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  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 8 (1976), S. 143-153 
    ISSN: 1432-1432
    Keywords: 5S rRNA ; Comparative Analysis ; Secondary Structure ; Evolution ; Tuned Helix
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The available comparative data on procaryotic 5S rRNA was extended through sequencing studies of eight gram positive procaryotes. Complete nucleotide sequences were presented for 5S rRNA fromBacillus subtilis, B. firmus, B.pasteurii, B.brevis, Lactobacillus brevis andStreptococcus faecalis. In addition, 5S rRNA oligonucleotide catalogs and partial sequence data were provided forB.cereus andSporosarcina ureae. These sequences and catalogs were discussed in terms of known features of procaryotic 5S rRNA architecture.
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  • 2
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 10 (1977), S. 1-6 
    ISSN: 1432-1432
    Keywords: Evolution ; Ribosomes ; Genotype-Phenotype ; Cytoplasm ; Endosymbiosis ; Procaryote ; Eucaryote ; Progenote
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A central evolutionary question is whether the eucaryotic cytoplasm represents a line of descent that is separate from the typical bacterial line. It is argued on the basis of differences between their respective translation mechanisms that the two lines do represent separate phylogenetic trees in the sense that each line of descent independently evolved to a level of organization that could be called procaryotic. The two lines of descent, nevertheless shared a common ancestor, that was far simpler than the procaryote. This primitive entity is called a progenote, to recognize the possibility that it had not yet completed evolving the link between genotype and phenotype. This concept changes considerably the view one takes toward cellular evolution.
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 5 (1975), S. 35-46 
    ISSN: 1432-1432
    Keywords: Photobacter Strain 8265 ; 5S Ribosomal RNA ; Primary Structure ; Comparative Characterization ; Evolution ; Energetically Constrained Helix
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Comparative sequencing studies provide powerful insights into molecular function and evolution. The sequence for 5S ribosomal RNA from Photobacter strain 8265 is eighteen base replacements removed from that ofEscherichia coli. Of these, the vast majority involve a G or C becoming an A or U. These variations also define unequivocally a hexanucleotide base paired region, which appears to be a universal feature of the 5S RNA molecule. The base composition of this helix seems to be under rather stringent, and so unusual, energetic constraints. The possible implications of this are discussed - in particular the prospect of a 5S RNA molecule that undergoes conformational transitions as a part of the overall state changes that constitute the function of the ribosome.
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 31 (1990), S. 18-24 
    ISSN: 1432-1432
    Keywords: Plant and algae evolution ; 5S rRNA phylogeny ; Streptophyta ; Charophyceae ; Chlorophyceae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary 5S rRNA sequences from six additional green algae lend strong molecular support for the major outlines of higher plant and green algae phylogeny that have been proposed under varying naming conventions by several authors. In particular, the molecular evidence now available unequivocally supports the existence of at least two well-separated divisions of the Chlorobionta: the Chlorophyta and the Streptophyta (i.e., charophytes) (according to the nomenclature of Bremer). The chlamydomonad 5S rRNAs are, however, sufficiently distinct from both clusters that it may ultimately prove preferable to establish a third taxon for them. In support of these conclusions 5S rRNA sequence data now exist for members of four diverse classes of chlorophytes. These sequences all exhibit considerably more phylogenetic affinity to one another than any of them show toward members of the other cluster, the Streptophyta, or the twoChlamydomonas strains. Among the Charophyceae, new 5S rRNA sequences are provided herein for three genera,Spirogyra, Klebsormidium, andColeochate. All of these sequences and the previously publishedNitella sequence show greater resemblance among themselves and to the higher plants than they do to any of the other green algae examined to date. These results demonstrate that an appropriately named taxon that includes these green algae and the higher plants is strongly justified. The 5S rRNA data lack the resolution needed, however, to unequivocally determine which of several subdivisions of the charophytes is the sister group of the land plants. The evolutionary diversity ofChlamydomonas relative to the other green algae was recognized in earlier 5S rRNA studies but was unanticipated by ultrastructural work. These new data provide further evidence for the relative uniqueness of the chlamydomonads and are discussed further.
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  • 5
    ISSN: 1432-1432
    Keywords: Enzyme Polymorphism ; 5S rRNA ; Caenorhabditis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Electrophoretic comparisons have been made for 24 enzymes in theBergerac andBristol strains ofCaenorhabditis elegans and the related species,Caenorhabditis briggsae. No variation was detected between the two strains ofC. elegans. In contrast, the two species,C. elegans andC. briggsae exhibited electrophoretic differences in 22 of 24 enzymes. A consensus 5S rRNA sequence was determined forC. elegans and found to be identical to that fromC. briggsae. By analogy with other species with relatively well established fossil records it can be inferred that the time of divergence between the two nematode species is probably in the tens of millions of years. The limited anatomical evolution during a time period in which proteins undergo extensive changes supports the hypothesis that anatomical evolution is not dependent on overall protein changes.
