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At least 1,297 records · Page 72Linked to original sources
PubMed1995

Sequence evolution of the porB gene of Neisseria gonorrhoeae and Neisseria meningitidis: evidence of positive Darwinian selection.

Protein 1 (PI) is a major porin of Neisseria gonorrhoeae and Neisseria meningitidis and is encoded by a single locus, porB. Alleles of the porB locus of N. gonorrhoeae are assigned to two homology groups, PI(A) and PI(B), on the basis of immunological and structural similarity. In a like manner, alleles of the porB locus of the closely related bacterium, N. meningitidis, are allocated into class 2 and class 3 homology groups. An individual strain of N. gonorrhoeae or N. meningitidis expresses either one or other of these porin homology groups but never both, and the antigenic reactions of these highly diverse outer membrane proteins form part of the N. gonorrhoeae and N. meningitidis serotyping schemes. A comparison of the number of synonymous and nonsynonymous substitutions per site between the two most divergent alleles of each of these four groups of porB alleles shows that PI(A) alleles have accumulated significantly more nonsynonymous substitutions per site than synonymous substitutions. In contrast the distribution of synonymous and nonsynonymous substitutions between alleles of class 2 and class 3 porins are not significantly different from random. We localize the regions of the PI(A) alleles with an excess of amino acid changes to the surface-exposed loops of these outer membrane proteins and suggest that positive Darwinian selection for diversity, driven by the human immune system, can most easily explain the allelic polymorphism and the pattern of synonymous and nonsynonymous substitutions.

Alleles↗
PubMed1983

Evolution of antibiotic resistance genes: the DNA sequence of a kanamycin resistance gene from Staphylococcus aureus.

The kanamycin resistance gene from Staphylococcus aureus has been sequenced and its structure compared with similar genes isolated from Streptomyces fradiae and from two transposons, Tn5 and Tn903, originally isolated from Klebsiella pneumoniae and Salmonella typhimurium, respectively. The genes are all homologous but, since their common ancestor, have undergone extensive divergence, with more than 43% divergence between the closest pair. The phylogeny of the genes cannot be made congruent to the phylogeny of the taxa from which they were isolated without requiring rather improbable differences in rates. One is therefore led to conclude that there have been multiple occurrences of gene transfer between these species. Thus, although they are homologous, they are neither orthologous nor paralogous. It is suggested that homologous genes of this type be called xenologous.

Amino Acid Sequence↗
PubMed1984

Retention of cryptic genes in microbial populations.

Cryptic genes are silenced genes that can still be reactivated by mutation. Since they can make no positive contribution to the fitness of their carriers, it is not clear why many cryptic genes in microbial populations have not degenerated into useless DNA sequences. Hall et al. (1983) have suggested that cryptic genes have persisted because of occasional strong environmental selection for reactivated genes. The present mathematical study supports their suggestion. It shows that a cryptic gene can be retained without having any selective advantage over a useless DNA sequence, if selection for the reactivated gene occasionally occurs for a substantially long time.

Bacteria↗
PubMed1988

Mitochondrial DNA evolution in the Drosophila obscura group.

We report a restriction-site study of the mitochondrial DNA (mtDNA) of seven species of the Drosophila obscura group. One species (D. azteca) belongs to the affinis subgroup; the other six species are classified in the obscura subgroup, three of them being from the old-world species (D. obscura, D. ambigua, and D. subobscura) and three from the new-world species (D. pseudoobscura, D. persimilis, and D. miranda). The mtDNA patterns suggest that the phylogeny of the group needs to be revised. The Nearctic obscura species appear as more closely related to D. azteca (affinis subgroup) than to the Palearctic species. The three Palearctic species are, in turn, a very heterogeneous group, with D. obscura no more closely related to D. subobscura and D. ambigua than to D. affinis or the Nearctic obscura species. The rates of mtDNA evolution are variable: some lineages have evolved at rates two or three times greater than others. If an average rate of 0.5% nucleotide substitutions/Myr is assumed, the divergence among the four main lineages in the phylogeny would have occurred 12-15 Myr ago, during the Miocene, which is consistent with biogeographic information.

