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At least 1,639 records · Page 91Linked to original sources
PubMed2006

Local migration promotes competitive restraint in a host-pathogen 'tragedy of the commons'.

Fragmented populations possess an intriguing duplicity: even if subpopulations are reliably extinction-prone, asynchrony in local extinctions and recolonizations makes global persistence possible. Migration is a double-edged sword in such cases: too little migration prevents recolonization of extinct patches, whereas too much synchronizes subpopulations, raising the likelihood of global extinction. Both edges of this proverbial sword have been explored by manipulating the rate of migration within experimental populations. However, few experiments have examined how the evolutionary ecology of fragmented populations depends on the pattern of migration. Here, we show that the migration pattern affects both coexistence and evolution within a community of bacterial hosts (Escherichia coli) and viral pathogens (T4 coliphage) distributed across a large network of subpopulations. In particular, different patterns of migration select for distinct pathogen strategies, which we term 'rapacious' and 'prudent'. These strategies define a 'tragedy of the commons': rapacious phage displace prudent variants for shared host resources, but prudent phage are more productive when alone. We find that prudent phage dominate when migration is spatially restricted, while rapacious phage evolve under unrestricted migration. Thus, migration pattern alone can determine whether a de novo tragedy of the commons is resolved in favour of restraint.

Animals↗
PubMed2002

The genetics of plant morphological evolution.

Considerable progress has been made in identifying genes that are involved in the evolution of plant morphologies. Elements of the ABC model of flower development are conserved throughout angiosperms, and homologous MADS-box genes function in gymnosperm reproduction. Candidate gene and mapping analyses of floral symmetry, sex determination, inflorescence architecture, and compound leaves provide intriguing glimpses into the evolution of morphological adaptations.

ATP-Binding Cassette Transporters↗
PubMed1986

Plasmid-mediated resistance to beta-lactam antibiotics in gram-negative bacteria: the role of in-vivo recyclization reactions in plasmid evolution.

Over 20 different plasmid-encoded beta-lactamases have so far been discovered. This paper considers genetic mechanisms by which beta-lactamase genes encoded by plasmids are disseminated across generic boundaries. Particular emphasis is placed on the evolution of plasmids carrying all or part of Tn3 and encoding TEM-1 beta-lactamase in Haemophilus and Neisseria species. Examples of the acquisition of broad host range plasmids carrying Tn3 sequences and of rescue of transposon sequences to indigenous plasmids or to the host chromosome have been found in these two genera. Studies on nonconjugative beta-lactamase plasmids in Neisseria and Haemophilus are consistent with the evolution of a family of plasmids originating from the insertion of Tn3 into an indigenous progenitor plasmid. A series of subsequent insertional and deletional events, most probably occurring as a consequence of genetic transfer, have given rise to the existing group of small, closely related ampicillin-resistance plasmids found currently in these genera. A general model for deletional and other rearrangements caused by recombinational recyclization during the evolution of resistance plasmids is described.

Anti-Bacterial Agents↗
PubMed1993

Sequence divergence in two tandemly located pilin genes of Eikenella corrodens.

Eikenella corrodens normally inhabits the human respiratory and gastrointestinal tracts but is frequently the cause of abscesses at various sites. Using the N-terminal portion of the Moraxella nonliquefaciens pilin gene as a hybridization probe, we cloned two tandemly located pilin genes of E. corrodens 31745, ecpC and ecpD, and expressed the two pilin genes separately in Escherichia coli. A comparison of the predicted amino acid sequences of E. corrodens 31745 EcpC and EcpD revealed considerable divergence between the sequences of these two pilins and even less similarity to EcpA and EcpB of E. corrodens type strain ATCC 23834. EcpC from E. corrodens 31745 displayed high degrees of homology to the pilins of Neisseria gonorrhoeae and Pseudomonas aeruginosa. EcpD from E. corrodens 31745 showed the highest homologies with the pilin of one of the three P. aeruginosa classes, whereas EcpA and EcpB of strain ATCC 23834 most closely resemble Moraxella bovis pilins. These findings raise interesting questions about potential genetic transfer between different bacterial species, as opposed to convergent evolution.

Amino Acid Sequence↗
PubMed1995

Understanding cellular responses to toxic agents: a model for mechanism-choice in bacterial metal resistance.

