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PubMed2005

Bacterial genome adaptation to niches: divergence of the potential virulence genes in three Burkholderia species of different survival strategies.

BACKGROUND: Two closely related species Burkholderia mallei (Bm) and Burkholderia pseudomallei (Bp) are serious human health hazards and are potential bio-warfare agents, whereas another closely related species Burkholderia thailandensis (Bt) is a non-pathogenic saprophyte. To investigate the genomic factors resulting in such a dramatic difference, we first identified the Bm genes responsive to the mouse environment, and then examined the divergence of these genes in Bp and Bt. RESULTS: The genes down-expressed, which largely encode cell growth-related proteins, are conserved well in all three species, whereas those up-expressed, which include potential virulence genes, are less well conserved or absent notably in Bt. However, a substantial number of up-expressed genes is still conserved in Bt. Bm and Bp further diverged from each other in a small number of genes resulting from unit number changes in simple sequence repeats (ssr) in the homologs. CONCLUSION: Our data suggest that divergent evolution of a small set of genes, rather than acquisition or loss of pathogenic islands, is associated with the development of different life styles in these bacteria of similar genomic contents. Further divergence between Bm and Bp mediated by ssr changes may reflect different adaptive processes of Bm and Bp fine-tuning into their host environments.

Animals↗
PubMed1988

Localization of the human X-linked gene for chronic granulomatous disease to the mouse X chromosome: implications for X-chromosome evolution.

The gene encoded at the human X-linked chronic granulomatous disease locus (cytochrome b245 beta subunit) has been mapped to the mouse X chromosome using an interspecific Mus domesticus x M. spretus cross. The localization of this gene provides detailed information on one of the proposed ancestral breakpoints that account for the divergent evolution of the mouse and human X chromosomes.

Animals↗
PubMed1995

Conservation and dynamics of microsatellite loci over 300 million years of marine turtle evolution.

Microsatellite loci consisting of (CA)n repetitive arrays were obtained from three species of marine turtle, and primers were designed to test for polymorphism within species and the persistence of microsatellites across species. Homologous loci were found in each test of six marine species within two families (Cheloniidae and Dermochelyidae), as well as in a freshwater species (Emydidae, Trachemys scripta), which indicates a conservation of flanking sequences spanning approximately 300 million years of divergent evolution. The persistence of homologous microsatellites across marine turtles was confirmed by direct sequencing of loci across species and by the discovery of polymorphism in 24 of 30 cross species tests. The conservation of flanking sequences could be due to a slow rate of base substitution in turtle nuclear DNA, as previously reported for mtDNA. In contrast, the presence of up to 25 alleles per locus per species indicates that the replication slippage events responsible for changes in allele length operate as in mammals. Comparisons of alleles among species revealed that alleles of the same length may not be homologous due to mutations within the flanking sequences. Levels of heterozygosity were consistently higher in species from which the primers were designed, which suggests problems with cross-species comparisons of variability. Within species, microsatellite variation between divergent populations was consistent with results from previous mtDNA studies indicating the usefulness of microsatellites for comparing male- versus female-mediated gene flow.

Animals↗
PubMed1998

An evolutionary approach to the design of glutathione-linked enzymes.

Studies of protein structure provide information about principles of protein design that have come into play in natural evolution. This information can be exploited in the redesign of enzymes for novel functions. The glutathione-binding domain of glutathione transferases has similarities with structures in other glutathione-linked proteins, such as glutathione peroxidases and thioredoxin (glutaredoxin), suggesting divergent evolution from a common ancestral protein fold. In contrast, the binding site for glutathione in human glyoxalase I is located at the interface between the two identical subunits of the protein. Comparison with the homologous, but monomeric, yeast glyoxalase I suggests that new domains have originated through gene duplications, and that the oligomeric structure of the mammalian glyoxalase I has arisen by 'domain swapping'. Recombinant DNA techniques are being used for the redesign of glutathione-linked proteins in attempts to create binding proteins with novel functions and catalysts with tailored specificities. Enzymes with desired properties are selected from libraries of variant structures by use of phage display and functional assays.

Binding Sites↗
PubMed1992

Refined atomic model of wheat serine carboxypeptidase II at 2.2-A resolution.

