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  • phylogeny  (82)
  • Saccharomyces cerevisiae
  • Springer  (163)
  • Institute of Physics
  • 1995-1999  (70)
  • 1990-1994  (93)
  • 1940-1944
  • 1999  (70)
  • 1993  (93)
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  • 1995-1999  (70)
  • 1990-1994  (93)
  • 1940-1944
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  • 1
    Electronic Resource
    Electronic Resource
    Identification of a fungal triacetylfusarinine C siderophore transport gene (TAF1) in Saccharomyces cerevisiae as a member of the major facilitator superfamily (1999)
    Springer
    BioMetals 12 (1999), S. 301-306 
    Details
    ISSN: 1572-8773
    Keywords: iron ; siderophores ; transport ; Saccharomyces cerevisiae ; fungi
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract Transport proteins of microorganisms may either belong to the ATP-binding cassette (ABC) superfamily or to the major facilitator (MFS)-superfamily. MFS transporters are single-polypeptide membrane transporters that transport small molecules via uniport, symport or antiport mechanisms in response to a chemiosmotic gradient. Although Saccharomyces cerevisiae is a non-siderophore producer, various bacterial and fungal siderophores can be utilized as an iron source. From yeast genome sequencing data six genes of the unknown major facilitator (UMF) family were known of which YEL065w Sce was recently identified as a transporter for the bacterial siderophore ferrioxamine B (Sit1p). The present investigation shows that another UMF gene, YHL047c Sce, encodes a transporter for the fungal siderophore triacetylfusarinine C. The gene YHL047c Sce (designated TAF1) was disrupted using the kanMX disruption module in a fet3 background (strain DEY 1394 Δfet3), possessing a defect in the high affinity ferrous iron transport. Growth promotion assays and transport experiments with 55Fe-labelled triacetylfusarinine C showed a complete loss of iron utilization and uptake in the disrupted strain, indicating that TAF1 is the gene for the fungal triacetylfusarinine transport in Saccharomyces cerevisiae and possibly in other siderophore producing fungi.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1009252118050
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  • 2
    Electronic Resource
    Electronic Resource
    Interaction of Saccharomyces cerevisiae with gold: toxicity and accumulation (1999)
    Springer
    BioMetals 12 (1999), S. 289-294 
    Details
    ISSN: 1572-8773
    Keywords: accumulation ; gold ; proton efflux ; Saccharomyces cerevisiae ; toxicity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract This paper examines the effects of ionic gold on Saccharomyces cerevisiae, as determined by long-term (growth in gold-containing media) and short-term interactions (H+ efflux activity). An increasing gold concentration inhibited growth and at 〈0.2 mM Au, growth was not observed. Transmission electron microscopy revealed no differences in ultrastructure but fine electron dense particles were observed in unstained preparations from gold-containing medium. After glucose addition (to 10mM) to starved suspensions of S. cerevisiae, glucose-dependent reduction of external pH occurred as the cells extruded protons. In the presence of increasing gold concentrations, the lag time before proton extrusion did not change but the rate and duration decreased significantly with a marked influence on proton efflux rate being observed at ≤ 10 μM. Extension of preincubation time of yeast cells in gold-containing medium resulted in a decreasing proton efflux rate and colloidal phase formation in the cell suspensions, the time between gold addition and the beginning of colloidal phase formation depending on the gold concentration used. Both Ca and Mg enhanced the inhibitory effect of gold on the yeast cells with Ca showing a stronger inhibitory effect than Mg.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1009210101628
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  • 3
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    Phylogenetic relation of Epidermophyton floccosum to the species of Microsporum and Trichophyton in chitin synthase 1 (CHS1) gene sequences (1999)
    Springer
    Mycopathologia 146 (1999), S. 111-113 
    Details
    ISSN: 1573-0832
    Keywords: chitin synthase gene 1 ; dermatophyte ; Epidermophyton floccosum ; Microsporum ; phylogeny ; Trichophyton
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract The Nucleotide sequence of the chitin synthase1 (CHS1) gene of Epidermophyton floccosum, an anthrophophilic dermatophyte which is the type species of the genus Epidermophyton was analyzed to determine its phylogenetic relation to eight other dermatophyte species belonging to the genera Microsporum and Trichophyton, which were sequenced in our previous studies. A genomic DNA fragment about 620 bp in length of the CHS1 genewas amplified from E. floccosum by polymerasechain reaction (PCR) and was sequenced. The CHS1 nucleotide sequence showed more than 85% similarity with sequences derived from the other dermatophytes. Phylogenetic analyses of the sequences from E. floccosum revealed that the genus Epidermophyton may be genetically distinct from Microsporum and Trichophyton.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1007091031124
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  • 4
    Electronic Resource
    Electronic Resource
    Molecular confirmation of a Trichophyton violaceum isolate from human black-dot ringworm (1999)
    Springer
    Mycopathologia 146 (1999), S. 127-130 
    Details
    ISSN: 1573-0832
    Keywords: black-dot ringworm ; chitin synthase gene ; phylogeny ; Trichophyton rubrum ; T. tonsurans ; T. violaceum
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract A clinical isolate from a black-dot ringworm lesion of a 28-year-old female Japanese was investigated by morphological and biochemical analyses as well as molecular analyses. The isolate grew well onthiamine enriched agar and did not produce violetpigment, macroconidia or microconidia on Sabouraud's dextrose agar. Approximately 620-bp genomic DNA fragments of the CHS1 gene were amplified from Trichophyton mentagrophytes, T. rubrum, T. tonsurans and T. violaceum by polymerase chain reaction (PCR) and sequenced. The chitin synthase 1 (CHS1) nucleotide sequences of the clinical isolate showed more than 97% similarity to that of T. violaceum and less than 96% similarity to that of T. mentagrophytes, T. rubrum and T. tonsurans. The phylogenetic analysis of their sequences revealed that the clinical isolate was genetically close to T. violaceum and distinct from T. mentagrophytes, T. rubrum and T. tonsurans. Therefore, the isolate was confirmed as T. violaceum by mycological examination and molecular analyses.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1007091607889
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  • 5
    Electronic Resource
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    Naturalists, Molecular Biologists, and the Challenges of Molecular Evolution (1999)
    Springer
    Journal of the history of biology 32 (1999), S. 321-341 
    Details
    ISSN: 1573-0387
    Keywords: molecular biology ; molecular evolution ; natural history ; phylogeny ; systematics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , History
    Notes: Abstract Biologists and historians often present natural history and molecular biology as distinct, perhaps conflicting, fields in biological research. Such accounts, although supported by abundant evidence, overlook important areas of overlap between these areas. Focusing upon examples drawn particularly from systematics and molecular evolution, I argue that naturalists and molecular biologists often share questions, methods, and forms of explanation. Acknowledging these interdisciplinary efforts provides a more balanced account of the development of biology during the post-World War II era.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1004660202226
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  • 6
    Electronic Resource
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    Origin and Evolution of Feather Mites (Astigmata) (1999)
    Springer
    Experimental and applied acarology 23 (1999), S. 437-454 
    Details
    ISSN: 1572-9702
    Keywords: feather mites ; morphological adaptations ; phylogeny ; coevolution ; co-speciation ; birds ; ectoparasites
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Feather mites are highly specialized plumage and skin ectoparasites that are variously adapted for inhabiting certain microhabitats on a bird's body. Different feather mite taxa of higher (familial) rank adapted to the same microhabitats display similar main morphological adaptations even if they are rather distantly related to one another. Hypotheses on the evolution of general adaptations in morphology of feather mites during colonization and establishment in different microhabitats are presented. According to recent data, feather mites are a paraphyletic group consisting of three superfamilies: Analgoidea, Pterolichoidea and Freyanoidea. We present our view on the general feather mite phylogeny course at the familial rank for the Analgoidea by means of cladistic analysis. Co-speciation of parasites with their hosts is postulated as a main factor driving feather mite evolution. Examples are given of non-coevolutionary events, for example recolonization from one host species onto another, extinction and multiple speciation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1006180705101
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  • 7
    Electronic Resource
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    Presence in and effects of pineal indoleamines at very low level of phylogeny (1993)
    Springer
    Cellular and molecular life sciences 49 (1993), S. 627-634 
    Details
    ISSN: 1420-9071
    Keywords: Serotonin ; melatonin ; Tetrahymena ; Planaria ; hormonal imprinting ; phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract The unicellular organism Tetrahymena contains serotonin and is able to take up the hormone from its mileiu. The serotonin content of the cell changes as a function of the presence of foreign exogenous hormones. This indicates a possible role of serotonin as a chemical mediator. Exogenous serotonin stimulates the RNA synthesis of Tetrahymena, and it was the only one among the hormones studied which kept the RNA level durably high. Serotonin stimulates phagocytosis and growth of Tetrahymena, and its precursors also stimulate growth. Serotonin can imprint Tetrahymena, and as a consequence of this the effect of the hormone increases in the case of further encounters. Treatment with serotonin-related molecules soon after imprinting can reduce the effect of imprinting. Melatonin can contract the pigment cells of Planaria; however, its precursors serotonin and tryptamine can do this more intensely. Both melatonin and serotonin can influenc the regeneration of Planaria, with effects which differ when different phenomena are studied. Evolutionary theories are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01923943
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  • 8
    Electronic Resource
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    Cloning and expression of Hormoconis resinae glucoamylase P cDNA in Saccharomyces cerevisiae (1993)
    Springer
    Current genetics 24 (1993), S. 38-44 
    Details
    ISSN: 1432-0983
    Keywords: Glucoamylase ; Gene cloning ; Hormoconis resinae ; Saccharomyces cerevisiae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A cDNA coding for glucoamylase P of Hormoconis resinae was cloned using a synthetic oligonucleotide probe coding for a peptide fragment of the purified enzyme and polyclonal anti-glucoamylase antibodies. Nucleotide-sequence analysis revealed an open reading frame of 1848 base pairs coding for a protein of 616 amino-acid residues. Comparison with other fungal glucoamylase amino-acid sequences showed homologies of 37–48%. The glucoamylase cDNA, when introduced into Saccharomyces cerevisiae under the control of the yeast ADC1 promoter, directed the secretion of active glucoamylase P into the growth medium.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00324663
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  • 9
    Electronic Resource
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    Normal mitochondrial structure and genome maintenance in yeast requires the dynamin-like product of the MGM1 gene (1993)
    Springer
    Current genetics 24 (1993), S. 141-148 
    Details
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Dynamin ; Mitochondria ; GTP binding protein
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The isolation and characterization of MGM1, and yeast gene with homology to members of the dynamin gene family, is described. The MGM1 gene is located on the right arm of chromosome XV between STE4 and PTP2. Sequence analysis revealed a single open reading frame of 902 residues capable of encoding a protein with an approximate molecular mass of 101 kDa. Loss of MGM1 resulted in slow growth on rich medium, failure to grow on non-fermentable carbon sources, and loss of mitochondrial DNA. The mitochondria also appeared abnormal when visualized with an antibody to a mitochondrial-matrix marker. MGM1 encodes a dynamin-like protein involved in the propagation of functional mitochondria in yeast.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00324678
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  • 10
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    Molecular cloning of the PEL1 gene of Saccharomyces cerevisiae that is essential for the viability of petite mutants (1993)
    Springer
    Current genetics 24 (1993), S. 307-312 
    Details
    ISSN: 1432-0983
    Keywords: Growth control ; Genetic mapping ; Molecular cloning ; Nucleo-mitochondrial interaction ; Saccharomyces cerevisiae ; Viability of petites
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The PEL1 gene of Saccharomyces cerevisiae is essential for the cell viability of mitochondrial petite mutants, for the ability to utilize glycerol and ethanol on synthetic medium, and for cell growth at higher temperatures. By tetrad analysis the gene was assigned to chromosome III, centromere proximal of LEU2. The PEL1 gene has been isolated and cloned by the complementation of a pel1 mutation. The molecular analysis of the chromosomal insert carrying PEL1 revealed that this gene corresponds to the YCL4W open reading frame on the complete DNA sequence of chromosome III. The putative Pel1 protein is characterized by a low molecular weight of approximately 17 kDa, a low codon adaptation index, and a high leucine content.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00336781
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  • 11
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    Sequence analysis of a Papaver somniferum L. mitochondrial DNA fragment promoting autonomous plasmid replication in Saccharomyces cerevisiae and Kluyveromyces lactis (1993)
    Springer
    Current genetics 24 (1993), S. 366-367 
    Details
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Papaver somniferum L. ; ARS ; Mitochondrial DNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The minimal fragment of mitochondrial DNA from Papaver somniferum L. (poppy) able to promote autonomous plasmid replication in the yeast Saccharomyces cerevisiae was sequenced. Sequence analysis of the 917-bp MK4/8 DNA fragment revealed a high AT content, and the presence of two 12-bp sequences differing from the ARS core consensus of S. cerevisiae only by a T and C insertion, respectively. The mitochondrial insert contains a further six 11-bp sequences with one mismatch to the S. cerevisiae core consensus, more then 20 related sequences with two base pair exchanges, numerous direct and inverted repeats, and many copies of a sequence motif called the ARS box. The original 4.2-kb mitochondrial DNA fragment, as well as the minimal 917-bp subfragment in vector pFL1-E (a variant of YIP5, lacking an origin of replication in yeast), were then tested for their ability to replicate autonomously in another fungus, Kluyveromyces lactis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00336790
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  • 12
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    The ogd1 and kgd1 mutants lacking 2-oxoglutarate dehydrogenase activity in yeast are allelic and can be differentiated by the cloned amber suppressor (1993)
    Springer
    Current genetics 24 (1993), S. 377-381 
    Details
    ISSN: 1432-0983
    Keywords: 2-Oxoglutarate dehydrogenase ; Molecular cloning ; Saccharomyces cerevisiae ; Sequencing ; Suppressor ; Yeast
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The activity of mitochondrial 2-oxoglutarate dehydrogenase in S. cerevisiae can be impaired either by the ogd1 or the kgd1 mutation. The OGD1 gene and two suppressor genes were isolated by complementation of the ogd1 mutant. The complementation of the kdg1 mutant by the OGD1 gene, an allelism test, and meiotic mapping, revealed that the ogd1 and kgd1 mutations are allelic. The two mutations were differentiated by the cloned suppressor gene which was able to partially complement ogd1, but not kgd1. The molecular analysis of the suppressor gene revealed its identity with the natural tRNA CAG Gln gene found in the upstream region of URA10.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00351844
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  • 13
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    Use of reporter genes for the isolation and characterisation of different classes of sporulation mutants in the yeast Saccharomyces cerevisiae (1993)
    Springer
    Current genetics 24 (1993), S. 451-454 
    Details
    ISSN: 1432-0983
    Keywords: Yeast ; Saccharomyces cerevisiae ; Sporulation mutants ; Reporter genes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Reporter genes consisting of sporulation-specific promoters fused to lacZ were used as markers to monitor the sporulation pathway of the yeast Saccharomyces cerevisiae. Strains transformed with these lacZ gene fusions expressed β-galactosidase (assayable on plates using the substrate 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside, X-gal) in a sporulation-dependent manner. Mutagenesis experiments performed on transformed strains resulted in the recovery of a number of novel sporulation mutants. Three classes of mutants were obtained: those which overexpressed the reporter gene under sporulation conditions, those which did not express the gene under any conditions, and those which expressed the gene in vegetative cells not undergoing sporulation. On the basis of the blue colony-colour produced in the presence of X-gal these have been described as superblue, white, and blue vegetative mutants, respectively. These were further characterised using earlier reporter genes and other marker systems. This study established that the multicopy reporter plasmids chosen do not interfere with sporulation; they are valid tools for monitoring the pathway and they provide a way to isolate mutations not readily selected by other markers.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00351856
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  • 14
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    Physical mapping of the MEL gene family in Saccharomyces cerevisiae (1993)
    Springer
    Current genetics 24 (1993), S. 461-464 
    Details
    ISSN: 1432-0983
    Keywords: Chromosome fragmentation ; MEL gene family ; Saccharomyces cerevisiae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Nine members, MEL2–MEL10, of the MEL gene family coding for α-galactosidase were physically mapped to the ends of the chromosomes by chromosome fragmentation. Genetic mapping of the genes supported the location of all the MEL genes in the left arm of their resident chromosomes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00351706
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  • 15
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    Parameters affecting lithium acetate-mediated transformation of Saccharomyces cerevisiae and development of a rapid and simplified procedure (1993)
    Springer
    Current genetics 24 (1993), S. 455-459 
    Details
    ISSN: 1432-0983
    Keywords: Yeast ; Saccharomyces cerevisiae ; Transformation ; Plasmid
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have compared a number of procedures for the transformation of whole cells of the yeast Saccharomyces cerevisiae and assessed the effects of dimethylsulphoxide (DMSO) or ethanol, both of which have been reported to enhance transformation efficiency. We find that simplified methods benefit from the addition of one of these compounds, and although differences are observed between strains as to the more beneficial reagent, peak transformation efficiency is, in general obtained with 10% DMSO or 10% EtOH. Increases of between six- and 50-fold are observed, despite a reduction in cell viability, and at this concentration the two compounds are not additive in their effects. The optimum level appears to depend on a balance between improved DNA uptake and reduced cell viability. As a result of this work we present a straightforward and rapid transformation procedure.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00351857
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  • 16
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    Cysteine uptake by Saccharomyces cerevisiae is accomplished by multiple permeases (1999)
    Springer
    Current genetics 35 (1999), S. 609-617 
    Details
    ISSN: 1432-0983
    Keywords: Key words Cysteine uptake ; Amino-acid permeases ; Saccharomyces cerevisiae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Uptake by Saccharomyces cerevisiae of the sulphur-containing amino acid L-cysteine was found to be non-saturable under various conditions, and uptake kinetics suggested the existence of two or more transport systems in addition to the general amino-acid permease, Gap1p. Overexpression studies identified BAP2, BAP3, AGP1 and GNP1 as genes encoding transporters of cysteine. Uptake studies with disruption mutants confirmed this, and identified two additional genes for transporters of cysteine, TAT1 and TAT2, both very homologous to BAP2, BAP3, AGP1 and GNP1. While Gap1p and Agp1p appear to be the main cysteine transporters on the non-repressing nitrogen source proline, Bap2p, Bap3p, Tat1p, Tat2p, Agp1p and Gnp1p are all important for cysteine uptake on ammonium-based medium. Furthermore, whereas Bap2p, Bap3p, Tat1p and Tat2p seem most important under amino acid-rich conditions, Agp1p contributes significantly when only ammonium is present, and Gnp1p only contributes under the latter condition.
