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PubMed1981

Causes of more frequent deletions than insertions in mutations and protein evolution.

Deletions and insertions of base pairs in dNA, jointly called gap events, are one of the major sources of evolutionary change at the molecular level. On the basis of very limited data, Fitch has suggested that deletions might be expressed more often than insertions in proteins. We have examined the presently available homologous protein sequences, and observed that in the course of evolution, deletions of amino acids have indeed occurred about four times more frequently than insertions. An even higher preponderance of deletions over insertions (ten times or more) is found in recent spontaneous and induced mutants of genes or proteins. We propose here a mutational mechanism to explain this predominance of deletions.

Animals↗
PubMed2002

Genome and protein evolution in eukaryotes.

The past year has seen the completion of the genome sequence of the flowering plant Arabidopsis thaliana and the initial sequence reports of the human genome. The availability of completely sequenced eukaryotic genomes from disparate phylogenetic lineages has opened the door to comparative analyses and a better understanding of the evolutionary processes shaping genomes. Complex many-to-many relationships between genes from different species appear to be the norm, suggesting that transfer of detailed functional annotation will not be straightforward. In addition to expansion and contraction of gene families, new genes evolve from recombination of pre-existing domains, although some domain families do appear to have evolved recently and to be specific to restricted phylogenetic lineages. The overall picture is of a huge diversity of gene content within eukaryotic genomes, reflecting different functional demands in different species.

Animals↗
PubMed2002

A new zinc binding fold underlines the versatility of zinc binding modules in protein evolution.

Many different zinc binding modules have been identified. Their abundance and variety suggests that the formation of zinc binding folds might be relatively common. We have determined the structure of CH1(1), a 27-residue peptide derived from the first cysteine/histidine-rich region (CH1) of CREB binding protein (CBP). This peptide forms a highly ordered zinc-dependent fold that is distinct from known folds. The structure differs from a subsequently determined structure of a larger region from the CH3 region of CBP, and the CH1(1) fold probably represents a nonphysiologically active form. Despite this, the fold is thermostable and tolerant to both multiple alanine mutations and changes in the zinc-ligand spacing. Our data support the idea that zinc binding domains may arise frequently. Additionally, such structures may prove useful as scaffolds for protein design, given their stability and robustness.

Amino Acid Sequence↗
PubMed1997

Hox genes in evolution: protein surfaces and paralog groups.

The clustered Hox genes, which encode homeodomain transcription factors, control cell fates along the anterior-posterior axis. Differences between Hox proteins cause differences between body parts. Vertebrates have 13 Hox subgroups, called paralog groups, which can be correlated with some of the insect and Amphioxus genes, and have remained distinctive for hundreds of millions of years. We identify characteristic residues that define the different paralog groups. Some paralog groups can be recognized by the homeodomain sequence alone; others only by using characteristic residues outside the homeodomain. Mapping characteristic residues onto the known homeodomain crystal structure reveals that most of the homeodomain amino acids that distinguish paralog groups are oriented away from the DNA, in positions where they might engage in protein-protein interactions.

Amino Acid Sequence↗
PubMed2006

Fast protein evolution and germ line expression of a Drosophila parental gene and its young retroposed paralog.

This is the first detailed study of the evolution, phylogenetic distribution, and transcription of one young retroposed gene, CG13732, and its parental gene CG15645, whose functions are unknown. CG13732 is a recognizable retroposed copy of CG15645 retaining the signals of this process. We name the parental gene Cervantes and the retrogene Quijote. To determine when this duplication occurred and the phylogenetic distribution of Quijote, we employed polymerase chain reaction, Southern blotting, and the available information on sequenced Drosophila genomes. Interestingly, these analyses revealed that Quijote is present only in 4 species of Drosophila (Drosophila melanogaster, Drosophila simulans, Drosophila sechellia, and Drosophila mauritiana) and that retroposed copies of Cervantes have also originated in the lineages leading to Drosophila yakuba and Drosophila erecta independently in the 3 instances. We name the new retrogene in the D. yakuba lineage Rocinante and the new retrogene in the D. erecta lineage Sancho. In this work, we present data on Quijote and its parental gene Cervantes. Polymorphism analysis of the derived gene and divergence data for both parental and derived genes were used to determine that both genes likely produce functional proteins and that they are changing at a fast rate (KA/KS approximately 0.38). The negative value of H of Fay and Wu in the non-African sample reveals an excess of derived variants at high frequency. This could be explained either by positive selection in the region or by demographic effects. The comparative expression pattern shows that both genes express in the same adult tissues (male and female germ line) in D. melanogaster. Quijote is also expressed in male and female in D. simulans, D. sechellia, and D. mauritiana. We argue that the fast rate of evolution of these genes could be related to their putative germ line function and are further studying the independent recruitment of Cervantes-derived retrogenes in multiple lineages.

Animals↗
PubMed1999

Protein evolution by molecular breeding.

Natural evolution has guided the development of 'molecular breeding' processes used in the laboratory for the rapid modification of subgenomic sequences including single genes. The most significant recent development has been the in vitro permutation of natural diversity. Homologous recombination of multiple related sequences produced high-quality libraries of chimeric sequences encoding proteins with functions that differ dramatically from any of the parents. Increasingly powerful screening methods are also being developed, allowing these libraries to be screened for novel biocatalysts.

Animals↗
PubMed2003

Sequence divergence, functional constraint, and selection in protein evolution.