Animals↗
PubMed2001

Intimate interactions of enteropathogenic Escherichia coli at the host cell surface.

Unlike many gastrointestinal pathogens, enteropathogenic Escherichia coli orchestrates the modulation of host cellular and immune responses from the exterior of the infected cell, chiefly via the secreted and translocated components of a type III secretion system. Close inspection of these enteropathogenic Escherichia coli proteins and the interactions they mediate provides an increasingly coherent picture of the pathogenic mechanisms that enteropathogenic Escherichia coli uses to exploit its host.

Adhesins, Bacterial↗
PubMed1986

The evolution of DNA sequences in Escherichia coli.

It is proposed that certain families of transposable elements originally evolved in plasmids and functioned in forming replicon fusions to aid in the horizontal transmission of non-conjugational plasmids. This hypothesis is supported by the finding that the transposable elements Tn3 and gamma delta are found almost exclusively in plasmids, and also by the distribution of the unrelated insertion sequences IS4 and IS5 among a reference collection of 67 natural isolates of Escherichia coli. Each insertion sequence was found to be present in only about one-third of the strains. Among the ten strains found to contain both insertion sequences, the number of copies of the elements was negatively correlated. With respect to IS5, approximately half of the strains containing a chromosomal copy of the insertion element also contained copies within the plasmid complement of the strain.

Base Sequence↗
PubMed1992

Phylogenetic relationship of Cowdria ruminantium, agent of heartwater, to Anaplasma marginale and other members of the order Rickettsiales determined on the basis of 16S rRNA sequence.

The phylogenetic relationship between Cowdria ruminantium and representative members of the orders Rickettsiales and Chlamydiales has been examined on the basis of the sequence of the 16S rRNA. Phylogeny reconstruction by using both parsimony and distance methods supports the conclusion that C. ruminantium is closely related to the Rickettsiales and in particular to the family Anaplasmataceae. A signature of nine base substitutions delineated the linkage of Anaplasma marginale with C. ruminantium and differentiated these two species from the 45 other members of the alpha group of Proteobacteria examined, and five of these base substitutions were unique among all members of the class Proteobacteria examined to date.

Alphaproteobacteria↗
PubMed1993

The phylogenetic position of Helicobacter nemestrinae.

Comparison of the Helicobacter nemestrinae 16S ribosomal DNA with published homologous sequences from members of the genera Helicobacter, Wolinella, and Campylobacter reveals a close relationship between H. nemestrinae, H. pylori, and H. acinonyx. This finding is unexpected since these species differ significantly in their DNA guanine-plus-cytosine contents (24 to 38 mol%).

Biological Evolution↗
PubMed1999

Sequence changes in six variants of rice tungro bacilliform virus and their phylogenetic relationships.

The DNA of three biological variants, G1, Ic and G2, which originated from the same greenhouse isolate of rice tungro bacilliform virus (RTBV) at the International Rice Research Institute (IRRI), was cloned and sequenced. Comparison of the sequences revealed small differences in genome sizes. The variants were between 95 and 99% identical at the nucleotide and amino acid levels. Alignment of the three genome sequences with those of three published RTBV sequences (Phi-1, Phi-2 and Phi-3) revealed numerous nucleotide substitutions and some insertions and deletions. The published RTBV sequences originated from the same greenhouse isolate at IRRI 20, 11 and 9 years ago. All open reading frames (ORFs) and known functional domains were conserved across the six variants. The cysteine-rich region of ORF3 showed the greatest variation. When the six DNA sequences from IRRI were compared with that of an isolate from Malaysia (Serdang), similar changes were observed in the cysteine-rich region in addition to other nucleotide substitutions and deletions across the genome. The aligned nucleotide sequences of the IRRI variants and Serdang were used to analyse phylogenetic relationships by the bootstrapped parsimony, distance and maximum-likelihood methods. The isolates clustered in three groups: Serdang alone; Ic and G1; and Phi-1, Phi-2, Phi-3 and G2. The distribution of phylogenetically informative residues in the IRRI sequences shared with the Serdang sequence and the differing tree topologies for segments of the genome suggested that recombination, as well as substitutions and insertions or deletions, has played a role in the evolution of RTBV variants. The significance and implications of these evolutionary forces are discussed in comparison with badnaviruses and caulimoviruses.