The crystal structure of the homodimeric serine carboxypeptidase II from wheat (CPDW-II, M(r) 120K) has been determined and fully refined at 2.2-A resolution to a standard crystallographic R factor of 16.9% using synchrotron data collected at the Brookhaven National Laboratory. The model has an rms deviation from ideal bond lengths of 0.018 A and from bond angles of 2.8 degrees. The model supports the general conclusions of an earlier study at 3.5-A resolution and will form the basis for investigation into substrate binding and mechanistic studies. The enzyme has an alpha + beta fold, consisting of a central 11-stranded beta-sheet with a total of 15 helices on either side. The enzyme, like other serine proteinases, contains a "catalytic triad" Ser146-His397-Asp338 and a presumed "oxyanion hole" consisting of the backbone amides of Tyr147 and Gly53. The carboxylate of Asp338 and imidazole of His397 are not coplanar in contrast to the other serine proteinases. A comparison of the active site features of the three families of serine proteinases suggests that the "catalytic triad" should actually be regarded as two diads, a His-Asp diad and a His-Ser diad, and that the relative orientation of one diad with respect to the other is not particularly important. Four active site residues (52, 53, 65, and 146) have unfavorable backbone conformations but have well-defined electron density, suggesting that there is some strain in the active site region. The binding of the free amino acid arginine has been analyzed by difference Fourier methods, locating the binding site for the C-terminal carboxylate of the leaving group. The carboxylate makes hydrogen bonds to Glu145, Asn51, and the amide of Gly52. The carboxylate of Glu145 also makes a hydrogen bond with that of Glu65, suggesting that one or both may be protonated. Thus, the loss of peptidase activity at pH > 7 may in part be due to deprotonation of Glu145. The active site does not reveal exposed peptide amides and carbonyl oxygen atoms that could interact with substrate in an extended beta-sheet fashion. The fold of the polypeptide backbone is completely different than that of trypsin or subtilisin, suggesting that this is a third example of convergent molecular evolution to a common enzymatic activity. Furthermore, it is suggested that the active site sequence motif "G-X-S-X-G/A", often considered the hallmark of serine peptidase or esterase activity, is fortuitous and not the result of divergent evolution.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed2005

Structure and sequence conservation of hao cluster genes of autotrophic ammonia-oxidizing bacteria: evidence for their evolutionary history.

Comparison of the organization and sequence of the hao (hydroxylamine oxidoreductase) gene clusters from the gammaproteobacterial autotrophic ammonia-oxidizing bacterium (aAOB) Nitrosococcus oceani and the betaproteobacterial aAOB Nitrosospira multiformis and Nitrosomonas europaea revealed a highly conserved gene cluster encoding the following proteins: hao, hydroxylamine oxidoreductase; orf2, a putative protein; cycA, cytochrome c(554); and cycB, cytochrome c(m)(552). The deduced protein sequences of HAO, c(554), and c(m)(552) were highly similar in all aAOB despite their differences in species evolution and codon usage. Phylogenetic inference revealed a broad family of multi-c-heme proteins, including HAO, the pentaheme nitrite reductase, and tetrathionate reductase. The c-hemes of this group also have a nearly identical geometry of heme orientation, which has remained conserved during divergent evolution of function. High sequence similarity is also seen within a protein family, including cytochromes c(m)(552), NrfH/B, and NapC/NirT. It is proposed that the hydroxylamine oxidation pathway evolved from a nitrite reduction pathway involved in anaerobic respiration (denitrification) during the radiation of the Proteobacteria. Conservation of the hydroxylamine oxidation module was maintained by functional pressure, and the module expanded into two separate narrow taxa after a lateral gene transfer event between gamma- and betaproteobacterial ancestors of extant aAOB. HAO-encoding genes were also found in six non-aAOB, either singly or tandemly arranged with an orf2 gene, whereas a c(554) gene was lacking. The conservation of the hao gene cluster in general and the uniqueness of the c(554) gene in particular make it a suitable target for the design of primers and probes useful for molecular ecology approaches to detect aAOB.

Amino Acid Sequence↗
PubMed1979

Evolution of human influenza A viruses in nature: sequential mutations in the genomes of new H1N1.

The genetic variation of the new pandemic H1N1 influenza A viruses isolated in 1977 was analyzed by two-dimensional oligonucleotide fingerprinting and RNA sequencing. Differences were observed in the fingerprints of the RNAs of these viruses, and analysis of the changes suggested that sequential mutations occurred in their genomes. Based on these data, a scheme is presented which proposes divergent evolution of strains from a common ancestry. Furthermore, it was found that mutations were not restricted to the genes coding for the hemagglutinin and the neuraminidase, but were scattered throughout the genome, suggesting that selective antibody pressure is not solely responsible for the emergence of genetic variants. Our data also strengthen the hypothesis that the new H1N1 influenza virus strains are derived from strains circulating in 1950.

Antigens, Viral↗
PubMed2001

The evolution of ribonucleotide reduction revisited.

