CiteULike: hpaces's bacteria

Genomic plasticity in prokaryotes: the case of the square haloarchaeon.

S Cuadros-Orellana — 2007-12-02T15:44:29-00:00

ISME J, Vol. 1, No. 3. (July 2007), pp. 235-245.

The variability in genome content among closely related strains of prokaryotes has been one of the most remarkable discoveries of genomics. One way to approach the description of this so-called pan-genome is to compare one reference strain genome with metagenomic sequences from the environment. We have applied this approach to one extreme aquatic habitat, saturated brines in a solar saltern. The genome of Haloquadratum walsbyi strain DSM 16790 was compared to an environmental metagenome obtained from the exact site of its isolation. This approach revealed that some regions of the strain genome were scarcely represented in the metagenome. Here we have analyzed these genomic islands (GI) in the genome of DSM 16790 and compared them with the complete sequence of some fosmids from the environmental library. Two of the islands, GI 2 and GI 4, overlapped with two large guanine and cytosine (GC)-rich regions that showed evidence of high variability through mobile elements. GI 3 seemed to be a phage or phage-remnant acquired by the reference genome, but not present in most environmental lineages. Most differential gene content was related to small molecule transport and detection, probably reflecting adaptation to different pools of organic nutrients. GI 1 did not possess traces of mobile elements and had normal GC content. This island contained the main cluster of cell envelope glycoproteins and the variability found was different from the other GIs. Rather than containing different genes it consisted of homologs with low similarity. This variation might reflect a phage evasion strategy.The ISME Journal (2007) 1, 235-245; doi:10.1038/ismej.2007.35; published online 31 May 2007.

Comparative analysis of the complete genome sequence of the plant growth–promoting bacterium Bacillus amyloliquefaciens FZB42

Xiao Chen — 2007-09-11T23:43:23-00:00

Nature Biotechnology, Vol. 25, No. 9. (19 August 2007), pp. 1007-1014.

Genome-wide transcriptional changes in Streptococcus gordonii in response to competence signaling peptide.

MM Vickerman — 2007-12-11T09:06:57-00:00

J Bacteriol, Vol. 189, No. 21. (November 2007), pp. 7799-7807.

Streptococcus gordonii is a primary colonizer of the multispecies biofilm on tooth surfaces forming dental plaque and a potential agent of endocarditis. The recent completion of the genome sequence of the naturally competent strain Challis allowed the design of a spotted oligonucleotide microarray to examine a genome-wide response of this organism to environmental stimuli such as signal peptides. Based on temporal responses to synthetic competence signaling peptide (CSP) as indicated by transformation frequencies, the S. gordonii transcriptome was analyzed at various time points after CSP exposure. Microarray analysis identified 35 candidate early genes and 127 candidate late genes that were up-regulated at 5 and 15 min, respectively; these genes were often grouped in clusters. Results supported published findings on S. gordonii competence, showing up-regulation of 12 of 16 genes that have been reported to affect transformation frequencies in this species. Comparison of CSP-induced S. gordonii transcriptomes to results published for Streptococcus pneumoniae strains identified both conserved and species-specific genes. Putative intergenic regulatory sites, such as the conserved combox sequence thought to be a binding site for competence sigma factor, were found preceding S. gordonii late responsive genes. In contrast, S. gordonii early CSP-responsive genes were not preceded by the direct repeats found in S. pneumoniae. These studies provide the first insights into a genome-wide transcriptional response of an oral commensal organism. They offer an extensive analysis of transcriptional changes that accompany competence in S. gordonii and form a basis for future intra- and interspecies comparative analyses of this ecologically important phenotype.

The complete genome sequence of Campylobacter jejuni strain 81116 (NCTC11828).

BM Pearson — 2007-12-11T09:04:30-00:00

J Bacteriol, Vol. 189, No. 22. (November 2007), pp. 8402-8403.

Campylobacter jejuni is a major human enteric pathogen that displays genetic variability via genomic reorganization and phase variation. This variability can adversely affect the outcomes and reproducibility of experiments. C. jejuni strain 81116 (NCTC11828) has been suggested to be a genetically stable strain (G. Manning, B. Duim, T. Wassenaar, J. A. Wagenaar, A. Ridley, and D. G. Newell, Appl. Environ. Microbiol. 67:1185-1189, 2001), is amenable to genetic manipulation, and is infective for chickens. Here we report the finished annotated genome sequence of C. jejuni strain 81116.

