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At least 1,423 records · Page 79Linked to original sources
PubMed2003

Proteorhodopsin genes are distributed among divergent marine bacterial taxa.

Proteorhodopsin (PR) is a retinal-binding bacterial integral membrane protein that functions as a light-driven proton pump. The gene encoding this photoprotein was originally discovered on a large genome fragment derived from an uncultured marine gamma-proteobacterium of the SAR86 group. Subsequently, many variants of the PR gene have been detected in marine plankton, via PCR-based gene surveys. It has not been clear, however, whether these different PR genes are widely distributed among different bacterial groups, or whether they have a restricted taxonomic distribution. We report here comparative analyses of PR-bearing genomic fragments recovered directly from planktonic bacteria inhabiting the California coast, the central Pacific Ocean, and waters offshore the Antarctica Peninsula. Sequence analysis of an Antarctic genome fragment harboring PR (ANT32C12) revealed moderate conservation in gene order and identity, compared with a previously reported PR-containing genome fragment from a Monterey Bay gamma-proteobacterium (EBAC31A08). Outside the limited region of synteny shared between these clones, however, no significant DNA or protein identity was evident. Analysis of a third PR-containing genome fragment (HOT2C01) from the North Pacific subtropical gyre showed even more divergence from the gamma-proteobacterial PR-flanking region. Subsequent phylogenetic and comparative genomic analyses revealed that the Central North Pacific PR-containing genome fragment (HOT2C01) originated from a planktonic alpha-proteobacterium. These data indicate that PR genes are distributed among a variety of divergent marine bacterial taxa, including both alpha- and gamma-proteobacteria. Our analyses also demonstrate the utility of cultivation-independent comparative genomic approaches for assessing gene content and distribution in naturally occurring microbes.

Antarctic Regions↗
PubMed2002

Leishmania priming of human dendritic cells for CD40 ligand-induced interleukin-12p70 secretion is strain and species dependent.

A major question in the study of leishmaniasis is what dictates clinical disease expression produced by different Leishmania species, i.e., cutaneous versus systemic and healing versus nonhealing. Animal models using a Leishmania species associated with self-limiting cutaneous disease (L. major) have revealed that protective immunity requires CD40/CD40 ligand (CD40L)-dependent, interleukin-12 (IL-12)-driven Th1 responses. We recently showed that L. major can prime human dendritic cells (DCs) for CD40L-triggered IL-12p70 secretion and that these cells can drive a Th1 response in autologous T cells from sensitized individuals. Here we show that in contrast to L. major, Leishmania species responsible for visceral disease (L. donovani), as well as species associated with persistent, cutaneous lesions and occasional systemic disease (L. tropica), did not induce CD40L-dependent IL-12p70 production, despite comparable levels of uptake by DCs. Up-regulated surface expression of CD40 did not correlate with IL-12p70 production, and appreciable CD40L-induced IL-12p40 secretion was observed in uninfected as well as infected DCs, regardless of species. Reverse transcription-PCR analysis confirmed that the production of heterodimeric IL-12 was limited by expression of IL-12p35 mRNA, which was dependent on both a microbial priming signal and CD40 engagement for its high-level induction. The intrinsic differences in the ability of Leishmania species to prime DCs for CD40L-dependent IL-12p70 secretion may account, at least in part, for the evolution of healing and nonhealing forms of leishmanial disease.

Animals↗
PubMed1994

Nucleotide composition as a driving force in the evolution of retroviruses.

All complete retrovirus sequences in the GenEMBL database were examined with the goal of assessing possible relationships between the nucleotide composition of retroviral genomes, the amino acid composition of retroviral proteins, and evolutionary strategies used by retroviruses. The results demonstrated that the genome of each viral lineage has a characteristic base composition and that the variations between groups are related to retroviral phylogeny. By analogy to microbial species, we suggest that the variations arise from group-specific patterns of directional mutations where the bias can be exerted on any of the four nucleotides. It is most likely that the mutational patterns are introduced during reverse transcription, and a direct participation of reverse transcriptase in the process is suspected. A straightforward strategy was used to analyze the compositional relationship between nucleotides and encoded amino acids. The procedure entailed calculations of amino acid frequencies from nucleotide content and the comparison of the calculated values to the observed amino acid frequencies in retroviruses. The results revealed an excellent correspondence between variation in genomic base composition and variation in amino acid composition of proteins with the compositional differences extending into all major coding regions of the viruses. Because of the magnitude and dispersion of these effects, and because of the nonconservative nature of many of the substitutions between groups with different genomic biases, we suggest that the variations in protein composition driven by biased nucleotide frequencies are an important factor in shaping the characteristic phenotypes of the different viral lineages. A clue to the nature of the evolutionary forces that are responsible for the generation of nucleotide biases was provided by the observation that viruses with radically different base frequencies most often inhabit the same cell type. This observation, along with analysis of amino acid and nucleotide replacement patterns between and within reverse transcriptase sequences from the various groups, permitted us to advance a model for the evolution of retroviruses. According to the model, speciation could initiate when daughter virions from a single progenitor vary in the direction of their mutational bias. These variations would exert a pleiotropic effect on the frequencies of nucleotides in all viral genes and consequently on the frequencies of amino acids in the encoded proteins. The variants with the most extreme compositional differences would have a selective advantage because their different precursor requirements would enable them to occupy different ecological niches within a single cell.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed2006

