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PubMed1998

Resistance gene evolution.

Plant resistance genes are highly polymorphic and have diverse recognition specificities. These genes often occur as members of clustered gene families that have evolved through duplication and diversification. Regions of nucleotides conserved between family members and flanking sequences facilitate equal or unequal recombination events. Transposition contributes to allelic diversity. Resistance gene clusters appear to evolve more rapidly than other regions of the genome, and domains responsible for recognitional specificity, such as the leucine-rich repeat domain, are subject to adaptive selection.

Adaptation, Physiological↗
PubMed1991

Structure, chromosome location, and expression of the human smooth muscle (enteric type) gamma-actin gene: evolution of six human actin genes.

Recombinant phages that carry the human smooth muscle (enteric type) gamma-actin gene were isolated from human genomic DNA libraries. The amino acid sequence deduced from the nucleotide sequence matches those of cDNAs but differs from the protein sequence previously reported at one amino acid position, codon 359. The gene containing one 5' untranslated exon and eight coding exons extends for 27 kb on human chromosome 2. The intron between codons 84 and 85 (site 3) is unique to the two smooth muscle actin genes. In the 5' flanking region, there are several CArG boxes and E boxes, which are regulatory elements in some muscle-specific genes. Hybridization with the 3' untranslated region, which is specific for the human smooth muscle gamma-actin gene, suggests the single gene in the human genome and specific expressions in enteric and aortic tissues. From characterized molecular structures of the six human actin isoform genes, we propose a hypothesis of evolutionary pathway of the actin gene family. A presumed ancestral actin gene had introns at least sites 1, 2, and 4 through 8. Cytoplasmic actin genes may have directly evolved from it through loss of introns at sites 5 and 6. However, through duplication of the ancestral actin gene with substitutions of many amino acids, a prototype of muscle actin genes had been created. Subsequently, striated muscle actin and smooth muscle actin genes may have evolved from this prototype by loss of an intron at site 4 and acquisition of a new intron at site 3, respectively.

Actins↗
PubMed1991

Glutamine synthetase gene evolution: a good molecular clock.

Glutamine synthetase (EC 6.3.1.2) gene evolution in various animals, plants, and bacteria was evaluated by a general stationary Markov model. The evolutionary process proved to be unexpectedly regular even for a time span as long as that between the divergence of prokaryotes from eukaryotes. This enabled us to draw phylogenetic trees for species whose phylogeny cannot be easily reconstructed from the fossil record. Our calculation of the times of divergence of the various organelle-specific enzymes led us to hypothesize that the pea and bean chloroplast genes for these enzymes originated from the duplication of nuclear genes as a result of the different metabolic needs of the various species. Our data indicate that the duplication of plastid glutamine synthetase genes occurred long after the endosymbiotic events that produced the organelles themselves.

Amino Acid Sequence↗
PubMed2003

Hox gene evolution in nematodes: novelty conserved.

The conserved homeobox (Hox) gene cluster is neither conserved nor clustered in the nematode Caenorhabditis elegans. Instead, C. elegans has a reduced and dispersed gene complement that is the result the loss of Hox genes in stages throughout its evolutionary history. The roles of Hox genes in patterning the nematode body axis are also divergent, although there are tantalising remnants of ancient regulatory systems. Hox patterning also differs greatly between C. elegans and a second 'model' nematode, Pristionchus pacificus. The pattern of Hox gene evolution may be indicative of the move to deterministic developmental modes in nematodes.

Animals↗
PubMed1992

Analysis of gene evolution: the software AGE.

The software AGE (Analysis of Gene Evolution) has been developed both to study a genetic reality, i.e. the identification of statistical properties in genes (e.g. periodicities), and to simulate this observed genetic reality, by models of molecular evolution. AGE has two types of models: (i) models of sequence creation from oligonucleotides: concatenation model in series of an oligonucleotide, independent (or Markov) mixing model of oligonucleotides according to given probabilities (or a Markov matrix); (ii) models of sequence evolution from created sequences: insertion/deletion process of (mono,di,tri)nucleotides, base mutation process. The study of a reality and the development of simulation models are based on several new algorithms: approximated simulation and exact calculus to compute various autocorrelation functions, Fourier transformation of autocorrelation curves, recognition of a curve form, etc. AGE is implemented on IBM or compatible microcomputers and can be used by biologists without any computer knowledge to identify statistical properties in their newly determined DNA sequence and to explain them by models of molecular evolution.

