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At least 163 records · Page 9Linked to original sources
PubMed1990

Implications of thermodynamics of protein folding for evolution of primary sequences.

Natural proteins exhibit essentially two-state thermodynamics, with one stable fold that dominates thermodynamically over a vast number of possible folds, a number that increases exponentially with the size of the protein. Here we address the question of whether this feature of proteins is a rare property selected by evolution or whether it is in fact true of a significant proportion of all possible protein sequences. Using statistical procedures developed to study spin glasses, we show that, given certain assumptions, the probability that a randomly synthesized protein chain will have a dominant fold (which is the global minimum of free energy) is a function of temperature, and that below a critical temperature the probability rapidly increases as the temperature decreases. Our results suggest that a significant proportion of all possible protein sequences could have a thermodynamically dominant fold.

Amino Acid Sequence↗
PubMed1989

Allelic variation in HLA-B and HLA-C sequences and the evolution of the HLA-B alleles.

Several new HLA-B (B8, B51, Bw62)- and HLA-C (Cw6, Cw7)-specific genes were isolated either as genomic cosmid or cDNA clones to study the diversity of HLA antigens. The allele specificities were identified by sequence analysis in comparison with published HLA-B and -C sequences, by transfection experiments, and Southern and northern blot analysis using oligonucleotide probes. Comparison of the classical HLA-A, -B, and -C sequences reveals that allele-specific substitutions seem to be rare events. HLA-B51 codes only for one allele-specific residue: arginine at position 81 located on the alpha 1 helix, pointing toward the antigen binding site. HLA-B8 contains an acidic substitution in amino acid position 9 on the first central beta sheet which might affect antigen binding capacity, perhaps in combination with the rare replacement at position 67 (F) on the alpha 1 helix. HLA-B8 shows greatest homology to HLA-Bw42, -Bw41, -B7, and -Bw60 antigens, all of which lack the conserved restriction sites Pst I at position 180 and Sac I at position 131. Both sites associated with amino acid replacements seem to be genetic markers of an evolutionary split of the HLA-B alleles, which is also observed in the leader sequences. HLA-Cw7 shows 98% sequence identity to the JY328 gene. In general, the HLA-C alleles display lower levels of variability in the highly polymorphic regions of the alpha 1 and alpha 2 domains, and have more distinct patterns of locus-specific residues in the transmembrane and cytoplasmic domains. Thus we propose a more recent origin for the HLA-C locus.

Amino Acid Sequence↗
PubMed1992

Evolution of DNA sequence homologies between the sex chromosomes in primate species.

Cloned DNA sequences from 18 X-Y homologous loci have been used to examine the evolution of regions of homology between the human X and Y chromosomes. The pattern of X-Y linkage in different primate species has enabled the charting of the chronology of their appearance and removal from the sex chromosomes during evolution. Examination of the pattern of differences in restriction enzyme sites at different loci has been used to estimate the degree of divergence in three different regions of homology. These studies have indicated that (1) blocks of homology have arisen at different points in evolution, (2) different regions of homology are heterogeneous in composition in that they contain X-Y homologous sequences of different age, and (3) the combination of X and Y locations together with the point of evolutionary origin has defined five new patterns of homology.

Animals↗
PubMed1984

Molecular evolution of chloroplast DNA sequences.

Comparative data on the evolution of chloroplast genes are reviewed. The chloroplast genome has maintained a similar structural organization over most plant taxa so far examined. Comparisons of nucleotide sequence divergence among chloroplast genes reveals marked similarity across the plant kingdom and beyond to the cyanobacteria (blue-green algae). Estimates of rates of nucleotide substitution indicate a synonymous rate of 1.1 x 10(-9) substitutions per site per year. Noncoding regions also appear to be constrained in their evolution, although addition/deletion events are common. There have also been evolutionary changes in the distribution of introns in chloroplast encoded genes. Relative to mammalian mitochondrial DNA, the chloroplast genome evolves at a conservative rate.

Biological Evolution↗
PubMed1988

Identification of an orthologous mammalian cytokeratin gene. High degree of intron sequence conservation during evolution of human cytokeratin 10.