Vancomycin resistance in gram-positive cocci.

The first vancomycin-resistant clinical isolates of Enterococcus species were reported in Europe in 1988. Similar strains were later detected in hospitals on the East Coast of the United States. Since then, vancomycin-resistant enterococci have spread with unexpected rapidity and are now encountered in hospitals in most countries. This article reviews the mode of action and the mechanism of bacterial resistance to glycopeptides, as exemplified by the VanA type, which is mediated by transposon Tn1546 and is widely spread in enterococci. The diversity, regulation, evolution, and recent dissemination of methicillin-resistant Staphylococcus aureus are then discussed.

Anti-Bacterial Agents↗
PubMed1998

Comparative and library epidemiological typing systems: outbreak investigations versus surveillance systems.

A number of high-resolution molecular typing systems have been developed in recent years. Their availability raises the new issues of selecting the method (s) best suited for a particular purpose and interpreting and communicating typing results. Most of the currently available methods are comparative only: they allow testing of a sample of isolates for delineation of those closely related from those markedly different in genomic backgrounds. This approach is adequate for outbreak investigation, allowing determination of clonal spread in a microenvironment and identification of the source of infection. Comparative methods with sufficient resolution for most pathogens include restriction fragment-length polymorphism (RFLP), pulsed-field gel electrophoresis (PFGE), and arbitrarily primed and randomly amplified polymorphic DNA-polymerase chain reaction (PCR) analysis. For surveillance systems, monitoring clonal spread and prevalence in populations over extended periods of time requires library typing systems. These must be standardized, must have a high throughput, and must use a uniform nomenclature. Promising or validated methods include serotyping, insertion sequence fingerprinting, ribotyping, PFGE, amplified fragment-length polymorphism (AFLP), infrequent-restriction-site amplification PCR, interrepetitive element PCR typing (rep-PCR) and PCR-RFLP of polymorphic loci. PCR methods generating arrays of size-specific amplicons (AFLP, rep-PCR) can be more reproducibly analyzed by using denaturing polyacrylamide gel or capillary electrophoresis with automated laser detection. Binary probe typing systems appear optimal and should be enhanced further through use of DNA chip technology. In these systems, amplification of polymorphic regions is followed by solid-phase hybridization with a reference panel of sequence-variant specific probes. The resulting binary type results allow determination of reproducible, numeric profiles. However, interpretation and nomenclature of typing results for large-scale surveillance purposes still require a better understanding of population structure and microevolution of most microbial pathogens.

Bacterial Infections↗
PubMed1995

Single amino acid replacements at positions altered in naturally occurring extended-spectrum TEM beta-lactamases.

By directed mutagenesis, we constructed a set of seven TEM-1 derivatives containing single replacements in each one of the amino acids substituted in naturally occurring extended-spectrum TEM beta-lactamases. The exact contribution of each mutation to the resistance phenotype was determined. In addition, mutant enzyme production and stabilities were studied. Five of seven mutations determined to some extent variations in cephalosporin and/or monobactam activity. Dramatic changes in the hydrolysis of ceftazidime and aztreonam occurred when a serine was at position 164. Changes at positions 104, 238, and 240 showed more leaky variation in activity towards cephalosporins and aztreonam. Replacements at positions 237 and 265 caused no variation in susceptibility to cephalosporins. Interestingly, the change from Gln to Lys at position 39 found in TEM-2, classically considered a neutral change, slightly but consistently increased the MIC of ceftazidime and aztreonam. The in vitro construction of mutations appearing in naturally occurring TEM-beta-lactamases, studied in the same genetic context, may help to understand the evolution of extended-spectrum beta-lactamases.