Ribonucleotide reductases (RNRs) catalyze the conversion of both purine and pyrimidine nucleotides to deoxynucleotides in all organisms and provide all the monomeric precursors essential for both DNA replication and repair. RNRs have been divided into three classes on the basis of their unique metallo-cofactors. The exquisitely controlled free radical chemistry used by all RNRs, and the commonality of the structures of the subunits where the nucleotide reduction process occurs, together provide compelling evidence for the importance of chemistry in the divergent evolution of RNRs from a common progenitor.

Allosteric Site↗
PubMed1987

The complex Arom locus of Aspergillus nidulans. Evidence for multiple gene fusions and convergent evolution.

The physical positions of the DNA sequences encoding the five consecutive enzyme activities required to metabolise 3-deoxy-D-arabino-heptulosonic acid-7-phosphate to 5-enolpyruvyl-shikimate-3phosphate, which are encoded by the A. nidulans Arom polypeptide have been determined. Subfragments of the Arom locus encoding EPSP synthase and 3-dehydroquinase have been expressed in appropriate E. coli aro mutants. The DNA sequence of the A. nidulans Arom locus has been shown to have homology with the corresponding unlinked E. coli aro loci strongly suggesting (I) divergent evolution from common ancestral sequences and (II) that the complex A. nidulans Arom locus arose by multiple gene fusion. The DNA and protein sequence of the two 3-dehydroquinase isoenzymes of A. nidulans share no homology, strongly indicating separate phylogenetic origins and their convergent evolution. The 5' and 3' non-translated DNA sequence of the A. nidulans Arom locus is presented along with the presumed sites for transcription initiation and polyadenylation determined by S1 nuclease protection experiments.

3-Phosphoshikimate 1-Carboxyvinyltransferase↗
PubMed2005

Male genital size reflects a tradeoff between attracting mates and avoiding predators in two live-bearing fish species.

Male genitalia may experience more rapid, divergent evolution than any other animal character, but why? Research during the past several decades has culminated in the view that genital diversification primarily results from postmating sexual selection (e.g., sperm competition or cryptic female choice). However, the potential roles of premating sexual selection (e.g., mate choice) and natural selection have received little attention. We examined the possible importance of these mechanisms by investigating divergence in male genitalia among populations differing in predator regime for two species of live-bearing fish (Gambusia affinis in Texas and Gambusia hubbsi in The Bahamas). When controlled for body size, males exhibited a larger gonopodium (sperm-transfer organ) in predator-free environments than in predatory environments, a trend that persisted across space (multiple populations), time (multiple years), and species. By conducting laboratory experiments with G. affinis, we found that premating sexual selection seems to favor larger male genitalia (females exhibited mating preference for males having larger gonopodia), but natural selection in the presence of predatory fishes seems to favor reduced genital size (larger gonopodium size was associated with reduced burst-swimming performance, an important antipredator behavior). Although postmating sexual selection is widely presumed to be the most important mechanism driving genital diversification, these findings suggest that alternative mechanisms, particularly for organisms that cannot retract their genitalia, may also prove important.

Analysis of Variance↗
PubMed1967

Evolution of structure and function of proteases.

One of the striking features of the proteolytic enzymes as a group is the immense variety of biological functions served by enzymes employing one of a few basic mechanisms. For example, in the higher animals, enzymes for activation of zymogens (trypsin), for digestion of dietary proteins (trypsin, chymotrypsin, elastase), for blood clotting (thrombin), for clot lysis (plasmin), and for sensing pain (kallikrein) all appear to use the same mechanism and to have evolved from the same ancestral gene by the process of gene duplication and subsequent divergent evolution. Equally striking is the variety of chemical solutions of the same functional problem, such as the peptide-bond cleavage by sulfhydryl proteases on the one hand and serine proteases on the other.

Amino Acid Sequence↗
PubMed2003

Concerted and nonconcerted evolution of the Hsp70 gene superfamily in two sibling species of nematodes.

