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PubMed1998

Intragenic recombination and diversifying selection contribute to the evolution of downy mildew resistance at the RPP8 locus of Arabidopsis.

Pathogen resistance (R) genes of the NBS-LRR class (for nucleotide binding site and leucine-rich repeat) are found in many plant species and confer resistance to a diverse spectrum of pathogens. Little is known about the mechanisms that drive NBS-LRR gene evolution in the host-pathogen arms race. We cloned the RPP8 gene (for resistance to Peronospora parasitica) and compared the structure of alleles at this locus in resistant Landsberg erecta (Ler-0) and susceptible Columbia (Col-0) accessions. RPP8-Ler encodes an NBS-LRR protein with a putative N-terminal leucine zipper and is more closely related to previously cloned R genes that confer resistance to bacterial pathogens than it is to other known RPP genes. The RPP8 haplotype in Ler-0 contains the functional RPP8-Ler gene and a nonfunctional homolog, RPH8A. In contrast, the rpp8 locus in Col-0 contains a single chimeric gene, which was likely derived from unequal crossing over between RPP8-Ler and RPH8A ancestors within a Ler-like haplotype. Sequence divergence among RPP8 family members has been accelerated by positive selection on the putative ligand binding region in the LRRs. These observations indicate that NBS-LRR molecular evolution is driven by the same mechanisms that promote rapid sequence diversification among other genes involved in non-self-recognition.

Alleles↗
PubMed1996

SpHbox7, a new Abd-B class homeobox gene from the sea urchin Strongylocentrotus purpuratus: insights into the evolution of hox gene expression and function.

Hox genes, by virtue of their key functions in axial patterning, have long been thought to be pivotal players in the evolution of developmental mechanisms. Despite their potential importance in evolution, there is little information about Hox genes in animal groups that are most closely related to ancestral Chordates. Accordingly, we have taken the step of analyzing Hox gene expression and function in the sea urchin embryo, whose simple bilateral body plan is thought to resemble that of a stem organism in the Chordate lineage. Here we describe the isolation, sequences analysis and spatiotemporal expression pattern of a sea urchin (Strongylocentrotus purpuratus) Abd-B-like gene, designated SpHbox7. We show that this gene is one of at least two Abd-B-like genes in the S. purpuratus genome, a result that argues against the simple hypothesis that Hox gene duplications occurred only during the evolution of the chordates. SpHbox7 transcripts are first detectable in midblastula stage embryos, increase in amount during gastrulation, decline slightly by the pluteus stage, and are not detectable in any tissue of the adult. Whole mount in situ hybridization and antibody staining with an SpHbox7-specific antibody reveal that both SpHbox7 mRNA and protein are present throughout the embryo in the blastula. Subsequently, they are localized in the invaginating archenteron, secondary mesenchyme, and oral ectoderm. By the pluteus larva stage, SpHbox7 protein and mRNA are present in the gut, larval arms, and portions of the oral ectoderm. This complex and dynamic expression pattern suggests that SpHbox7 has a role in the patterning of the gut, the mesoderm, and the oral surface.

Aging↗
PubMed1993

Sequence of the growth hormone (GH) gene from the silver carp (Hypophthalmichthys molitrix) and evolution of GH genes in vertebrates.

The silver carp (Hypophthalmichthys molitrix) growth hormone (GH) gene was isolated and sequenced following amplification from genomic DNA by the polymerase chain reaction. The gene spans a region of approx. 2.5 kb nucleotides (nt) and consists of five exons. The sequence predicts a polypeptide of 210 amino acids (aa) including a putative signal peptide of 22 hydrophobic aa residues. The arrangement of exons and introns is identical to the GH genes of common carp, grass carp, and very similar to mammals and birds, but quite different from that for the GH genes of tilapia and salmonids. The silver carp GH gene shares a high homology at the nt and aa levels with those of grass carp (95.3% nt, 99.5% aa) and of common carp (81% nt, 95.7% aa).

Amino Acid Sequence↗
PubMed2005

Sex-specific functional specialization and the evolutionary rates of essential fertility genes.

Genes related to sex and reproduction are known to evolve rapidly, however, the mechanism for rapid evolutionary change is proving to be more complex than a simple relaxation of selective constraint. We compared the divergence between orthologous human and mouse fertility genes according to their degree of dispensability as suggested by mouse knockout mutation phenotypes. The dataset consisted of 161 orthologous genes affecting fertility and 803 orthologous genes affecting viability. We find that essential fertility genes affecting both sexes evolve at a similar rate as essential viability genes, but that within sexes the degree of dispensability is not an important factor affecting the rate of fertility gene evolution. We also find no difference in the evolutionary rates of fertility genes that affect the male versus the female, however, there are a greater number of sterility genes that affect the male. Generally there are a significantly greater number of fertility genes that affect one sex rather than both, suggesting that fertility genes tend toward sex-specific functions, particularly in the male. Our findings support the hypothesis that the rapid evolution of sex- and reproduction-related genes is facilitated through an increased specialization of gene function and that dispensability is not a major factor determining their evolutionary rate.