Amino Acids↗
PubMed1987

Cloning and analysis of ermG, a new macrolide-lincosamide-streptogramin B resistance element from Bacillus sphaericus.

To analyze the regulation of a newly discovered macrolide-lincosamide-streptogramin B resistance element (ermG) found in a soil isolate of Bacillus sphaericus, we cloned this determinant and obtained its DNA sequence. Minicell analysis revealed that ermG specifies a 29,000-dalton protein, the synthesis of which is induced by erythromycin. S1 nuclease mapping was used to identify the transcriptional start site. These experiments demonstrated the presence on the ermG mRNA of a 197 to 198-base leader. Within the leader are two small open reading frames (ORFs) capable of encoding 11- and 19-amino-acid peptides. Each ORF is preceded by a suitably spaced Shine-Dalgarno sequence. The ermG protein is encoded by a large ORF that encodes a 244-amino-acid protein, in agreement with the minicell results. This protein and the 19-amino-acid peptide are highly homologous to the equivalent products of ermC and ermA. We conclude, on the basis of this homology, that ermG encodes an rRNA transmethylase. The leader of ermG can be folded into a structure that sequesters the Shine-Dalgarno sequence and start codon for the large ORF (SD3). On the basis of these data and on the observed greater responsiveness of the ermG system than of the ermC system to low concentrations of erythromycin, we propose a model for the regulation of this gene in which the stalling of a ribosome under the influence of an inducer, while reading either peptide, suffices to uncover SD3 and allow translation of the rRNA transmethylase. The evolution of ermG is discussed.

Amino Acid Sequence↗
PubMed2004

[Antibiotic resistance and molecular epidemiology of Shigella spp. in northeastern Argentina].

OBJECTIVES: To evaluate the antibiotic resistance of strains of Shigella spp. isolated from feces samples from northeastern Argentina and to characterize the strains in terms of their molecular epidemiology. METHODS: We studied 132 isolates of Shigella spp. obtained from feces samples from 132 patients with diarrhea who were seen at various private and public laboratories in the Argentine provinces of Chaco and Corrientes during the period of 1998 to 2002. Each strain was characterized according to its serotype, its resistance to 13 individual or combination antibiotics, and its sensitivity to pyocins. With 52 strains selected in relation to their antimicrobial susceptibility profiles we conducted plasmid profile analysis using alkaline lysis, and the repetitive extragenic palindromic sequences were determined by amplifying repetitive DNA segments using polymerase chain reaction. The chi-square test was used to compare proportions, with a level of statistical significance of 0.05. RESULTS: Shigella flexneri was the most common species (78%), followed by S. sonnei (22%). In general, the resistance of S. flexneri to the antibiotics studied was greater than that of S. sonnei, and this difference was statistically significant (P < 0.001) for ampicillin, tetracycline, chloramphenicol, and the combination of ampicillin and sulbactam. The S. flexneri strains also showed multiple resistance more often than S. sonnei strains (84.5% vs. 31.0%; P < 0.001). The strains isolated from S. flexneri were grouped into five pyocin types, three plasmid profiles, and five patterns of repetitive palindromic sequences. The strains of S. sonnei formed three pyocin types, two plasmid profiles, and three patterns of repetitive palindromic sequences. CONCLUSIONS: Given that the Shigella species that were studied showed a high level of resistance to the most frequently used antibiotics, surveillance activities should be implemented in order to detect and control the appearance of new resistant strains. Applying epidemiological typing techniques can provide more precise information about the distribution and evolution of resistant strains of circulating microorganisms.

Argentina↗
PubMedDate not supplied

[Non-culturable Koch bacilli during antitubercular chemotherapy].

The authors have performed 58435 microscopic examinations, of which 3813 were positive, and found 209 (5,48%) cases of non-cultivable Koch bacilli. The major bacteriological, clinico-evolutive and therapeutical aspects are examined. Most of the cases showing a syndrome of positive homogenate with a negative culture were rather recent ones (an evolution of less than 2 years in 73,68% of the total) and the highest frequency was found in those in which the treatment was in its first year. No direct relationship could be demonstrated between the number of germs (the Gaffky scale) and the frequency of the syndrome. The factors influencing the occurrence and the development of the syndrome are: the structure of the lesions, the method of bacteriologic examination, the therapy applied, and a certain immunologic reactivity. According to the authors the significance of this syndrome is positive in most of the cases, indicating a regression that has not been completed. The most reasonable attitude is a differentiated one, depending on each case, integrating the data obtained by the bacteriological examination in the therapeutic and evolutive clinico-radiologic context.