The genome sequences of multiple species has enabled functional inferences from comparative genomics. A primary objective is to infer biological functions from the conservation of homologous DNA sequences between species. A second, more difficult, objective is to understand what functional DNA sequences have changed over time and are responsible for species' phenotypic differences. The neutral theory of molecular evolution provides a theoretical framework in which both objectives can be explicitly tested. Development of statistical tests within this framework has provided insight into the evolutionary forces that constrain and in some cases change DNA sequences and the resulting patterns that emerge. In this article, we review recent work on how functional constraint and changes in protein function are inferred from protein polymorphism and divergence data. We relate these studies to our understanding of the neutral theory and adaptive evolution.

DNA↗
PubMed2003

The insertion of palindromic repeats in the evolution of proteins.

The current theory of protein evolution is that all contemporary proteins are derived from an ancestral subset. However, each new sequenced genome exhibits many genes with no detectable homologues in other species, leading to the paradoxical picture of a universal ancestor with more genes than any of its progeny. Standard explanations indicate that fast evolving genes might disappear into the 'twilight zone' of sequence similarity. Regardless of the size of the original ancestral subset, its origin and the potential mechanisms of its subsequent enlargement are rarely addressed. Sequencing of Rickettsia conorii genome recently led to the discovery of three families of repeat-mobile elements frequently inserted into the middle of protein coding genes. Although not yet identified in other species of bacteria, this discovery has provided the first clear evidence for the de novo creation of long protein segments (up to 50 amino acid residues) by repeat insertion. Based on previous results and theories on the coding potential of palindromic elements, we speculate that their insertion and mobility might have played a significant role in the early stages of protein evolution.

Amino Acid Sequence↗
PubMed1995

Three different rearrangements in a single intron truncate sterol regulatory element binding protein-2 and produce sterol-resistant phenotype in three cell lines. Role of introns in protein evolution.

The cholesterol analogue 25-hydroxycholesterol kills animal cells by blocking the proteolytic activation of two sterol-regulated transcription factors designated sterol regulatory element binding protein-1 and -2 (SREBP-1 and SREBP-2). These proteins, each approximately 1150 amino acids in length, are embedded in the membranes of the nucleus and endoplasmic reticulum by virtue of hydrophobic COOH-terminal segments. In cholesterol-depleted cells the proteins are cleaved to release soluble NH2-terminal fragments of approximately 480 amino acids that enter the nucleus and activate genes encoding the low density lipoprotein receptor and enzymes of cholesterol synthesis. 25-Hydroxycholesterol blocks this cleavage, and cells die of cholesterol deprivation. We previously described a mutant 25-hydroxycholesterol-resistant hamster cell line (SRD-1 cells) in which the SREBP-2 gene had undergone a recombination between the intron following codon 460 and an intron in an unrelated gene. The SREBP-2 sequence terminated at residue 460, eliminating the membrane attachment domain and producing a constitutively active factor that no longer required proteolysis and thus was not inhibited by 25-hydroxycholesterol. Here, we report that two additional sterol-resistant cell lines (SRD-2 and SRD-3) have also undergone genomic rearrangements in the intron following codon 460 of the SREBP-2 gene. Although the molecular rearrangements differ in the three mutant lines, each leads to the production of a constitutively active transcription factor whose SREBP-2 sequence terminates at residue 460. These findings provide a dramatic illustration of the advantage that introns provide in allowing proteins to gain new functions in response to new environmental challenges.

Amino Acid Sequence↗
PubMed2005

Patterns of protein evolution in Tetrahymena thermophila: implications for estimates of effective population size.

High levels of synonymous substitutions among alleles of the surface antigen SerH led to the hypothesis that Tetrahymena thermophila has a tremendously large effective population size, one that is greater than estimated for many prokaryotes (Lynch, M., and J. S. Conery. 2003. Science 302:1401-1404.). Here we show that SerH is unusual as there are substantially lower levels of synonymous variation at five additional loci (four nuclear and one mitochondrial) characterized from T. thermophila populations. Hence, the effective population size of T. thermophila, a model single-celled eukaryote, is lower and more consistent with estimates from other microbial eukaryotes. Moreover, reanalysis of SerH polymorphism data indicates that this protein evolves through a combination of vertical transmission of alleles and concerted evolution of repeat units within alleles. SerH may be under balancing selection due to a mechanism analogous to the maintenance of antigenic variation in vertebrate immune systems. Finally, the dual nature of ciliate genomes and particularly the amitotic divisions of processed macronuclear genomes may make it difficult to estimate accurately effective population size from synonymous polymorphisms. This is because selection and drift operate on processed chromosomes in macronuclei, where assortment of alleles, disruption of linkage groups, and recombination can alter the genetic landscape relative to more canonical eukaryotic genomes.

Alleles↗
PubMed1986

Micro-complement fixation: a quantitative estimator of protein evolution.

The quantitative immunological technique of micro-complement fixation (MC'F) has been routinely used during the past decade to assess evolutionary relationships among living vertebrate species. The large data base that has been generated, along with the excellent correlations between immunologically measured genetic distances and paleontologically derived estimates of divergence times, have formed the basis for the albumin molecular clock. Immunological distance (ID) involves a logarithmic transformation of experimentally measured antibody concentrations. The justification for this transformation has rested entirely on empirical correlations. Consequently, several other transformations have been proposed as giving better fits to particular data sets. We derive, from first principles, the relationship between ID and the amino acid sequence replacements (AAR) between compared albumins. ID is shown to be a linear estimator of AAR. This ID-AAR relationship is based on a proposed process of antibody assortment and exclusion. We present experimental data confirming that such an antibody assortment-exclusion process occurs in MC'F. This process can explain both the high sensitivity and the quantitative phylogenetic nature of the MC'F assay. The assortment-exclusion process also predicts a divergence limit beyond which MC'F data no longer provide robust phylogenetic data.

Biological Evolution↗