Algorithms↗
PubMed1988

Immunoglobulin heavy chain variable region gene evolution: structure and family relationships of two genes and a pseudogene in a teleost fish.

Nucleotide sequences for two immunoglobulin heavy chain variable region (VH) genes and one pseudogene in the goldfish (Carassius auratus) and the family relationships and distribution of these genes in individual fish are presented. Comparison of the nucleotide and inferred amino acid sequences of goldfish and other vertebrate VH genes indicates that goldfish VH genes show the major VH gene regulatory and structural features (5'-putative promoter region, split hydrophobic leader, three framework and two complementarity-determining regions, and 3'-recombination signals for VH to diversity region joining) and that goldfish VH genes are not more closely related to one another than they are to VH genes of evolutionarily distant vertebrates such as the mammals. Goldfish VH genes appear to exist in distinct families, and individual goldfish can carry from none to apparently greater than 15 genes of a given family. These results suggest that whereas the basic structure of VH genes has been conserved in evolution, there may be substantial variation in the nature and population distribution of VH gene families in the vertebrates.

Amino Acid Sequence↗
PubMed1982

An evaluation of mitochondrial tRNA gene evolution and its relation to the genetic code.

Extensive sequence data on mitochondrial (mt) tRNAs give for the first time an opportunity to evaluate tRNA gene evolution in this organelle. Deductions from these gene structures relate to the evolution of tRNA genes in other cellular systems and to the origin of the genetic code. Mt tRNAs, in contrast to the prokaryotic nature of chloroplastic tRNA structure, can not at the present time be definitely related to either prokaryotic or eukaryotic tRNAs, probably because of a higher mutation rate in mitochondria. Fungal mt tRNAs having the same anticodon and function are generally similar enough to be considered homologous. Comparisons af all mt tRNA sequences contained in the same mitochondrion indicate that some tRNAs originated by duplication of a prototypic gene which, after divergence, led to tRNAs having different amino acid specificities. The deviant mt genetic code, although admittedly permitting a simpler decoding mechanism, is not useful in determining whether the origin of mitochondria had preceded or was derived from prokaryotes or eukaryotes, since the genetic code is variable even among mitochondria. Variants of the mt genetic code lead to speculation on the nature of the primordial code and its relation to the present "universal" code.

Animals↗
PubMed1993

Mouse alpha-1-microglobulin/bikunin precursor: cDNA analysis, gene evolution and physical assignment of the gene next to the orosomucoid locus.

alpha-1-Microglobulin (A1m) is a member of the lipocalin superfamily whereas bikunin is a Kunitz-type proteinase inhibitor. A1m and bikunin originate from a shared precursor. A comparison of mammalian cDNAs for the precursor indicates a highly conserved amino acid sequence along with muridae-specific deletions in both A1m and bikunin. In rodents, the gene for this precursor is less than 300 kb apart from the orosomucoid gene, another lipocalin gene. This precursor likely results from the assembly of two lipocalin and Kunitz-type genes, between 270 and 80 million years ago.

Alpha-Globulins↗
PubMed1993

Mammalian gene evolution: nucleotide sequence divergence between mouse and rat.

As a paradigm of mammalian gene evolution, the nature and extent of DNA sequence divergence between homologous protein-coding genes from mouse and rat have been investigated. The data set examined includes 363 genes totalling 411 kilobases, making this by far the largest comparison conducted between a single pair of species. Mouse and rat genes are on average 93.4% identical in nucleotide sequence and 93.9% identical in amino acid sequence. Individual genes vary substantially in the extent of nonsynonymous nucleotide substitution, as expected from protein evolution studies; here the variation is characterized. The extent of synonymous (or silent) substitution also varies considerably among genes, though the coefficient of variation is about four times smaller than for nonsynonymous substitutions. A small number of genes mapped to the X-chromosome have a slower rate of molecular evolution than average, as predicted if molecular evolution is "male-driven." Base composition at silent sites varies from 33% to 95% G+C in different genes; mouse and rat homologues differ on average by only 1.7% in silent-site G+C, but it is shown that this is not necessarily due to any selective constraint on their base composition. Synonymous substitution rates and silent site base composition appear to be related (genes at intermediate G+C have on average higher rates), but the relationship is not as strong as in our earlier analyses. Rates of synonymous and nonsynonymous substitution are correlated, apparently because of an excess of substitutions involving adjacent pairs of nucleotides. Several factors suggest that synonymous codon usage in rodent genes is not subject to selection.