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    URL: http://dx.doi.org/10.1007/s002940050459
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  • 17
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    Starvation in yeast increases non-adaptive mutation (1999)
    Springer
    Current genetics 35 (1999), S. 77-81 
    Details
    ISSN: 1432-0983
    Keywords: Key words Adaptive mutations ; 6-N-hydroxylaminopurine ; Saccharomyces cerevisiae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The frequency of reversion in a histidine-requiring mutant of Saccharomyces cerevisiae increases about ten-fold in stationary cells during histidine starvation. Histidine starvation enhances a similar frequency of reversion in a tryptophan-requiring mutant. Starvation, therefore, enhances mutation frequencies in a non-adaptive manner. The base analogue 6-N-hydroxylaminopurine (HAP) added prior to plating on medium with limited histidine strongly increases reversion of the histidine mutant. HAP-induced reversion increases further in stationary starving cells with the same kinetics as that which increases spontaneous reversion. Adding HAP to the stationary starving cells does not produce any effect.
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    URL: http://dx.doi.org/10.1007/s002940050435
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  • 18
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    Strand interruptions confer strand preference during intracellular correction of a plasmid-borne mismatch in Saccharomyces cerevisiae (1999)
    Springer
    Current genetics 35 (1999), S. 499-505 
    Details
    ISSN: 1432-0983
    Keywords: Key words Heteroduplex repair ; Strand discrimina-tion ; Strand interruptions ; Saccharomyces cerevisiae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Site-directed mutagenesis was used to construct yeast centromere plasmids in which a strand nick or gap could be placed 5′ or 3′, on either strand, to a reporter gene (SUP4-o) carrying defined base mismatches. The plasmids were then transformed into yeast cells and the direction and efficiency of mismatch repair were assayed by scoring colouring of the transformant colonies. Strands that were nicked were consistently corrected more often than intact strands, but the effect was very small. However, placement of a small gap at the same positions as the nicks resulted in a marked increase in selection for the gapped strand and an enhanced efficiency of mismatch repair. Both the preference for the gapped strand and correction of the mismatch were offset by deletion of the mismatch repair gene PMS1. Together, the results suggest that strand interruptions can direct intracellular mismatch correction of plasmid-borne base mispairs in yeast.
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    URL: http://dx.doi.org/10.1007/s002940050445
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  • 19
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    Analysis of the genes activated by the FLO8 gene in Saccharomyces cerevisiae (1999)
    Springer
    Current genetics 36 (1999), S. 256-261 
    Details
    ISSN: 1432-0983
    Keywords: Key wordsFLO8 ; Transcriptional regulation ; Saccharomyces cerevisiae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract It is thought that the FLO8 gene encodes a transcriptional activator of the dominant flocculation gene FLO1 in Saccharomycescerevisiae. To determine other genes which are regulated by FLO8, a detailed comparison of the transcripts from the FLO8 and Δflo8 strains was carried out. In addition to the FLO1 gene, it was found that transcription of the FLO11 and STA1 genes is positively regulated by FLO8. In flo8 strains, not only transcripts of the FLO11, STA1, and FLO1 genes but also invasive growth, extracellular glucoamylase production, and flocculation were undetected. From these results, it is suggested that FLO8 regulates these characteristics via the transcriptional regulation of the FLO11, STA1, and FLO1 genes.
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    URL: http://dx.doi.org/10.1007/s002940050498
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  • 20
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    Evolutionary conservation of genomic sequences related to the GGP1 gene encoding a yeast GPI-anchored glycoprotein (1993)
    Springer
    Current genetics 23 (1993), S. 19-21 
    Details
    ISSN: 1432-0983
    Keywords: Glycosylphosphatidylinositol anchored-protein ; Southern analysis ; Saccharomyces cerevisiae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The GGP1 gene encodes the only GPI-anchored glycoprotein (gp115) that has been purified todate in the budding yeast Saccharomyces cerevisiae. It is a single-copy gene whose deduced amino-acid sequence shares no significant homology to any other known protein. In this paper we report a Southern hybridization analysis of genomic DNA from different eukaryotic organisms to identify homologues of the GGP1 gene. We have analyzed DNA prepared from a unicellular green alga (Chlamydomonas eugametos), from two distantly related yeast species (Candida cylindracea and Schizosaccharomyces pombe), and from the common bean Phasoleus vulgaris. The moderate stringency of the experimental conditions and the high specificity of the probes used indicate that a single-copy of GGP1-related sequences exists in all these eukaryotic organisms. The chromosomal localization of the GGP1 gene in S. cerevisiae has also been determined.
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    URL: http://dx.doi.org/10.1007/BF00336744
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  • 21
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    The STA2 and MEL1 genes of Saccharomyces cerevisiae are idiomorphic (1993)
    Springer
    Current genetics 23 (1993), S. 92-94 
    Details
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Gene mapping ; Idiomorphism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The STA2 (glucoamylase) gene of Saccharomyces cerevisiae has been mapped close to the end of the left arm of chromosome II. Meiotic analysis of a cross between a haploid strain containing STA2, and another strain carrying the melibiase gene MEL1 (which is known to be at the end of the left arm of chromosome II) produced parental ditype tetrads only. Since there is no significant DNA sequence similarity between the STA2 and MEL1 genes, or their respective flanking regions, we conclude that these two genes are carried by separate non-hybridizing sequences of chromosomal DNA, either of which can reside at the end of the left arm of chromosome II. By analogy with the mating-type locus of Neurospora crassa, we suggest that the STA2 and MEL1 genes are idiomorphs with respect to one another.
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    URL: http://dx.doi.org/10.1007/BF00336753
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  • 22
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    Molecular cloning of the yeast OPI3 gene as a high copy number suppressor of the cho2 mutation (1993)
    Springer
    Current genetics 23 (1993), S. 95-101 
    Details
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Phospholipid synthesis ; Phospholipid-N-methyltransferase ; Mutant ; Over-expression
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract By functional complementation of the auxotrophic requirements for choline of a cdg1, cho2 double-mutant, by transformation with a genomic DNA library in a high copy number plasmid, two different types of complementing DNA inserts were identified. One type of insert was earlier shown to represent the CHO2 structural gene. In this report we describe the molecular and biochemical characterization of the second type of complementing activity. The transcript encoded by the cloned gene was about 1000-nt in length and was regulated in response to the soluble phospholipid precursors, inositol and choline. A gene disruption resulted in no obvious growth phenotype at 23°C or 30°C, but in a lack of growth at 37°C in the presence of monomethylethanolamine. Null-mutants exhibited an inositol-secretion phenotype, indicative of mutations in the lipid biosynthetic pathway. Complementation analysis, biochemical analysis of the phospholipid methylation pathway in vivo, and comparison of the restriction pattern of the cloned gene to published sequences, unequivocally identified the cloned gene as the OPI3 gene, encoding phospholipid-N-methyltransferase in yeast. When present in multiple copies the OPI3 gene efficiently suppresses the phospholipid methylation defect of a cho2 mutation. As a result of impaired synthesis of phosphatidylcholine, the INO1-deregulation phenotype is abolished in cho2 mutants transformed with the OPI3 gene on a high copy number plasmid. Taken together, these data demonstrate a significantly overlapping specificity of the OPI3 gene product for three sequential phospholipid methylation reactions in the de novo Ptd-Cho biosynthetic pathway.
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    Epitope-tagging vectors designed for yeast (1993)
    Springer
    Current genetics 23 (1993), S. 181-183 
    Details
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; c-myc epitope ; Fusion
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In order to facilitate the process of epitope-tagging of yeast proteins, we have constructed two Saccharomyces cerevisiae-Escherichia coli shuttle vectors that allow fusion of a sequence encoding an epitope of the human c-myc protein at the 3′ end of any gene. An example of the use of this technique is presented.
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    Genetic and molecular analysis of REC114, an early meiotic recombination gene in yeast (1993)
    Springer
    Current genetics 23 (1993), S. 295-304 
    Details
    ISSN: 1432-0983
    Keywords: Meiosis ; Meiotic recombination ; Saccharomyces cerevisiae ; REC114
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Four new meiotic recombination genes were previously isolated by selecting for mutations that rescue the meiotic lethality of rad52 spo13 strains. One of these genes, REC114, is described here, and the data confirm that REC114 is a meiosis-specific recombination gene with no detectable function in mitosis. REC114 is located on chromosome XIII approximately 4,9 cM from CIN4. The nucleotide sequence reveals an open reading frame of 1262 bp, consensus intron splice sites close to the 3′ end, and indicates that the second exon codes for only seven amino acids. In the promoter region, a URS1 consensus sequence (TGGGCGGCTA), identical to the URS1 found in the promoter of SPO16, is present 93 bp upstream of the translation start site. Northern-blot hybridization demonstrates that REC114 is transcribed only during meiosis and that it is not expressed in the absence of the IME1 gene product, even when IME2 is constitutively expressed.
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    URL: http://dx.doi.org/10.1007/BF00310890
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    Lack of correlation between trehalase activation and trehalose-6 phosphate synthase deactivation in cAMP-altered mutants of Saccharomyces cerevisiae (1993)
    Springer
    Current genetics 23 (1993), S. 382-387 
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    ISSN: 1432-0983
    Keywords: Trehalase ; Trehalose-6-P synthase ; cAMP mutants ; Saccharomyces cerevisiae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The rise in cAMP level that follows the addition of glucose or 2,4-dinitrophenol (DNP) to stationaryphase cells of Saccharomyces cerevisiae was accompanied by a marked activation of trehalase (3-fold increase) and a concomitant deactivation of trehalose-6 phosphate synthase (50% of the basal levels). In glucose-grown exponential cells, which are deficient in glucose-induced cAMP signalling, the addition of glucose also prompted a decrease in trehalose-6 phosphate synthase, but had no effect on trehalase activity. Mutants defective in the RAS-adenylate cyclase pathway (ras1 ras2 bcy1 strain), as well as mutants containing greatly reduced protein kinase activity either cAMP-dependent (tpk w1 BCY1 strains) or cAMP-independent (tpk1 w1 bcy1 strains), were unable to show glucose- or DNP-induced trehalase activation but still displayed a clear decrease in trehalose-6 phosphate synthase activity upon addition of these compounds. These data suggest that the activity of trehalose-6 phosphate synthase, as opposed to that of trehalase, is not controlled by the cAMP signalling pathway “in vivo”. Trehalose-6 phosphate synthase was competitively inhibited by glucose (Ki=15 mM) and resulted unaffected by ATP in assays performed “in vitro”.
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    Structure and regulation of the isocitrate lyase gene ICL1 from the yeast Saccharomyces cerevisiae (1993)
    Springer
    Current genetics 23 (1993), S. 375-381 
    Details
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Isocitrate lyase ; Gene regulation ; Ethanol induction
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The ICL1 gene encoding the isocitrate lyase from Saccharomyces cerevisiae was cloned and sequenced. A reading frame of 557 amino acids showing significant similarity to isocitrate lyases from seven other species could be identified. Construction of icl1 null mutants led to growth defects on C2 carbon sources while utilization of sugars or C3 substrates remained unaffected. Using an ICL1-lacZ fusion integrated at the ICL1 locus, a more than 200-fold induction of β-galactosidase activity was observed after growth on ethanol when compared with glucose-repressed conditions. A preliminary analysis of the ICL1 upstream region identified a 364-bp fragment necessary and sufficient for this regulatory phenotype. Sequence motifs also present in the upstream regions of co-regulated genes were found within this region.
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    Phenotypic identification of amplifications of the ADH4 and CUP1 genes of Saccharomyces cerevisiae (1993)
    Springer
    Current genetics 23 (1993), S. 392-396 
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    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Gene amplification ; ADH4 ; CUP1
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Primary gene amplification, i.e., mutation from one gene copy to multiple gene copies per genome, is important in genomic evolution, as a means of producing anti-cancer drug resistance, and is associated with the progression of tumor malignancy. Primary amplification has not been studied in normal eukaryotic cells because amplifications are extremely rare in these cells. A system has been developed to phenotypically identify co-amplifications of the ADH4 and CUP1 genes of Saccharomyces cerevisiae and 21 independent spontaneous amplifications have been isolated.
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    Donation of information to the unbroken chromosome in double-strand break repair (1993)
    Springer
    Current genetics 23 (1993), S. 414-422 
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    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Donation ; Gene conversion ; Double-strand break repair ; Heteroduplex DNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have used transformation of yeast with lincarized plasmids to study the transfer of information to the unbroken chromosome during double-strand break repair. Using a strain which carried the wild-type HIS3 allele, and a linearized plasmid which carried a mutant his3 allele, we have obtained His- transformants. In these, double-strand break repair has resulted in precise transfer of genetic information from the plasmid to the chromosome. Such repair events, we suggest, are gene conversions which entail the formation of heteroduplex DNA on the (unbroken) chromosome. If this suggestion is correct, our results reflect the spatial distribution of such heteroduplex DNA. Transfer of information from the plasmid to the chromosome was obtained at a maximal frequency of 1.5% of the repair events, and showed a dependence with distance. Transformation to His- was also obtained with a 2-kbp insertion and with a deletion of 200 bp. The latter results suggest that gene conversion of large heterologies can occur via repair of a heteroduplex DNA intermediate.
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    MCB elements and the regulation of DNA replication genes in yeast (1993)
    Springer
    Current genetics 24 (1993), S. 185-192 
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    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Cell cycle ; Transcription ; DNA replication
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In eukaryotic organisms, genes involved in DNA replication are often subject to some form of cell cycle control. In the yeast Saccharomyces cerevisiae, most of the DNA replication genes that have been characterized to date are regulated at the transcriptional level during G1 to S phase transition. A cis-acting element termed the MluI cell cycle box (or MCB) conveys this pattern of regulation and is common among more than 20 genes involved in DNA synthesis and repair. Recent findings indicate that the MCB element is well conserved among fungi and may play a role in controlling entry into the cell division cycle. It is evident from studies in higher systems, however, that transcriptional regulation is not the only form of control that governs the cell-cycle-dependent expression of DNA replication genes. Moreover, it is unclear why this general pattern of regulation exists for so many of these genes in various eukaryotic systems. This review summarizes recent studies of the MCB element in yeast and briefly discusses the purpose of regulating DNA replication genes in the eukaryotic cell cycle.
