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PubMed2005

Mitochondrial genome of Pogona vitticepes (Reptilia; Agamidae): control region duplication and the origin of Australasian agamids.

The complete mitochondrial DNA sequence for an Australian agamid Pogona vitticepes was determined. Twenty-two tRNA genes, two rRNA genes, thirteen protein-coding genes, and two control regions were identified in this mitochondrial genome. The second control region was inserted between NADH dehydrogenase subunits 5 and 6 genes. The duplication of the control region was found in all Australasian agamids examined and was not found in other Asian or African taxa. The two control regions had nearly identical sequences within species but they were divergent among species, suggesting their concerted sequence evolution. Phylogenetic analyses including divergence time estimation without assuming the molecular clock suggested that the duplication of the control region occurred on a lineage leading to the Australasian agamids 25-45 million years ago after their divergence from a Southeast Asian Physignathus cocincinus. Our finding thus supports the recent dispersal origin of Australasian agamids in connection with plate tectonic movement of Australia to the proximity of Southeast Asia.

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↗
PubMed2005

Specialization of the HOG pathway and its impact on differentiation and virulence of Cryptococcus neoformans.

The human pathogenic fungus Cryptococcus neoformans has diverged from a common ancestor into three biologically distinct varieties or sibling species over the past 10-40 million years. During evolution of these divergent forms, serotype A C. neoformans var. grubii has emerged as the most virulent and cosmopolitan pathogenic clade. Therefore, understanding how serotype A C. neoformans is distinguished from less successful pathogenic serotypes will provide insights into the evolution of fungal virulence. Here we report that the structurally conserved Pbs2-Hog1 MAP kinase cascade has been specifically recruited as a global regulator to control morphological differentiation and virulence factors in the highly virulent serotype A H99 clinical isolate, but not in the laboratory-generated and less virulent serotype D strain JEC21. The mechanisms of Hog1 regulation are strikingly different between the two strains, and the phosphorylation kinetics and localization pattern of Hog1 are opposite in H99 compared with JEC21 and other yeasts. The unique Hog1 regulatory pattern observed in the H99 clinical isolate is widespread in serotype A strains and is also present in some clinical serotype D isolates. Serotype A hog1delta and pbs2delta mutants are attenuated in virulence, further underscoring the role of the Pbs2-Hog1 MAPK cascade in the pathogenesis of cryptococcosis.

Cryptococcus neoformans↗
PubMed2001

Reproductive character displacement in Lymantria monacha from northern Japan?

Our objective was to test the hypothesis that the pheromone blend and/or diel periodicity of pheromonal communication differ in populations of the nun moth, Lymantria monacha (Lepidoptera: Lymantriidae), from eastern Asia (northern Honshu, Japan) and Central Europe (Bohemia, Czech Republic). Coupled gas chromatographic-electroantennographic detection (GC-EAD) analyses of pheromone gland extract of female L. monacha from Japan confirmed the presence of compounds previously identified in pheromone extracts of L. monacha from Bohemia, as follows: (Z)-7-octadecene, 2-methyl-(Z)-7-octadecene (2me-Z7-18Hy), cis-7,8-epoxy-octadecane (monachalure), and cis-7,8-epoxy-2-methyloctadecane (disparlure). Field experiments in Honshu suggested that (+)-monachalure is the major pheromone component of L. monacha. 2me-Z7-18Hy significantly enhanced attractiveness of (+)-monachalure. Addition of (+)-disparlure to (+)-monachalure plus 2me-Z7-18Hy in Honshu and Bohemia increased attractiveness of lures by 1.2 and 20 times, respectively, indicating that (+)-disparlure is of least and most significance in the respective L. monacha populations. Moreover, capture of male L. monacha in pheromone-baited traps between 18:00 and 24:00 hr in Bohemia and 2:00 and 5:00 hr in Honshu revealed a markedly different diel periodicity of pheromonal communication. Pheromonal communication late at night and use of (+)-monachalure, rather than (+)-disparlure, as the major pheromone component by L. monacha in Honshu may have resulted from interspecific competition with coseasonal L. fumida, which uses the early night for pheromonal communication and (+)-disparlure as major pheromone component. Whether communication channel divergence of L. monacha in Honshu indeed constitutes a case of reproductive character displacement is difficult to prove. The evolution of such divergence in sympatric populations of L. fumida and L. monacha would have to be demonstrated.

