Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We uniformly (re-) annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Within the ∼18,000 families of orthologous genes, we found ∼2,000 common to all strains. Although recombination rates are much higher than mutation rates, we show, both theoretically and using phylogenetic inference, that this does not obscure the phylogenetic signal, which places the B2 phylogenetic group and one group D strain at the basal position. Based on this phylogeny, we inferred past evolutionary events of gain and loss of genes, identifying functional classes under opposite selection pressures. We found an important adaptive role for metabolism diversification within group B2 and Shigella strains, but identified few or no extraintestinal virulence-specific genes, which could render difficult the development of a vaccine against extraintestinal infections. Genome flux in E. coli is confined to a small number of conserved positions in the chromosome, which most often are not associated with integrases or tRNA genes. Core genes flanking some of these regions show higher rates of recombination, suggesting that a gene, once acquired by a strain, spreads within the species by homologous recombination at the flanking genes. Finally, the genome's long-scale structure of recombination indicates lower recombination rates, but not higher mutation rates, at the terminus of replication. The ensuing effect of background selection and biased gene conversion may thus explain why this region is A+T-rich and shows high sequence divergence but low sequence polymorphism. Overall, despite a very high gene flow, genes co-exist in an organised genome

Comparative Analysis of Acinetobacters: Three Genomes for Three Lifestyles

Acinetobacter baumannii is the source of numerous nosocomial infections in humans and therefore deserves close attention as multidrug or even pandrug resistant strains are increasingly being identified worldwide. Here we report the comparison of two newly sequenced genomes of A. baumannii. The human isolate A. baumannii AYE is multidrug resistant whereas strain SDF, which was isolated from body lice, is antibiotic susceptible. As reference for comparison in this analysis, the genome of the soil-living bacterium A. baylyi strain ADP1 was used. The most interesting dissimilarities we observed were that i) whereas strain AYE and A. baylyi genomes harbored very few Insertion Sequence elements which could promote expression of downstream genes, strain SDF sequence contains several hundred of them that have played a crucial role in its genome reduction (gene disruptions and simple DNA loss); ii) strain SDF has low catabolic capacities compared to strain AYE. Interestingly, the latter has even higher catabolic capacities than A. baylyi which has already been reported as a very nutritionally versatile organism. This metabolic performance could explain the persistence of A. baumannii nosocomial strains in environments where nutrients are scarce; iii) several processes known to play a key role during host infection (biofilm formation, iron uptake, quorum sensing, virulence factors) were either different or absent, the best example of which is iron uptake. Indeed, strain AYE and A. baylyi use siderophore-based systems to scavenge iron from the environment whereas strain SDF uses an alternate system similar to the Haem Acquisition System (HAS). Taken together, all these observations suggest that the genome contents of the 3 Acinetobacters compared are partly shaped by life in distinct ecological niches: human (and more largely hospital environment), louse, soil

A Tribute to Disorder in the Genome of the Bloom- Forming Freshwater Cyanobacterium Microcystis aeruginosa

International audienceMicrocystis aeruginosa is one of the most common bloom-forming cyanobacteria in freshwater ecosystems worldwide. This species produces numerous secondary metabolites, including microcystins, which are harmful to human health. We sequenced the genomes of ten strains of M. aeruginosa in order to explore the genomic basis of their ability to occupy varied environments and proliferate. Our findings show that M. aeruginosa genomes are characterized by having a large open pangenome, and that each genome contains similar proportions of core and flexible genes. By comparing the GC content of each gene to the mean value of the whole genome, we estimated that in each genome, around 11% of the genes seem to result from recent horizontal gene transfer events. Moreover, several large gene clusters resulting from HGT (up to 19 kb) have been found, illustrating the ability of this species to integrate such large DNA molecules. It appeared also that all M. aeruginosa displays a large genomic plasticity, which is characterized by a high proportion of repeat sequences and by low synteny values between the strains. Finally, we identified 13 secondary metabolite gene clusters, including threenew putative clusters. When comparing the genomes of Microcystis and Prochlorococcus, one of the dominant picocyanobacteria living in marine ecosystems, our findings show that they are characterized by having almost opposite evolutionary strategies, both of which have led to ecological success in their respective environments

Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium

Acinetobacter sp. strain ADP1 is a nutritionally versatile soil bacterium closely related to representatives of the well-characterized Pseudomonas aeruginosa and Pseudomonas putida. Unlike these bacteria, the Acinetobacter ADP1 is highly competent for natural transformation which affords extraordinary convenience for genetic manipulation. The circular chromosome of the Acinetobacter ADP1, presented here, encodes 3325 predicted coding sequences, of which 60% have been classified based on sequence similarity to other documented proteins. The close evolutionary proximity of Acinetobacter and Pseudomonas species, as judged by the sequences of their 16S RNA genes and by the highest level of bidirectional best hits, contrasts with the extensive divergence in the GC content of their DNA (40 versus 62%). The chromosomes also differ significantly in size, with the Acinetobacter ADP1 chromosome <60% of the length of the Pseudomonas counterparts. Genome analysis of the Acinetobacter ADP1 revealed genes for metabolic pathways involved in utilization of a large variety of compounds. Almost all of these genes, with orthologs that are scattered in other species, are located in five major ‘islands of catabolic diversity’, now an apparent ‘archipelago of catabolic diversity’, within one-quarter of the overall genome. Acinetobacter ADP1 displays many features of other aerobic soil bacteria with metabolism oriented toward the degradation of organic compounds found in their natural habitat. A distinguishing feature of this genome is the absence of a gene corresponding to pyruvate kinase, the enzyme that generally catalyzes the terminal step in conversion of carbohydrates to pyruvate for respiration by the citric acid cycle. This finding supports the view that the cycle itself is centrally geared to the catabolic capabilities of this exceptionally versatile organism

Distribution of the core and flexible genes from all the <i>Microcystis</i> genomes in the Clusters of Orthologous Groups (COGs).