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    Pentose-phosphate pathway in Saccharomyces cerevisiae: analysis of deletion mutants for transketolase, transaldolase, and glucose 6-phosphate dehydrogenase (1993)
    Springer
    Current genetics 24 (1993), S. 373-376 
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    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Pentose-phosphate pathway ; Transketolase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Deletion mutants for the yeast transketolase gene TKL1 were constructed by gene replacement. Transketolase activity was below the level of detection in mutant crude extracts. Transketolase protein could be detected as a single protein band of the expected size by Western-blot analysis in wild-type strains but not in the delection mutant. Deletion of TKL1 led to a reduced but distinct growth in synthetic medium without an aromatic amino-acid supplement. We also isolated double and triple mutants for transketolase (tkl1), transaldolase (tal1), and glucose 6-phosphate dehydrogenase (zwf1) by crossing the different mutants. A tal1 tkl1 double mutant grew nearly like wild-type in rich medium. Only the tkl1 zwf1 double and the tal1 tkl1 zwf1 triple mutant grew more slowly than the wild-type in rich medium. This growth defect could be partly alleviated by the addition of xylulose but not ribose. The triple mutant still grew slowly on a synthetic mineral salts medium without a supplement of aromatic amino acids. This suggests the existence of an alternative but limited source of pentose phosphates and erythrose 4-phosphate in the tkl1 zwf1 double mutants. Hybridization with low stringency showed the existence of a sequence with homology to transketolase, possibly a second gene.
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    Mutant allele pso7-1, that sensitizes Saccharomyces cerevisiae to photoactivated psoralen, is allelic with COX11, encoding a protein indispensable for a functional cytochrome c oxidase (1999)
    Springer
    Current genetics 36 (1999), S. 124-129 
    Details
    ISSN: 1432-0983
    Keywords: Key words Psoralen sensitivity ; Cytochrome oxidase ; Saccharomyces cerevisiae ; Oxidative stress
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The yeast gene PSO7 was cloned from a genomic library by complementation of the pso7-1 mutant's sensitivity phenotype to 4-nitroquinoline-1-oxide (4NQO). Sequence analysis revealed that PSO7 is allelic to the 1.1-kb ORF of the yeast gene COX11 which is located on chromosome XVI and encodes a protein of 28-kDa localized in the inner mitochondrial membrane. Allelism of PSO7/COX11 was verified by non-complementation of 4NQO-sensitivity in diploids homo- and hetero-allelic for the pso7-1 and cox11::TRP1 mutant alleles. Sensitivity to 4NQO was the same in exponentially growing cells of the pso7-1 mutant and the cox11::TRP1 disruptant. Allelism of COX11 and PSO7 indicates that the pso7 mutant's sensitivity to photoactivated 3-carbethoxypsoralen and to 4NQO is not caused by defective DNA repair, but rather is due to an altered metabolism of the pro-mutagen 4NQO in the absence of cytochrome oxidase (Cox) in pso7-1/cox11::TRP1 mutants/disruptants. Lack of Cox might also lead to a higher reactivity of the active oxygen species produced by photoactivated 3-carbethoxypsoralen. The metabolic state of the cells is important for their sensitivity phenotype since the largest enhancement of sensitivity to 4NQO between wild-type (WT) and the pso7 mutant occurs in exponentially growing cells, while cells in stationary phase or growing cells in phosphate buffer have the same 4NQO resistance, irrespective of their WT/mutant status. Strains containing the pso7-1 or cox11::TRP1 mutant allele were also sensitive to the oxidative stress-generating agents H2O2 and paraquat. Mutant pso7-1, as well as disruptant cox11::TRP1, harboured mitochondria that in comparison to WT contained less than 5% and no detectable Cox activity, respectively.
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    Induction of pyruvate decarboxylase in glycolysis mutants of Saccharomyces cerevisiae correlates with the concentrations of three-carbon glycolytic metabolites (1993)
    Springer
    Archives of microbiology 160 (1993), S. 324-328 
    Details
    ISSN: 1432-072X
    Keywords: Saccharomyces cerevisiae ; Pyruvate decarboxylase ; Pyruvate kinase ; Signalling ; Glycolysis mutants
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Pyruvate decarboxylase, PDCase, activity in wild-type yeast cells growing on ethanol is quite low but increases up to tenfold upon addition of glucose, less with galactose and only slightly with glycerol. PDCase levels in glycolysis mutant strains growing on ethanol or acetate were higher than in the wild-type strain. These levels correlated with the sum of the concentrations of three-carbon glycolytic metabolites. The highest accumulation was observed in a fructose bisphosphate aldolase deletion mutant concomintant with the highest PDCase activity wild-type level. On the other hand, the PDCase levels in the different mutants again correlated with the sum of the concentrations of the three-carbon glycolytic metabolites. This was interpreted to mean that full induction of PDCase activity requires the accumulation of hexose-and triosephosphates.
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    Characterization of acetyl-CoA: l-lysine N6-acetyltransferase, which catalyses the first step of carbon catabolism from lysine in Saccharomyces cerevisiae (1993)
    Springer
    Archives of microbiology 160 (1993), S. 397-400 
    Details
    ISSN: 1432-072X
    Keywords: Saccharomyces cerevisiae ; Acetyl-CoA ; l-Lysine N6 ; acetytransferase ; Lysine catabolism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The carbon catabolism of l-lysine starts in Saccharomyces cerevisiae with acetylation by an acetyl-CoA: l-lysine N6-acetyltransferase. The enzyme is strongly induced in cells grown on l-lysine as sole carbon source and has been purified about 530-fold. Its activity was specific for acetyl-CoA and, in addition to l-lysine, 5-hydroxylysine and thialysine act as acetyl acceptor. The following apparent Michaelis constants were determined: acetyl-CoA 0.8 mM, l-lysine 5.8 mM, dl-5-hydroxylysine 2.8 mM, l-thialysine 100 mM. The enzyme had a maximum activity at pH 8.5 and 37°C. Its molecular mass, estimated by sodium dodecyl sulphate-polyacrylamide gel electrophoresis, was 52 kDa. Since the native molecular mass, determined by gel filtration, was 48 kDa, the enzyme is a monomer.
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    Comparative effects of Saccharomyces cerevisiae cultivation under copper stress on the activity and kinetic parameters of plasma-membrane-bound H+-ATPases PMA1 and PMA2 (1999)
    Springer
    Archives of microbiology 171 (1999), S. 273-278 
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    ISSN: 1432-072X
    Keywords: Key words Plasma membrane H+-ATPase ; PMA1 ; ATPase ; PMA2 ATPase ; Saccharomyces cerevisiae ; Copper stress ; Copper tolerance
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The major yeast plasma membrane H+-ATPase is encoded by the essential PMA 1 gene. The PMA 2 gene encodes an H+-ATPase that is functionally interchangeable with the one encoded by PMA 1 , but it is expressed at a much lower level than the PMA 1 gene and it is not essential. Using genetically manipulated strains of Saccharomyces cerevisiae that exclusively synthesize PMA1 ATPase or PMA2 ATPase under control of the PMA1 promoter, we found that yeast cultivation under mild copper stress leads to a similar activation of PMA2 and PMA1 isoforms. At high inhibitory copper concentrations (close to the maximum that allowed growth), ATPase activity was reduced from maximal levels; this decrease in activity was less important for PMA2 ATPase than for PMA1 ATPase. The higher tolerance to high copper stress of the artificial strain synthesizing PMA2 ATPase exclusively, as compared to that synthesizing solely PMA1 ATPase, correlated both with the lower sensitivity of PMA2 ATPase to the deleterious effects of copper in vivo and with its higher apparent affinity for MgATP, and suggests that plasma membrane H+-ATPase activity plays a role in yeast tolerance to copper.
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    A strange calmodulin of yeast (1999)
    Springer
    Molecular and cellular biochemistry 190 (1999), S. 47-54 
    Details
    ISSN: 1573-4919
    Keywords: calmodulin ; yeast calmodulin ; Ca2+ binding ; Ca2+ binding protein ; Saccharomyces cerevisiae ; interdomain interaction
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: Abstract Calmodulin of Saccharomyces cerevisiae has different Ca2+ binding properties from other calmodulins. We previously reported that the maximum number of Ca2+ binding was 3 mol/mol and the fourth binding site was defective, which was different from 4 mol/mol for others. Their macroscopic dissociation constants suggested the cooperative three Ca2+ bindings rather than a pair of cooperative two Ca2+ bindings of ordinary calmodulin. Here we present evidence for yeast calmodulin showing the intramolecular close interaction between the N-terminal half domain and the C-terminal half domain, while the two domains of ordinary calmodulin are independent of each other. We will discuss the relationship of the shape and the shape change caused by the Ca2+ binding to the enzyme activation in yeast. The functional feature of calmodulin in yeast will also be considered, which might be different from the one of vertebrate calmodulin.
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    Intracellular pH inSchizosaccharomyces pombe — Comparison withSaccharomyces cerevisiae (1993)
    Springer
    Molecular and cellular biochemistry 124 (1993), S. 131-140 
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    ISSN: 1573-4919
    Keywords: Schizosaccharomyces pombe ; Saccharomyces cerevisiae ; H+-ATPase ; intracellular pH ; carboxy-seminaphthorhodafluor-1
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: Abstract We examined cytoplasmic pH regulation inSchizosaccharomyces pombe andSaccharomyces cerevisiae using pH-sensitive fluorescent dyes. Of several different fluorescent compounds tested, carboxy-seminaphthorhodafluor-1 (C.SNARF-1) was the most effective. Leakage of C.SNARF-1 fromS. pombe was much slower than leakage fromC. cerevisiae. Using the pH-dependent fluorescence of C.SNARF-1 we showed that at an external pH of 7, mean resting internal pH was 7.0 forS. pombe and 6.6 forS. cerevisiae. We found that internal pH inS. pombe was maintained over a much narrower range in response to changes in external pH, especially at acidic pH. The addition of external glucose caused an intracellular alkalinization in both species, although the effect was much greater inS. cerevisiae than inS. pombe. The plasma membrane H+-ATPase inhibitor diethylstilbestrol reduced both the rate and extent of alkalinisation, with an IC50 of approximately 35 μM in both species. Amiloride also inhibited internal alkalinisation with IC50's of 745 μM forS. cerevisiae and 490 μM forS. pombe.
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    Characterization of Saccharomyces cerevisiae strains expressing ira1 mutant alleles modeled after disease-causing mutations in NF1 (1999)
    Springer
    Molecular and cellular biochemistry 202 (1999), S. 109-118 
    Details
    ISSN: 1573-4919
    Keywords: NF1 mutations ; IRA1 ; Saccharomyces cerevisiae ; RAS2 ; GAP activity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: Abstract The 2818 amino acids of neurofibromin, the product of the human NF1 gene, include a 230 amino acid Ras-GAP related domain (GRD). Functions which may be associated with the rest of the protein remain unknown. However, many NF1 mutations in neurofibromatosis 1 patients are found downstream of the GRD, suggesting that the C-terminal region of the protein is also functionally important. Since the C-terminal region of neurofibromin encompassing these mutations is homologous with the corresponding regions in the two Saccharomyces cerevisiae Ras-GAPs, Ira1p and Ira2p, we chose yeast as a model system for functional exploration of this region (Ira-C region). Three missense mutations that affect the Ira-C region of NF1 were used as a model for the mutagenesis of IRA1. The yeast phenotypes of heat shock sensitivity, iodine staining, sporulation efficiency, pseudohyphae formation, and GAP activity were scored. Even though none of the mutations directly affected the Ira1p-GRD, mutations at two of the three sites resulted in a decrease in the GAP activity present in ira1 cells. The third mutation appeared to disassociate the phenotypes of sporulation ability and GAP activity. This and other evidence suggest an effector function for Ira1p.
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    Direct observation of oxidative stress on the cell wall of Saccharomyces cerevisiae strains with atomic force microscopy (1999)
    Springer
    Molecular and cellular biochemistry 201 (1999), S. 17-24 
    Details
    ISSN: 1573-4919
    Keywords: Saccharomyces cerevisiae ; atomic force microscope ; bioscope ; organic synthesis ; molecular biology ; oxidative stress ; pore enlargement ; cell wall ; baker's yeast ; biotechnology
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: Abstract We imaged pores on the surface of the cell wall of three different industrial strains of Saccharomyces cerevisiae using atomic force microscopy. The pores could be enlarged using 10 mM diamide, an SH residue oxidant that attacks surface proteins. We found that two strains showed signs of oxidative damage via changes in density and diameter of the surface pores. We found that the German strain was resistant to diamide induced oxidative damage, even when the concentration of the oxidant was increased to 50 mM. The normal pore size found on the cell walls of American strains had diameters of about 200nm. Under conditions of oxidative stress the diameters changed to 400nm. This method may prove to be a useful rapid screening process (45-60 min) to determine which strains are oxidative resistant, as well as being able to screen for groups of yeast that are sensitive to oxidative stress. This rapid screening tool may have direct applications in molecular biology (transference of the genes to inside of living cells) and biotechnology (biotransformations reactions to produce chiral synthons in organic chemistry.
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    Antibodies raised against yeast HSP 104 cross-react with a heat-and abscisic acid-regulated polypeptide in rice (1993)
    Springer
    Plant molecular biology 22 (1993), S. 1177-1180 
    Details
    ISSN: 1573-5028
    Keywords: abscisic acid ; developmental regulation ; heat shock proteins ; Oryza sativa ; Saccharomyces cerevisiae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Antibodies raised against yeast heat shock protein (HSP) 104 recognized a heat-inducible polypeptide with a molecular mass of 110 kDa in shoot tissue of young rice seedlings. Root tissue of the same age showed no immuno-reaction with yeast HSP 104 antibodies. The 110 kDa polypeptide of rice was also shown to be abscisic acid-inducible in young seedlings. Though this polypeptide was seen to be constitutively present in the flag leaf of 90-day-old field-grown plant, it was not much affected by either heat shock or abscisic acid in this case.
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    Characterization of the Oxaloacetate Decarboxylase and Pyruvate Kinase-like Activities of Saccharomyces cerevisiae and Anaerobiospirillum succiniciproducens Phosphoenolpyruvate Carboxykinases (1999)
    Springer
    The protein journal 18 (1999), S. 659-664 
    Details
    ISSN: 1573-4943
    Keywords: Phosphoenolpyruvate carboxykinase ; oxaloacetate decarboxylase ; pyruvate kinase-like activity ; Anaerobiospirillum succiniciproducens ; Saccharomyces cerevisiae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Two members of the ATP-dependent class of phosphoenolpyruvate carboxykinases (PEPCKs) (Saccharomyces cerevisiae and Anaerobiospirillum succiniciproducens) have been comparatively studied with regard to their oxaloacetate (OAA) decarboxylase and pyruvate kinase-like activities. The pyruvate kinase-like activities were dependent on the presence of Mn2+; at the same concentrations Mg2+ was not effective. These activities were synergistically activated by a combination of both metal ions. V max for these activities in A. succiniciproducens and S. cerevisiae PEPCKs was 0.13% and 1.2% that of the principal reaction, respectively. The OAA decarboxylase activity was nucleotide independent and, with decreasing order of effectiveness, these activities were supported by Mn2+ and Mg2+. AMP is an activator of these reactions. V max for the OAA decarboxylase activities in A. succiniciproducens and S. cerevisiae PEPCKs was 4% and 0.2% that of the PEP-forming reaction, respectively.
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    Fluorescence staining of yeast cells permeabilized by killer toxin K1: Determination of optimum conditions (1993)
    Springer
    Journal of fluorescence 3 (1993), S. 241-244 
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    ISSN: 1573-4994
    Keywords: Killer toxin K1 ; bromocresol purple staining ; Saccharomyces cerevisiae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract Optimal assay conditions were established for the previously described method used to determine the activity ofSaccharomyces cerevisiae pore-forming killer toxin K1. The method is based on cell staining with bromocresol purple. Sensitive cells ofS. cerevisiae from the early exponential phase under nongrowth conditions and in the presence of glucose were the most convenient for determining the killer toxin activity. Maximum killing war reached when the suspension was buffered with 10 mM citrate-phosphate at pH 4.6.
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    Identification and characterization of a second plasma membrane H+-ATPase gene subfamily in Nicotiana plumbaginifolia (1993)
    Springer
    Plant molecular biology 21 (1993), S. 955-963 
    Details
    ISSN: 1573-5028
    Keywords: multigene family ; Nicotiana ; phylogeny ; plasma membrane H+-ATPase ; sequence
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A cDNA clone was isolated for a fourth pma gene encoding a putative plasma membrane H+-ATPase of Nicotiana plumbaginifolia. The sequence of the predicted 952 residue PMA4 polypeptide was compared with those of other known plant PMAs, revealing a higher identity with the Arabidopsis thaliana proteins (86–89%) than with the other three N. plumbaginifolia PMA proteins (80–82%). This supports the view that there are two pma subfamilies which probably arose from a gene duplication predating the separation of the Dilleniidae and Asteridae plant subclasses. Measured pma4 transcript levels indicate that pma4 is similarly expressed in root, stem, leaf, and flower tissues, contrary to the pmal-3 subfamily whose members displayed differential expression according to the organ.