Animal Communication↗
PubMed1985

Evolution of Alu family repeats since the divergence of human and chimpanzee.

The DNA sequences of three members of the Alu family of repeated sequences located 5' to the chimpanzee alpha 2 gene have been determined. The base sequences of the three corresponding human Alu family repeats have been previously determined, permitting the comparison of identical Alu family members in human and chimpanzee. Here we compare the sequences of seven pairs of chimpanzee and human Alu repeats. In each case, with the exception of minor sequence differences, the identical Alu repeat is located at identical sites in the human and chimpanzee genomes. The Alu repeats diverge at the rate expected for nonselected sequences. Sequence conversion has not replaced any of these 14 Alu family members since the divergence between chimpanzee and human.

Animals↗
PubMed1998

Runaway ornament diversity caused by Fisherian sexual selection.

Fisher's runaway process of sexual selection is potentially an important force generating character divergence between closely related populations. We investigated the evolution of multiple female preferences by Fisher's runaway process. There are two outcomes of runaway. The first is the evolution of mate preference to a stable equilibrium. This evolution occurs if the benefits of mate choice are sufficiently large relative to the cost of choice. Alternatively, mate preferences evolve cyclically. The rate and pattern of cyclic evolution depends primarily on the individual cost of choice and epistasis in the joint cost of choice. If there are small differences in natural selection (e.g., predation risk) between populations, cyclic evolution quickly leads to divergence in mate preferences and sexual ornaments and so to sexual isolation.

Animals↗
PubMed1975

Intrinsic asymmetry of oligomer transitions and biomolecular evolution.

Structural transitions in oligomeric proteins due to ligand binding are important in biomolecular regulatory processes. The transitions may occur on the secondary, tertiary or quarternary structure levels. Detailed consideration of the time sequence of ligand binding to the oligomer shows that there is an intrinsic dynamic asymmetry in all oligomer transitions, even if the initial and the final state are completely symmetric. This asymmetry has important bearing on the evolution and the divergence of the primary structure (amino acid sequence) of oligomeric proteins. It may explain (at least in part) the occurrence of oligomeric proteins with similar but not identical protomers. Certain specific groups of oligomers are shown to be under greater evolutionary pressure for protomer structure divergence. The dynamic asymmetry of oligomer transitions also results in higher complexity in reaction kinetics. Some implications on ribosome structural evolution are discussed.

Biological Evolution↗
PubMed2000

Structure and phylogeny of the venom group I phospholipase A(2) gene.

Phospholipases A(2) (PLA(2)s) catalyzing the hydrolysis of phospholipids form a family of proteins with diverse physiological and pharmacological properties. While there have been several reports on the cloning of PLA(2) cDNAs, very few studies have been carried out on the PLA(2) genes and, most importantly, no information has been available on the gene structure and function of group I venom PLA(2). This study, on the PLA(2) gene from a spitting cobra, besides being the very first report on any venom group I PLA(2) gene, constitutes the missing link in the biology and evolution of phospholipases. The 4-kb gene consists of four exons and three introns and resembles the human pancreatic PLA(2) gene. However, the size of intron 3 in particular is much smaller than that in the pancreatic gene. Interestingly, the information for the toxic and most of the pharmacological properties of the venom PLA(2) can be attributed to the end of exon 3 and the whole of exon 4 of the gene. This functional delineation fits in well with the theory of adaptive evolution exhibited by the venom PLA(2)s. We also show that the mammalian pancreatic and elapid PLA(2)s have similar paths of evolution (probably following gene duplication) from a common ancestral gene. Venom group II phospholipases, although evolved from the same ancestor, diverged early in evolution from the group I PLA(2) genes. Intriguingly, CAT reporter gene assays and DNase 1 footprinting studies on the promoter and its deletion constructs using CHO and HepG2 cell lines identified the possible involvement of cis elements such as Sp1, AP2, gamma-IRE, and (TG)(12) repeats in the expression of the gene in a tissue-specific manner.