Paradoxical DNA Repair and Peroxide Resistance Gene Conservation in Bacillus pumilus SAFR-032.

J Gioia — 2007-12-11T09:03:25-00:00

PLoS ONE, Vol. 2, No. 9. (2007)

BACKGROUND: Bacillus spores are notoriously resistant to unfavorable conditions such as UV radiation, gamma-radiation, H(2)O(2), desiccation, chemical disinfection, or starvation. Bacillus pumilus SAFR-032 survives standard decontamination procedures of the Jet Propulsion Lab spacecraft assembly facility, and both spores and vegetative cells of this strain exhibit elevated resistance to UV radiation and H(2)O(2) compared to other Bacillus species. PRINCIPAL FINDINGS: The genome of B. pumilus SAFR-032 was sequenced and annotated. Lists of genes relevant to DNA repair and the oxidative stress response were generated and compared to B. subtilis and B. licheniformis. Differences in conservation of genes, gene order, and protein sequences are highlighted because they potentially explain the extreme resistance phenotype of B. pumilus. The B. pumilus genome includes genes not found in B. subtilis or B. licheniformis and conserved genes with sequence divergence, but paradoxically lacks several genes that function in UV or H(2)O(2) resistance in other Bacillus species. SIGNIFICANCE: This study identifies several candidate genes for further research into UV and H(2)O(2) resistance. These findings will help explain the resistance of B. pumilus and are applicable to understanding sterilization survival strategies of microbes.

Identification of disulfide reductases in Campylobacterales: a bioinformatics investigation.

NO Kaakoush — 2007-12-11T09:02:25-00:00

Antonie Van Leeuwenhoek, Vol. 92, No. 4. (November 2007), pp. 429-441.

Disulfide reductases of host-colonising bacteria are involved in the expression of virulence factors, resistance to drugs, and elimination of toxic compounds. Large-scale genome analyses of 281 prokaryotes identified CXXC and CXXC-derived motifs in each microorganism. The total number of these motifs showed correlations with genome size and oxygen tolerance of the prokaryotes. Specific bioinformatic analyses served to identify putative disulfide reductases in the Campylobacterales Campylobacter jejuni, Helicobacter pylori, Wolinella succinogenes and Arcobacter butzleri which colonise the gastrointestinal tract of higher animals. Three filters applied to the genomes of these species yielded 35, 25, 28 and 34 genes, respectively, encoding proteins with the characteristics of disulfide reductases. Ten proteins were common to the four species, including four belonging to the thioredoxin system. The presence of thioredoxin reductase activities was detected in the four bacterial species by observing dithiobis-2-nitrobenzoic acid reduction with beta-nicotinamide adenine dinucleotide phosphate as cofactor. Phylogenetic analyses of the thioredoxin reductases TrxB(1) and TrxB(2) of the four Campylobacterales were performed. Their TrxB(1) proteins were more closely related to those of Firmicutes than to the corresponding proteins of other Proteobacteria. The Campylobacterales TrxB(2) proteins were closer to glutathione reductases of other organisms than to their respective TrxB(1) proteins. The phylogenetic features of the Campylobacterales thioredoxin reductases suggested a special role for these enzymes in the physiology of these bacteria.

Lateral gene transfer between obligate intracellular bacteria: Evidence from the Rickettsia massiliae genome

Guillaume Blanc — 2007-12-01T22:11:29-00:00

Genome Res., Vol. 17, No. 11. (1 November 2007), pp. 1657-1664.

Rickettsia massiliae is a tick-borne obligate intracellular alpha-proteobacteria causing spotted fever in humans. Here, we present the sequence of its genome, comprising a 1.3-Mb circular chromosome and a 15.3-kb plasmid. The chromosome exhibits long-range colinearity with the other Spotted Fever Group Rickettsia genomes, except for a large fragment specific to R. massiliae that contains 14 tra genes presumably involved in pilus formation and conjugal DNA transfer. We demonstrate that the tra region was acquired recently by lateral gene transfer (LGT) from a species related to Rickettsia bellii. Further analysis of the genomic sequences identifies additional candidates of LGT between Rickettsia. Our study indicates that recent LGT between obligate intracellular Rickettsia is more common than previously thought. 10.1101/gr.6742107

Rhizobial factors required for stem nodule maturation and maintenance in Sesbania rostrata-Azorhizobium caulinodans ORS571 symbiosis.

S Suzuki — 2007-12-11T08:58:54-00:00

Appl Environ Microbiol, Vol. 73, No. 20. (October 2007), pp. 6650-6659.