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    Phylogenetic relationships ofMicrosphaera andErysiphe sectionErysiphe (powdery mildews) inferred from the rDNA ITS sequences (1999)
    Springer
    Mycoscience 40 (1999), S. 259-268 
    Details
    ISSN: 1618-2545
    Keywords: Erysiphe ; internal transcribed spacer ; Microsphaera ; phylogeny ; powdery mildew
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The genusMicrosphaera has been considered to be derived from sectionErysiphe of the genusErysiphe by a single event. Cleistothecial appendages are the most distinct difference between the two genera and have an important role for overwintering. To understand the phylogenetic relationship betweenErysiphe sectionErysiphe andMicrosphaera more precisely, phylogenetic trees were constructed using the nucleotide sequences of the rDNA ITS region from 11Erysiphe (sectionErysiphe) and 16Microsphaera taxa. The phylogenetic trees indicated the close relationship between the two genera. However, the generaErysiphe (sectionErysiphe) andMicrosphaera did not group into separate monophyletic lineages; instead, they formed several small clusters that were mixed together. This result suggests that the differentiations of the genera occurred two or more times independently. This also supports the idea that appendage morphology does not always accurately reflect the phylogeny of the powdery mildews because the morphology of appendages may evolve convergently under the selection pressure of their particular biotopes (host plants).
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    Phylogenetic relationships ofPythium species based on ITS and 5.8S sequences of the ribosomal DNA (1999)
    Springer
    Mycoscience 40 (1999), S. 321-331 
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    ISSN: 1618-2545
    Keywords: Chromista ; internal transcribed spacer ; phylogeny ; Pythium ; 5.8S rDNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The sequences of ITS regions in 30 species and two groups of the genusPythium were resolved. In the phylogenetic trees, the species were generally divided into two clusters, referred to here as the F and S groups. The species in the two groups correspond in terms of their sporangial morphology, with the F group being filamentous/lobulate and the S group being spherical. Genetic divergence within the F group was lower than that within the S group. Other morphological characteristics such as oogonial structure and sexual nature appeared to be unrelated to the groupings in these trees. An alignment analysis revealed common sequences to all the species and arrangements specific to each F or S group. It was found that the ITS region was a good target in designing species-specific primers for the identification and detection ofPythium species. In the tree based on 5.8S rDNA sequences, oomycetes are distantly related to other fungi but separated from algae in Chromista.
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    Genetic evidence for interaction between components of the yeast 26S proteasome: combination of a mutation in RPN12 (a lid component gene) with mutations in RPT1 (an ATPase gene) causes synthetic lethality (1999)
    Springer
    Molecular genetics and genomics 262 (1999), S. 145-153 
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    ISSN: 1617-4623
    Keywords: Key words Proteasome ; Synthetic lethality ; Saccharomyces cerevisiae ; AAA-ATPase ; 19S Regulatory particle
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The 19S regulatory particle of the yeast 26S proteasome consists of six related ATPases (Rpt proteins) and at least 11 non-ATPase proteins (Rpn proteins). RPN12 (formerly NIN1) encodes an Rpn component of the 19S regulatory particle and is essential for growth. To determine which subunit(s) of the 26S proteasome interact(s) with Rpn12, we attempted to screen for mutations that cause synthetic lethality in the presence of the rpn12-1 (formerly nin1-1) mutation. Among the candidates recovered was a new allele of RPT1 (formerly CIM5). This mutant allele was designated rpt1-2; on its own this mutation caused no phenotypic change, whereas the rpn12-1 rpt1-2 double mutant was lethal, suggesting a strong interaction between Rpn12 and Rpt1. The site of the rpt1-2 mutation was determined by DNA sequencing of the RPT1 locus retrieved from the mutant, and a single nucleotide alteration was found. This changes amino acid 446 of the RPT1 product from alanine to valine. The alanine residue is conserved in all Rpt proteins, except Rpt5, but no function has yet been assigned to the region that contains it. We propose that this region is necessary for Rpt1 to interact with Rpn12. The terminal phenotype of the rpn12-1 rpt1-2 double mutant was not cell cycle specific, suggesting that in the double mutant cells the function of the 26S proteasome is completely eliminated, thereby inducing multiple defects in cellular functions.
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    Cat8p, the activator of gluconeogenic genes in Saccharomyces cerevisiae, regulates carbon source-dependent expression of NADP-dependent cytosolic isocitrate dehydrogenase (Idp2p) and lactate permease (Jen1p) (1999)
    Springer
    Molecular genetics and genomics 262 (1999), S. 869-875 
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    ISSN: 1617-4623
    Keywords: Key wordsCAT8 ; Transcriptional regulation ; IDP2 ; JEN1 ; Saccharomyces cerevisiae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The yeast transcriptional activator Cat8p has been identified as a factor that is essential for the derepression of genes involved in gluconeogenesis (like FBP1, PCK1, ACR1, ICL1 and MLS1) when only non-fermentable carbon sources are provided. Cat8p-dependent expression is mediated by cis-acting elements in the respective promoters, which are named UAS/CSREs (upstream activating sequence/carbon source responsive element). To establish whether the function of Cat8p is restricted to the activation of gluconeogenesis or is also involved in the regulation of a greater variety of genes, we investigated the transcriptional regulation of two genes, IDP2 and JEN1, which exhibit a similar expression pattern to gluconeogenic genes, although IDP2 at least is not linked directly to the gluconeogenic pathway. We identified functional UAS/CSRE elements in the promoters of both genes. Expression studies revealed that JEN1 is regulated negatively by the repressors Mig1p and Mig2p, and that Cat8p is needed for full derepression of the gene under non-fermentative growth conditions. Furthermore, we showed that Mig2p is also involved in the repression of CAT8 itself. The results presented in this study support a model in which Cat8p-dependent gene activation is not restricted to gluconeogenesis, but targets a wide variety of genes which are strongly derepressed under non-fermentative growth conditions.
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    Yeast genes GIS1–4: multicopy suppressors of the Gal− phenotype of snf1 mig1 srb8/10/11 cells (1999)
    Springer
    Molecular genetics and genomics 262 (1999), S. 589-599 
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    ISSN: 1617-4623
    Keywords: Key words Ras/cAMP pathway ; Saccharomyces cerevisiae ; Snf1 ; Mig1 ; Mediator
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Cyclin C and the cyclin C-dependent protein kinase are associated with the RNA polymerase II Mediator complex, which regulates initiation of transcription in response to signals from activators and repressors bound to upstream promoter elements. Disruption of the corresponding genes, SRB11 and SRB10, in budding yeast causes a reduction in expression of the GAL genes, which is particularly pronounced in a mig1 snf1 background. We have screened two yeast genomic libraries for genes that can suppress this phenotype when overexpressed. Seven suppressor genes were identified, GIS1–7. GIS1 encodes one of two related zinc-finger proteins, which also share two other highly conserved domains present in several eukaryotic transcription factors. GIS2 encodes a homologue of the mammalian CNBP and fission yeast Byr3 proteins. GIS3 and GIS4 predict proteins with no obvious similarities to any known proteins. GIS5–7 are identical to the previously described genes PDE2, SGE1 and TUB3, respectively. None of the suppressor genes seem to be involved in Mediator function. Instead, we find that the GIS1, GIS2 and GIS4 genes interact with the CDC25 gene, indicating a possible involvement of these genes in the RAS/cAMP signaling pathway.
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    Growth-related expression of ribosomal protein genes in Saccharomyces cerevisiae (1993)
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    Molecular genetics and genomics 239 (1993), S. 196-204 
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    ISSN: 1617-4623
    Keywords: Saccharomyces cerevisiae ; Ribosomal protein genes ; Transcription activation ; cAMP ; Growth control
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The rate of ribosomal protein gene (rp-gene) transcription in yeast is accurately adjusted to the cellular requirement for ribosomes under various growth conditions. However, the molecular mechanisms underlying this co-ordinated transcriptional control have not yet been elucidated. Transcriptional activation of rp-genes is mediated through two different multifunctional trans-acting factors, ABF1 and RAP1. In this report, we demonstrate that changes in cellular rp-mRNA levels during varying growth conditions are not parallelled by changes in the in vitro binding capacity of ABF1 or RAP1 for their cognate sequences. In addition, the nutritional upshift response of rp-genes observed after addition of glucose to a culture growing on a non-fermentative carbon source turns out not to be the result of increased expression of the ABF1 and RAP1 genes or of elevated DNA-binding activity of these factors. Therefore, growth rate-dependent transcription regulation of rp-genes is most probably not mediated by changes in the efficiency of binding of ABF1 and RAP1 to the upstream activation sites of these genes, but rather through other alterations in the efficiency of transcription activation. Furthermore, we tested the possibility that cAMP may play a role in elevating rp-gene expression during a nutritional shift-up. We found that the nutritional upshift response occurs normally in several mutants defective in cAMP metabolism.
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    Inducible removal of UV-induced pyrimidine dimers from transcriptionally active and inactive genes of Saccharomyces cerevisiae (1993)
    Springer
    Molecular genetics and genomics 239 (1993), S. 28-32 
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    ISSN: 1617-4623
    Keywords: Saccharomyces cerevisiae ; UV damage ; Mating type ; Inducible repair
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The prior UV irradiation of α haploid Saccharomyces cerevisiae with a UV dose of 25 J/m2 substantially increases the repairability of damage subsequently induced by a UV dose of 70 J/m2 given 1 h after the first irradiation. This enhancement of repair is seen at both the MATa and HMLα loci, which are, respectively, transcriptionally active and inactive in α haploid cells. The presence in the medium of the protein synthesis inhibitor, cycloheximide in the period between the two irradiations eliminated this effect. Enhanced repair still occurred if cycloheximide was present only after the final UV irradiation. This indicated that the first result is not due to cycloheximide merely blocking the synthesis of repair enzymes associated with a hypothetical rapid turnover of such molecules. The enhanced repairability is not the result of changes in chromatin accessibility without protein synthesis, merely caused by the repair of the damage induced by the prior irradiation. The data clearly show that a UV-inducible removal of pyrimidine dimers has occurred which involves the synthesis of new proteins. The genes known to possess inducible promoters, and which are involved in excision are RAD2, RAD7, RAD16 and RAD23. Studies with the rad7 and rad16 mutants which are defective in the ability to repair HMLα and proficient in the repair' of MATα showed that in rad7, preirradiation enhanced the repair at MATα, whereas in rad16 this increased repair of MATα was absent. The preirradiation did not modify the inability to repair HMLα in either strain. Thus RAD16 has a role in this inducible repair. Inducible repair is also absent in a rad2 strain which cannot repair MATα or HMLα after a single UV dose.
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    Cladistic interrelationships and major clades of theEricales (1993)
    Springer
    Plant systematics and evolution 184 (1993), S. 207-231 
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    ISSN: 1615-6110
    Keywords: Angiosperms ; Ericales ; Cladistics ; phylogeny ; taxonomy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A cladistic analysis of theEricales based on morphological, anatomical, embryological, and phytochemical data has been undertaken. Resulting from the analysis, 56 equally parsimonious cladograms were obtained. The tribeEnkiantheae was found to be the sister-group of the rest of theEricaceae, in which theEmpetraceae, theEpacridaceae, Pyrolaceae, andMonotropaceae are forming derived ingroups. It is thus concluded that theEricaceae are a paraphyletic assemblage as presently circumscribed, and thatEmpetraceae andEpacridaceae are better treated as members of theEricaceae.
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    A cladistic analysis of the tribeAstereae (Asteraceae) with notes on their evolution and subtribal classification (1993)
    Springer
    Plant systematics and evolution 184 (1993), S. 259-283 
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    ISSN: 1615-6110
    Keywords: Angiosperms ; Asteraceae ; Astereae ; Cladistics ; evolution ; phylogeny ; classification
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract TheAstereae were surveyed and the genera arranged in 23 informal groups. The generic groups were used to sample representative genera for a cladistic analysis based on morphological characters. The resulting cladogram was used for discussion of evolution and subtribal classification within the tribe. The lower basic chromosome numbers x = 4, 5, 6, and 8 are interpreted as reductions from a primitive x = 9. The subtribeGrangeinae occupies a phylogenetically basal position as sister group to the rest of the tribe. This may be divided into two large groups, largely corresponding to the homochromousSolidagininae and to the heterochromousAsterinae sensu lato, i.e. including theBellidinae, Hinterhuberinae, Conyzinae, andBaccharidinae. The latter four subtribes are derived within theAsterinae, and hence reduced to synonymy. Several intercontinental relationships indicate that a geographical subdivision of the tribe should be avoided, although in our analysis most of the groups proved to be restricted to one of five major regions.
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    Phylogeny of thePolygalaceae and its taxonomic implications (1993)
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    Plant systematics and evolution 186 (1993), S. 33-55 
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    ISSN: 1615-6110
    Keywords: Polygalaceae ; Carpolobieae ; Ancylotropis ; Pteromonnina ; Taxonomy ; phylogeny ; cladistics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The phylogeny of thePolygalaceae is analysed cladistically. The two tribesXanthophylleae andMoutabeae are maintained in their former circumscription while a new tribe, theCarpolobieae, comprising the African generaCarpolobia andAtroxima is detached from thePolygaleae. Within thePolygaleae, the generaPolygala andMonnina appears to be polyphyletic. It is concluded thatMonnina subg.Monninopsis andM. subg.Pterocarya are better recognized as independent genera, here described asAncylotropis andPteromonnina, respectively. More work needs to be done before taxonomical decisions are made regardingPolygala. Bredemeyera andComesperma, which are often joined in a single genus, are found to be only distantly related.
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    Chloroplast DNA variation and phylogeny of theRanunculaceae (1993)
    Springer
    Plant systematics and evolution 187 (1993), S. 29-49 
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    ISSN: 1615-6110
    Keywords: Angiosperms ; Ranunculaceae ; Chloroplast DNA ; rearrangements ; mutation frequency ; phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Restriction site mapping of chloroplast DNA from 31 species representing 26 genera of theRanunculaceae was performed using eleven restriction endonucleases. The chloroplast genome varies in length from approximately 152 to 160 kb. Length variants are frequent in theRanunculaceae and range from usually less than 300 bp to rarely 1.5 kb. The inverted repeat is extended into the large single copy (LSC) region by 4–4.5 kb inAnemone, Clematis, Clematopsis, Hepatica, Knowltonia, andPulsatilla. Several inversions are present in the LSC-region of the cpDNA in all these genera and inAdonis. The frequency of restriction site mutations varies within the chloroplast genome in theRanunculaceae between 4 and 32 mutations per kilobase, and is lowest in the inverted repeat and the regions containing the ATPase-genes and the genespsaA, psaB, psbA, rpoB, andrbcL. A total of 547 phylogenetically informative restriction sites was utilized in cladistic analyses of the family using Wagner, Dollo, and weighted parsimony. These three parsimony analyses result in different tree topologies. Four, six, and one equally most parsimonious trees were obtained with Wagner, Dollo, and weighted parsimony, respectively. The amount of support for the monophyletic groups was evaluated using bootstrapping and decay analysis. All three parsimony methods suggest thatHydrastis is the sister group to the remainder of theRanunculaceae, and that theAnemone-Clematis group, which shares several derived cpDNA rearrangements, is monophyletic. Only a few of the traditional groups in theRanunculaceae are supported by cpDNA restriction side data. Only Dollo parsimony provides support for the hypothesis thatThalictroideae andRanunculoideae are monophyletic.
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    Chloroplast DNA variation in the genusSecale (Poaceae) (1993)
    Springer
    Plant systematics and evolution 187 (1993), S. 115-125 
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    ISSN: 1615-6110
    Keywords: Poaceae ; Secale ; cpDNA variation ; RFLP ; phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The chloroplast genomes of 44 accessions ofSecale were surveyed for restriction site polymorphisms. The accessions were chosen to represent the geographic as well as taxonomic range of the genus. Using 12 restriction enzymes a total of 348 sites were detected. Twenty-nine mutation sites were phylogenetically informative and used in a cladistic analysis. Further, a 0.1 kb insertion separatedSecale from the outgroup species. Only the annual speciesS. sylvestre was distinct from the rest of the taxa. Cultivated rye together with both wild annual and wild perennial accessions were mixed among each other. Sequence divergence (p) among taxa ofSecale was low, varying from 0.000 to 0.005, suggesting a rather recent origin of the genus.
