Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction

Variably present genes and pseudogenes in Rickettsia species tend to have been acquired more recently and to be more divergent from the genes conserved across all specie

Genome dynamics of Bartonella grahamii in micro-populations of woodland rodents

<p>Abstract</p> <p>Background</p> <p>Rodents represent a high-risk reservoir for the emergence of new human pathogens. The recent completion of the 2.3 Mb genome of <it>Bartonella grahamii</it>, one of the most prevalent blood-borne bacteria in wild rodents, revealed a higher abundance of genes for host-cell interaction systems than in the genomes of closely related human pathogens. The sequence variability within the global <it>B. grahamii </it>population was recently investigated by multi locus sequence typing, but no study on the variability of putative host-cell interaction systems has been performed.</p> <p>Results</p> <p>To study the population dynamics of <it>B. grahamii</it>, we analyzed the genomic diversity on a whole-genome scale of 27 <it>B. grahamii </it>strains isolated from four different species of wild rodents in three geographic locations separated by less than 30 km. Even using highly variable spacer regions, only 3 sequence types were identified. This low sequence diversity contrasted with a high variability in genome content. Microarray comparative genome hybridizations identified genes for outer surface proteins, including a repeated region containing the <it>fha </it>gene for filamentous hemaggluttinin and a plasmid that encodes a type IV secretion system, as the most variable. The estimated generation times in liquid culture medium for a subset of strains ranged from 5 to 22 hours, but did not correlate with sequence type or presence/absence patterns of the <it>fha </it>gene or the plasmid.</p> <p>Conclusion</p> <p>Our study has revealed a geographic microstructure of <it>B. grahamii </it>in wild rodents. Despite near-identity in nucleotide sequence, major differences were observed in gene presence/absence patterns that did not segregate with host species. This suggests that genetically similar strains can infect a range of different hosts.</p

Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade

Zaremba-Niedzwiedzka K, Viklund J, Zhao W, et al. Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade. Genome biology. 2013;14(11): R130.BACKGROUND: The SAR11 group of Alphaproteobacteria is highly abundant in the oceans. It contains a recently diverged freshwater clade, which offers the opportunity to compare adaptations to salt- and freshwaters in a monophyletic bacterial group. However, there are no cultivated members of the freshwater SAR11 group and no genomes have been sequenced yet. RESULTS: We isolated ten single SAR11 cells from three freshwater lakes and sequenced and assembled their genomes. A phylogeny based on 57 proteins indicates that the cells are organized into distinct microclusters. We show that the freshwater genomes have evolved primarily by the accumulation of nucleotide substitutions and that they have among the lowest ratio of recombination to mutation estimated for bacteria. In contrast, members of the marine SAR11 clade have one of the highest ratios. Additional metagenome reads from six lakes confirm low recombination frequencies for the genome overall and reveal lake-specific variations in microcluster abundances. We identify hypervariable regions with gene contents broadly similar to those in the hypervariable regions of the marine isolates, containing genes putatively coding for cell surface molecules. CONCLUSIONS: We conclude that recombination rates differ dramatically in phylogenetic sister groups of the SAR11 clade adapted to freshwater and marine ecosystems. The results suggest that the transition from marine to freshwater systems has purged diversity and resulted in reduced opportunities for recombination with divergent members of the clade. The low recombination frequencies of the LD12 clade resemble the low genetic divergence of host-restricted pathogens that have recently shifted to a new host

Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria

Most free-living planktonic cells are streamlined and in spite of their limitations in functional flexibility, their vast populations have radiated into a wide range of aquatic habitats. Here we compared the metabolic potential of subgroups in the Alphaproteobacteria lineage SAR11 adapted to marine and freshwater habitats. Our results suggest that the successful leap from marine to freshwaters in SAR11 was accompanied by a loss of several carbon degradation pathways and a rewiring of the central metabolism. Examples for these are C1 and methylated compounds degradation pathways, the Entner–Doudouroff pathway, the glyoxylate shunt and anapleuretic carbon fixation being absent from the freshwater genomes. Evolutionary reconstructions further suggest that the metabolic modules making up these important freshwater metabolic traits were already present in the gene pool of ancestral marine SAR11 populations. The loss of the glyoxylate shunt had already occurred in the common ancestor of the freshwater subgroup and its closest marine relatives, suggesting that the adaptation to freshwater was a gradual process. Furthermore, our results indicate rapid evolution of TRAP transporters in the freshwater clade involved in the uptake of low molecular weight carboxylic acids. We propose that such gradual tuning of metabolic pathways and transporters toward locally available organic substrates is linked to the formation of subgroups within the SAR11 clade and that this process was critical for the freshwater clade to find and fix an adaptive phenotype.This work was supported by the Swedish Research Council (Grant Numbers 2012-4592 to AE and 2012-3892 to SB) and the Communiy Sequencing Programme of the US Department of Energy Joint Genome Institute. The work conducted by the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under Contract No. DE-AC02-05CH11231

Visualization of variable segments using the GenComp visualization tool

Segments are shown that contain variable open reading frames (ORFs) that are present in all seven species, in most but not all species, in members of the spotted fever group (SFG) , and in a single species. The visualization tool displays (in blue) the location of positional orthologs that are conserved across all seven spp. and differ by less than 20% in size. Interspersed among these are segments with strain-variable ORFs shown (in green) that differ in sizes and are normally present in only a subset of the spp. Vertical lines show positional orthologs and horizontal lines indicate the six frames (+1, +2, +3, -1, -2, and -3, in that order). Each set of six lines represents a species, with (Rp), (Rt), (Rf), (Ra), (Rc), (Rs), and (Rr) shown from the top to the bottom, in accordance with their phylogenetic relationships. Numbers inside boxes show ORF numbers, and designations above boxes show gene annotations. The first digits in the numbers below the boxes indicate homologous strain-variable ORFs that are members of the same ORF-cluster, and the last two digits indicate ORFs in the ORF-clusters that differ by less than 80% in size. Arrows illustrate the fragmentation process for sequences that are similar across species.<p><b>Copyright information:</b></p><p>Taken from "Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction"</p><p>http://genomebiology.com/2008/9/2/R42</p><p>Genome Biology 2008;9(2):R42-R42.</p><p>Published online 26 Feb 2008</p><p>PMCID:PMC2374718.</p><p></p

Substitution frequency at nonsynonymous and synonymous sites plotted by genes present in different numbers of species

The nonsynonymous substitution frequency (dN) values were plotted against the synonymous substitution frequency (dS) values for R7 core genes and strain-variable open reading frames (ORFs) present in two to seven species and core genes and strain-variable ORFs present in seven species that are longer than one kilobase in size.<p><b>Copyright information:</b></p><p>Taken from "Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction"</p><p>http://genomebiology.com/2008/9/2/R42</p><p>Genome Biology 2008;9(2):R42-R42.</p><p>Published online 26 Feb 2008</p><p>PMCID:PMC2374718.</p><p></p

Number of R7 core genes and strain-variable ORFs placed at different nodes of the species tree

The relative proportions of R7 core genes (open boxes) and strain-variable open reading frames (ORFs; black boxes) are indicated at each node of the tree. Arrows show the nodes that contain the majority of core genes (ROW*) and strain-variable ORFs (R8). Species abbreviations are as in Figure 3, plus Ot (), wMel ([]), and wBm ([]). The underlying phylogenetic tree was constructed using the maximum likelihood method from a concatenated alignment of adenylate kinase, SecY, and ribosomal proteins S3, S8, S10, S11, S13, S14, S19 and L2, L3, L4, L5, L6, L14, L16, L18, L22, L23, L24 and L29.<p><b>Copyright information:</b></p><p>Taken from "Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction"</p><p>http://genomebiology.com/2008/9/2/R42</p><p>Genome Biology 2008;9(2):R42-R42.</p><p>Published online 26 Feb 2008</p><p>PMCID:PMC2374718.</p><p></p