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  • 1
    Electronic Resource
    Electronic Resource
    Evidence of recent lateral gene transfer among hyperthermophilic Archaea (2000)
    Oxford, UK : Blackwell Science, Ltd
    Molecular microbiology 38 (2000), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: A total of 153 nucleotide differences were found over a contiguous 16 kb region between two hyperthermophilic Archaea, Pyrococcus furiosus and Thermococcus litoralis. The 16 kb region in P. furiosus is flanked by insertion sequence (IS) elements with inverted and direct repeats. Both IS elements contain a single open reading frame (ORF) encoding a putative protein of 233 amino acids identified as a transposase. This 16 kb region has the features of a typical bacterial composite transposon and represents a possible mechanism for lateral gene transfer between Archaea or possibly between Archaea and Bacteria. A total of 23 homologous IS elements was found in the genome sequence of P. furiosus, whereas no full-length IS elements were identified in the genomes of Pyrococcus abyssi and Pyrococcus horikoshii. Only one IS element was found in T. litoralis. In P. furiosus and T. litoralis, the 16 kb region contains an ABC transport system for maltose and trehalose that was characterized biochemically for T. litoralis. Regulation of expression studies showed that the malE gene, located on the transposon, and the encoded trehalose/maltose-binding protein (TMBP) are induced in the presence of maltose and trehalose in both P. furiosus and T. litoralis. The implications of transposition as a mechanism for lateral gene transfer among Archaea are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2958.2000.02161.x
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  • 2
    Electronic Resource
    Electronic Resource
    Microbial survival of space vacuum and extreme ultraviolet irradiation: strain isolation and analysis during a rocket flight (2002)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 215 (2002), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: We have recovered new isolates from hot springs, in Yellowstone National Park and the Kamchatka Peninsula, after γ-irradiation and exposure to high vacuum (10−6 Pa) of the water and sediment samples. The resistance to desiccation and ionizing radiation of one of the isolates, Bacillus sp. strain PS3D, was compared to that of the mesophilic bacterium, Deinococcus radiodurans, a species well known for its extraordinary resistance to desiccation and high doses of ionizing radiation. Survival of these two microorganisms was determined in real and simulated space conditions, including exposure to extreme UV radiation (10–100 nm) during a rocket flight. We found that up to 15 days of desiccation alone had little effect on the viability of either bacterium. In contrast, exposure to space vacuum (∼10−6 Pa) decreased cell survival by two and four orders of magnitude for Bacillus sp. strain PS3D and D. radiodurans, respectively. Simultaneous exposure to space vacuum and extreme UV radiation further decreased the survival of both organisms, compared to unirradiated controls. This is the first report on the isolated effect of extreme UV at 30 nm on cell survival. Extreme UV can only be transmitted through high vacuum, therefore its penetration into the cells may only be superficial, suggesting that in contrast to near UV, membrane proteins rather than DNA were damaged by the radiation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.2002.tb11386.x
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  • 3
    Electronic Resource
    Electronic Resource
    Genetic analysis of Carboxydothermus hydrogenoformans carbon monoxide dehydrogenase genes cooF and cooS (2000)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 191 (2000), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Carboxydothermus hydrogenoformans is an extremely thermophilic, Gram-positive bacterium growing on carbon monoxide (CO) as single carbon and energy source and producing only H2 and CO2. Carbon monoxide dehydrogenase is a key enzyme for CO metabolism. The carbon monoxide dehydrogenase genes cooF and cooS from C. hydrogenoformans were cloned and sequenced. These genes showed the highest similarity to the cooF genes from the archaeon Archaeoglobus fulgidus and the cooS gene from the bacterium Rhodospirillum rubrum, respectively. The cooS gene was identified immediately downstream of cooF, however, the cooF and cooS genes from C. hydrogenoformans have substantially different codon usage, and the cooF gene Arg codon usage pattern, dominated by AGA and AGG, resembles the archaeal pattern. The data therefore suggest lateral transfer of these genes, possibly from different donor species.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.2000.tb09346.x
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  • 4
    Electronic Resource
    Electronic Resource