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    A phylogenetic analysis of the lichen familySphaerophoraceae (Caliciales); a new generic classification and notes on character evolution (1993)
    Springer
    Plant systematics and evolution 187 (1993), S. 213-241 
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    ISSN: 1615-6110
    Keywords: Ascomycetes ; Bunodophoron ; Caliciales ; Calycidium ; Leifidium ; Sphaerophoraceae ; Sphaerophorus ; Cladistics ; classification ; evolution ; systematics ; phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A phylogenetic analysis of the familySphaerophoraceae (Caliciales, lichenized ascomycetes) has resulted in a new generic classification. Notes on character evolution are given. The generaSphaerophorus s. str.,Bunodophoron andLeifidium, gen. nov., are accepted.Pleurocybe andPseudosphaerophorus are considered synonyms ofBunodophoron andThysanophoron is considered synonym toSphaerophorus. The following new combinations are proposed:Bunodophoron coomerense (Ohlsson)Wedin,B. diplotypum (Vain.)Wedin,B. dodgei (Ohlsson)Wedin,B. flaccidum (Kantvilas & Wedin)Wedin,B. formosanum (Zahlbr.)Wedin,B. imshaugii (Ohlsson)Wedin,B. insigne (Laurer)Wedin,B. kinabaluense (M. Satô)Wedin,B. macrocarpum (Ohlsson)Wedin,B. madagascareum (Nyl.)Wedin,B. microsporum (Ohlsson)Wedin,B. murrayi (Ohlsson)Wedin,B. notatum (Tibell)Wedin,B. ohlssonii (Wedin)Wedin,B. patagonicum (C. W. Dodge)Wedin,B. ramuliferum (I. M. Lamb)Wedin,B. scrobiculatum (C. Bab.)Wedin,B. tibellii (Wedin)Wedin,B. whakapapaense (Wedin)Wedin, andLeifidium tenerum (Laurer)Wedin.
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    Ribosomal DNA variation and its phylogenetic implication in the genusBrachypodium (Poaceae) (1993)
    Springer
    Plant systematics and evolution 188 (1993), S. 125-138 
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    ISSN: 1615-6110
    Keywords: Poaceae ; Brachypodium ; rDNA repeat units ; restriction map ; phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The structure of ribosomal DNA ofBrachypodium and several other grass species was investigated using a heterologous rDNA probe from wheat. Several different rDNA families were present among perennial and annual species within the genus. In contrast to the annual species the perennial species exhibited a very low degree of repeat length variation. An extra Eco RI site and a Hin dIII site were observed in the IGS, which distinguishedBrachypodium from other grass genera. The restriction fragment length polymorphism and length variation of the repeat units have taxonomic value withinBrachypodium and are correlated with the classification ofBrachypodium derived from other data.
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    A revision of the moss genusCrossidium (Pottiaceae) with the description of the new genusMicrocrossidium (1993)
    Springer
    Plant systematics and evolution 188 (1993), S. 213-235 
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    ISSN: 1615-6110
    Keywords: Bryophyta ; Musci ; Pottiaceae ; Crossidium ; Microcrossidium gen. nov. ; Taxonomy ; phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A world revision of the genusCrossidium Jur. recognizes 11 species, which are described and discussed in the context of important taxonomic characters. An identification key is provided.C. asirense Frey & Kürschner is reduced to synonymy withC. davidai Catcheside, and the geographical range ofC. laevipilum Ther. & Trab. is extended to Europe. Phylogenetic trends are interpreted on the basis of two main evolutionary lines associated with the presence or absence of hyaline hair-points on the leaves. A twelfth species is transferred toMicrocrossidium Guerra & Cano, gen. nov., asM. apiculatum (Magill)Guerra & Cano, comb. nova, because of differences in stem anatomy, peristome configuration, and spore morphology.
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    The phylogeny of land plants: A cladistic analysis based on male gametogenesis (1993)
    Springer
    Plant systematics and evolution 188 (1993), S. 237-269 
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    ISSN: 1615-6110
    Keywords: Bryophytes ; ferns ; gymnosperms ; seed plants ; land plants ; Antheridia ; cladistics ; gametogenesis ; phylogeny ; spermatogenesis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A cladistic analysis was carried out to resolve phylogenetic pattern among bryophytes and other land plants. The analysis used 22 taxa of land plants and 90 characters relating to male gametogenesis.Coleochaete orChara/Nitella were the outgroups in various analyses using HENNIG86, PAUP, and MacClade, and the land plant phylogeny was unchanged regardless of outgroup utilized. The most parsimonious cladograms from HENNIG86 (7 trees) have treelengths of 243 (C.I. = 0.58, R.I. = 0.82). Bryophytes are monophyletic as are hornworts, liverworts, and mosses, with hornworts identified as the sister group of a liverwort/moss assemblage. In vascular plants, lycophytes are polyphyletic andSelaginella is close to the bryophytes.Lycopodium is the sister group of the remaining vascular plants (minusSelaginella). Longer treelengths (over 250) are required to produce tree topologies in which either lycophytes are monophyletic or to reconstruct the paraphyletic bryophyte phylogeny of recent authors. This analysis challenges existing concepts of bryophyte phylogeny based on more classical data and interpretations, and provides new insight into land plant evolution.
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    Seed oil fatty acid patterns of theAconitum-Delphinium-Helleborus complex (Ranunculaceae) (1999)
    Springer
    Plant systematics and evolution 215 (1999), S. 37-47 
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    ISSN: 1615-6110
    Keywords: Ranunculaceae ; Aconitum ; Delphinium ; Helleborus ; Nigella ; Seed oil ; fatty acids ; phylogeny ; evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Many members ofRanunculaceae contain unusual fatty acids in their seed oils. This leads to rather typical genus-specific fatty acid patterns or “fingerprints” in these seed oils. The members of theDelphinioideae and/orHelleboroideae, however, do not contain highly unusual fatty acids. Nevertheless, their seed oil fatty acid fingerprints are also fairly typical and genus-specific, and the patterns found are rather consistent throughout several species of one genus. It was found that species ofAconitum do not contain fatty acids with 20 carbon atoms.Delphinium, Consolida, Helleborus, Nigella and others do contain C20 fatty acids. In allHelleborus species, for example, there was a consistent C20 fatty acid pattern of 20:0≪20:1≫20:2〉20:3. Species ofNigella andGaridella contain high levels,Helleborus low levels, of 20:2n-6 in their seed oils.Delphinium andAconitum both contain low levels of 18:3n-3, whereasHelleborus spp. consistently show high levels of this fatty acid. The genus-specific fatty acid patterns found are discussed, and a correlation with the subfamily and tribe affiliation of the genera investigated here is attempted.
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    Chromosome number evolution in the tribeBrassiceae (Brassicaceae): Evidence from isozyme number (1999)
    Springer
    Plant systematics and evolution 215 (1999), S. 255-285 
    Details
    ISSN: 1615-6110
    Keywords: Brassiceae ; Isozyme number ; chromosome number ; phylogeny ; gene duplication
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Variation in isozyme number was used to assess the evolution of haploid chromosome numbers (n=6−75) and systematic relationships in the tribeBrassiceae, which is believed to be one of the few monophyletic tribes in theBrassicaceae. Ten enzyme systems were surveyed among 108 species in 35 genera of tribeBrassiceae and for 11 species from seven other tribes. The data indicated that taxa with n=7−13 and n=14−18 were similar in isozyme number, suggesting that genera with n=14−18 did not arise from polyploidy (i.e. entire duplication) of the n=7−13 genomes. These results suggest that aneuploidy and/or chromosome fusion/splitting have played a more significant role than polyploidy in the evolution of higher base chromosome numbers in the tribe. The detection of widespread isozyme duplication in the tribe is consistent with reports of extensive gene duplication in theBrassica crop species, and suggests that the common ancestor of the tribe already had undergone a polyploid event, i.e. complete genome duplication, prior to aneuploid divergence. Inheritance studies conducted onSinapis arvensis showed that segregation ratios at seven loci (Fbp-2,Gpi-2,Idh-2,Pgm-2,Pgm-2′,Tpi-1,Tpi-1′) conformed to those expected under Mendelian inheritance. Isozyme duplications were phylogenetically informative at various taxonomic levels in the tribe. In particular, duplications for cytosolic phosphoglucomutase (Pgm-2,Pgm-2′) and plastid triosephosphate isomerase (Tpi-1,Tpi-1′) were evident in 33 of the 35 genera examined, supporting the monophyletic status of theBrassiceae with the inclusion ofOrychophragmus and the exclusion of controversial membersCalepina andConringia.
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    URL: http://dx.doi.org/10.1007/BF00984659
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    Phylogeny and biosystematics ofPseudomonotes (Dipterocarpaceae) based on molecular and morphological data (1999)
    Springer
    Plant systematics and evolution 216 (1999), S. 197-205 
    Details
    ISSN: 1615-6110
    Keywords: Dipterocarpaceae ; Monotoideae ; Dipterocarpoideae ; Pakaraimoideae ; Pseudomonotes ; Monotes ; Marquesia ; rbcL ; phylogeny ; biosystematics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The placement of a recently discovered South American monotypic genus,Pseudomonotes tropenbosii, in subfam.Monotoideae (Dipterocarpaceae) extends the geographical range of the subfamily from Africa to the Neotropics. Although morphological and anatomical evidence suggest similarities betweenPseudomonotes andMonotes, the close alliance of these two genera was questionable due to their disjunct distribution and a lack of phylogenetic analysis. In the present study, we reconstructed the phylogeny ofPseudomonotes and other putatively related taxa usingrbcL sequence data. The analysis ofrbcL sequences of 20 taxa belonging to 15 genera and eight families recovered a single most parsimonious tree. The genusSarcolaena (Sarcolaenaceae) formed a clade sister to the monophyleticDipterocarpaceae clade.Monotes andPseudomonotes formed a strongly supported group, sister to the monophyletic clade withPakaraimaea and the remaining Asiatic dipterocarp species studied. The study strongly supports the placement ofPseudomonotes within subfam.Monotoideae of theDipterocarpaceae.
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    URL: http://dx.doi.org/10.1007/BF01084398
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    The phylogeny ofActaea (Ranunculaceae): A biogeographical approach (1999)
    Springer
    Plant systematics and evolution 216 (1999), S. 251-263 
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    ISSN: 1615-6110
    Keywords: Ranunculaceae ; Cimicifugeae ; Actaea ; Cimicifuga ; Souliea ; Anemonopsis ; Biogeography ; morphology ; ecology ; phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Phylogenetic analyses of the genusActaea were performed using morphological, ecological and biogeographical characters. Using solely morphological characters, the relationships of the three identified species-groups remain uncertain. Close biogeographical examination and comparison of the areas with ecological peculiarities as well as climate data gave important insight into the phylogeny ofActaea and the whole tribe. Consequently, the obtained biogeographical data were used for phylogenetic reconstructions. Both, from the point of view of morphological and biogeographical data,A. pachypoda andA. asiatica are the most ancestral species. They grow on the east sides of the continents, mainly in broad-leaved forests. In West Eurasia the apomorphicA. spicata andA. acuminata occur under similar climatic and ecological conditions, but these species are adapted to another climate rhythm. The most advanced species (A. erythrocarpa, A. rubra) are to be found in the boreal forests where they are widely distributed. This biogeographical approach revealed that the evolution of the species led to a gradual widening and shifting of their ecological constitutions.
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    URL: http://dx.doi.org/10.1007/BF01084402
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    The Concept of Monophyly: A Speculative Essay (1999)
    Springer
    Biology and philosophy 14 (1999), S. 331-348 
    Details
    ISSN: 1572-8404
    Keywords: cladistics ; evolutionary genomics ; monophyly ; origins of life ; origins of tetrapods ; phylogeny ; systematics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Philosophy
    Notes: Abstract The concept of monophyly is central to much of modern biology. Despite many efforts over many years, important questions remain unanswered that relate both to the concept itself and to its various applications. This essay focuses primarily on four of these: i) Is it possible to define monophyly operationally, specifically with respect to both the structures of genomes and at the levels of the highest phylogenetic categories (kingdoms, phyla, classes)? ii) May the mosaic and chimeric structures of genomes be sufficiently important factors in phylogeny that situations exist in which the concept may not be applicable? iii) In the history of life on earth were there important groups of organisms that probably had polyphyletic, rather than monophyletic, origins? iv) Does the near universal search for monophyletic origins of clades lead, on occasion, to both undesirable narrowing of acceptable options for development of evolutionary scenarios and sometimes actual omission from consideration of less conventional types of both data and modes of thought, possibly at the expense of biological understanding? Three sections in the essay consider possible answers to these questions: i) A reassessment is made of major features of both the concept and some of its applications. Recent research results make it seem improbable that there could have been single basal forms for many of the highest categories of evolutionary differentiation (kingdoms, phyla, classes). The universal tree of life probably had many roots. Facts contributing to this perception include the phylogenetically widespread occurrences of: horizontal transfers of plasmids, viral genomes, and transposons; multiple genomic duplications; the existence and properties of large numbers of gene families and protein families; multiple symbioses; broad-scale hybridizations; and multiple homoplasys. Next, justifications are reassessed for the application of monophyletic frameworks to two major evolutionary developments usually interpreted as having been monophyletic: ii) the origins of life; and iii) the origins of the vertebrate tetrapods. For both cases polyphyletic hypotheses are suggested as more probable than monophyletic hypotheses. Major conclusions are, as answers to the four questions posed above: probably not, yes, yes, and yes.
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    URL: http://dx.doi.org/10.1023/A:1006535524246
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    Molecular phylogeny of onygenalean fungi based on small subunit ribosomal DNA (SSU rDNA) sequences (1999)
    Springer
    Mycoscience 40 (1999), S. 251-258 
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    ISSN: 1618-2545
    Keywords: Onygenales ; phylogeny ; small subunit rDNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Phylogenetic analysis of nucleotide data from small subunit ribosomal DNA (SSU rDNA) sequences (ca. 1685 bp.) was performed on 19 taxa of the Onygenales and three related mitosporic fungi. Phylogenetic trees were constructed by the neighbor-joining method with the sequence data of related taxa obtained from DNA databases. The species in the Onygenales form two clusters and seven subclusters, and the tree topology reflects the traditional classification by Currah (1985) with some exceptions. The Myxotrichaceae is placed in the different lineage, separate from other plectomycetous taxa and among the Leotiales and the Erysiphales. Furthermore, two separate lineages in the Myxotrichaceae were found. Tree topology suggested the Onygenaceae is polyphyletic and composed of three subgroups; 1) most members of Onygenaceae, 2)Spiromastix warcupii, and 3) pathogenic dimorphic fungi classified inAjellomyces.
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    URL: http://dx.doi.org/10.1007/BF02463962
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    Modus Darwin (1999)
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    Biology and philosophy 14 (1999), S. 253-278 
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    ISSN: 1572-8404
    Keywords: ancestry ; Bayesianism ; creationism ; Darwin ; evolution ; likelihood ; natural selection ; phylogeny ; probability ; Reichenbach
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Philosophy
    Notes: Abstract Modus Darwin is a principle of inference that licenses the conclusion that two species have a common ancestor, based on the observation that they are similar. The present paper investigates the principle's probabilistic foundations.
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    URL: http://dx.doi.org/10.1023/A:1006626115852
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    Reflections on higher mammalian phylogenetics (1993)
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    Journal of mammalian evolution 1 (1993), S. 3-30 
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    ISSN: 1573-7055
    Keywords: Mammalia ; phylogeny ; comparative data
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract For well over a decade, the higher-level relationships of mammals has been the focus of intensive and broad-ranging investigations. The sources of evidence drawn upon for this purpose are both traditional (e.g., paleontology, skeletal morphology) and newly sampled (e.g., comparative gene sequencing). A basic methodology, nonetheless, pervades this diversity of sampling. Issues that concern all types of data include the assumptions for recognizing homology, the techniques for building trees, the justification of parsimony and weighting, and the means of evaluating and comparing different results. In some areas (e.g., paleontology, molecular comparisons), we have been continual or even explosive expansion of the data base. In other areas (e.g., comparative behavior, physiology, or comparisons involving many aspects of nonskeletal morphology), the expansion has been far less dramatic. Codifying large arrays of characters is no substitute for penetrating studies of comparative form, function, and ontogeny or careful sampling of a diversity of genes. It is hoped that the latter emphases are maintained and nourished. The results of all this recent activity show a mixed profile of resolution for higher-level patterns of phylogeny. Particularly, the higher eutherian mammal radiation still presents many problems. Such challenges, however, have attracted an unprecedented level of synthesis and interaction.
