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  • 1
    Electronic Resource
    Electronic Resource
    Copper/Zinc superoxide dismutase: How likely is gene transfer from ponyfish toPhotobacterium leiognathi? (1986)
    Springer
    Journal of molecular evolution 23 (1986), S. 250-258 
    Details
    ISSN: 1432-1432
    Keywords: Superoxide dismutase ; Gene transfer ; Phylogenetic tree ; Rate of evolution ; Molecular evolution ; Protein evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The proposed transfer of the gene for Cu/Zn superoxide dismutase from the ponyfish to its symbiotic bacteriumPhotobacterium leiognathi has been evaluated by an extensive analysis of all available Cu/Zn superoxide dismutase sequences. By the use of four different computer programs, phylogenetic trees were constructed from the sequences of the superoxide dismutases of human, ox, pig, horse, swordfish, fruit fly, yeast, andNeurospora crassa to find out whether superoxide dismutase sequences can reliably be used for the reconstruction of genealogical relationships. All programs arrived at the same most parsimonious tree (one requiring 232 amino acid replacements), the topology of which conformed to established opinions about the phylogenetic relations among these eukaryotes, except that it placed humans closer to the artiodactyls ox and pig than it placed horses. This could be corrected at the cost of two amino acid replacements. The sequence ofP. leiognathi superoxide dismutase was then connected at all possible positions to the corrected eukaryotic tree. It was slighly more parsimonious to link the bacterial sequence to the root of the tree than to the fish branch: The former required 316 (or 317) amino acid replacements, versus 319 for the latter. This relative lack of discrimination between such distinct alternative topologies may be a general complication in the comparison of prokaryotic and eukaryotic proteins: Bacterial cytochrome c sequences also were found to be connected as parsimoniously to the root of the eukaryotic tree as to any terminal or ancestral branch. It was calculated that the rate of evolution of the bacterial superoxide dismutase gene, if transfer occurred 30 million years (Myr) ago, must have amounted to 487 amino acid replacements per 100 residues per 100 Myr. This is more than 5 times the highest rate observed in any protein (that found for fibrinopeptides), and even much higher than the maximum rate of protein evolution that can be deduced from the neutral mutation rate of unconstrained DNA. Also, no significant evidence that shared derived amino acid replacements are present in swordfish andP. leiognathi superoxide dismutase, as might be expected had gene transfer occurred, was found. On the basis of the available data it seems more reasonable to ascribe the isolated occurrence of Cu/Zn superoxide dismutase inP. leiognathi (as well as inCaulobacter crescentus) to irregular patterns of gene expression and inactivation in the course of divergent evolution than to undocumented processes of gene transfer from eukaryotes to prokaryotes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02115581
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  • 2
    Electronic Resource
    Electronic Resource
    Extreme differences in charge changes during protein evolution (1990)
    Springer
    Journal of molecular evolution 31 (1990), S. 33-39 
    Details
    ISSN: 1432-1432
    Keywords: Amino acid replacements ; Codon usage ; Electrostatic interactions ; Mitochondrial code ; Molecular evolution ; Mutations
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The maintenance of a proper distribution of charged amino acid residues might be expected to be an important factor in protein evolution. We therefore compared the inferred changes in charge during the evolution of 43 protein families with the changes expected on the basis of random base substitutions. It was found that certain proteins, like the eye lens crystallins and most histones, display an extreme avoidance of changes in charge. Other proteins, like phospholipase A2 and ferredoxin, apparently have sustained more charged replacements than expected, suggesting a positive selection for changes in charge. Depending on function and structure of a protein, charged residues apparently can be important targets for selective forces in protein evolution. It appears that actual biased codon usage tends to decrease the proportion of charged amino acid replacements. The influence of nonrandomness of mutations is more equivocal. Genes that use the mitochondrial instead of the universal code lower the probability that charge changes will occur in the encoded proteins.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02101790
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  • 3
    Electronic Resource
    Electronic Resource
    The expanding small heat-shock protein family, and structure predictions of the conserved “α-crystallin domain” (1995)
    Springer
    Journal of molecular evolution 40 (1995), S. 238-248 
    Details
    ISSN: 1432-1432
    Keywords: Molecular chaperones ; Molecular phylogeny ; Molecular evolution ; Structural domains ; Structure prediction
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The ever-increasing number of proteins identified as belonging to the family of small heat-shock proteins (shsps) and α-crystallins enables us to reassess the phylogeny of this ubiquitous protein family. While the prokaryotic and fungal representatives are not properly resolved, most of the plant and animal shsps and related proteins are clearly grouped in distinct clades, reflecting a history of repeated gene duplications. The members of the shsp family are characterized by the presence of a conserved homologous “α-crystallin domain,” which sometimes is present in duplicate. Predictions are made of secondary structure and solvent accessibility of this domain, which together with hydropathy profiles and intron positions support the presence of two similar hydrophobic β-sheet-rich motifs, connected by a hydrophilic α-helical region. Together with an overview of the newly characterized members of the shsp family, these data help to define this family as being involved as stable structural proteins and as molecular chaperones during normal development and induced under pathological and stressful conditions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00163229
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  • 4
    Electronic Resource
    Electronic Resource
    Presence of hybridizing DNA sequences homologous to bovine acidic and basicβ-crystallins in all classes of vertebrates (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 457-463 
    Details
    ISSN: 1432-1432
    Keywords: Eye lens proteins ; Molecular evolution ; Gene family