    Geochemistry and microbial diversity of a trichloroethene-contaminated Superfund site undergoing intrinsic in situ reductive dechlorination (2002)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 40 (2002), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: This study explored the geochemistry and microbial diversity of a Superfund site containing trichloroethene (TCE) and an unusual co-pollutant, tetrakis(2-ethylbutoxy)silane. Geochemical analysis of contaminated groundwater indicated subsurface anaerobiosis, reductive dechlorination of TCE to predominantly cis-1,2-dichloroethene, and (transient) accumulation of 2-ethylbutanol and 2-ethylbutyrate as a result of tetrakis(2-ethylbutoxy)silane breakdown. Comparative analysis of 106 16S rDNA and 61 16S–23S rDNA intergenic spacer region sequences – obtained from pristine and contaminated groundwater via DNA extraction, PCR amplification, cloning and sequencing – revealed that the contaminated groundwater featured (i) a distinct microbial community, (ii) reduced species diversity, (iii) various anaerobes, and (iv) bacteria closely related to the TCE-dechlorinating, dichloroethene-accumulating genus Dehalobacter, whereas (v) the TCE-dechlorinating, ethene-producing species Dehalococcoides ethenogenes was not detectable. Thus, geochemical and molecular biological results were in excellent agreement in this first ecological field study linking in situ reductive dechlorination of TCE to metabolism of tetraalkoxysilanes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.2002.tb00944.x
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  • 5
    Electronic Resource
    Electronic Resource
    Regulation of ribosomal RNA transcription by growth rate of the hyperthermophilic Archaeon, Pyrococcus furiosus (1993)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 111 (1993), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract We have studied the single rRNA gene cluster from the Archaeon, Pyrococcus furiosus. This isolate grows optimally at 100°C and is thus a hyperthermophile. In P. furiosus, transcription of 16S rRNA is subject to regulation over a 7.5-fold range in response to a 20-fold increase in growth rate. The single cluster encoding the 16S and 23S rRNA genes of P. furiosus was cloned and the 1.9 kb region upstream of the 16S rRNA gene was sequenced.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.1993.tb06379.x
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  • 6
    Electronic Resource
    Electronic Resource
    Regulation of nitrogen catabolic enzymes in Vibrio alginolyticus (1983)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 19 (1983), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.1983.tb00536.x
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  • 7
    Electronic Resource
    Electronic Resource
    DNA Repair Systems in Archaea: Mementos from the Last Universal Common Ancestor? (1999)
    Springer
    Journal of molecular evolution 49 (1999), S. 474-484 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Hyperthermophile — Archaea — DNA repair — Endonuclease — Recombinase — Last universal common ancestor
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. DNA repair in the Archaea is relevant to the consideration of genome maintenance and replication fidelity in the last universal common ancestor (LUCA) from two perspectives. First, these prokaryotes embody a mix of bacterial and eukaryal molecular features. Second, DNA repair proteins would have been essential in LUCA to maintain genome integrity, regardless of the environmental temperature. Yet we know very little of the basic molecular mechanisms of DNA damage and repair in the Archaea in general. Many studies on DNA repair in archaea have been conducted with hyperthermophiles because of the additional stress imposed on their macromolecules by high temperatures. In addition, of the six complete archaeal genome sequences published so far, five are thermophilic archaea. We have recently shown that the hyperthermophile Pyrococcus furiosus has an extraordinarily high capacity for repair of radiation-induced double-strand breaks and we have identified and sequenced several genes involved in DNA repair in P. furiosus. At the sequence level, only a few genes share homology with known bacterial repair genes. For instance, our phylogenetic analysis indicates that archaeal recombinases occur in two paralogous gene families, one of which is very deeply branched, and both recombinases are more closely related to the eukaryotic RAD51 and Dmc1 gene families than to the Escherichia coli recA gene. We have also identified a gene encoding a repair endo/exonuclease in the genomes of several Archaea. The archaeal sequences are highly homologous to those of the eukaryotic Rad2 family and they cluster with genes of the FEN-1 subfamily, which are known to be involved in DNA replication and repair in eukaryotes. We argue that there is a commonality of mechanisms and protein sequences, shared between prokaryotes and eukaryotes for several modes of DNA repair, reflecting diversification from a minimal set of genes thought to represent the genome of the LUCA.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006570