The molecular and physiological mechanisms behind the maturation and maintenance of N(2)-fixing nodules during development of symbiosis between rhizobia and legumes still remain unclear, although the early events of symbiosis are relatively well understood. Azorhizobium caulinodans ORS571 is a microsymbiont of the tropical legume Sesbania rostrata, forming N(2)-fixing nodules not only on the roots but also on the stems. In this study, 10,080 transposon-inserted mutants of A. caulinodans ORS571 were individually inoculated onto the stems of S. rostrata, and those mutants that induced ineffective stem nodules, as displayed by halted development at various stages, were selected. From repeated observations on stem nodulation, 108 Tn5 mutants were selected and categorized into seven nodulation types based on size and N(2) fixation activity. Tn5 insertions of some mutants were found in the well-known nodulation, nitrogen fixation, and symbiosis-related genes, such as nod, nif, and fix, respectively, lipopolysaccharide synthesis-related genes, C(4) metabolism-related genes, and so on. However, other genes have not been reported to have roles in legume-rhizobium symbiosis. The list of newly identified symbiosis-related genes will present clues to aid in understanding the maturation and maintenance mechanisms of nodules.

Mineralization of individual congeners of linear alkylbenzenesulfonate by defined pairs of heterotrophic bacteria.

D Schleheck — 2007-12-11T08:52:47-00:00

Appl Environ Microbiol, Vol. 70, No. 7. (July 2004), pp. 4053-4063.

Parvibaculum lavamentivorans DS-1(T) utilized the commercial surfactant linear alkylbenzenesulfonate (LAS) (20 congeners with C(10) to C(13) side chains) as a carbon and energy source by shortening the side chain, and sulfophenylcarboxylates (SPCs) and similar compounds (e.g., alpha,beta-unsaturated SPCs [SPC-2Hs]) were excreted with quantitative recovery of the sulfophenyl moiety. 2-(4-Sulfophenyl)decane (2-C10-LAS) was converted largely to 3-(4-sulfophenyl)butyrate (3-C4-SPC), as were 2-C12-LAS and 2-C14-LAS; the other products were 5-C6-SPC (SPC+2C) and 3-C4-SPC-2H. 2-C11-LAS was converted largely to 4-C5-SPC with the corresponding SPC+2C and SPC-2H; similarly, 3-C12-LAS yielded 4-C6-SPC with the corresponding SPC+2C and SPC-2H. This pattern of products confirmed that LAS is degraded by omega-oxygenation and chain shortening through beta-oxidation. At least nine major SPCs were formed from commercial LAS. The novel isolates Comamonas testosteroni SPB-2 and KF-1 utilized 3-C4-SPC; Delftia acidovorans SPH-1 utilized 4-C6-SPC enantioselectively. The substrate-dependent oxygen uptake of whole cells of strain SPB-2 indicated that there was inducible oxygenation of 3-C4-SPC and of 4-sulfophenol in whole cells of the strains of C. testosteroni during growth with 3-C4-SPC or 4-sulfophenol. The degradative pathways apparently involved 4-sulfocatechol and 4-sulfocatechol 1,2-dioxygenase. Strain SPB-2 and strain DS-1(T) grew together in LAS-salts medium, and only seven of the nine major SPCs were recovered. Strain SPB-2 utilized 3-C4-SPC, 3-C5-SPC, and 3-C4-SPC-2H. Strain SPH-1 grew together with strain DS-1(T) in LAS-salts medium, and a different set of seven major SPCs was recovered. Strain SPH-1 utilized 4-C6-SPC, 4-C5-SPC, 4-C6-SPC-2H, and 4-C5-SPC-2H. A three-member community consisting of strains DS-1(T), SPB-2, and SPH-1 utilized four major SPCs. We inferred that this community mineralized the major SPCs derived from 8 of the 20 LAS congeners.

Genome sequence of Lactobacillus helveticus: an organism distinguished by selective gene loss and IS element expansion.