Bacterial resistances to metals are heterogeneous in both their genetic and biochemical bases. Metal resistance may be chromosomally-, plasmid- or transposon-encoded, and one or more genes may be involved: at the biochemical level at least six different mechanisms are responsible for resistance. Various types of resistance mechanisms can occur singly or in combination and for a particular metal different mechanisms of resistance can occur in the same species. To understand better the diverse responses of bacteria to metal ion challenge we have constructed a qualitative model for the selection of metal resistance in bacteria. How a bacterium becomes resistant to a particular metal depends on the number and location of cellular components sensitive to the specific metal ion. Other important selective factors include the nature of the uptake systems for the metal, the role and interactions of the metal in the normal metabolism of the cell and the availability of plasmid (or transposon) encoded resistance mechanisms. The selection model presented is based on the interaction of these factors and allows predictions to be made about the evolution of metal resistance in bacterial populations. It also allows prediction of the genetic basis and of mechanisms of resistance which are in substantial agreement with those in well-documented populations. The interaction of, and selection for resistance to, toxic substances in addition to metals, such as antibiotics and toxic analogues, involve similar principles to those concerning metals. Potentially, models for selection of resistance to any substance can be derived using this approach.

Bacteria↗
PubMed1995

Molecular cloning of the hom-thrC-thrB cluster from Bacillus sp. ULM1: expression of the thrC gene in Escherichia coli and corynebacteria, and evolutionary relationships of the threonine genes.

A 6.5 kb DNA fragment containing the gene (thrC) encoding threonine synthase, the last enzyme of the threonine biosynthetic pathway, has been cloned from the DNA of Bacillus sp. ULM1 by complementation of Escherichia coli and Brevibacterium lactofermentum thrC auxotrophs. Complementation studies showed that the thrB gene (encoding homoserine kinase) is found downstream from the thrC gene, and analysis of nucleotide sequences indicated that the hom gene (encoding homoserine dehydrogenase) is located upstream of the thrC gene. The organization of this cluster of genes is similar to the Bacillus subtilis threonine operon (hom-thrC-thrB). An 1.9 kb BclI fragment from the Bacillus sp. ULM1 DNA insert 351 amino acids was found corresponding to a protein of 37462 Da. The thrC gene showed a low G + C content (39.4%) and the encoded threonine synthase is very similar to the B. subtilis enzyme. Expression of the 1.9 kb BcI DNA fragment in E. coli minicells resulted in the formation of a 37 kDa protein. The upstream region of this gene shows promoter activity in E. coli but not in corynebacteria. A peptide sequence, including a lysine that is known to bind the pyridoxal phosphate cofactor, is conserved in all threonine synthase sequences and also in the threonine and serine dehydratase genes. Amino acid comparison of nine threonine synthases revealed evolutionary relationships between different groups of bacteria.

Amino Acid Sequence↗
PubMed1997

The Staphylococcus aureus collagen adhesin-encoding gene (cna) is within a discrete genetic element.

Although the gene (cna) encoding the Staphylococcus aureus (Sa) collagen adhesin is not present in all strains, the DNA both upstream and downstream of cna is present in all Sa strains. Using oligo primers corresponding to the conserved nt flanking cna and template DNA from Sa strains that do not encode cna, we amplified a 372-bp fragment. These results illustrate that the conserved regions upstream and downstream of cna are contiguous in strains that do not encode cna. Using primers corresponding to the conserved flanking DNA together with primers corresponding to the 5' and 3' ends of cna, we also amplified DNA fragments containing the junctions between the cna genetic element and the conserved flanking sequences. Sequence comparisons of the amplification products from four cna negative and four cna positive strains revealed that cna is within a discrete genetic element that extends 202 bp upstream from the cna start codon and 100 bp downstream of the cna stop codon. Sequence analysis of the ends of the cna element did not reveal any of the repeats characteristic of transposable elements. These results suggest that cna may be part of a larger element (e.g., a phage) that may or may not contain cna. Alternatively, cna may be a subject to a precise excision event resulting in its deletion from the chromosome. Based on sequence analysis of the flanking DNA amplified from strains that do not encode cna, the presence of a cna genetic element does not disrupt an ORF.

Adhesins, Bacterial↗
PubMed1991

Waterborne transmission and the evolution of virulence among gastrointestinal bacteria.

Diarrhoeal diseases are primary contributors to millions of deaths annually. Yet, little is known about the evolutionary reasons for the differences in virulence among gastrointestinal pathogens. Applying the comparative, cost/benefit approach of evolutionary biology this paper proposes that waterborne transmission should favour evolution towards high virulence. This hypothesis is supported by a cross-specific test, which shows that waterborne transmission is strongly correlated with the virulence of bacterial gastrointestinal pathogens of humans. Alternative explanations of this correlation are not supported by available data. These findings bear on public health policy because they draw attention to a previously unrecognized long-range benefit gained from purification of water supplies; diarrhoeal pathogens may evolve to lower levels of virulence.

Bacteria↗
PubMed2003

Linear plasmid SLP2 of Streptomyces lividans is a composite replicon.