Among the human acidic (type I) cytokeratins, components 10 and 11 are especially interesting, as they are under various kinds of expression control. They are synthesized in the suprabasal cell layers of certain stratified epithelia, notably epidermis, in an endogenous differentiation program; they are expressed in certain epithelial tumours but not in others; they can appear de novo in certain pathological situations such as in squamous metaplasias; and their expression in vivo and in vitro is under positive influence of extracellular calcium concentrations and is reduced in the presence of vitamin A or other retinoids. To provide a basis for studies of the various regulatory elements, we have isolated the human gene encoding cytokeratin 10, using a cDNA probe derived from the corresponding bovine gene, and have sequenced the mRNA coding region as well as adjacent regions approximately 1500 bases 5' upstream and 1000 bases 3' downstream. The eight exons encode a polypeptide 59,535 Mr, i.e. somewhat larger than the corresponding bovine and murine proteins. The deduced amino acid sequences display a high degree of homology, which is not restricted to the exons and the 5' and 3' adjacent regions but, surprisingly, is also evident in the seven introns, some of which contain extended sequence elements with 70% identical nucleotides and more, i.e. similar to the homology in the adjacent exons. This exceptionally high level of conservation of intron sequences is discussed in relation to the recently accumulating evidence of the occurrence of intron sequences important in the regulation of the expression of members of other multigene families during development.

Base Sequence↗
PubMed1991

Molecular evolution in hypotrichous ciliates: sequence of the small subunit ribosomal RNA genes from Onychodromus quadricornutus and Oxytricha granulifera (Oxytrichidae, Hypotrichida, Ciliophora).

The small subunit ribosomal RNA (16S-like rRNA) coding regions of the hypotrichous ciliates Onychodromus quadricornutus and Oxytricha granulifera were amplified using polymerase chain reaction techniques. Complete sequences were determined for the amplified genes and compared to those of other ciliated protozoa. In phylogenetic trees inferred using distance matrix methods oxytrichids are not seen as a cohesive phylogenetic group. Oxytricha nova is most closely related to Stylonychia pustulata in a lineage that also includes O. quadricornutus. This phylogeny contradicts phylogenetic schemes in which Onychodromus is considered to be a primitive hypotrichous ciliate and suggests that O. nova was misidentified as members of the genus Oxytricha.

Animals↗
PubMed1979

The use of amino acid sequence analysis in assessing evolution.

The thirteen year history of assessing evolution by amino acid sequence analysis has made apparent the limitations imposed upon this system by the finite nature of the characters. This finiteness exists on several levels and ultimately expresses itself as parallelism, back mutation and the retention of primitive characters in the sequences of proteins from present day species and the putative ancestral protein chains. Sequence analysis shares these problems with other molecular approaches, but because it is concerned both with the nucleotide substitutions in the genome and with the functional roles of proteins, it has unique advantages. For example, the large fluctuation in the rate of fixation of mutations in a protein's evolution can be detected and used to point out the unreliability of any molecular clock for estimating divergence dates. Moreover, when consideration is given to studies which assign functional significance to specific amino acid sites in a protein, changes in function during the descent of a protein can be appreciated and their significance correlated with organismal evolution.

Amino Acid Sequence↗
PubMed1978

The evolution of protein sequences by repetitious gene duplication: clostridial flavodoxin.

Internal regularities of amino acid sequences of flavodoxins, FMN-containing, low molecular weight flavoproteins, were statistically examined using the minimum mutation method. The sequence of Clostridium pasteurianum flavodoxin shows statistically significant evidence of repetitious internal gene duplications at different levels of structure. Peptide pairs with a low chance probabilitiy of occurrence were frequently observed at a shift of 5 residues. The pairs with the lowest chance probabilities are a pair of heptapeptides at positions39--45 vs. 44--50, a 5 residue shift (p = 9 x 10(-6)). Most of the related pairs are consistent and could best be explained by the repeating pentapeptide sequence: (Lys-Gly-Ala-Asp-Val-)n and appropriate gaps. Internal repetitions with longer shifts were also suggested for other flavodoxins. Repetitious gene duplication is proposed for the early stages of flavodoxin evolution.

Amino Acid Sequence↗
PubMed1989

Multiple cDNA sequences and the evolution of bovine stomach lysozyme.