Michael Callanan — 2007-12-11T08:46:23-00:00

J Bacteriol (9 November 2007)

Mobile genetic elements are major contributing factors to the generation of genetic diversity in prokaryotic organisms. For example insertion sequence (IS) elements have been shown to specifically contribute to niche adaptation by promoting a variety of genetic rearrangements. The complete genome sequence of the cheese culture Lactobacillus helveticus DPC 4571 was determined and revealed significant conservation when compared to three non-dairy gut lactobacilli. Despite originating from significantly different environments, 65-75% of genes were conserved between the commensal and dairy lactobacilli which allowed key niche-specific gene sets to be described. However, the primary distinguishing feature was two hundred and thirteen IS elements in the DPC 4571 genome, ten times more than the other lactobacilli. Moreover, genome alignments revealed an unprecedented level of genome stability between these four Lactobacillus species considering the number of IS elements in the L. helveticus genome. Comparative analysis also indicated that the IS elements were not the primary agents of niche adaptation for the L. helveticus genome. A clear bias towards the loss of genes reported to be important for gut colonization was observed for the cheese culture but there was no clear evidence of IS-associated gene deletion and decay for the majority of genes lost. Furthermore, an extraordinary level of sequence diversity exists between copies of certain IS elements in the DPC 4571 genome indicating they may represent an ancient component of the L. helveticus genome. These data suggests a special unobtrusive relationship between the DPC 4571 genome and its mobile DNA complement.

Subtle genetic changes enhance virulence of methicillin resistant and sensitive Staphylococcus aureus

Sarah Highlander — 2007-11-07T21:43:29-00:00

BMC Microbiology, Vol. 7 (06 November 2007), 99.

Using Likelihood-Free Inference to Compare Evolutionary Dynamics of the Protein Networks of H. pylori and P. falciparum

Oliver Ratmann — 2007-12-01T08:59:40-00:00

PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e230.

Gene duplication with subsequent interaction divergence is one of the primary driving forces in the evolution of genetic systems. Yet little is known about the precise mechanisms and the role of duplication divergence in the evolution of protein networks from the prokaryote and eukaryote domains. We developed a novel, model-based approach for Bayesian inference on biological network data that centres on approximate Bayesian computation, or likelihood-free inference. Instead of computing the intractable likelihood of the protein network topology, our method summarizes key features of the network and, based on these, uses a MCMC algorithm to approximate the posterior distribution of the model parameters. This allowed us to reliably fit a flexible mixture model that captures hallmarks of evolution by gene duplication and subfunctionalization to protein interaction network data of Helicobacter pylori and Plasmodium falciparum. The 80% credible intervals for the duplication–divergence component are [0.64, 0.98] for H. pylori and [0.87, 0.99] for P. falciparum. The remaining parameter estimates are not inconsistent with sequence data. An extensive sensitivity analysis showed that incompleteness of PIN data does not largely affect the analysis of models of protein network evolution, and that the degree sequence alone barely captures the evolutionary footprints of protein networks relative to other statistics. Our likelihood-free inference approach enables a fully Bayesian analysis of a complex and highly stochastic system that is otherwise intractable at present. Modelling the evolutionary history of PIN data, it transpires that only the simultaneous analysis of several global aspects of protein networks enables credible and consistent inference to be made from available datasets. Our results indicate that gene duplication has played a larger part in the network evolution of the eukaryote than in the prokaryote, and suggests that single gene duplications with immediate divergence alone may explain more than 60% of biological network data in both domains.

Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation

Letunic — 2006-12-25T11:16:04-00:00

Bioinformatics, Vol. 23, No. 1. (1 January 2007), pp. 127-128.

Whole-genome analysis of photosynthetic prokaryotes.

J Raymond — 2006-07-03T23:01:10-00:00

Science, Vol. 298, No. 5598. (22 November 2002), pp. 1616-1620.

The process of photosynthesis has had profound global-scale effects on Earth; however, its origin and evolution remain enigmatic. Here we report a whole-genome comparison of representatives from all five groups of photosynthetic prokaryotes and show that horizontal gene transfer has been pivotal in their evolution. Excluding a small number of orthologs that show congruent phylogenies, the genomes of these organisms represent mosaics of genes with very different evolutionary histories. We have also analyzed a subset of "photosynthesis-specific" genes that were elucidated through a differential genome comparison. Our results explain incoherencies in previous data-limited phylogenetic analyses of phototrophic bacteria and indicate that the core components of photosynthesis have been subject to lateral transfer.

EVOLUTION: Passages Found Through Labyrinth of Bacterial Evolution

Elizabeth Pennisi — 2007-12-09T08:01:03-00:00

Science, Vol. 301, No. 5634. (8 August 2003), pp. 745a-746.

10.1126/science.301.5634.745a

The entire organization of transcription units on the Bacillus subtilis genome

Hirokazu Kobayashi — 2007-06-29T10:54:07-00:00

BMC Genomics, Vol. 8 (28 June 2007), 197.