SLP2 is a 50 kb linear plasmid in Streptomyces lividans that contains short (44 bp) terminal inverted repeats and covalently bound terminal proteins. The nucleotide sequence of SLP2 was determined. The rightmost 15.4 kb sequence is identical to that of the host chromosome, including the Tn4811 sequence at the border, which is interrupted by an insertion sequence (IS) element in SLP2. Examination of the flanking target sequences of Tn4811 suggests a previous recombinational event there. The 43 putative protein coding sequences contained many involved in replication (including two terminal protein homologues), partitioning, conjugal transfer and intramycelial spread. The terminally located helicase-like gene ttrA was necessary for conjugal transfer. The two telomeres diverge significantly in primary sequence, while preserving similar secondary structures. Mini-linear plasmids containing these telomeres replicated in S. lividans using the chromosomally encoded terminal protein. In addition, two pseudotelomere sequences are present near the left telomere. The G+C content and GC or AT skew profiles exhibit complex distributions. These, plus the inferred recombination at the right arm, indicate that SLP2 has evolved through rounds of exchanges involving at least three replicons.

Bacterial Proteins↗
PubMed2003

Evolutionary engineering of a beta-Lactamase activity on a D-Ala D-Ala transpeptidase fold.

The beta-Lactamase hydrolytic activity has arisen several times from DD-transpeptidases. We have been able to replicate the evolutionary process of beta-Lactamase activity emergence on a PBP2X DD-transpeptidase. Some of the most interesting changes, like modifying the catalytic properties of an enzyme, may require several mutations in concert; therefore it is essential to explore efficiently sequence space by generating the right diversity. We designed a biased combinatorial library in which biochemical and structural information were incorporated by site directed mutagenesis on relevant residues and then subjected to random mutagenesis to allow for mutations in unforeseen positions. We isolated mutants from this library conferring 10-fold higher cefotaxime resistance levels than the background wild-type through mutations exclusively in the coding sequence. We demonstrate that only three substitutions in the DD-transpeptidase active site, two produced by the directed and one by the random mutagenesis, are sufficient to acquire this activity. The purified product of one mutant (MutE) had a 10(5)-fold increase in cefotaxime deacylation rate allowing it to hydrolyze beta-Lactams yet it has apparently conserved DD-peptidase activity. This work is the first to show a possible evolutionary intermediate between a beta-Lactamase and a DD-transpeptidase necessary for the development of antibiotic resistance.

Amino Acid Sequence↗
PubMed1992

Molecular evolutionary genetics of the cattle-adapted serovar Salmonella dublin.

An electrophoretic analysis of allelic variation at 24 enzyme loci among 170 isolates of the serovar Salmonella dublin (serotype 1,9,12[Vi]:g,p:-) identified three electrophoretic types (Du 1, Du 3, and Du 4), marking three closely related clones, one of which (Du 1) is globally distributed and was represented by 95% of the randomly selected isolates. All but 1 of 114 nonmotile isolates of serotype 1,9,12:-:- recovered from cattle and swine in the United States were genotypically Du 1. The virulence capsular polysaccharide (Vi antigen) is confined to clone Du 3, which apparently is limited in distribution to France and Great Britain. For all 29 isolates of Du 3, positive signals were detected when genomic DNA was hybridized with a probe specific for the ViaB region, which contains the structurally determinant genes for the Vi antigen; and 23 of these isolates had been serologically typed as Vi positive. In contrast, all 30 isolates of Du 1 tested with the ViaB probe were negative. These findings strongly suggest that the ViaB genes were recently acquired by S. dublin via horizontal transfer and additive recombination. The clones of S. dublin are closely similar to the globally predominant clone (En 1) of Salmonella enteritidis (serotype 1,9,12:g,m:-) in both multilocus enzyme genotype and nucleotide sequence of the fliC gene encoding phase 1 flagellin. Comparative sequencing of fliC has revealed the molecular genetic basis for expression of the p and m flagellar epitopes by which these serovars are distinguished in the Kauffmann-White serological scheme of classification.

Alleles↗
PubMed2003

On the origin of mitochondria: a genomics perspective.

The availability of complete genome sequence data from both bacteria and eukaryotes provides information about the contribution of bacterial genes to the origin and evolution of mitochondria. Phylogenetic analyses based on genes located in the mitochondrial genome indicate that these genes originated from within the alpha-proteobacteria. A number of ancestral bacterial genes have also been transferred from the mitochondrial to the nuclear genome, as evidenced by the presence of orthologous genes in the mitochondrial genome in some species and in the nuclear genome of other species. However, a multitude of mitochondrial proteins encoded in the nucleus display no homology to bacterial proteins, indicating that these originated within the eukaryotic cell subsequent to the acquisition of the endosymbiont. An analysis of the expression patterns of yeast nuclear genes coding for mitochondrial proteins has shown that genes predicted to be of eukaryotic origin are mainly translated on polysomes that are free in the cytosol whereas those of putative bacterial origin are translated on polysomes attached to the mitochondrion. The strong relationship with alpha-proteobacterial genes observed for some mitochondrial genes, combined with the lack of such a relationship for others, indicates that the modern mitochondrial proteome is the product of both reductive and expansive processes.