We have identified the Hsp70 gene superfamily of the nematode Caenorhabditis briggsae and investigated the evolution of these genes in comparison with Hsp70 genes from C. elegans, Drosophila, and yeast. The Hsp70 genes are classified into three monophyletic groups according to their subcellular localization, namely, cytoplasm (CYT), endoplasmic reticulum (ER), and mitochondria (MT). The Hsp110 genes can be classified into the polyphyletic CYT group and the monophyletic ER group. The different Hsp70 and Hsp110 groups appeared to evolve following the model of divergent evolution. This model can also explain the evolution of the ER and MT genes. On the other hand, the CYT genes are divided into heat-inducible and constitutively expressed genes. The constitutively expressed genes have evolved more or less following the birth-and-death process, and the rates of gene birth and gene death are different between the two nematode species. By contrast, some heat-inducible genes show an intraspecies phylogenetic clustering. This suggests that they are subject to sequence homogenization resulting from gene conversion-like events. In addition, the heat-inducible genes show high levels of sequence conservation in both intra-species and inter-species comparisons, and in most cases, amino acid sequence similarity is higher than nucleotide sequence similarity. This indicates that purifying selection also plays an important role in maintaining high sequence similarity among paralogous Hsp70 genes. Therefore, we suggest that the CYT heat-inducible genes have been subjected to a combination of purifying selection, birth-and-death process, and gene conversion-like events.

Animals↗
PubMed2004

Complete sequence and genetic organization of pDTG1, the 83 kilobase naphthalene degradation plasmid from Pseudomonas putida strain NCIB 9816-4.

The complete 83,042 bp sequence of the circular naphthalene degradation plasmid pDTG1 from Pseudomonas putida strain NCIB 9816-4 was determined in order to examine the process by which the nah and sal operons may have been compiled and distributed in nature. Eighty-nine open reading frames were predicted using computer analyses, comprising 80.0% of the pDTG1 DNA sequence. The most distinctive feature of the plasmid is the upper and lower naphthalene degradation operons, which occupy 9.5 kb and 13.4 kb regions, respectively, bordered by numerous defective mobile genetic element fragments. Identified on this plasmid were homologues of genes required for large plasmid replication, maintenance, and conjugation, as well as transposases, resolvases, and integrases, suggesting an evolution that involved the lateral transfer of DNA between bacterial species. Also found were genes that contain a high degree of sequence similarity to other known degradation genes, as well as genes involved in chemotaxis. Although the incompatibility group designation of pDTG1 remains unresolved, striking sequence organization and homology exists between the plasmid backbones of pDTG1 and the IncP-9 toluene-degradation plasmid pWW0, which suggests a divergent evolution from a progenitor plasmid prior to degradative gene incorporation.

Catalytic Domain↗
PubMed1999

Allosteric control of three B12-dependent (class II) ribonucleotide reductases. Implications for the evolution of ribonucleotide reduction.

Three separate classes of ribonucleotide reductases are known, each with a distinct protein structure. One common feature of all enzymes is that a single protein generates each of the four deoxyribonucleotides. Class I and III enzymes contain an allosteric substrate specificity site capable of binding effectors (ATP or various deoxyribonucleoside triphosphates) that direct enzyme specificity. Some (but not all) enzymes contain a second allosteric site that binds only ATP or dATP. Binding of dATP to this site inhibits the activity of these enzymes. X-ray crystallography has localized the two sites within the structure of the Escherichia coli class I enzyme and identified effector-binding amino acids. Here, we have studied the regulation of three class II enzymes, one from the archaebacterium Thermoplasma acidophilum and two from eubacteria (Lactobacillus leichmannii and Thermotoga maritima). Each enzyme has an allosteric site that binds ATP or various deoxyribonucleoside triphosphates and that regulates its substrate specificity according to the same rules as for class I and III enzymes. dATP does not inhibit enzyme activity, suggesting the absence of a second active allosteric site. For the L. leichmannii and T. maritima enzymes, binding experiments also indicate the presence of only one allosteric site. Their primary sequences suggest that these enzymes lack the structural requirements for a second site. In contrast, the T. acidophilum enzyme binds dATP at two separate sites, and its sequence contains putative effector-binding amino acids for a second site. The presence of a second site without apparent physiological function leads to the hypothesis that a functional site was present early during the evolution of ribonucleotide reductases, but that its function was lost from the T. acidophilum enzyme. The other two B12 enzymes lost not only the function, but also the structural basis for the site. Also a large subgroup (Ib) of class I enzymes, but none of the investigated class III enzymes, has lost this site. This is further indirect evidence that class II and I enzymes may have arisen by divergent evolution from class III enzymes.

Allosteric Regulation↗
PubMed2006

The role of transposable element clusters in genome evolution and loss of synteny in the rice blast fungus Magnaporthe oryzae.