<p>Only the COG categories containing >1% of the genes in at least one of the two core genomes, are shown in the figure. The functional classifications of the COGs are: <b>Cellular process and signaling:</b> (D) Cell cycle control, cell division, chromosome partitioning; (M) Cell wall/membrane/envelope biogenesis; (N) Cell motility (O) Post-translational modification, protein turnover, and chaperones; (T) Signal transduction mechanisms; (U) Intracellular trafficking, secretion, and vesicular transport; (V) Defense mechanisms; (W) Extracellular structures; (Y) Nuclear structure; (Z) Cytoskeleton. <b>Information storage and processing:</b> (J) Translation, ribosomal structure and biogenesis; (K) Transcription; (L) Replication, recombination and repair. <b>Metabolism:</b> (C) Energy production and conversion; (E) Amino acid transport and metabolism; (F) Nucleotide transport and metabolism; (G) Carbohydrate transport and metabolism; (H) Coenzyme transport and metabolism; (I) Lipid transport and metabolism; (P) Inorganic ion transport and metabolism; (Q) Secondary metabolites biosynthesis, transport, and catabolism. <b>Poorly characterized:</b> (R) General function prediction only; (S) Function unknown.</p

Proportions of repeated sequences according to the size of the genomes in the ten new <i>Microcystis aeruginosa</i> genomes (black diamonds), the two previously-available genomes (PCC 7806 and NIES-843) (gray diamonds) and other cyanobacterial genomes (<i>Prochlorococcus</i> AS9601 (number 1 in the figure) & MIT 9301 (2); <i>Oscillatoria</i> PCC 6506 (16); <i>Nostoc</i> ATCC 29133/PCC 73102 (18) & PCC 7120 (15); <i>Synechococcus</i> PCC 6301 (4), JA-2-3B (7); JA-3-3ab (5); PCC 7002 (5) & CC 9311 (3); <i>Synechocystis</i> PCC 6803 (8), <i>Trichodesmium</i> IMS 101 (17); <i>Anabaena</i> ATCC 29413 (14); <i>Cyanothece</i> PCC 7424 (13), PCC 7425 (12), PCC 8801 (9) & PCC 8802 (11); <i>Gloeobacter</i> PCC 7421 (10); white diamonds).

<p>Proportions of repeated sequences according to the size of the genomes in the ten new <i>Microcystis aeruginosa</i> genomes (black diamonds), the two previously-available genomes (PCC 7806 and NIES-843) (gray diamonds) and other cyanobacterial genomes (<i>Prochlorococcus</i> AS9601 (number 1 in the figure) & MIT 9301 (2); <i>Oscillatoria</i> PCC 6506 (16); <i>Nostoc</i> ATCC 29133/PCC 73102 (18) & PCC 7120 (15); <i>Synechococcus</i> PCC 6301 (4), JA-2-3B (7); JA-3-3ab (5); PCC 7002 (5) & CC 9311 (3); <i>Synechocystis</i> PCC 6803 (8), <i>Trichodesmium</i> IMS 101 (17); <i>Anabaena</i> ATCC 29413 (14); <i>Cyanothece</i> PCC 7424 (13), PCC 7425 (12), PCC 8801 (9) & PCC 8802 (11); <i>Gloeobacter</i> PCC 7421 (10); white diamonds).</p

General features of the ten new <i>Microcystis aeruginosa</i> genomes and of the two previously available (PCC 7806 and NIES-843).

<p>SC number: Number of scaffolds; GC%: Percentage of G/C bases in the genome; CDS number: Number of Coding DNA Sequence; IG length: Average intergenic length; Ref: Reference.</p

Phylogenetic relationships (Maximum likelihood method) between the twelve <i>Microcystis aeruginosa</i> genomes (including the two previously-available genomes of PCC 7806 and NIES-843).

<p>A. Phylogeny based on the alignment of seven housekeeping genes (<i>ftsZ</i>, <i>glnA</i>, <i>gltX</i>, <i>gyrB</i>, <i>pgi</i>, <i>recA</i> and <i>tpi</i>; 217 informative sites). B. Phylogeny based on the alignment of 1989 genes belonging to the core genome (SC = Subclade ; 144276 informative sites).</p

Estimation of the sizes of the pangenome (A) and core genome (B) of <i>Microcystis aeruginosa</i> from the twelve <i>Microcystis aeruginosa</i> genomes (including the two previously-available genomes of PCC 7806 and NIES-843). The upper and lower edges of the boxes indicate the first quartile and third quartile, respectively, of all different input orders (1000) of the genomes. The central horizontal line indicates the sample median (50th percentile). The central vertical lines extend above and below each box as far as the data extend, to a distance of at most 1.5 times the interquartile range.

<p>Estimation of the sizes of the pangenome (A) and core genome (B) of <i>Microcystis aeruginosa</i> from the twelve <i>Microcystis aeruginosa</i> genomes (including the two previously-available genomes of PCC 7806 and NIES-843). The upper and lower edges of the boxes indicate the first quartile and third quartile, respectively, of all different input orders (1000) of the genomes. The central horizontal line indicates the sample median (50th percentile). The central vertical lines extend above and below each box as far as the data extend, to a distance of at most 1.5 times the interquartile range.</p