Antitubercular Agents↗
PubMedDate not supplied

Heterogeneous plasmid population from enterotoxigenic Escherichia coli strains isolated in Venezuelan children with acute diarrhea.

Thirty eight enterotoxigenic Escherichia coli (ETEC) isolated from children with acute diarrhea were analyzed in order to assess the possible associations among enterotoxigenicity, antibiotic resistance and other plasmid-mediated virulence properties such as CoIV, Hly and CFA/I. Eighty four percent of ETEC strains were multiresistant. Twenty strains (52.63%) were able to transfer one or more properties studied and 92.68% of the transconjugants were multiresistant. The simultaneous transfer of genes encoding ST enterotoxin and CoIV, Hly or CFA/I was very low (1.82%). The plasmid analysis revealed the presence of a heterogeneous enterotoxigenic (Ent) plasmid population. Additionally, the existence of a conjugative plasmid of approximately 31 megadaltons (Md) of molecular weight encoding for ST and resistance to ampicillin, kanamycin and streptomycin was found. However, this plasmid was not present in all isolates. These results show a diversity of Ent plasmid population which is probably a consequence of the indiscriminate use of antibiotics and the molecular mechanism of transposition of ST and drug-resistance in the evolution of bacterial strains.

Anti-Bacterial Agents↗
PubMed1998

Genotypes of Helicobacter pylori in Lithuanian families.

BACKGROUND: Infection by Helicobacter pylori is very common in Eastern Europe, but the genotypes of predominant strains and prevalence of single vs. multiple infection in this geographic region have not been much studied. MATERIALS AND METHODS: H. pylori was cultured from 13 Lithuanians belonging to six families, and characterized by arbitrarily primed PCR (RAPD) DNA fingerprinting, and by hybridization and PCR tests for polymorphic virulence-associated and neutral genetic markers. RESULTS: Eleven distinct strains were identified: seven carried the cag pathogenicity island (PAI) and the s1 (generally toxigenic) allele of the vacuolating cytotoxin gene (vacA); the other four were cag- and carried the vacA s2 (nontoxigenic) allele; five of the seven vacA s1 strains carried an m1 middle region allele of vacA, whereas all other strains carried m2 alleles, which are generally less toxigenic; four strains carried the virulence-associated iceA1 gene, and the other seven carried the completely unrelated iceA2 gene at the same locus. Insertion sequences IS605 and IS606 and a plasmid replication gene (repA) were also found in some strains. RAPD fingerprinting identified a mixed infection in just one of the 13 persons. In two families, two of the members harbored the same strain, whereas in the other four families each member tested carried a different strain. Resistance to metronidazole (Mtz) was found in two persons; each of them also carried MtzS strains that were indistinguishable from the coresident MtzR strain by RAPD fingerprinting, and that were thus closely related in overall genotype. CONCLUSION: The distribution of genotypes of Lithuanian H. pylori strains resembles that seen in Western Europe. This finding has important implications for understanding modes of H. pylori transmission and evolution.

Adolescent↗
PubMed1996

A modular domain of NifU, a nitrogen fixation cluster protein, is highly conserved in evolution.

hnifU, a gene exhibiting similarity to nifU genes of nitrogen fixation gene clusters, was identified in the course of expressed sequence tag (EST) generation from a human fetal heart cDNA library. Northern blot of human tissues and polymerase chain reaction (PCR) using human genomic DNA verified that the hnifU gene represented a human gene rather than a microbial contaminant of the cDNA library. Conceptual translation of the hnifU cDNA yielded a protein product bearing 77% and 70% amino acid identity to NifU-like hypothetical proteins from Haemophilus influenzae and Saccharomyces cerevisiae, respectively, and 40-44% identity to the N-terminal regions of NifU proteins from several diazatrophs (i.e., nitrogen-fixing organisms). Pairwise determination of amino acid identities between the NifU-like proteins of nondiazatrophs showed that these NifU-like proteins exhibited higher sequence identity to each other (63-77%) than to the diazatrophic NifU proteins (40-48%). Further, the NifU-like proteins of non-nitrogen-fixing organisms were similar only to the N-terminal region of diazatrophic NifU proteins and therefore identified a novel modular domain in these NifU proteins. These findings support the hypothesis that NifU is indeed a modular protein. The high degree of sequence similarity between NifU-like proteins from species as divergent as humans and H. influenzae suggests that these proteins perform some basic cellular function and may be among the most highly conserved proteins.