Animals↗
PubMed1979

The evolution and sequence comparison of two recently diverged mouse chromosomal beta--globin genes.

We have determined the entire nucleotide sequence of a cloned mouse beta--globinminor gene and compared it to the closely related sequence of the betamajor gene. These two genes differ by nine amino acids and presumably evolved from a common ancestral gene as recently as 50 million years ago. Since these genes are closely linked and coordinately expressed, they provide an especially favorable opportunity to assess selection and mutation as these processes affect genes under similar constraints. We find that evolution has preserved these two genes in two short segments of DNA which include their immediately adjacent flanking regions. These regions presumably encode functions that are necessary for proper globin gene expression. In contrast, the more distal flanking sequences and major segments of the long intervening sequences have diverged much more sharply. The homology pattern in these genes also provides considerable insight into the mechanisms by which less constrained nucleotide sequences diverge rapidly. Change in such regions apparently occurs less by point mutation than by insertion, deletion and duplication of relatively short segments of the genome.

Amino Acid Sequence↗
PubMed2002

Evolution of the PP2C family in Caenorhabditis: rapid divergence of the sex-determining protein FEM-2.

To investigate the causes and functional significance of rapid sex-determining protein evolution we compared three Caenorhabditis elegans genes encoding members of the protein phosphatase 2C (PP2C) family with their orthologs from another Caenorhabditis species (strain CB5161). One of the genes encodes FEM-2, a sex-determining protein, while the others have no known sex-determining role. FEM-2's PP2C domain was found to be more diverged than the other PP2C domains, supporting the notion that sex-determining proteins are subjected to selective pressures that allow for or cause rapid divergence. Comparison of the positions of amino acid substitutions in FEM-2 with a solved three-dimensional structure suggests that the catalytic face of the protein is highly conserved among C. elegans, CB5161, and another closely related species C. briggsae. However, the non-conserved regions of FEM-2 cannot be said to lack functional importance, since fem-2 transgenes from the other species were unable to rescue the germ-line defect caused by a C. elegans fem-2 mutation. To test whether fem-2 functions as a sex-determining gene in the other Caenorhabditis species we used RNA-mediated interference (RNAi). fem-2 (RNAi) in C. elegans and C. briggsae caused germ-line feminization, but had no noticeable effect in CB5161. Thus the function of fem-2 in CB5161 remains uncertain.

Amino Acid Sequence↗
PubMed2005

Unravelling the evolution of the head lice and body lice of humans.

Recent studies of mitochondrial genes of the head and body lice of humans indicate that present-day lice comprise two lineages that diverged before the evolution of modern humans. To test if this was a locus-specific phenomenon, we studied two nuclear genes, elongation factor-1alpha (EF-1alpha) and small subunit ribosomal RNA (ssu rRNA). Our ssu rRNA phylogeny was concordant with the phylogenies from mitochondrial genes, but the EF-1alpha phylogeny was not concordant either with the mitochondrial phylogenies or with the ssu rRNA phylogeny. So both nuclear (ssu rRNA) and mitochondrial data indicate that there are two lineages of lice: one lineage with head lice only (H-only lineage) the other lineage with head and body lice (H+B lineage). Thus, body lice apparently evolved from just one of the two main lineages of lice. However, the date of divergence and geographical origins of the two lineages are controversial. Kittler et al. (Curr Biol 13:1414-1417, 2003; Curr Biol 14:2309, 2004) proposed that these two lineages diverged 0.77 mya, whereas Reed et al. (PLoS Biol 2:e340, 2004) proposed that they diverged 1.18 mya and suggested that one of the lineages, the H-only lineage, evolved in the New World on Homo erectus. We discuss this hypothesis in light of our results from ssu rRNA.

Animals↗
PubMed1995

The CD36, CLA-1 (CD36L1), and LIMPII (CD36L2) gene family: cellular distribution, chromosomal location, and genetic evolution.