Animals↗
PubMed2001

The horizontal transfer of Agrobacterium rhizogenes genes and the evolution of the genus Nicotiana.

With the aim of understanding better the distribution and evolution of Agrobacterium rhizogenes genes transferred in the genus Nicotiana, 42 species were screened for presence of rolB, rolC, ORF13, and ORF14. The transferred sequences were then compared within the genus and with current bacterial sequences. The results obtained showed the presence of at least one bacterial gene in 15 species belonging to different subgenera. Sequence analyses supported the hypothesis of coevolution of bacterial and plant sequences, thus suggesting a possible role for the transferred genes in the early events of Nicotiana species differentiation. The high level of conservation of Agrobacterium sequences and the dependence of their expression from the plant physiological context along with previous data suggesting their involvement in the determination of the plant hormonal balance were all consistent with this hypothesis. The results are finally discussed also as to their relevance for the hypothesis of mono and multi ancient infection by Agrobacterium.

Bacterial Proteins↗
PubMed2006

The gain and loss of genes during 600 million years of vertebrate evolution.

BACKGROUND: Gene duplication is assumed to have played a crucial role in the evolution of vertebrate organisms. Apart from a continuous mode of duplication, two or three whole genome duplication events have been proposed during the evolution of vertebrates, one or two at the dawn of vertebrate evolution, and an additional one in the fish lineage, not shared with land vertebrates. Here, we have studied gene gain and loss in seven different vertebrate genomes, spanning an evolutionary period of about 600 million years. RESULTS: We show that: first, the majority of duplicated genes in extant vertebrate genomes are ancient and were created at times that coincide with proposed whole genome duplication events; second, there exist significant differences in gene retention for different functional categories of genes between fishes and land vertebrates; third, there seems to be a considerable bias in gene retention of regulatory genes towards the mode of gene duplication (whole genome duplication events compared to smaller-scale events), which is in accordance with the so-called gene balance hypothesis; and fourth, that ancient duplicates that have survived for many hundreds of millions of years can still be lost. CONCLUSION: Based on phylogenetic analyses, we show that both the mode of duplication and the functional class the duplicated genes belong to have been of major importance for the evolution of the vertebrates. In particular, we provide evidence that massive gene duplication (probably as a consequence of entire genome duplications) at the dawn of vertebrate evolution might have been particularly important for the evolution of complex vertebrates.

Animals↗
PubMed2005

Magmas gene structure and evolution.

Magmas is a nuclear encoded protein found in the mitochondria of mammalian cells. It participates in granulocyte-macrophage-colony stimulating factor (GM-CSF) signaling in hematopoietic cells and has an essential role in invertebrate development. In order to characterize the protein structural features and gene evolution of Magmas, a dataset containing 61 Magmas homologs from 52 species distributed among animals, plants and fungi was analyzed. All Magmas members were found to possess three novel sequence motifs in addition to a conserved leader peptide. Phylogenetic tree and dN/dS rate ratios showed that Magmas was evolutionarily conserved. Analysis of Magmas gene organization demonstrated incremental intron acquisition in plants and vertebrates. Significant genetic diversity in Magmas was observed from kingdom specific amino acid signatures, the presence of predicted signal peptides that target the protein to other intracellular locations besides the mitochondria, and the detection of multiple isoforms in higher animals. These studies demonstrate that Magmas members constitute an important family of conserved proteins having multifunctional activities, and provide a basis for future experiments.

Alternative Splicing↗
PubMed2002

In vitro molecular evolution of antibody genes mimicking receptor revision.

Antibody evolution in vivo proceeds mainly by stepwise improvements, accomplished by single base pair substitutions. Lately, receptor revision, i.e. exchange of large parts of the V gene for another sequence, has been suggested to provide a complementary route for affinity maturation. By employing a receptor revision like evolution process in vitro using combinatorial libraries and phage display selection, we demonstrate here that maturation of a clone may preferentially proceed through exchange of a large gene segment rather than via minor sequence changes. These modifications of a CD40-specific human antibody fragment outline how receptor revision like events may provide an advantage to a particular clonotype put under selective pressure.

Amino Acid Sequence↗
PubMed2005

The evolutionary dynamics of plant duplicate genes.