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 45 (1997), S. 278-284 
    ISSN: 1432-1432
    Keywords: Key words: Sequence space — Shape space — 5S rRNA — Parsimony —Vibrio proteolyticus— Evolutionary paths
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. An experimental system for determining the potential ability of sequences resembling 5S ribosomal RNA (rRNA) to perform as functional 5S rRNAs in vivo in the Escherichia coli cellular environment was devised previously. Presumably, the only 5S rRNA sequences that would have been fixed by ancestral populations are ones that were functionally valid, and hence the actual historical paths taken through RNA sequence space during 5S rRNA evolution would have most likely utilized valid sequences. Herein, we examine the potential validity of all sequence intermediates along alternative equally parsimonious trajectories through RNA sequence space which connect two pairs of sequences that had previously been shown to behave as valid 5S rRNAs in E. coli. The first trajectory requires a total of four changes. The 14 sequence intermediates provide 24 apparently equally parsimonious paths by which the transition could occur. The second trajectory involves three changes, six intermediate sequences, and six potentially equally parsimonious paths. In total, only eight of the 20 sequence intermediates were found to be clearly invalid. As a consequence of the position of these invalid intermediates in the sequence space, seven of the 30 possible paths consisted of exclusively valid sequences. In several cases, the apparent validity/invalidity of the intermediate sequences could not be anticipated on the basis of current knowledge of the 5S rRNA structure. This suggests that the interdependencies in RNA sequence space may be more complex than currently appreciated. If ancestral sequences predicted by parsimony are to be regarded as actual historical sequences, then the present results would suggest that they should also satisfy a validity requirement and that, in at least limited cases, this conjecture can be tested experimentally.
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  • 7
    ISSN: 1432-1432
    Keywords: Key words: Genomics — Gene regulation — RNA world — Progenote
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Five complete bacterial genome sequences have been released to the scientific community. These include four (eu)Bacteria, Haemophilus influenzae, Mycoplasma genitalium, M. pneumoniae, and Synechocystis PCC 6803, as well as one Archaeon, Methanococcus jannaschii. Features of organization shared by these genomes are likely to have arisen very early in the history of the bacteria and thus can be expected to provide further insight into the nature of early ancestors. Results of a genome comparison of these five organisms confirm earlier observations that gene order is remarkably unpreserved. There are, nevertheless, at least 16 clusters of two or more genes whose order remains the same among the four (eu)Bacteria and these are presumed to reflect conserved elements of coordinated gene expression that require gene proximity. Eight of these gene orders are essentially conserved in the Archaea as well. Many of these clusters are known to be regulated by RNA-level mechanisms in Escherichia coli, which supports the earlier suggestion that this type of regulation of gene expression may have arisen very early. We conclude that although the last common ancestor may have had a DNA genome, it likely was preceded by progenotes with an RNA genome.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 17 (1981), S. 52-55 
    ISSN: 1432-1432
    Keywords: 5S rRNA ; Beneckea harveyi ; Procaryotic phylogeny ; Sequence heterogeneity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The complete sequence of the 5S rRNA from the bioluminescent bacterium,Beneckea harveyi has been determined to be p U G C U U G G C G $$\mathop A\limits^{10} $$ C C A U A G C G A $$\mathop U\limits^{20} $$ U U-G G A C C C A $$\mathop C\limits^{30} $$ C U G A (U) C U U C $$\mathop C\limits^{40} $$ A U U C C-G A A C $$\mathop U\limits^{50} $$ C A G A A G U G A $$\mathop A\limits^{60} $$ A C G A A U U A-G $$\mathop C\limits^{70} $$ G C C G A U G G U $$\mathop A\limits^{80} $$ G U G U G G G G C $$\mathop U\limits^{90} $$ U-C C C C A U G U $$\mathop G\limits^{100} $$ A G A G U A G G A $$\mathop C\limits^{110} $$ A U C G-C C A G G $$\mathop C\limits^{120} $$ U (U)OH. Two sites of sensitivity to ribonuclease T2 cleavage were identified; at A41 and either A54 or A55. Comparison with existing sequence information fromEscherichia coli andPhotobacterium phosphoreum clarifies the amount of diversity among the bioluminescent bacteria and provides further insight into their phylogenetic position. Sequence heterogeneities were encountered and the importance of these in interpreting 5S rRNA data is discussed.
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  • 9
    ISSN: 1432-1432
    Keywords: Symbiosis ; Plant mitochondria ; 5S RNA ; Evolution ; Purple bacteria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The complete nucleotide sequences of 5S ribosomal RNAs fromRhodocyclus gelatinosa, Rhodobacter sphaeroides, andPseudomonas cepacia were determined. Comparisons of these 5S RNA sequences show that rather than being phylogenetically related to one another, the two photosynthetic bacterial 5S RNAs share more sequence and signature homology with the RNAs of two nonphotosynthetic strains.Rhodobacter sphaeroides is specifically related toParacoccus denitrificans andRc. gelatinosa is related toPs. cepacia.These results support earlier 16S ribosomal RNA studies and add two important groups to the 5S RNA data base. Unique 5S RNA structural features previously found inP. denitrificans are present also in the 5S RNA ofRb. sphaeroides; these provide the basis for subdivisional signatures. The immediate consequence of our obtaining these new sequences is that we are able to clarify the phylogenetic origins of the plant mitochondrion. In particular, we find a close phylogenetic relationship between the plant mitochondria and members of the alpha subdivision of the purple photosynthetic bacteria, namely,Rb. sphaeroides, P. denitrificans, andRhodospirillum rubrum.
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  • 10
    Electronic Resource
    Electronic Resource
    [s.l.] : Nature Publishing Group
    Nature 256 (1975), S. 505-507 
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] A comparative analysis5 of 5S RNA primary structure is one approach to defining functionally significant secondary (and tertiary) structure whose interpretation is not open to the above caveat. A phylogenetically broad range of prokaryotic 5S RNAs have been shown to be functionally equivalent (that ...
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