BACKGROUND: Transposable elements are abundant in the genomes of many filamentous fungi, and have been implicated as major contributors to genome rearrangements and as sources of genetic variation. Analyses of fungal genomes have also revealed that transposable elements are largely confined to distinct clusters within the genome. Their impact on fungal genome evolution is not well understood. Using the recently available genome sequence of the plant pathogenic fungus Magnaporthe oryzae, combined with additional bacterial artificial chromosome clone sequences, we performed a detailed analysis of the distribution of transposable elements, syntenic blocks, and other features of chromosome 7. RESULTS: We found significant levels of conserved synteny between chromosome 7 and the genomes of other filamentous fungi, despite more than 200 million years of divergent evolution. Transposable elements are largely restricted to three clusters located in chromosomal segments that lack conserved synteny. In contradiction to popular evolutionary models and observations from other model organism genomes, we found a positive correlation between recombination rate and the distribution of transposable element clusters on chromosome 7. In addition, the transposable element clusters are marked by more frequent gene duplications, and genes within the clusters have greater sequence diversity to orthologous genes from other fungi. CONCLUSION: Together, these data suggest that transposable elements have a profound impact on the M. oryzae genome by creating localized segments with increased rates of chromosomal rearrangements, gene duplications and gene evolution.

Base Sequence↗
PubMed1996

Antigenic and genetic evolution of equine H3N8 influenza A viruses.

Evolution of equine influenza a H3N8 viruses was examined by antigenic and genetic analysis of a collection isolates from around the world. It was noted that antigenic and genetic variants of equine H3N8 viruses cocirculate, and in particular that variants currently circulating in Europe and the USA are distinguishable from one another both in terms of antigenic reactivity and genetic structure of the HA1 portion of the haemagglutinin (HA) molecule. Whilst the divergent evolution of American and European isolates may be due to geographical isolation of the two gene pools, some mixing is believed to occur as 'American-like' viruses have been isolated during outbreaks of equine influenza in the UK. The cocirculation of two antigenically and genetically distinct lineages of equine influenza H3N8 viruses has serious implications for vaccine strain selection.

Amino Acid Sequence↗
PubMed1996

Molecular evidence supporting the existence of two major groups in uropathogenic Escherichia coli.

Molecular methods allow an extremely fine strain typing that can be used to establish the population structure of bacterial species. This methodology has been used to characterize a collection of 74 uropathogenic Escherichia coli obtained from three hospitals located in geographically distant towns in Spain, some representatives of the ECOR collection and other reference strains. Genomic DNA was analyzed by RAPD (Random Amplified Polymorphic DNA) that can characterize a bacterial strain to the level of defining individual clones. The 16S rDNA-23S rDNA spacers were amplified by PCR and submitted to restriction analysis. Finally, the presence or absence of G adhesins in Escherichia coli as well as the type of adhesin (three types are known) have been shown by PCR amplification followed by digestion with restriction enzymes. As expected a wide diversity was shown by RAPD and identical patterns were only found in the case of strains isolated from the same individual, an obvious case of relapse. Analysis of the spacers' restriction patterns showed the presence of two markedly differentiated clusters that we have named alpha and beta. Both RAPD and spacer restriction patterns originated similar clusters of strains showing a consistency in the evolution of the global genome with the sequence variation of the ribosomal spacers. Furthermore, most of the strains having G-adhesin, with only a few exceptions, corresponded to the alpha rRNA spacer group. The two spacer types detected were also consistent with some phenotypic markers such as sucrose and raffinose utilization. The alpha and beta clusters could be intraspecific groups produced by partial sexual isolation or other barriers that are originating a divergent evolution.

Adhesins, Bacterial↗
PubMed2005

Utility of nuclear DNA intron markers at lower taxonomic levels: phylogenetic resolution among nine Tragelaphus spp.

Phylogenetic relationships among the nine spiral-horn antelope species of the African bovid tribe Tragelaphini are controversial. In particular, mitochondrial DNA sequencing studies are not congruent with previous morphological investigations. To test the utility of nuclear DNA intron markers at lower taxonomic levels and to provide additional data pertinent to tragelaphid evolution, we sequenced four nuclear DNA segments (MGF, PRKCI, SPTBN, and THY) and combined these data with mitochondrial DNA sequences from three genes (cytochrome b, 12S rRNA, and 16S rRNA). Our molecular supermatrix comprised 4682 characters which were analyzed independently and in combination. Parsimony and model based phylogenetic analyses of the combined nuclear DNA data are congruent with those derived from the analysis of mitochondrial gene sequences. The corroboration between nuclear and mtDNA gene trees reject the possibility that genetic processes such as lineage sorting, gene duplication/deletion and hybrid speciation account for the conflict evident in the previously published phylogenies. It suggests rather that the morphological characters used to delimit the Tragelaphid species are subject to convergent evolution. Divergence times among species, calculated using a relaxed Bayesian molecular clock, are consistent with hypotheses proposing that climatic oscillations and their impact on habitats were the major forces driving speciation in the tribe Tragelaphini.

Animals↗