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  • 8
    Electronic Resource
    Electronic Resource
    Evidence for the Early Divergence of Tryptophanyl- and Tyrosyl-tRNA Synthetases (1997)
    Springer
    Journal of molecular evolution 45 (1997), S. 9 -16 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Archaea — Aminoacyl-tRNA synthetases — Evolution — Universal tree
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Each amino acid is attached to its cognate tRNA by a distinct aminoacyl-tRNA synthetase (aaRS). The conventional evolutionary view is that the modern complement of synthetases existed prior to the divergence of eubacteria and eukaryotes. Thus comparisons of prokaryotic and eukaryotic aminoacyl-tRNA synthetases of the same type (charging specificity) should show greater sequence similarities than comparisons between synthetases of different types—and this is almost always so. However, a recent study [Ribas de Pouplana L, Furgier M, Quinn CL, Schimmel P (1996) Proc Natl Acad Sci USA 93:166–170] suggested that tryptophanyl- (TrpRS) and tyrosyl-tRNA (TyrRS) synthetases of the Eucarya (eukaryotes) are more similar to each other than either is to counterparts in the Bacteria (eubacteria). Here, we reexamine the evolutionary relationships of TyrRS and TrpRS using a broader range of taxa, including new sequence data from the Archaea (archaebacteria) as well as species of Eucarya and Bacteria. Our results differ from those of Ribas de Pouplana et al.: All phylogenetic methods support the separate monophyly of TrpRS and TyrRS. We attribute this result to the inclusion of the archaeal data which might serve to reduce long branch effects possibly associated with eukaryotic TrpRS and TyrRS sequences. Furthermore, reciprocally rooted phylogenies of TrpRS and TyrRS sequences confirm the closer evolutionary relationship of Archaea to eukaryotes by placing the root of the universal tree in the Bacteria.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006206
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  • 9
    Electronic Resource
    Electronic Resource
    Regulation of exoprotease production by temperature and oxygen in Vibrio alginolyticus (1981)
    Springer
    Archives of microbiology 130 (1981), S. 276-280 
    Details
    ISSN: 1432-072X
    Keywords: Collagenase ; Alkaline protease ; Temperature control ; Oxygen control ; Regulation ; Vibrio alginolyticus ; Secretion exoproteins ; Cerulenin ; Quinacrine ; Microbial ecology
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The production of an extracellular collagenase and an alkaline protease by Vibrio alginolyticus during stationary phase was inhibited by a temperature shift from 30 to 37°C and by a lack of oxygen. The stability of the exoproteases was unaffected by incubation at 37°C and aeration. The optimum growth temperature for the V. alginolyticus strain was 33.5°C Aeration enhanced the rate of growth of exponential phase cells. Temperature and oxygen did not affect the growth of stationary phase cells when the exoproteases were being produced. Macromolecular synthesis in stationary phase cells was not affected by temperature. There was no rapid release of the exoproteases after temperature shift down and chloramphenicol inhibited the production of the enzymes when added at time of temperature shift down from 37 to 30°C. The regulation of exoprotease production by temperature and oxygen was specific and has implications regarding the ecology of V. alginolyticus. Cerulenin, quinacrine and O-phenanthroline inhibited the production of the exoproteases.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00425940
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  • 10
    Electronic Resource
    Electronic Resource
    Temperature and oxygen regulated expression of a glutamine synthetase gene fromVibrio alginolyticus cloned inEscherichia coli (1986)
    Springer
    Archives of microbiology 146 (1986), S. 30-34 
    Details
    ISSN: 1432-072X
    Keywords: Vibrio alginolyticus ; Glutamine synthetase ; Cloning glutamine synthetase ; Temperature and oxygen regulation glutamine synthetase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Glutamine synthetase (GS) synthesis inVibrio alginolyticus was regulated by temperature, oxygen and nitrogen levels. A GS gene,glnA fromV. alginolyticus was cloned on a 5.67 kb insert in the recombinant plasmid pRM210, which enabledEscherichia coli glnA, ntrB, ntrC deletion mutants to utilize (NH4)2SO4 as a sole source of nitrogen. TheV. alginolyticus glnA gene was expressed from a regulatory region contained within the cloned fragment.V. alginolyticus glnA expression from pRM210 was subject to regulation by temperature, oxygen and nitrogen levels. GS specific activity in anE. coli wild-type strain was not affected by temperature or oxygen. pRM211 was a deletion derivative of pRM210 and GS production by pRM211 was not regulated by temperature, oxygen or nitrogen levels inE. coli.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00690154
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