Given the prevalence of duplicate genes and genomes in plant species, the study of their evolutionary dynamics has been a focus of study in plant evolutionary genetics over the past two decades. The past few years have been a particularly exciting time because recent theoretical and experimental investigations have led to a rethinking of the classic paradigm of duplicate gene evolution. By combining recent advances in genomic analysis with a new conceptual framework, researchers are determining the contributions of single-gene and whole-genome duplications to the diversification of plant species. This research provides insights into the roles that gene and genome duplications play in plant evolution.

Evolution, Molecular↗
PubMed1999

Stat protein transactivation domains recruit p300/CBP through widely divergent sequences.

The signal transduction and activator of transcription (Stat) gene family has been highly conserved throughout evolution. Gene duplication and divergence has produced 7 mammalian Stat genes, each of which mediates a distinct process. While some Stat proteins are activated by multiple cytokines, Stat2 is highly specific for responses to type I interferon. We have cloned mouse Stat2 and found that while its sequence was more divergent from its human homologue than any other mouse-human Stat pairs, it was fully functional even in human cells. Overall sequence identity was only 69%, compared with 85-99% similarity for other Stat genes, and several individual domains that still served similar or identical functions in both species were even less well conserved. The coiled-coil domain responsible for interaction with IRF9 was only 65% identical and yet mouse Stat2 interacted with either human or mouse IRF9; the carboxyl terminus was only 30% identical and yet both regions functioned as equal transactivation domains. Both mouse and human transactivation domains recruited the p300/CBP coactivator and were equally sensitive to inhibition by adenovirus E1A protein. Interestingly, the Stat3 carboxyl terminus also functioned as a transactivator capable of recruiting p300/CBP, as does the Stat1 protein, although with widely differing potencies. Yet these proteins share no sequence similarity with Stat2. These data demonstrate that highly diverged primary sequences can serve similar or identical functions, and that the minimal regions of similarity between human and mouse Stat2 may define the critical determinants for function.

Amino Acid Sequence↗
PubMed1984

Analysis of the mouse gamma-crystallin gene family: assignment of multiple cDNAs to discrete genomic sequences and characterization of a representative gene.

Blot hybridization analysis of mouse DNA with gamma-crystallin-specific cDNAs has detected the presence of a multigene family comprised of at least four related genes. The detailed structure of one of these genes, mouse gamma 4-crystallin (M gamma 4.1), and its corresponding cDNA has been determined. The gene spans approximately 2.6 kilobases (kb) and contains two introns. The gene predicts a polypeptide of 174 amino acids that shares extensive sequence homology with gamma-crystallin polypeptides of other species. The two similar structural domains of the protein correspond exactly to the second and third exons of the gene, supporting an exon-duplication model of gene evolution. The similarity in structure of this gene to that recently reported for a gamma-crystallin gene of the rat (1) suggests that a common structure may exist for all gamma-crystallin genes of the two species. Moreover, a highly conserved region, 50 nucleotides in length, immediately precedes the TATA box of both the mouse and rat genes, suggesting that this sequence may be important in gene regulation.

Amino Acid Sequence↗
PubMed2004

Occurrence and consequences of coding sequence insertions and deletions in Mammalian genomes.

Nucleotide insertion and deletion (indel) events, together with substitutions, represent the major mutational processes of gene evolution. Through the alignment of 8148 orthologous genes from human, mouse, and rat, we have identified 1743 indel events within rodent protein-coding sequences. Using human as an out-group, we reconstructed the mutational event underlying each of these indels. Overall, we found an excess of deletions over insertions, particularly for the rat lineage (70% excess). Sequence slippage accounts for at least 52% of insertions and 38% of deletions. We have also evaluated the selective tolerance of identifiable protein structures to indels. Transmembrane domains are the least, and low complexity regions, the most tolerant. Mapping of indels onto known protein structures demonstrated that structural cores are markedly less tolerant to indels than are loop regions. There is a specific enrichment of CpG dinucleotides in close proximity to insertion events, and both insertions and deletions are more common in higher G+C content sequences.

Amino Acid Sequence↗
PubMed2003

Comparative sequence analysis of the PRKAG3 region between human and pig: evolution of repetitive sequences and potential new exons.

The PRKAG3 gene encodes the gamma3 chain of AMP-activated protein kinase (AMPK). A non-conservative missense mutation in the PRKAG3 gene causes a dominant phenotype involving abnormally high glycogen content in pig skeletal muscle. We have determined >126 kb (in 13 contigs) of porcine genomic sequence surrounding the PRKAG3 gene and the corresponding mouse region covering the gene. A comparison of these PRKAG3 sequences and the human sequence was conducted and used to predict evolutionarily conserved regions, including regulatory regions. A comparison of the human genomic sequence and a porcine BAC sequence containing the PRKAG3 gene, revealed a conserved organization and the presence of three additional genes, CYP27A1 (cytochrome P450, family 27, subfamily A, polypeptide 1), STK36 (Serine Threonine Kinase 36), and the homolog of the unidentified human mRNA KIAA0173. Interspersed repetitive elements constituted 51.4 and 38.6% of this genomic region in human and pig, respectively. We were able to reliably align 12.6 kb of orthologous repeats shared between pig and human and these showed an average sequence identity of 72.4%. Our analysis revealed that the human KIAA0173 gene harbors alternative 5' untranslated exons originating from repetitive elements. This provides an obvious example how transposable elements may affect gene evolution.