Amino Acid Sequence↗
PubMed2000

Effect of soil on microbial responses to metal contamination.

An experiment was conducted to investigate microbial responses to metal inputs in five soils with varying clay and organic contents; one soil had also a higher pH. These soils were treated with a low metal, sewage sludge control or with this sludge contaminated to achieve Cu=112, Ni=58 and Zn=220 mg kg(-1) in medium and Cu=182, Ni=98 and Zn=325 mg kg(-1) in high metal soils. CO(2) evolution rates were measured at 1 week and at 4-5-day intervals thereafter until the end of the incubation (7 weeks). Extractable metals (CaCl(2) and water), biomass C, metabolic quotient, ergosterol, bacterial-fungal phospholipid fatty acid (PLFA-3 weeks only) ratio and mineral N were measured at 3 and 7 weeks. Metal inputs caused a marked increase in metal availability in the slightly acidic sandy loams, a smaller increase in slightly acidic clays and had little effect in the alkaline loam. After an initial increase in CO(2) evolution with metal inputs in all soils, the high metal treatment alone caused a significant decrease at later stages, mainly in sandy loams. Although biomass C and metabolic quotient decreased in all soils with higher metal inputs, the effect was more pronounced in the sandy loams. Metal inputs increased ergosterol and decreased bacterial-fungal PLFA ratios in most soils. Larger mineral N contents were found in all high metal soils at 3 weeks but, after 7 weeks, metals caused a significant decrease in sandy loams. CaCl(2) and water-extractable Cu, Ni and Zn contents were closely correlated with microbial indices in sandy loam but not in clay soils. Overall, the effect of treatments on microbial and extractable metal indices was greater in loams. Within a single series, higher organic soils showed less pronounced responses to metal inputs, although this trend was not always consistent.

Journal Article↗
PubMed2006

Biodegradation of hydrocarbons vapors: Comparison of laboratory studies and field investigations in the vadose zone at the emplaced fuel source experiment, Airbase Vaerløse, Denmark.

The natural attenuation of volatile organic compounds (VOCs) in the unsaturated zone can only be predicted when information about microbial biodegradation rates and kinetics are known. This study aimed at determining first-order rate coefficients for the aerobic biodegradation of 13 volatile petroleum hydrocarbons which were artificially emplaced as a liquid mixture during a field experiment in an unsaturated sandy soil. Apparent first-order biodegradation rate coefficients were estimated by comparing the spatial evolution of the resulting vapor plumes to an analytical reactive transport model. Two independent reactive numerical model approaches have been used to simulate the diffusive migration of VOC vapors and to estimate degradation rate coefficients. Supplementary laboratory column and microcosm experiments were performed with the sandy soil at room temperature under aerobic conditions. First-order kinetics adequately matched the lab column profiles for most of the compounds. Consistent compound-specific apparent first-order rate coefficients were obtained by the three models and the lab column experiment, except for benzene. Laboratory microcosm experiments lacked of sensitivity for slowly degrading compounds and underestimated degradation rates by up to a factor of 5. Addition of NH3 vapor was shown to increase the degradation rates for some VOCs in the laboratory microcosms. All field models suggested a significantly higher degradation rate for benzene than the rates measured in the lab, suggesting that the field microbial community was superior in developing benzene degrading activity.

Bacteria↗
PubMed2006

The unusual adaptive expansion of pancreatic ribonuclease gene in carnivora.

Pancreatic ribonuclease (RNASE1) is a digestive enzyme that has been recognized to be one of the most attractive model systems for molecular evolutionary studies. The contribution of RNASE1 gene duplication to the functional adaptation of digestive physiology in foregut-fermenting herbivores, mostly in ruminants, has been well documented. However, no one has ever done a comprehensive study on the carnivores, which are sister to the artiodactyls. Here, we sequenced this gene from 15 species of the superfamily Caniformia in order Carnivora, which all have a relatively simple digestive system and lack the microbial digestion in rumen or cecum typical of most herbivores. In contrast to our initial expectation that only a single RNASE1 gene is present in these carnivores, we observed a "birth (gene duplication)-and-death (gene deactivation)" process for the evolution of RNASE1 genes in all 3 species of Mustelidae family examined here, adding the growing diversity of RNASE1 gene family evolution. In addition, bursts of positive selection have been shown to contribute the enigmatic diversification of these RNASE1 genes in Mustelidae. The finding of the adaptive expansion of RNASE1 in animals without foregut fermentation provides another opportunity for further studies of the structure, function, and evolution of this gene, raising the possibility that new tissue specificity or other functions of RNASE1 genes might have developed in these species.