CD36, CLA-1, and LIMPII are single polypeptide membrane glycoproteins, and the genes encoding them constitute a recently described gene family (D. Calvo and M. A. Vega (1993) J. Biol. Chem. 268: 18929). In the present paper, a cDNA encoding the human lysosomal membrane protein LIMPII was used to determine its expression pattern in cells of various lineages. Like CLA-1, and in contrast with the restricted expression of CD36, the expression of LIMPII is widespread. Mapping of the human LIMPII and CLA-1 genes (gene symbols CD36L2 and CD36L1, respectively) to specific chromosomes revealed that CLA-1, LIMPII, and CD36 do not form a gene cluster, but are found dispersed on chromosomes 12, 4, and 7, respectively. These data, together with the phylogenetic analysis carried out for the members of this family, indicate that the LIMPII, CLA-1, and CD36 genes diverged early in evolution from an ancestor gene, possibly before the divergence between the arthropods and the vertebrates.

Amino Acid Sequence↗
PubMed1998

Solution structure of the IRF-2 DNA-binding domain: a novel subgroup of the winged helix-turn-helix family.

BACKGROUND: The transcription of interferon (IFN) and IFN-inducible genes is mainly regulated by the interferon regulatory factor (IRF) family of proteins, which recognize a unique AAGTGA hexamer repeat motif in the regulatory region of IFN genes. A DNA-binding domain of approximately 100 amino acids has been commonly found in the IRF family of proteins, but it has no sequence homology to known DNA-binding motifs. Elucidation of the structures of members of the IRF family is therefore useful to the understanding of the regulation and evolution of the immune system at the structural level. RESULTS: The solution structure of the DNA-binding domain of interferon regulatory factor-2 (IRF-2) has been determined by NMR spectroscopy. It is composed of a four-stranded antiparallel beta sheet and three alpha helices, and its global fold is similar to those of the winged helix-turn-helix (wHTH) family of proteins. A long loop (Pro37-Asp51) is found immediately before the HTH motif, which is not found in other wHTH proteins. The NMR signals of residues in this long loop, as well as the second helix of the HTH motif, are strongly affected upon the addition of the hexamer repeat DNA, suggesting that these structural elements participate in DNA recognition and binding. CONCLUSIONS: The structural similarity of the DNA-binding domain of IRF-2 with those of proteins in the wHTH family shows that the IRF proteins belong to the wHTH family, even though there is no apparent sequence homology among proteins of the two families. The sequential structure alignment program (SSAP) shows that IRF-2 has a slightly different structure from typical wHTH proteins, mainly in the orientation of helix 2. The IRF family of proteins should therefore be categorized into a subfamily of the wHTH family. The evidence here implies that the evolutional pathway of the IRF family is distinct from that of the other wHTH proteins, in other words, the immune system diverged from an evolutional stem at an early stage.

Amino Acid Sequence↗
PubMed1996

Evolution of sex determination in caenorhabditis: unusually high divergence of tra-1 and its functional consequences.

The tra-1 gene is a terminal regulator of somatic sex in Caenorhabditis elegans: high tra-1 activity elicits female development, low tra-1 activity elicits male development. To investigate the function and evolution of tra-1, we examined the tra-1 gene from the closely related nematode C. briggsae. Ce-tra-1 and Cb-tra-1 are unusually divergent. Each gene generates two transcripts, but only one of these is present in both species. This common transcript encodes TRA-1A, which shows only 44% amino acid identity between the species, a figure much lower than that for previously compared genes. A Cb-tra-1 transgene rescues many tissues of tra-1(null) mutants of C. elegans but not the somatic gonad or germ line. This transgene also causes nongonadal feminization of XO animals, indicating incorrect sexual regulation. Alignment of Ce-TRA-1A and Cb-TRA-1A defines several conserved regions likely to be important for tra-1 function. The phenotypic differences between Ce-tra-1(null) mutants rescued by Cb-tra-1 transgenes and wild-type C. elegans indicate significant divergence of regulatory regions. These molecular and functional studies suggest that evolution of sex determination in nematodes is rapid and genetically complex.

Amino Acid Sequence↗
PubMed2004

Conservation and coevolution in the scale-free human gene coexpression network.