5' Untranslated Regions↗
PubMed2006

Evolution of the vertebrate ABC gene family: analysis of gene birth and death.

Vertebrate evolution has been largely driven by the duplication of genes that allow for the acquisition of new functions. The ATP-binding cassette (ABC) proteins constitute a large and functionally diverse family of membrane transporters. The members of this multigene family are found in all cellular organisms, most often engaged in the translocation of a wide variety of substrates across lipid membranes. Because of the diverse function of these genes, their large size, and the large number of orthologs, ABC genes represent an excellent tool to study gene family evolution. We have identified ABC proteins from the sea squirt (Ciona intestinalis), zebrafish (Danio rerio), and chicken (Gallus gallus) and, using phylogenetic analysis, identified those genes with a one-to-one orthologous relationship to human ABC proteins. All ABC protein subfamilies found in Ciona and zebrafish correspond to the human subfamilies, with the exception of a single ABCH subfamily gene found only in zebrafish. Multiple gene duplication and deletion events were identified in different lineages, indicating an ongoing process of gene evolution. As many ABC genes are involved in human genetic diseases, and important drug transport phenotypes, the understanding of ABC gene evolution is important to the development of animal models and functional studies.

ATP-Binding Cassette Transporters↗
PubMed1992

Structure and sequence of the Cu,Zn Sod gene in the Mediterranean fruit fly, Ceratitis capitata: intron insertion/deletion and evolution of the gene.

We have cloned a 4-kb region encompassing the Cu,Zn superoxide dismutase (Sod) gene from a genomic library of the Mediterranean fruit fly, Ceratitis capitata, using a cDNA probe from Drosophila melanogaster. The coding sequence of 462 bases is equally as long as that in Drosophila species. The rate of amino acid replacement over the past 100 million years is approximately the same in the Diptera and in mammals, thus excluding the hypothesis (proposed to account for an apparent acceleration in rate of evolution of Sod over geological time) that the evolution of the SOD protein is much higher in the mammals than in other organisms. The coding region is interrupted by two introns in Ceratitis, whereas only one occurs in Drosophila. Phylogenetic comparisons indicate that the second intron was present in the common dipteran ancestor, but was lost shortly after the divergence of the Drosophila lineage from other Diptera. Analysis of the exon/intron structure of Sod in various animal phyla, plants, and fungi indicates that intron insertions as well as deletions have occurred in the evolution of the Sod gene.

Amino Acid Sequence↗
PubMed2004

Antigen receptor genes and the evolution of a recombinase.

Antigen receptor genes exist in the germline in a "split" configuration and are assembled in developing B and T lymphocytes by V(D)J recombination. This site-specific recombination reaction is initiated by a complex containing the RAG1 and RAG2 proteins and completed by general DNA repair factors. RAG1 and RAG2, like the adaptive immune system itself, are found exclusively in jawed vertebrates, and are thought to have entered the vertebrate genome by horizontal transmission as components of a transposable element. This review discusses the structure of antigen receptor genes and the mechanisms by which they are assembled and diversified, and then goes on to consider the evolutionary implications of the arrival of the hypothetical "RAG transposon".

Animals↗
PubMed2002

Evolution of Ig DNA sequence to target specific base positions within codons for somatic hypermutation.

Ig variable (V) region genes are subjected to a somatic hypermutation process as B lymphocytes participate in immune reactions to protein Ags. Although little is known regarding the mechanism of mutagenesis, a consistent hierarchy of trinucleotide target preferences is evident. Analysis of trinucleotide regional distributions predicted and we now empirically confirm the surprising finding that the framework 2 region of kappa V region genes is highly mutable despite its importance to the structural integrity and function of the Ab molecule. Interestingly, much of this mutability appears to be focused on the third codon position where synonymous substitutions are most likely to occur. We also observed a trend for high predicted mutability for codon positions 1 and 2 in complementarity-determining regions. Consequently, amino acid replacements should occur at a higher rate in complementarity-determining regions than in framework regions due to the distribution and subsequent targeting of microsequences by the mutation mechanism. Our results reveal a subtle tier of V region gene evolution in which DNA sequence has been molded to direct mutations to specific base positions within codons in a manner that minimizes damage and maximizes the benefits of the somatic hypermutation process.

Animals↗