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    URL: http://dx.doi.org/10.1007/BF01027597
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    Disparate Data Sets Resolve Squirrel Monkey (Saimiri) Taxonomy: Implications for Behavioral Ecology and Biomedical Usage (1999)
    Springer
    International journal of primatology 20 (1999), S. 237-256 
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    ISSN: 1573-8604
    Keywords: squirrel monkey ; capuchin ; speciation ; phylogeny ; research model
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Squirrel monkeys (Saimiri spp.) are the most commonly used neotropical (platyrrhine) monkeys in biomedical research; however, no consensus exists as to the phylogenetic relationships amongst geographic variants or whether these variants represent species or subspecies. Here we report a strongly supported squirrel monkey phylogeny, congruent across multiple data sets, including new field data and the first molecular (mtDNA) cladogram. These data support species-level classification for the three major groups in this study. Approximately the same amount of molecular divergence exists among Saimiri oerstedii, S. sciureus, and S. boliviensis. The S. sciureus/S. oerstedii ancestor diverged from S. boliviensis and shortly thereafter S. sciureus and S. oerstedii diverged. Until now, lack of a robust taxonomy has hindered exploitation of the massive potential of Saimiri for comparative studies. No other primate genus displays such widely divergent, genetically-based social behaviors. Our taxonomy also provides robust support for previous warnings against the widespread use of hybrid squirrel monkeys as research models.
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    URL: http://dx.doi.org/10.1023/A:1020522519946
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    Phylogeny of the slow lorises (genusNycticebus): An approach using mitochondrial DNA restriction enzyme analysis (1993)
    Springer
    International journal of primatology 14 (1993), S. 167-175 
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    ISSN: 1573-8604
    Keywords: Nycticebus ; phylogeny ; mitochondrial DNA ; Restriction enzyme analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Mitochondrial DNA polymorphisms in 15 specimens of three species of slow lorises-Nycticebus coucang, N. intermedius, andN. pygmaeus-were analyzed in order to study the evolutionary relationships among the species. Eight restriction types were observed in the samples. Phylogenetic trees constructed on the basis of genetic distances showed that the slow lorises sort into two clusters: four types ofN. coucang and three types ofN. intermedius plus one type ofN. pygmaeus. Our results suggest that there are two valid species in the genusNycticebus-N. coucang, andN. pygmaeus-and thatN. intermedius should be included withinN. pygmaeus. Divergence between the two species may have begun 2.7 Ma (million years ago). Evolution of gross morphology, chromosomes, and mitochondrial DNA in the slow lorises appears to be concordant.
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    Phylogeny of rheusus monkeys (Macaca mulatta) as revealed by mitochondrial DNA restriction enzyme analysis (1993)
    Springer
    International journal of primatology 14 (1993), S. 587-605 
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    ISSN: 1573-8604
    Keywords: Macaca mulatta ; mitochondrial DNA ; restriction enzyme analysis ; phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Mitochondrial DNA, purified from 36 samples of 23 local populations which are widely distributed in Vietnam, Burma, and 10 provinces of China, has been analyzed to model the phylogeny of rhesus monkeys. The 20 local populations of China may represent nearly all major populations in China. Using 20 restriction endonucleases of 6-bp recognition, we observed a total of 50–61 sites in the various samples. By combining the cleavage patterns for each enzyme, the 36 samples were classified into 23 restriction types, each of which was found exclusively in the respective population from which samples were obtained. By combining the earlier study of Indian rheusus monkeys, phylogenetic trees, which have been constructed on the basis of genetic distance, indicate that rhesus monkeys in China, Vietnam, India, and Burma can be divided into seven groups. Integrating morphological and geographical data, we suggest that rhesus monkeys in China, Vietnam, and Burma may be classified into six subspecies—M. m. mulatta, M. m. brevicaudus, M. m. lasiotis, M. m. littoralis, M. m. vestita, and M. m. tcheliensis-and rhesus monkeys in India may be another valid subspecies.M. m. tcheliensis is the most endangered subspecies in China. Divergence among subspecies may have begun 0.9–1.6 Ma. The radiation of rhesus monkeys in China may have spread from the southwest toward the east. The taxonomic status of the Hainan monkey and the Taiwan monkey require further investigation.
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    URL: http://dx.doi.org/10.1007/BF02215449
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    The use of a non-coding region of chloroplast DNA in phylogenetic studies of the subtribeSonchinae (Asteraceae:Lactuceae) (1999)
    Springer
    Plant systematics and evolution 215 (1999), S. 85-99 
    Details
    ISSN: 1615-6110
    Keywords: Sonchinae ; Asteraceae ; cpDNA ; non-coding region (psbA-trnHGUG) ; phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The systematic utility of sequences from a non-coding region of chloroplast DNA (cpDNA) betweenpsbA andtrnH(GUG) was examined by assessing phylogenetic relationships in subtribeSonchinae (Asteraceae:Lactuceae). Primers constructed against highly conserved regions of tRNA genes were used for PCR amplification and sequencing. ThepsbA-trnH intergenic spacer contains several insertions and deletions (indels) inSonchinae with the length varying from 385 to 450 bp. Sequence divergence ranges from 0.00% to 7.54% withinSonchinae, with an average of 2.4%. Average sequence divergence inSonchus subg.Sonchus is 2.0%, while the mean for subg.Dendrosonchus and its close relatives in Macaronesia (the woodySonchus alliance) is 1.0%. Our results suggest that this region does not evolve rapidly enough to resolve relationships among closely related genera or insular endemics in theAsteraceae. The phylogenetic utility ofpsbA-trnH sequences of the non-coding cpDNA was compared to sequences from the ITS region of nuclear ribosomal DNA. The results suggest that ITS sequences evolve nearly four times faster thanpsbA-trnH intergenic spacer sequences. Furthermore, the ITS sequences provide more variable and phylogenetically informative sites and generate more highly resolved trees with more strongly supported clades, and thus are more suitable for phylogenetic comparisons at lower taxonomic levels than thepsbA-trnH intergenic chloroplast sequences.
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    Phylogenetic relationships of epacrids and vaccinioids (Ericaceae s. l.) based onmatK sequence data (1999)
    Springer
    Plant systematics and evolution 218 (1999), S. 55-65 
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    ISSN: 1615-6110
    Keywords: Ericaceae ; Vaccinieae ; Epacridaceae Vaccinioids ; matK ; phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Cladistic relationships of epacrids and vaccinioids (Ericaceae) are investigated using nucleotide sequence data from the chloroplast encodedmatK gene. Sequences of 56 taxa were aligned and analyzed using parsimony methods. Results show thatVaccinioideae as currently recognized are not monophyletic. The epacrids are sister to a clade that includes theLyonia group, theGaultheria group, and theVaccinieae. Arbutus andPyrola branch early inEricaceae, before the rhododendroid group.Enkianthus is sister to the remainingEricaceae (includingEpacridaceae).Vaccinieae are strongly supported as monophyletic, butVaccinium andAgapetes are polyphyletic.
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    Differential expression of two genes encoding isoforms of the ATPase involved in sodium efflux in Saccharomyces cerevisiae (1993)
    Springer
    Molecular genetics and genomics 236 (1993), S. 363-368 
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    ISSN: 1617-4623
    Keywords: Saccharomyces cerevisiae ; Sodium efflux ; Lithium efflux ; ATPase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The ENA2 gene encoding a P-type ATPase involved in Na+ and Li+ effluxes in Saccharomyces cerevisiae has been isolated. The putative protein encoded by ENA2 differs only in thirteen amino acids from the protein encoded by ENA1/PMR2. However, ENA2 has a very low level of expression and for this reason did not confer significant Li+ tolerance on a Li+ sensitive strain. ENA1 and ENA2 are the first two units of a tandem array of four highly homologous genes with probably homologous functions.
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    Post-transcriptional regulation of IME1 determines initiation of meiosis in Saccharomyces cerevislae (1993)
    Springer
    Molecular genetics and genomics 237 (1993), S. 375-384 
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    ISSN: 1617-4623
    Keywords: Regulation of meiosis ; Saccharomyces cerevisiae ; IME1
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The IME1 gene of Saccharomyces cerevisiae is required for initiation of meiosis. Transcription of IME1 is detected under conditions which are known to induce initiation of meiosis, namely starvation for nitrogen and glucose, and the presence of MATa1 and MATα2 gene products. In this paper we show that IME1 is also subject to translational regulation. Translation of IME1 mRNA is achieved either upon nitrogen starvation, or upon G1 arrest. In the presence of nutrients, constitutively elevated transcription of IME1 is also sufficient for the translation of IME1 RNA. Four different conditions were found to cause expression of Imel protein in vegetative cultures: elevated transcription levels due to the presence of IME1 on a multicopy plasmid; elevated transcription provided by a Gal-IME1 construct; G1 arrest due to α-factor treatment; G1 arrest following mild heat-shock treatment of cdc28 diploids. Using these conditions, we obtained evidence that starvation is required not only for transcription and efficient translation of IME1, but also for either the activation of Ime1 protein or for the induction/activation of another factor that, either alone or in combination with Ime1, induces meiosis.
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    Molecular and genetic characterization of SPT4, a gene important for transcription initiation in Saccharomyces cerevisiae (1993)
    Springer
    Molecular genetics and genomics 237 (1993), S. 449-459 
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    ISSN: 1617-4623
    Keywords: Saccharomyces cerevisiae ; Transcription ; spt mutants
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Mutations in the SPT4 gene of Saccharomyces cerevisiae were isolated as suppressors of δ insertion mutations that interfere with adjacent gene transcription. Recent genetic evidence indicates that the SPT4 protein functions with two other proteins, SPT5 and SPT6, in some aspect of transcription initiation. In this work we have characterized the SPT4 gene and we demonstrate that spt4 mutations, like spt5 and spt6 mutations, cause changes in transcription. Using the cloned SPT4 gene, spt4 null mutations were constructed; in contrast to spt5 and spt6 null mutants, which are inviable, spt4 null mutants are viable and have an Spt− phenotype. The DNA sequence of the SPT4 gene predicts a protein product of 102 amino acids that contains four cysteine residues positioned similarly to those of zinc binding proteins. Mutational analysis suggests that at least some of these cysteines are essential for SPT4 function. Genetic mapping showed that SPT4 is a previously unidentified gene that maps to chromosome VII, between ADE6 and CLY8.
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    Characterization of the cyrl-2 UGA mutation in Saccharomyces cerevisiae (1993)
    Springer
    Molecular genetics and genomics 237 (1993), S. 463-466 
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    ISSN: 1617-4623
    Keywords: Saccharomyces cerevisiae ; cyrl-2 ; Nonsense mutation ; CAMP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary cyrl-2 is a temperature-sensitive mutation of the yeast adenylate cyclase structural gene, CYR1. The cyrl-2 mutation has been suggested to be a UGA mutation since a UGA suppressor SUP201 has been isolated as a suppressor of the cyrl-2 mutation. Construction of chimeric genes restricted the region containing the cyrl-2 mutation, and the cyrl-2 UGA mutation was identified at codon 1282, which lies upstream of the region coding for the catalytic domain of adenylate cyclase. Alterations in the region upstream of the cyrl-2 mutation site result in null mutations. The complete open reading frame of the cyrl-2 gene expressed under the control of the GAL1 promoter complemented cyrl-dl in a galactose-dependent manner. These results suggest that at the permissive temperature weak readthrough occurs at the cyrl-2 mutation site to produce low levels of active adenylate cyclase. An endogenous suppressor in yeast cells is assumed to be responsible for this readthrough.
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    Characterization of the MKS1 gene, a new negative regulator of the Ras-cyclic AMP pathway in Saccharomyces cerevislae (1993)
    Springer
    Molecular genetics and genomics 238 (1993), S. 6-16 
    Details
    ISSN: 1617-4623
    Keywords: Saccharomyces cerevisiae ; cAMP MKS1 ; GAL11
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In order to isolate genes that function downstream of the Ras-cAMP pathway in Saccharomyces cerevisiae, a YEp13-based genomic library was screened for clones that inhibit growth of cells with diminished A-kinase activity. One such gene, MKS1, was found to encode a hydrophilic 52 kDa protein that shares weak homology with the yeast SPT2/SIN1 gene product. Three lines of evidence suggest that the MKS1 gene product is a negative regulator downstream of the Ras-cAMP pathway: (i) overexpression of MKS1 inhibits growth of cyrl disruptant cells on YPD medium containing a low concentration of cAMP; (ii) overexpression of MKS1 does not affect TPK1 expression; and (iii) the temperature-sensitive cyrl-230 mutation is partially suppressed by mks1 disruption. The mks1 mutant shows similar phenotypes to gal11/spt13, i.e., it cannot grow on YPGal containing ethidium bromide at 25°C, or on YPGly or SGal at 37°C. The mks1 gal11 double mutant shows more marked phenotypic changes than the single mutants. These results suggest that MKS1 is involved in transcriptional regulation of several genes by cAMP.
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    Budding yeast mutants showing constitutive basal levels of expression of DNA synthesis genes (1993)
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    Molecular genetics and genomics 240 (1993), S. 36-42 
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    ISSN: 1617-4623
    Keywords: Yeast ; Saccharomyces cerevisiae ; DNA synthesis genes ; Cell cycle regulation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Two mutants have been isolated in Saccharomyces cerevisiae in which transcripts from at least CDC8, CDC9, CDC21 (TMP1) and POL1 genes are expressed constitutively in cells blocked at START by use of either α-pheromone or the cdc28 mutation. The transcripts from these genes also persist in mutant stationary phase cells; however, cell cycle regulation of these four DNA synthesis genes occurs normally in late G1. The mutation therefore does not appear to lie in the MCB-DSC1 (MBF) system that controls the periodic regulation of the genes, but must affect some control mechanism regulating basal levels of expression.
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    MSl3, a multicopy suppressor of mutants hyperactivated in the RAS-CAMP pathway, encodes a novel HSP70 protein of Saccharomyces cerevisiae (1993)
    Springer
    Molecular genetics and genomics 240 (1993), S. 323-332 
    Details
    ISSN: 1617-4623
    Keywords: Heat shock response ; HSP70 ; Saccharomyces cerevisiae ; RAS-CAMP pathway ; Multicopy suppressor of ira1
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: abstract The MSI3 gene was isolated as a multicopy suppressor of the heat shock-sensitive phenotype of the iral mutation, which causes hyperactivation of the RAS-cAMP pathway. Overexpression of MSI3 also suppresses the heat shock-sensitive phenotype of the bcyl mutant. Determination of the DNA sequence of MSI3 revealed that MSI3 can encode a 77.4 kDa protein related to the HSP70 family. The amino acid sequence of Msi3p is about 30% identical to that of the Ssalp of Saccharomyces cerevisiae. This contrasts with the finding that members of the HSP70 family generally show at least 50% amino acid identity. The consensus nucleotide sequence of the heat shock element (HSE) was found in the upstream region of MSI3. Moreover, the steady-state levels of the MSI3 mRNA and protein were increased upon heat shock. These results indicate that the MSI3 gene encodes a novel HSP70-like heat shock protein. Disruption of the MSI3 gene was associated with a temperature sensitive growth phenotype but unexpectedly, thermotolerance was enhanced in the disruptant.
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    URL: http://dx.doi.org/10.1007/BF00280382
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    Characterisation of PDC2, a gene necessary for high level expression of pyruvate decarboxylase structural genes in Saccharomyces cerevlsiae (1993)
    Springer
    Molecular genetics and genomics 241 (1993), S. 657-666 
    Details
    ISSN: 1617-4623
    Keywords: Saccharomyces cerevisiae ; Pyruvate decarboxylase ; Transcription ; Glucose induction ; Autoregulation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The regulatory gene PDC2 was identified in a screen for mutations affecting pyruvate decarboxylase activity in yeast. I have cloned and sequenced this gene. The predicted protein of 925 amino acids has no homology to any sequence in the databases. However, the protein sequence is rich in asparagine and serine residues, as is often found for transcriptional regulators. The PDC2 deletion mutant exhibits a phenotype very similar to, but more severe than that of the point mutant: a strongly reduced pyruvate decarboxylase specific activity, slow, respiration-dependent growth on glucose, and accumulation of pyruvate. The activity of other glycolytic enzymes seems to be unaffected by the pdc2Δ mutation. Synthesis of pyruvate decarboxylase is regulated by PDC2 at the transcriptional level. Expression of the major structural gene for pyruvate decarboxylase, PDC1, is strongly reduced in pdc2Δ mutants. Transcription of the generally more weakly expressed PDC5 gene appears to be entirely abolished. However, glucose induction of pyruvate decarboxylase synthesis is unaffected. Thus, PDC2 is either important for a high basal level of PDC gene expression or it plays a positive role in the autoregulation that controls expression of PDC1 and PDC5.