Adenosine Triphosphate↗
PubMedDate not supplied

Thoughts on the evolution of strategies used by bacteria for evasion of host defenses.

The detailed study of the molecular biology of the mechanisms that pathogenic organisms employ to successfully parasitize their hosts has been very productive. An important part of the microbe's armamentarium is the ability to partially or totally evade one or more of the normal defenses of the host. While it is obvious that the molecular entities that produce these effects have an evolutionary history, as yet little attention has been devoted to this aspect. The study of the selective conditions that have given rise to a particular pathogenic property affords important perspectives on the process of mutual adaptation of the host and the parasite.

Antigens, Bacterial↗
PubMed1995

Dictyostelium discoideum mitochondrial DNA encodes a NADH:ubiquinone oxidoreductase subunit which is nuclear encoded in other eukaryotes.

Complex I, a key component of the mitochondrial electron transport system, is thought to have evolved from at least two separate enzyme systems prior to the evolution of mitochondria from a bacterial endosymbiont, but the genes for one of the enzyme systems are thought to have subsequently been transferred to the nuclear DNA. We demonstrated that the cellular slime mold Dictyostelium discoideum retains the ancestral characteristic of having mitochondria encoding at least one gene (80-kDa subunit) that is nuclear encoded in other eukaryotes. This is consistent with the cellular slime molds of the family Dictyosteliaceae having diverged from other eukaryotes at an early stage prior to the loss of the mitochondrial gene in the lineage giving rise to plants and animals. The D. discoideum mitochondrially encoded 80-kDa subunit of complex I exhibits a twofold-higher mutation rate compared with the homologous chromosomal gene in other eukaryotes, making it the most divergent eukaryotic form of this protein.

Animals↗
PubMed2002

Divergence of mitochondrial dna is not corroborated by nuclear dna, morphology, or behavior in Drosophila simulans.

We ask whether the observed mitochondrial DNA (mtDNA) population subdivision of Drosophila simulans is indicative of organismal structure or of specific processes acting on the mitochondrial genome. Factors either intrinsic or extrinsic to the host genome may influence the evolutionary dynamics of mtDNA. Potential intrinsic factors include adaptation of the mitochondrial genome and of nucleomitochondrial gene complexes specific to the local environment. An extrinsic force that has been shown to influence mtDNA evolution in invertebrates is the bacterial endosymbiont Wolbachia. Evidence presented in this study suggests that mtDNA is not a good indicator of organismal subdivision in D. simulans. Furthermore, there is no evidence to suggest that Wolbachia causes any reduction in nuclear gene flow in this species. The observed differentiation in mtDNA is not corroborated by data from NADH: ubiquinone reductase 75kD subunit precursor or the Alcohol dehydrogenase-related loci, from the shape or size of the male genital arch, or from assortative premating behavior. We discuss these results in relation to a mitochondrial genetic species concept and the potential for Wolbachia-induced incompatibility to be a mechanism of speciation in insects. We conclude with an iterated appeal to include phylogenetic and statistical tests of neutrality as a supplement to phylogenetic and population genetic analyses when using mtDNA as an evolutionary marker.

Animals↗
PubMed2005

Chicken orthologues of mammalian imprinted genes are clustered on macrochromosomes and replicate asynchronously.

In the chicken genome, most orthologues of mouse imprinted genes are clustered on macrochromosomes. Only a few orthologues are located in the microchromosome complement. Macrochromosomal and, to a lesser extent, microchromosomal regions containing imprinted gene orthologues exhibit asynchronous DNA replication. We conclude that highly conserved arrays of imprinted gene orthologues were selected during vertebrate evolution, long before these genes were recruited for parent-specific gene expression by genomic imprinting mechanisms. Evidently, the macrochromosome complement provides a better chromatin environment for the establishment of asynchronous DNA replication and imprinted gene expression later in evolution than microchromosomes.

Animals↗
PubMed2003

In search of the prototype of nitric oxide synthase.

Recent identification of the prokaryotic genes related to the catalytic oxygenase domain of mammalian nitric oxide synthase (NOS) has led to speculations on the origins of the NO signaling network. NOS activity in eukaryotes relies on the concerted action of the oxygenase domain with an electron-donating reductase domain that is fused to it. A fused reductase domain is, however, absent in prokaryotes. Consequently, we searched bacterial genomes for homologs of the reductase domain and identified candidate genes. On the basis of genomic sequence and protein structural analysis, we here propose that sulfite reductase flavoprotein is a prototype of the mammalian NOS reductase domain and a complementing interaction partner of the bacterial NOS oxygenase protein.

Amino Acid Sequence↗