Amino Acid Sequence↗
PubMed1991

Isolation and evolutionary analysis of a RepFVIB replicon of the plasmid pSU212.

We have isolated at least two different replication regions from pSU401, a Tn802 insertion derivative of the IncFVI plasmid pSU212. One of the replication regions (RepFVIB) is highly homologous to the RepFIIA replicon of IncFII plasmids, and thus belongs to the RepFIIA family. We have also cloned the incompatibility determinant (incFVI) and the copy number control gene (cop) from RepFVIB and determined their nucleotide sequences. The analysis of the sequences supports the idea of a modular evolution of RepFIIA plasmids.

Amino Acid Sequence↗
PubMed1993

Characterization of the 6-aminohexanoate-dimer hydrolase from Pseudomonas sp. NK87.

The DNA base sequence of the Pseudomonas sp. NK87 gene (P-nylB) for 6-aminohexanoate-dimer hydrolase (P-EII), a xenobiotic-compound-degrading enzyme, was determined. It has an open reading frame of 1188 bp, initiated by ATG and terminated by TAG, and coding for 396 amino acids. The base sequence of the open reading frame has 53% sequence similarity to that of the gene for the same enzyme of Flavobacterium sp. KI72 (F-nylB) and 35% sequence similarity with respect to the deduced amino acid sequence. The P-EII enzyme was purified from an Escherichia coli clone in which the P-EII gene was highly expressed. The P-EII enzyme was inhibited by a serine protease inhibitor, diisopropyl fluorophosphate, as was the F-EII enzyme. Double reciprocal plots obtained from various concentrations of 6-aminohexanoate-dimer indicated that the kcat value of the P-EII enzyme (9.2 s-1) was approximately half that of the F-EII enzyme (19 s-1), and the P-EII enzyme had higher affinity toward this substrate (Km for P-EII, 0.6 mM; Km for F-EII, 15 mM). The P-EII enzyme had a temperature optimum of 48 degrees C, and a pH optimum of 7.5. It is speculated that since the P-nylB and F-nylB genes are more diverged from each other than the corresponding nylA genes, the latter may have evolved more recently.

Amidohydrolases↗
PubMed1996

Genomic lineage of Salmonella enterica serotype Gallinarum.

Forty-eight strains of Salmonella enterica serotype Gallinarum of biotypes Gallinarum and Pullorum were characterised by three chromosomally based typing methods. The patterns obtained were compared with those of strains of eight other serotypes of Salmonella of O serogroup D. The same PvuII and PstI IS200 patterns were commonly observed among strains of both biotypes and the three SmaI ribotypes of serotype Gallinarum strains differed in only one or two bands, supporting the view that members of these two biotypes are closely related. The same IS200 patterns were also commonly observed among strains of serotype Enteritidis, indicating its evolutionary relationship with serotype Gallinarum. NotI pulsed-field gel electrophoresis (PFGE) patterns divided strains into 24 types. Based on a similarity analysis, two clusters were formed. One contained the majority of biotype Gallinarum strains and two atypical strains of Pullorum; the other contained strains of biotype Pullorum and an otherwise typical strain of biotype Gallinarum. Two atypical strains of biotype Pullorum remained unclustered by PFGE analysis. The grouping of strains differed according to the typing method used, but the majority of strains within each of the biotypes Gallinarum and Pullorum were very similar by the chromosomal markers analysed.