To investigate the origin of stomach expression of lysozyme in ruminants; we surveyed clones from a cow stomach cDNA library with a lysozyme cDNA probe. Ten percent of the clones in this library were lysozyme-specific. Thirty of the lysozyme clones were sequenced, and seven types of lysozyme mRNA sequence were found. They encode the three previously identified stomach isozymes of lysozyme. The seven sequences are closely related to one another and represent the products of a minimum of 4 of the approximately 10 cow lysozyme genes detected by genomic blotting. The most abundant form of stomach lysozyme (form 2) is encoded by at least two genes, whereas forms 1 and 3 are possibly each encoded by only one gene. The number of genes encoding each isozyme appears to contribute the largest factor in the relative abundance of each isozyme. The multiple lysozyme genes expressed in the cow stomach are the result of gene duplications that occurred during ruminant evolution. The recruitment of lysozyme as a major enzyme in the stomach may thus have involved an early regulatory event and a later 4-7-fold increase in expression allowed by gene amplification. During this period, the amino acid sequences of these lysozymes have been evolving more slowly than those of nonruminant lysozymes.

Abomasum↗
PubMed1987

L1 repeat elements in the human epsilon-G gamma-globin gene intergenic region: sequence analysis and concerted evolution within this family.

We have deduced the sequence of a composite long interspersed repeated DNA in primates and herein describe its relationship to a complex repeat element (L1Heg) located in the interval linking the human epsilon- and G gamma-globin genes. The main element of L1Heg is 3' truncated and interrupted by the insertion of the 3' end of a second L1 element. Transposition of L1Heg into this intergenic locus generated a 62-bp duplication of flanking sequences. In contrast, insertion of the second repeat may have been mediated by homology between donor and target sequences. The main repeat represents a novel class of abundant elements whose sequences have diverged from other rodent and primate LINES approximately 1.3 kb downstream from the 5' terminus of L1Heg. Comparison of L1Heg with the sequences of two other related L1 members revealed a complex set of rearrangements confined within a region that resembles the long terminal repeats of other types of retroposons. The boundaries of conversion-like events were defined on the basis of the clustering of nucleotide sequence variants common to two or more nonallelic 3' L1H elements. Several of these events are apparently initiated or resolved within a common 150-bp region that coincides with the 3' terminus of a pan-mammalian open reading frame. This analysis showed that concerted genetic interactions and random drift both contribute appreciably to sequence variation within this set of L1H members.

Animals↗
PubMed1980

Evolution of DNA sequences has been retarded in Malagasy primates.

It is generally accepted that there are six major groups of living primates: (1) lemurs (including all the primates of Madagascar), (2) lorises (including galago and potto), (3) tarsiers, (4) New World monkeys, (5) Old World monkeys and (6) apes (including man). Tree shrews, once considered to be primates, are now generally recognized as not significantly more closely related to the six groups than other mammals. The first surviving primate lines to diverge from the common primate ancestor are believed to have given rise to one or more of the first three groups. However, the fossil record is insufficient to determine their relative branching order. Furthermore, neither morphological considerations nor studies of protein evolution produce unanimity as to whether tarsiers are more closely related to the prosimians (the lemurs plus lorises) or the simians (the monkeys and apes). In an attempt to resolve these discrepancies, we have measured the DNA sequence difference between several primates. We report here that the evolution of DNA of primates from Madagascar is significantly less than that of all other groups of living primates. This is not expected in the simplest form of the theory of neutral selection and may be important for our understanding of evolution at the molecular level.

Animals↗
PubMed1983

Evolution of the nucleotide sequence of influenza virus RNA segment 7 during drift of the H3N2 subtype.

The complete genetic information contained in the influenza virus RNA segment 7 of the A/Bangkok/1/79 (H3N2) strain has been cloned by in vitro synthesis of the complementary dsDNA and its insertion into plasmid pBR322. The nucleotide sequence of the viral RNA segment has been determined from the cDNA insert. It is 1027 nucleotides long, and contains two open reading frames, as shown for other influenza virus strains. When compared with the previously published sequence for the A/Udorn/72 (H3N2) strain, 15 nucleotide exchanges are observed, most of them silent mutations, and only two causing amino acid changes in each of the M1 and M2 protein sequences.

Amino Acid Sequence↗