Adaptation, Biological↗
PubMed1996

Evidence for an in vivo superantigenic activity in human immunodeficiency virus-infected individuals.

In a previous study, we reported the existence of a specific anergy affecting selectively the V beta 8 subset in both CD4 and CD8 T cells from human immunodeficiency virus (HIV)-infected persons. Because this observation gives evidence for a previous in vivo activation of this subset by a superantigen, we further characterize, in the present study, this V beta 8-anergy associated with HIV infection. Molecular T cell receptor analysis indicates that the V beta 8-anergized T cells are polyclonal. Furthermore, we show the dependence of this anergy on the expression of allelic forms of HLA class II DRB1 molecules. These observations explain the frequency of anergic persons among HIV-infected donors (56%) and are consistent with a previous in vivo superantigenic activity. Comparative analyses of disease evolution between V beta 8 responder and anergic persons do not show any clear relation between the V beta 8 status and acquired immunodeficiency syndrome pathogenesis. However, the stability of the V beta 8 status, the absence of correlation with previous microbial infections, and the previously reported precocity of V beta 8 anergization are in favor of a strong association between the in vivo existence of a V beta 8-specific superantigen and HIV infection. Finally, the functional dichotomy we observe for all anergized donors between blood and lymph node T cells raises the question of the in vivo localization of the superantigenic activity.

Alleles↗
PubMed2026

Variations in carbapenem resistance associated with the VIM-1 metallo-&#x3b2;-lactamase across the Enterobacterales.

The VIM-1 metallo-&#x3b2;-lactamase enzyme, encoded within class 1 integrons, is found in Gram-negative clinical isolates worldwide and has been linked to outbreaks of bacterial pathogens in nosocomial settings. Six vim-1+ clinical isolates, from the genera Escherichia, Klebsiella and Enterobacter, were obtained from Kingston, Ontario, Canada. Whole-genome sequencing revealed that vim-1 was plasmid-borne in all strains and situated as the first gene in In916 or In110 integrons. Analysis of related plasmids suggested that these vim-1-containing plasmids are globally disseminated and have spread via horizontal gene transfer and autochthonous vertical spread within Ontario. Interestingly, the MICs of ertapenem and meropenem, two clinically relevant carbapenem antibiotics, against these six isolates varied more than tenfold, suggesting that the effects of VIM-1 are dependent on the genomic content of the host microbe. Introducing vim-1 into three common Enterobacterales laboratory strains was not sufficient to confer resistance to ertapenem and meropenem. Instead, adaptive laboratory evolution of the vim-1 + laboratory strains revealed that vim-1-mediated carbapenem resistance in these strains was dependent on epistatic interactions with ompC mutations, likely due to decreased outer membrane permeability to these antibiotics. Together, these results provide additional support for the role of gene epistasis in modulating the antimicrobial resistance phenotypes of acquired resistance genes, as well as previous results suggesting that the presence of a &#x3b2;-lactamase gene is insufficient to confer strong resistance to carbapenems without being paired with reduced outer membrane permeability.

beta-Lactamases↗
PubMed2006

Protein repertoire of double-stranded DNA bacteriophages.

The complexity and diversity of phage gene sets, which are produced by rapid evolution of phage genomes and rampant gene exchanges among phages, hamper the efforts to decipher the evolutionary relationships between individual phage proteins and reconstruct the complete set of evolutionary events leading to the known phages. To start unraveling the natural history of phages, we built the phage orthologous groups (POGs), a natural system of phage protein families that includes 6378 genes from 164 complete genome sequences of double-stranded DNA bacteriophages. Phage proteomes have high POG coverage: on average, 39 genes per phage genome belong to POGs, which is close to half of all genes in most phages. In an agreement with the notion of phage role in horizontal gene transfer, we see many cases of likely gene exchange between phages and their microbial hosts. At the same time, about 80% of all POGs are highly specific to phage genomes and are not commonly found in microbial genomes, indicating coherence and large degree of evolutionary independence of phage gene sets. The information on orthologous genes is essential for evolutionary classification of known bacteriophages and for reconstruction of ancestral phage genomes.

Bacteriophages↗