Animals↗
PubMed2006

Genetic and phenotypic characterization of Listeria monocytogenes lineage III.

Listeria monocytogenes has been previously grouped into three evolutionary groups, termed lineages I, II and III. While lineages I and II are commonly isolated from various sources, lineage III isolates are rare and have several atypical and unique phenotypic characteristics. Relative to their prevalence in other sources, lineage III strains are overrepresented among isolates from food-production animals, and underrepresented among isolates from human clinical cases and foods. This work describes an extensive genotypic and phenotypic characterization of 46 lineage III isolates. Phylogenetic analyses of partial sigB and actA sequences showed that lineage III represents three distinct subgroups, which were termed IIIA, IIIB and IIIC. Each of these lineage III subgroups is characterized by differentiating genotypic and phenotypic characteristics. Unlike typical L. monocytogenes, all subgroup IIIB and IIIC isolates lack the ability to ferment rhamnose. While all IIIC and most IIIB isolates carry the putative virulence gene lmaA, the majority of subgroup IIIA isolates lack this gene. All three lineage III subgroups contain isolates from human clinical cases as well as isolates that are cytopathogenic in a cell culture plaque assay, indicating that lineage III isolates have the potential to cause human disease. The identification of specific genotypic and phenotypic characteristics among the three lineage III subgroups suggests that these subgroups may occupy different ecological niches and, therefore, may be transmitted by different pathways.

Animals↗
PubMed2001

Capturing whole-genome characteristics in short sequences using a naïve Bayesian classifier.

Bacterial genomes have diverged during evolution, resulting in clearcut differences in their nucleotide composition, such as their GC content. The analysis of complete sequences of bacterial genomes also reveals the presence of nonrandom sequence variation, manifest in the frequency profile of specific short oligonucleotides. These frequency profiles constitute highly specific genomic signatures. Based on these differences in oligonucleotide frequency between bacterial genomes, we investigated the possibility of predicting the genome of origin for a specific genomic sequence. To this end, we developed a naïve Bayesian classifier and systematically analyzed 28 eubacterial and archaeal genomes. We found that sequences as short as 400 bases could be correctly classified with an accuracy of 85%. We then applied the classifier to the identification of horizontal gene transfer events in whole-genome sequences and demonstrated the validity of our approach by correctly predicting the transfer of both the superoxide dismutase (sodC) and the bioC gene from Haemophilus influenzae to Neisseria meningitis, correctly identifying both the donor and recipient species. We believe that this classification methodology could be a valuable tool in biodiversity studies.

Archaea↗
PubMed1990

The identification, characterization, sequencing and mutagenesis of the genes (hupSL) encoding the small and large subunits of the H2-uptake hydrogenase of Azotobacter chroococcum.

The structural genes (hupSL) of the membrane-bound NiFe-containing H2-uptake hydrogenase (Hup) of Azotobacter chroococcum were identified by oligonucleotide screening and sequenced. The small subunit gene (hupS) encodes a signal sequence of 34 amino acids followed by a 310-amino-acid, 34156D protein containing 12 cysteine residues. The large subunit gene (hupL) overlaps hupS by one base and codes for a predicted 601-amino-acid, 66433D protein. There are two regions of strong homology with other Ni hydrogenases: a Cys-Thr-Cys-Cys-Ser motif near the N-terminus of HupS and an Asp-Pro-Cys-Leu-Ala-Cys motif near the carboxy-terminus of HupL. Strong overall homology exists between Azotobacter, Bradyrhizobium japonicum and Rhodobacter capsulatus Hup proteins but less exists between the Azotobacter proteins and hydrogenases from Desulfovibrio strains. Mutagenesis of either hupS or hupL genes of A. chroococcum yielded Hup- phenotypes but some of these mutants retained a partial H2-evolving activity. Hybridization experiments at different stages of gene segregation confirmed the multicopy nature of the Azotobacter genome.

Amino Acid Sequence↗