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    URL: http://dx.doi.org/10.1007/BF00279908
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    Co-regulation with genes of phospholipid biosynthesis of the CTR/HNM1-encoded choline/nitrogen mustard permease in Saccbaromyces cerevisiae (1993)
    Springer
    Molecular genetics and genomics 241 (1993), S. 680-684 
    Details
    ISSN: 1617-4623
    Keywords: Nitrogen mustard resistance ; Regulation of choline permease ; Co-regulation ; Phospholipid biosynthesis ; Saccharomyces cerevisiae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract An 815 by region of the promoter of the Saccharomyces cerevisiae gene CTR/HNM1, encoding choline permease was sequenced and its regulatory function analysed by deletion studies in an in-frame promoter-lacZ construct. In addition to the TATA box, a 10 by motif (consensus 5′-CATGTGAAAT-3′) was found to be mandatory for CTR/HNM1 expression. This ‘decamer’ motif is located between nucleotides −262 and −271 and is identical in 9 of 10 by with the regulatory motif found in the S. cerevisiae INO1 and CHO1 genes. Constructs with the 10 by sequence show high constitutive expression, while elimination or alterations at three nucleotide positions, of the decamer motif in the context of an otherwise unchanged promoter leads to total loss of β-galactosidase production. Expression of the CTR/HNM1 gene in wild-type cells is regulated by the phospholipid precursors inositol and choline; no such influence is seen in cells bearing mutations in the phospholipid regulatory genes INO2, INO4, and OPI1. There is no regulation by INO2 and OPI1 in the absence of the decamer motif. However constructs not containing this sequence (promoter intact to positions −213 or −152) are still controlled by INO4. Other substrates of the choline permease, i.e. ethanolamine, nitrogen mustard and nitrogen half mustard do not regulate expression of CTR/HNM1.
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    Mitochondrial dysfunction in yeast expressing the cytoplasmic male sterility T-urf13 gene from maize: analysis at the population and individual cell level (1993)
    Springer
    Molecular genetics and genomics 236 (1993), S. 299-308 
    Details
    ISSN: 1617-4623
    Keywords: Texas maize cytoplasmic male sterility ; Saccharomyces cerevisiae ; Mitochondria ; Image and flow cytometry ; 3,3′-Dihexyloxacarbocyanine iodide
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The urf13TW gene, which is derived from the mitochondrial T-urf13 gene responsible for Texas cytoplasmic male sterility in maize, was expressed in Saccharomyces cerevisiae by targeting its translation product into mitochondria. Analysis by oxygraphy at the population level revealed that in the presence of methomyl the oxygen uptake of intact yeast cells carrying the targeted protein is strongly stimulated only with ethanol as respiratory substrate and not with glycerol, lactate, pyruvate, or acetate. When malate is the substrate oxidized by isolated mitochondria, interaction between the targeted protein and methomyl results in significant inhibition of oxygen uptake. This inhibition is eliminated and oxygen uptake is stimulated by subsequent addition of NAD+. Using 3,3′-dihexyloxacarbocyanine iodide [DiOC6(3)] as probe, interactive laser scanning and flow cytometry, which permit analysis at the individual cell level, demonstrated that specific staining of the mitochondrial compartment is obtained and that DiOC6(3) fluorescence serves as a measure of the membrane potential. Finally, it was shown that, as in T cytoplasm maize mitochondria, HmT toxin and methomyl dissipate the membrane potential of yeast mitochondria that carry the foreign protein. Furthermore, the results suggest that the HmT toxin and methomyl response is related to the plasmid copy number per cell and that the deleterious effect induced by HmT toxin is stronger than that of methomyl.
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    URL: http://dx.doi.org/10.1007/BF00277126
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    A point mutation in the core subunit gene of yeast mitochondrial RNA polymerase is suppressed by a high level of specificity factor MTF1 (1993)
    Springer
    Molecular genetics and genomics 237 (1993), S. 49-57 
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    ISSN: 1617-4623
    Keywords: Saccharomyces cerevisiae ; Nuclear pet mutants ; Mitochondrial transcription ; Mutant RNA polymerase ; Specificity factor
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The temperature-sensitive yeast mutant pet-ts798 is characterized by an altered mitochondrial transcription apparatus. The mutation has previously been shown to map in the RP041 gene encoding the core enzyme of mitochondrial RNA polymerase. In the present study the rpo41/pet-ts798 allele was cloned and sequenced, demonstrating that the mutant phenotype is caused by a single amino acid change in a conserved region of the core polymerase. The nuclear gene MTF1, previously isolated as a high copy suppressor of mutant rpo41/pet-ts798, and its gene product were characterized in more detail. Import of a MTF1-COXIV fusion protein in vivo and also import studies with in vitro synthesized MTF1 precursors indicate that MTF1 is a mitochondrial protein and that no apparent cleavage occurs during its import into mitochondria. DNA-binding assays demonstrate that the MTF1 protein alone interacts with DNA in a non-specific manner. An antibody directed against specificity factor MTF1 was raised and used for immunological quantification experiments. The results indicate that suppression is mediated by an increased level of MTF1 protein in mitochondria of the rpo41/pet-ts798 mutant. Possible implications of this finding for the mechanism of suppression are discussed.
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    URL: http://dx.doi.org/10.1007/BF00282783
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    Therps16 intron and the phylogeny of theRubioideae (Rubiaceae) (1999)
    Springer
    Plant systematics and evolution 214 (1999), S. 161-186 
    Details
    ISSN: 1615-6110
    Keywords: Rubiaceae ; Rubioideae ; Angiosperms ; cladistics ; DNA sequences ; phylogeny ; rps16 intron ; taxonomy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The phylogeny of the subfamilyRubioideae (Rubiaceae) was estimated from sequence variation in therps16 intron (cpDNA) in 143 ingroup and 5 outgroup taxa. The analysis largely confirms a recent one based onrbcL sequences, but branch support is often much stronger. Three of the traditional subfamilies are supported,Rubioideae, Cinchonoideae s. str., andIxoroideae s. l. while there is no support forAntirheoideae. TheRubioideae are the sister group of all otherRubiaceae and comprise the tribesAnthospermeae, Coccocypseleae, Cruckshanksieae, Coussareeae, Gaertnereae, Hedyotideae, Knoxieae, Morindeae, Ophiorrhizeae, Paederieae, Pauridiantheae, Perameae, Psychotrieae, Rubieae, Spermacoceae, Theligoneae, andUrophylleae. TheHamelieae andHillieae belong to theCinchonoideae. Rachicallis andSiemensia should be transferred from theHedyotideae to theCinchonoideae. ThePauridiantheae, Urophylleae, Ophiorrhizeae, andRaritebe form the basalmost subclade of theRubioideae. The second basalmost clade consists of the generaLasianthus andPerama. The third basalmost clade consists of the tribesCoussareeae, Coccocypseleae andCruckshanksieae, and the generaDeclieuxia andHindsia. The tribesKnoxieae, Anthospermeae, Argostemmateae, Paederieae, Theligoneae, Rubieae, Hedyotideae, andSpermacoceae are members of one clade. TheKnoxieae are monophyletic ifOtiophora, Otomeria, andPentas are included. The tribeAnthospermeae is supported as monophyletic, but its subtribes are not. ThePaederieae, together withTheligonum, form a paraphyletic grade basal to theRubieae. TheHedyotideae, includingSchismatoclada, form a grade at the base of theSpermacoceae. TheGaertnereae are monophyletic and distinct from thePsychotrieae. TheMorindeae are monophyletic and includeDamnacanthus andMitchella. Schradera is the sister group of theMorindeae. ThePsychotrieae are monophyletic when theGaertnereae, Lasianthus, andDeclieuxia are excluded. The recognition of a subtribeHydnophytineae leaves the rest of thePsychotrieae paraphyletic.Psychotria is paraphyletic with respect to all other genera of the tribe. Approximately 50 genera are here classified for the first time based on molecular data.
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    Analysis of the genetic diversity of wild Spanish populations of the genusHordeum through the study of their endosperm proteins (1999)
    Springer
    Plant systematics and evolution 214 (1999), S. 235-249 
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    ISSN: 1615-6110
    Keywords: Poaceae ; Hordeum ; Barley ; endosperm proteins ; variability ; phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A study was made of the genetic variability of 101 barley populations belonging to the four, wild, Spanish species of the genusHordeum (the autogamousH. marinum subspp.marinum andgussoneanum, andH. murinum subspp.murinum andleporinum, plus the allogamous speciesH. bulbosum andH. secalinum). Electrophoresis of endosperm proteins was performed using a large number of individuals from each population sampled, in order to determine intra- and interpopulational variation. The distribution of variability observed by population and taxonomic unit, is closely related to the breeding system.Hordeum bulbosum showed the greatest intrapopulational variability andH. marinum subsp.gussoneanum the least. In contrast to the autogamous species, the allogamous species showed low levels of interpopulational variation.
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    Towards a molecular phylogeny ofApiaceae subfamilyApioideae: Additional information from nuclear ribosomal DNA ITS sequences (1999)
    Springer
    Plant systematics and evolution 216 (1999), S. 167-195 
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    ISSN: 1615-6110
    Keywords: Apiaceae ; Umbelliferae ; Apioideae ; Nuclear ribosomal DNA internal transcribed spacer (ITS) region ; phylogeny ; phytochemistry ; systematics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Evolutionary relationships among 116 representatives (80 genera) ofApiaceae (Umbelliferae) subfam.Apioideae were investigated by comparative sequencing of the two internal transcribed spacers of the 18S–26S nuclear ribosomal DNA repeat. The resultant phylogenies, inferred using maximum parsimony and neighbor-joining methods, clarified the relationships of several genera whose phylogenetic placements have heretofore been problematic. Comparisons between the phylogenies inferred and the distribution of several phytochemical (coumarins, flavonoids, and phenylpropenes) and morphological (stomates, pollen, and cotyledonary shape) characters were also made, revealing that many of these characters (like those morphological and anatomical characters of the fruit) are highly homoplastic. It is not surprising then that systems of classification ofApioideae based on these characters, particularly with regard to tribal and subtribal designations and relationships, are unsatisfactory. The results of recent serological investigations of the subfamily support several relationships proposed herein using molecular data.
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    Phylogenetic utility of the nuclear rDNA ITS region in subfamilyIxoroideae (Rubiaceae): Comparisons with cpDNArbcL sequence data (1999)
    Springer
    Plant systematics and evolution 217 (1999), S. 119-135 
    Details
    ISSN: 1615-6110
    Keywords: Rubiaceae ; Ixoroideae ; cpDNA ; nrDNA ; rbcL ; ITS ; DNA sequences ; phylogeny ; incongruence ; combined analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract ITS of the nrDNA were sequenced for 21 taxa inIxoroideae and outgroups (Rubiaceae) and compared with sequences of the cp-generbcL. Separate and combined analyses were performed. ITS-variation was extensive and, because of alignment ambiguities, some sites were excluded from the analyses. Several topologies from therbcL analysis that conflicted with earlier classifications are corroborated by the ITS data: 1)Posoqueria should be excluded fromGardenieae. 2) The disputed genusBertiera, previously inGardenieae, is basal in an extendedCoffeeae, includingTricalysia. 3)Ixora should be excluded fromPavetteae. 4)Vangueria, (Antirheoideae), belongs toIxoroideae. This affiliation ofAntirheoideae tribes withIxoroideae is also shown by new ITS andrbcL data forAlberta. Incongruities found between the two data sets may be caused by density of taxon sampling, different evolutionary rates, phylogenetic sorting, homoplasy caused by functional constraints, or sampling of non-orthologous ITS types.
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    Phylogenetic evaluation of 5S ribosomal RNA gene and spacer in theCallistachys group (Fabaceae:Mirbelieae) (1999)
    Springer
    Plant systematics and evolution 218 (1999), S. 33-42 
    Details
    ISSN: 1615-6110
    Keywords: Fabaceae ; Mirbelieae ; Callistachys ; Brachysema ; Nemcia ; Jansonia ; 5S rDNA ; spacer variation ; phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Sequences of 5S rDNA from an Australian group of papilionoid legumes were evaluated for phylogenetic informativeness. Twenty four sequences were sampled from ten species in five closely related genera:Brachysema, Callistachys, Jansonia, Nemcia andPodolobium. These sequences fell into two size classes, 200bp and 600bp, which appear to represent paralogous copies of the 5S unit at different loci. As in previous studies, the 5S rRNA gene and both ends of the inter-gene spacer are found to be conserved and almost uninformative about phylogeny at this taxonomic level. By contrast, the middle part of the spacer is highly variable, both in substitutions at individual sites and in length. The short sequences contain virtually no duplications. The long sequences contain numerous short repeats (c.20 bp) which form a regular pattern in the middle section. Phylogenies estimated from these data support monophyly of the study group, and of species. Relationships among species and genera are less clear, perhaps because divergence of the 5S spacer between species is too great. However, non-monophyly ofNemcia andBrachysema, indicated by other data, is corroborated.
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    Phylogenetic relationships of the enigmatic fern families Hymenophyllopsidaceae and Lophosoriaceae: Evidence fromrbcL nucleotide sequences (1999)
    Springer
    Plant systematics and evolution 219 (1999), S. 263-270 
    Details
    ISSN: 1615-6110
    Keywords: Hymenophyllopsis ; Lophosoria ; molecular systematics ; evolution ; rbcL ; phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Nucleotide sequences fromrbcL were used to infer relationships of Lophosoriaceae and Hymenophyllopsidaceae. The phylogenetic positions of these two monotypic fern families have been debated, and neither group had been included in recent molecular systematic studies of ferns. Maximum parsimony analysis of our data supported a sister relationship betweenLophosoria andDicksonia, and also betweenHymenophyllopsis andCyathea. Thus, both newly-examined families appear to be part of a previously characterized and well-supported clade of tree ferns. The inferred relationships ofLophosoria are consistent with most (but not all) recent treatments. However,Hymenophyllopsis includes only small delicate plants superficially similar to filmy ferns (Hymenophyllaceae), very different from the large arborescent taxa. Nevertheless, some synapomorphic characteristics are shared with the tree fern clade. Further studies on gametophytes ofHymenophyllopsis are needed to test these hypotheses of relationship.
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    Genetic evidence for interactions between yeast importin α (Srp1p) and its nuclear export receptor, Cse1p (1999)
    Springer
    Molecular genetics and genomics 261 (1999), S. 788-795 
    Details
    ISSN: 1617-4623
    Keywords: Key words Cse1p ; Srp1p ; Importin ; Nuclear transport ; Saccharomyces cerevisiae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The yeast Srp1p protein functions as an import receptor for proteins bearing basic nuclear localization signals. Cse1p, the yeast homolog of mammalian CAS, recycles Srp1p back to the cytoplasm after import substrates have been released into the nucleoplasm. In this report we describe genetic interactions between SRP1 and CSE1. Results from genetic suppression and synthetic lethality studies demonstrate that these gene products interact to ensure accurate chromosome segregation. We also describe new mutant alleles of CSE1 and analyze a new temperature-sensitive allele of CSE1, cse1-2. This allele causes high levels of chromosome missegregation and cell cycle arrest during mitosis at the nonpermissive temperature.