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The eye lensβ-crystallins in cow and chicken are encoded by a family of at least six genes. In order to assess the distribution of the corresponding genes among other vertebrates we hybridized β-crystallin sequences (βA2, βA3/A1, βA4, βB1, βB2, βB3), isolated from a bovine lens cDNA library, to Southern blots on whichEcoR1-digested chromosomal DNA was blotted from different vertebrate species. These included human, chimpanzee, calf, rat, pigeon, duck, monitor lizard, toad, trout, and lamprey. Positive hybridization signals were found in the representatives of virtually all classes of vertebrates. The basic βB-crystallins gave hybridization signals in more species than the acidic βA ones. In monitor lizard and toad the weakest hybridization signals for basic crystallin probes were found. For acidic crystallin probes the distribution pattern was more simple; among cold-blooded vertebrates a signal for βA2 was found in trout and lamprey, for βA4 in trout, and for βA3/A1 only in toad. The results demonstrate that the duplications leading to the β-crystallin gene family occurred before or during the earliest stages of vertebrate evolution.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02103138
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  • 5
    Electronic Resource
    Electronic Resource
    Protein sequences indicate that turtles branched off from the amniote tree after mammals (1996)
    Springer
    Journal of molecular evolution 42 (1996), S. 580-586 
    Details
    ISSN: 1432-1432
    Keywords: Testudines ; Trachemys scripta elegans ; Tetrapod phylogeny ; Molecular evolution ; α-crystallin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The phylogenetic relationships among the major groups of amniote vertebrates remain a matter of controversy. Various alternatives for the position of the turtles have been proposed, branching off either before or after the mammals. To discover the phylogenetic position of turtles in relation to mammals and birds, we have determined cDNA sequences for the eye lens proteins αA- and αB-crystallin of the red-eared slider turtle (Trachemys scripta elegans). In addition, databases were searched for turtle protein sequences, for which mammalian, avian, and outgroup orthologs were available. All sequences were analyzed by three phylogenetic tree reconstruction methods (neighbor-joining, maximum parsimony, and maximum likelihood). Including the α-crystallins, 7 out of 12 proteins support a sister-group relation of turtles and birds with all 3 methods. For each of the other five proteins no topology was consistently preferred by the three approaches. Analyses of the combined amino acid data (1,695 aligned sites) also give extremely strong evidence that turtles are nearer to birds, indicating that mammals branched off before the divergence between turtles and birds occurred.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02352288
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  • 6
    Electronic Resource
    Electronic Resource
    Evolutionary changes ofα-crystallin and the phylogeny of mammalian orders (1977)
    Springer
    Journal of molecular evolution 10 (1977), S. 123-135 
    Details
    ISSN: 1432-1432
    Keywords: Ancestral sequence ; Eye lens protein ; Evolution ; Phylogenetic tree
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The sequences of the A chains of the eye lens proteinα-crystallin from seventeen mammalian species were compared. They showed a generally slow rate of evolution, but with marked variations in different lineages. Most substitutions have occurred in the C-terminal part of the chain, which probably forms part of the surface of theα-crystallin aggregate. The ancestral sequence method of Dayhoff revealed interesting indications about the phylogenetic relationships between the eleven mammalian orders that were represented by the investigated species. Most evident was the divergence of marsupial and placental orders. A notable resemblance between the hyrax and elephant sequences was observed, setting them apart from the ungulates, including whale. Primates, rodents, lagomorphs, insectivores and tupaiids seem to derive from a common stem group. These phylogenetic inferences are discussed in relation to current palaeontological and taxonomical opinions, and compared to evidence from other protein sequence data.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01751806
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  • 7
    Electronic Resource
    Electronic Resource
    The eye lens crystallins: Ambiguity as evolutionary strategy (1986)
    Springer
    Journal of molecular evolution 24 (1986), S. 121-129 
    Details
    ISSN: 1432-1432
    Keywords: Protein evolution ; Alternative splicing ; Translation initiation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Comparative studies of the different families of lens-specific proteins of the vertebrates, the crystallins, and their genes reveal several interesting evolutionary features. The origin of α-crystallin can be traced back to the small heat shock proteins, while the superfamily of βγ-crystallins shows structural similarities with a bacterial spore coat protein. The crystallins display a great diversity within and between species, as well as during development. Ambiguous transcription, mRNA-processing, and translation contribute to this diversity of the crystallins and their expression. These mechanisms include the occurrence of atypical poly-A addition signals, alternative splicing, and the use of two initiation codons on a single mRNA.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02099960
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  • 8
    Electronic Resource
    Electronic Resource
    Parallel adaptive radiations in two major clades of placental mammals (2001)
    [s.l.] : Macmillian Magazines Ltd.
    Nature 409 (2001), S. 610-614 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Higher level relationships among placental mammals, as well as the historical biogeography and morphological diversification of this group, remain unclear. Here we analyse independent molecular data sets, having aligned lengths of DNA of 5,708 and 2,947 base pairs, respectively, for all orders ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/35054544
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  • 9
    Electronic Resource
    Electronic Resource
    Ratites as oldest offshoot of avian stem—evidence from α -crystallin A sequences (1984)
    [s.l.] : Nature Publishing Group
    Nature 311 (1984), S. 257-259 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] The a-crystallin ?-chain is a suitable protein for comparative sequence analysis because (1) being a major eye lens constituent in all vertebrate classes7, it can often be isolated in considerable quantities, and (2) the sequence analysis of the 173-residues "?-chain is relatively simple8. There is ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/311257a0
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  • 10
    Electronic Resource
    Electronic Resource
    The enzyme lactate dehydrogenase as a structural protein in avian and crocodilian lenses (1987)
    [s.l.] : Nature Publishing Group
    Nature 326 (1987), S. 622-624 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Lens proteins occupy one of the more unusual environments in vertebrate biology. They have extraordinary requirements for structural stability, because they must be exposed to light and yet survive at high concentration (crystallins account for 20-50% of the wet weight of lenses) without ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/326622a0
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