Amino Acid Sequence↗
PubMed2005

Murine segmental duplications are hot spots for chromosome and gene evolution.

Mouse and rat genomic sequences permit us to obtain a global view of evolutionary rearrangements that have occurred between the two species and to define hallmarks that might underlie these events. We present a comparative study of the sequence assemblies of mouse and rat genomes and report an enrichment of rodent-specific segmental duplications in regions where synteny is not preserved. We show that segmental duplications present higher rates of molecular evolution and that genes in rearranged regions have evolved faster than those located elsewhere. Previous studies have shown that synteny breakpoints between the mouse and the human genomes are enriched in human segmental duplications, suggesting a causative connection between such structures and evolutionary rearrangements. Our work provides further evidence to support the role of segmental duplications in chromosomal rearrangements in the evolution of the architecture of mammalian chromosomes and in the speciation processes that separate the mouse and the rat.

Animals↗
PubMed2003

Introns in gene evolution.

Introns are integral elements of eukaryotic genomes that perform various important functions and actively participate in gene evolution. We review six distinct roles of spliceosomal introns: (1) sources of non-coding RNA; (2) carriers of transcription regulatory elements; (3) actors in alternative and trans-splicing; (4) enhancers of meiotic crossing over within coding sequences; (5) substrates for exon shuffling; and (6) signals for mRNA export from the nucleus and nonsense-mediated decay. We consider transposable capacities of introns and the current state of the long-lasting debate on the 'early-or-late' origin of introns. Cumulative data on known types of contemporary exon shuffling and the estimation of the size of the underlying exon universe are also discussed. We argue that the processes central to introns-early (exon shuffling) and introns-late (intron insertion) theories are entirely compatible. Each has provided insight: the latter through elucidating the transposon capabilities of introns, and the former through understanding the importance of introns in genomic recombination leading to gene rearrangements and evolution.

Alternative Splicing↗
PubMed2006

Evolutionary systems biology: links between gene evolution and function.

The recent accumulation of genome-wide data on various facets of gene expression, function and evolution stimulated the emergence of a new field, evolutionary systems biology. Many significant correlations were detected between variables that characterize the functioning of a gene, such as expression level, knockout effect, connectivity of genetic and protein-protein interaction networks, and variables that describe gene evolution, such as sequence evolution rate and propensity for gene loss. The first attempts on multidimensional analysis of genomic data yielded composite variables that describe the 'status' of a gene in the genomic community. However, it remains uncertain whether different functional variables affect gene evolution synergistically or there is a single, dominant factor. The number of translation events, linked to selection for translational robustness, was proposed as a candidate for such a major determinant of protein evolution. These developments show that, although the methodological basis of evolutionary systems biology is not yet fully solidified, this area of research is already starting to yield fundamental biological insights.

Evolution, Molecular↗
PubMed2006

Varying signals of the effects of natural selection during teleost growth hormone gene evolution.

The growth hormone (GH) gene of teleost fish exhibits a higher degree of variability compared with other vertebrate groups. However, the different selective constraints at the sequence level are not well understood. In this study, maximum-likelihood (ML) models of codon substitutions were used to investigate Darwinian adaptive evolution of the GH gene in teleost fishes. Complete GH gene sequences of 54 fish species were classified into 4 orders, and the variable nature of GH was examined by determining the dN and dS rate variation and the rates of molecular evolution for each teleost order. The results indicate that although the overall evolution rate for teleost GH is high ((1.15 +/- 0.01) x 10(-9) substitutions/(aa site x y)) compared with the "slow phases" in mammals ((0.21 to 0.28 +/- 0.05) x 10(-9)), the vital structure of this gene has been retained. While the majority of the amino acid changes appear to be due to relaxation of purifying selection, some positively selected sites were detected in regions with no specifically identified role in protein function. The positively selected regions observed in salmoniformes lineage suggests a possible role for positive selection driving functional divergence in paralogous forms of the GH gene after whole-genome duplication in this lineage.

Amino Acid Sequence↗