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    URL: http://dx.doi.org/10.1007/s004380050022
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    The Saccharomyces cerevisiae LEP1/SAC3 gene is associated with leucine transport (1999)
    Springer
    Molecular genetics and genomics 262 (1999), S. 332-341 
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    ISSN: 1617-4623
    Keywords: Key words Leucine transport ; Saccharomyces cerevisiae ; Trifluoroleucine resistance ; LEP1 ; SAC3
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Leucine uptake by Saccharomyces cerevisiae is mediated by three transport systems, the general amino acid transport system (GAP), encoded by GAP1, and two group-specific systems (S1 and S2), which also transport isoleucine and valine. A new mutant defective in both group-specific transport activities was isolated by employing a gap1 leu4 strain and selecting for trifluoroleucine-resistant mutants which also showed greatly reduced ability to utilize l-leucine as sole nitrogen source and very low levels of [14C]l-leucine uptake. A multicopy plasmid containing a DNA fragment which complemented the leucine transport defect was isolated by selecting for transformants that grew normally on minimal medium containing leucine as nitrogen source and subsequently assaying [14C]l-leucine uptake. Transformation of one such mutant, lep1, restored sensitivity to trifluoroleucine. The complementing gene, designated LEP1, was subcloned and sequenced. The LEP1 ORF encodes a large protein that lacks characteristics of a transporter or permease (i.e., lacks hydrophobic domains necessary for membrane association). Instead, Lep1p is a very basic protein (pI of 9.2) that contains a putative bipartite signal sequence for targeting to the nucleus, suggesting that it might be a DNA-binding protein. A database search revealed that LEP1 encodes a polypeptide that is identical to Sac3p except for an N-terminal truncation. The original identification of SAC3 was based on the isolation of a mutant allele, sac3-1, that suppresses the temperature-sensitive growth defect of an actin mutant containing the allele act1-1. Sac3p has been previously shown to be localized in the nucleus. When a lep1 mutant was crossed with a sac3 deletion mutant, no complementation was observed, indicating that the two mutations are functionally allelic.
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    Galactose induction in yeast involves association of Gal80p with Gal1p or Gal3p (1999)
    Springer
    Molecular genetics and genomics 261 (1999), S. 495-507 
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    ISSN: 1617-4623
    Keywords: Key wordsKluyveromyces lactis ; Saccharomyces cerevisiae ; GAL1 ; GAL80 ; Protein interaction
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Gal1p carries out two functions in the galactose pathway of yeast. It activates Gal4p by interacting with Gal80p – a function that can also served by Gal3p – and it catalyzes the formation of galactose-1-phosphate. Recently, we and others have presented biochemical evidence for complex formation between Gal1p and Gal80p. Here, we extend these data and present genetic evidence for an interaction between Gal1p and Gal80p in vivo, using a two-hybrid assay. Interaction between Gal1p and Gal80p depends on the presence of galactose, but not on the catalytic activity of Gal1p. A new class of Kluyveromyces lactis mutants was isolated, designated Klgal1-m, which have lost the derepressing activity but retain galactokinase activity, indicating that the two Gal1p activities are functionally independent. The KlGal1-m proteins are defective in their ability to interact with Gal80p in a two-hybrid assay. The locations of gal1-m mutations identify putative interaction sites in Gal1p and Gal80p. A dominant mutation, KlGAL1-d, leads to a high level of constitutive expression of genes of the galactose pathway. The behavior of chimeric proteins consisting of Gal3p and KlGal1p sequences indicates that both the N-terminal and C-terminal halves of KlGal1p are involved in specific interaction with KlGal80p.
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    The mitochondrial cytochrome c peroxidase Ccp1 of Saccharomyces cerevisiae is involved in conveying an oxidative stress signal to the transcription factor Pos9 (Skn7) (1999)
    Springer
    Molecular genetics and genomics 262 (1999), S. 437-447 
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    ISSN: 1617-4623
    Keywords: Key words Oxidative stress signalling ; Mitochondria ; Pos9 (Skn7) ; Ccp1 ; Saccharomyces cerevisiae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In Saccharomyces cerevisiae two transcription factors, Pos9 (Skn7) and Yap1, are involved in the response to oxidative stress. Fusion of the Pos9 response-regulator domain to the Gal4 DNA-binding domain results in a transcription factor which renders the expression of a GAL1-lacZ reporter gene dependent on oxidative stress. To identify genes which are involved in the oxygen-dependent activation of the Gal4-Pos9 hybrid protein we screened for mutants that failed to induce the heterologous test system upon oxidative stress (fap mutants for factors activating Pos9). We isolated several respiration-deficient and some respiration-competent mutants by this means. We selected for further characterization only those mutants which also displayed an oxidative-stress-sensitive phenotype. One of the respiration-deficient mutants (complementation group fap6) could be complemented by the ISM1 gene, which encodes mitochondrial isoleucyl tRNA synthetase, suggesting that respiration competence was important for signalling of oxidative stress. In accordance with this notion a rho0 strain and a wild-type strain in which respiration had been blocked (by treatment with antimycin A or with cyanide) also failed to activate Gal4-Pos9 upon imposition of oxidative stress. Another mutant, fap24, which was respiration-competent, could be complemented by CCP1, which encodes the mitochondrial cytochrome c peroxidase. Mitochondrial cytochrome c peroxidase degrades reactive oxygen species within the mitochondria. This suggested a possible sensor function for the enzyme in the oxidative stress response. To test this we used the previously described point mutant ccp1 W191F , which is characterized by a 104-fold decrease in electron flux between cytochrome c and cytochrome c peroxidase. The Ccp1W191F mutant was still capable of activating the Pos9 transcriptional activation domain, suggesting that the signalling function of Ccp1 is independent of electron flux rates.
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    Bending of DNA segments with Saccharomyces cerevisiae autonomously replicating sequence activity, isolated from basidiomycete mitochondrial linear plasmids (1993)
    Springer
    Molecular genetics and genomics 237 (1993), S. 1-9 
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    ISSN: 1617-4623
    Keywords: DNA bending ; Autonomously replicating sequence ; Saccharomyces cerevisiae ; Basidiomycete ; Linear plasmid
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Previous studies have indicated that DNA bending is a general structural feature of sequences (ARSs) from cellular DNAs of yeasts and nuclear and mitochondrial genomic DNAs of other eukaryotes that are capable of autonomous replication in Saccharomyces cerevisiae. Here we showed that bending activity is also tightly associated with S. cerevisiae ARS function of segments cloned from mitochondrial linear DNA plasmids of the basidiomycetes Pleurotus ostreatus and Lentinus edodes. Two plasmids, designated pLPO2-like (9.4 kb), and pLPO3 (6.6 kb) were isolated from a strain of P. ostreatus. A 1029 by fragment with high-level ARS activity was cloned from pLPO3 and it contained one ARS consensus sequence (A/T)TTTAT(A/G)TTT(A/T) indispensable for activity and seven dispersed ARS consensus-like (10/11 match) sequences. A discrete bent DNA region was found to lie around 500 by upstream from the ARS consensus sequence (T-rich strand). Removal of the bent DNA region impaired ARS function. DNA bending was also implicated in the ARS function associated with a 1430 by fragment containing three consecutive ARS consensus sequences which had been cloned from the L. edodes plasmid pLLE1 (11.0 kb): the three consecutive ARSs responsible for high-level ARS function occurred in, and immediately adjacent to, a bent DNA region. A clear difference exists between the two plasmid-derived ARS fragments with respect to the distance between the bent DNA region and the ARS consensus sequence(s).
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    Donation: a new, facile method of gene replacement in yeast (1993)
    Springer
    Molecular genetics and genomics 237 (1993), S. 306-310 
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    ISSN: 1617-4623
    Keywords: Saccharomyces cerevisiae ; Gene replacement ; Donation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We describe here a new method for the introduction of non-selectable alleles into Saccharomyces cerevisiae, gene replacement by donation. This method only requires the availability of an autonomously replicating, selectable plasmid containing the allele to be introduced into yeast. The plasmid is digested at a restriction site (or sites) within this allele, and introduced into yeast by transformation. In the course of double-strand break repair, the entering plasmid donates genetic information to the chromosome, replacing the chromosomal allele in a gene conversion-like event. Gene replacement events are identified by a phenotypic screen of the transformants. When necessary, the transforming plasmid may be subsequently lost by segregation during permissive growth. We have studied several parameters affecting the utility of this protocol as a method of gene replacement. Together with our previous results, the results show gene replacement by donation to be a useful, facile method, yielding gene replacement in up to 1.5% of transformants.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00282812
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  • 95
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    Molecular structure and genetic regulation of SFA, a gene responsible for resistance to formaldehyde in Saccharomyces cerevisiae, and characterization of its protein product (1993)
    Springer
    Molecular genetics and genomics 237 (1993), S. 351-358 
    Details
    ISSN: 1617-4623
    Keywords: Saccharomyces cerevisiae ; Formaldehyde hyper-resistance ; Alcohol dehydrogenase ; Glutathione ; Inducibility
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A 3.7 kb DNA fragment of yeast chromosome IV has been sequenced that contains the SFA gene which, when present on a multi-copy plasmid in Saccharomyces cerevisiae, confers hyper-resistance to formaldehyde. The open reading frame of SFA is 1158 by in size and encodes a polypeptide of 386 amino acids. The predicted protein shows strong homologies to several mammalian alcohol dehydrogenases and contains a sequence characteristic of binding sites for NAD. Overexpression of the SFA gene leads to enhanced consumption of formaldehyde, which is most probably the reason for the observed hyper-resistance phenotype. In sfa:LEU2 disruption mutants, sensitivity to formaldehyde is correlated with reduced degradation of the chemical. The SFA gene shares an 868 by divergent promoter with UGX2 a gene of yet unknown function. Promoter deletion studies with a SFA promoter-lacZ gene fusion construct revealed negative interference on expression of SFA by upstream sequences. The upstream region between positons − 145 and − 172 is totally or partially responsible for control of inducibility of SFA by chemicals such as formaldehyde (FA), ethanol and methyl methanesulphonate. The 41 kDa SFA-encoded protein was purified from a hyper-resistant transformant; it oxidizes long-chain alcohols and, in the presence of glutathione, is able to oxidize FA. SFA is predicted to code for a long-chain alcohol dehydrogenase (glutathione-dependent formaldehyde dehydrogenase) of the yeast S. cerevisiae.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00279438
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  • 96
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    Isolation of the DLD gene of Saccharomyces cerevisiae encoding the mitochondrial enzyme D-lactate ferricytochrome c oxidoreductase (1993)
    Springer
    Molecular genetics and genomics 238 (1993), S. 315-324 
    Details
    ISSN: 1617-4623
    Keywords: Saccharomyces cerevisiae ; Nuclear gene ; Mitochondrial enzyme ; Lactate dehydrogenase ; Flavoprotein
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In Saccharomyces cerevisiae the utilization of lactate occurs via specific oxidation of l- and d-lactate to pyruvate catalysed by l-lactate ferricytochrome c oxidoreductase (L-LCR) (EC 1.1.2.3) encoded by the CYB2 gene, and d-lactate ferricytochrome c oxidoreductase (D-LCR) (EC 1.1.2.4), respectively. We selected several lactate− pyruvate+ mutants in a cyb2 genetic background. Two of them were devoid of D -LCR activity (dld mutants, belonging to the same complementation group). The mutation mapped in the structural gene. This was demonstrated by a gene dosage effect and by the thermosensitivity of the enzyme activity of thermosensitive revertants. The DLD gene was cloned by complementation for growth on d-, l-lactate in the strain WWF18-3D, carrying both a CYB2 disruption and the dld mutation. The minimal complete complementing sequence was localized by subcloning experiments. From the sequence analysis an open reading frame (ORF) was identified that could encode a polypeptide of 576 amino-acids, corresponding to a calculated molecular weight of 64000 Da. The deduced protein sequence showed significant homology with the previously described microsomal flavoprotein l-gulono-γ-lactone oxidase isolated from Rattus norvegicus, which catalyses the terminal step of l-ascorbic acid biosynthesis. These results are discussed together with the role of L-LCR and D-LCR in lactate metabolism of S. cerevisiae.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00291989
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  • 97
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    Amplification and loss of repeat units of the human minisatellite MS1 integrated in chromosome III of a haploid yeast strain (1993)
    Springer
    Molecular genetics and genomics 238 (1993), S. 38-42 
    Details
    ISSN: 1617-4623
    Keywords: Saccharomyces cerevisiae ; DNA amplification ; Minisatellites ; VNTR ; MS1
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Minisatellites comprise arrays of tandemly repeated short DNA sequences which show extensive variation in repeat unit number. The mechanisms that underlie this length variation are not understood. In order to study processes influencing length changes of minisatellites, we integrated the human minisatellite MS1 into a haploid strain of the yeast Saccharomyces cerevisiae. Frequent spontaneous generation of MS1 alleles with new lengths were observed in this yeast strain. Hence it is concluded that recombination between members of a pair of homologous chromosomes is not a prerequisite for the generation of length changes in MS1 in yeast.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00279528
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  • 98
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    The centromere and promoter factor 1, CPFI, of Saccharomyces cerevisiae modulates gene activity through a family of factors including SPT21, RPD1 (SIN3), RPD3 and CCR4 (1993)
    Springer
    Molecular genetics and genomics 240 (1993), S. 374-386 
    Details
    ISSN: 1617-4623
    Keywords: Saccharomyces cerevisiae ; Centromere and promoter factor ; Chromatin ; SPT ; Transcription
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In Saccharomyces cerevisiae, the CPF1 gene encodes a ccntromere binding protein that also plays a role in transcription; cpf1 strains are methionine auxotrophs. In this paper we describe four strains that are methionine prototrophs despite containing a defective CPF1 gene. These strains, which contain mutations at either the SPT21, RPD1 (SINS), RPD3 or CCR4 loci, have defective centromere function and a chromatin structure around the CDEI elements in the MET25 promoter characteristic of strains lacking CPF1. This indicates that the roles of CPF1 in transcription, centromere function and chromatin modulation around CDEI sites are different. We propose that CPF1 functions to overcome the repressing action, mediated via inactive chromatin, of proteins such as SPT21 or RPDI (SIN3) on gene expression. The absence of proteins such as SPT21 or RPD1 (SIN3) relieves this respression and explains how methionine prototrophy is restored in the absence of CPF1.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00280389
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  • 99
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    Localization of a cruciform cutting endonuclease to yeast mitochondria (1993)
    Springer
    Molecular genetics and genomics 240 (1993), S. 414-418 
    Details
    ISSN: 1617-4623
    Keywords: Cruciform DNA ; Endonuclease ; Mitochondria ; Saccharomyces cerevisiae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have found a cruciform cutting endonuclease in the yeast, Saccharomyces cerevisiae, which localizes to the mitochondria. This activity apparently is associated with the mitochondrial inner membrane since the activity is not released into solution by osmolysis, in contrast to the matrix enzyme, isocitrate dehydrogenase. The cruciform cutting activity appears to be encoded by CCE1. This gene has been shown to encode one of the major cruciform cutting endonucleases present in a yeast cell. In ccel strains, which lack CCE1 endonuclease activity, the mitochondrial cruciform cutting endonucleolytic activity is also absent. Since CCE1 is allelic to MGT1, a gene required for the highly biased transmission of petite mitochondrial DNA in crosses between ϱ+ and hypersuppressive ϱ− cells, it seems likely that the CCE1 endonuclease functions within mitochondria.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00280395
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  • 100
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    Transcription of the yeast mitochondrial genome requires cyclic AMP (1993)
    Springer
    Molecular genetics and genomics 241 (1993), S. 213-224 
    Details
    ISSN: 1617-4623
    Keywords: Saccharomyces cerevisiae ; Mitochondria ; Transcriptional regulation ; Protein phosphorylation ; Stringent response
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Using various mutant strains and nutritional manipulations, we investigated a potential role for cyclic AMP (cAMP) in the regulation of mitochondrial (mt) gene expression in the yeast Saccharomyces cerevisiae. In RAS mutants known to have either abnormally low or high cellular levels of this nucleotide, we show that both mt transcription rate and overall mt transcript levels vary directly with cellular cAMP levels. We further show that nutritional downshift of actively growing cells causes a severe, rapid fall in cAMP levels, and that this fall is concomitant with the stringent mt transcriptional curtailment that we and others have previously shown to follow this nutritional manipulation. In in vitro mt transcription assays using intact organelles from downshifted and actively growing cells, stringently curtailed mt gene expression can be restored to 75% of control levels by addition of cAMP to the assay mix. Consistent with these observations a RAS2 vall9mutant strain, which cannot adjust cAMP levels in response to external stimuli, shows no mt stringent response following nutritional downshift. We also demonstrate a significant but transient increase in both mt transcript levels and mt transcription rate following shift of actively respiring wild-type cells to glucose-based medium, a manipulation known to cause a short-lived pulse of cAMP in yeast; similar manipulation of the RAS2 vall9mutant strain generates no such response. Taken together all these observations indicate that cellular cAMP levels are involved in the regulation of mt transcription in yeast. Moreover, the lack of a mt stringent transcriptional response following downshift in a strain in which the BCY1 gene had been insertionally inactivated suggests that cAMP may influence mt transcription via a mt cAMP-dependent protein kinase. These results link mt gene expression with mechanisms governing growth control and nutrient adaptation in yeast, and they provide a means by which nit gene expression might be coordinated with that of related nuclear genes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00280219
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