The role of natural selection in biology is well appreciated. Recently, however, a critical role for physical principles of network self-organization in biological systems has been revealed. Here, we employ a systems level view of genome-scale sequence and expression data to examine the interplay between these two sources of order, natural selection and physical self-organization, in the evolution of human gene regulation. The topology of a human gene coexpression network, derived from tissue-specific expression profiles, shows scale-free properties that imply evolutionary self-organization via preferential node attachment. Genes with numerous coexpressed partners (the hubs of the coexpression network) evolve more slowly on average than genes with fewer coexpressed partners, and genes that are coexpressed show similar rates of evolution. Thus, the strength of selective constraints on gene sequences is affected by the topology of the gene coexpression network. This connection is strong for the coding regions and 3' untranslated regions (UTRs), but the 5' UTRs appear to evolve under a different regime. Surprisingly, we found no connection between the rate of gene sequence divergence and the extent of gene expression profile divergence between human and mouse. This suggests that distinct modes of natural selection might govern sequence versus expression divergence, and we propose a model, based on rapid, adaptation-driven divergence and convergent evolution of gene expression patterns, for how natural selection could influence gene expression divergence.

3' Untranslated Regions↗
PubMed2001

Molecular evolutionary analysis of a histone gene repeating unit from Drosophila simulans.

A repeating unit of the histone gene cluster from Drosophila simulans containing the H1, H2A, H2B and H4 genes (the H3 gene region has already been analyzed) was cloned and analyzed. A nucleotide sequence of about 4.6 kbp was determined to study the nucleotide divergence and molecular evolution of the histone gene cluster. Comparison of the structure and nucleotide sequence with those of Drosophila melanogaster showed that the four histone genes were located at identical positions and in the same directions. The proportion of different nucleotide sites was 6.3% in total. The amino acid sequence of H1 was divergent, with a 5.1% difference. However, no amino acid change has been observed for the other three histone proteins. Analysis of the GC contents and the base substitution patterns in the two lineages, D. melanogaster and D. simulans, with a common ancestor showed the following. 1) A strong negative correlation was found between the GC content and the nucleotide divergence in the whole repeating unit. 2) The mode of molecular evolution previously found for the H3 gene was also observed for the whole repeating unit of histone genes; the nucleotide substitutions were stationary in the 3' and spacer regions, and there was a directional change of the codon usage to the AT-rich codons. 3) No distinct difference in the mode or pattern of molecular evolution was detected for the histone gene repeating unit in the D. melanogaster and D. simulans lineages. These results suggest that selectional pressure for the coding regions of histones, which eliminate A and T, is less effective in the D. melanogaster and D. simulans lineages than in the other GC-rich species.

Amino Acid Sequence↗
PubMed1991

Convergent evolution of similar function in two structurally divergent enzymes.

An example of two related enzymes that catalyse similar reactions but possess different active sites is provided by comparing the structure of Escherichia coli thioredoxin reductase with glutathione reductase. Both are dimeric enzymes that catalyse the reduction of disulphides by pyridine nucleotides through an enzyme disulphide and a flavin. Human glutathione reductase contains four structural domains within each molecule: the flavin-adenine dinucleotide (FAD)- and nicotinamide-adenine dinucleotide phosphate (NADPH)-binding domains, the 'central' domain and the C-terminal domain that provides the dimer interface and part of the active site. Although both enzymes share the same catalytic mechanism and similar tertiary structures, their active sites do not resemble each other. We have determined the crystal structure of E. coli thioredoxin reductase at 2 A resolution, and show that thioredoxin reductase lacks the domain that provides the dimer interface in glutathione reductase, and forms a completely different dimeric structure. The catalytically active disulphides are located in different domains on opposite sides of the flavin ring system. This suggests that these enzymes diverged from an ancestral nucleotide-binding protein and acquired their disulphide reductase activities independently.

Amino Acid Sequence↗
PubMed2003

Evolution of function in (beta/alpha)8-barrel enzymes.

The (beta/alpha)(8)-barrel is the most common fold in structurally characterized enzymes. Whether the functionally diverse enzymes that share this fold are the products of either divergent or convergent evolution (or both) is an unresolved question that will probably be answered as the sequence databases continue to expand. Recent work has examined natural, designed, and directed evolution of function in several superfamilies of (beta/alpha)(8)-barrel containing enzymes.

Animals↗