Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000

Abstract

The complete genomic sequence of Pseudomonas syringae pv. syringae B728a (Pss B728a) has been determined and is compared with that of P. syringae pv. tomato DC3000 (Pst DC3000). The two pathovars of this economically important species of plant pathogenic bacteria differ in host range and other interactions with plants, with Pss having a more pronounced epiphytic stage of growth and higher abiotic stress tolerance and Pst DC3000 having a more pronounced apoplastic growth habitat. The Pss B728a genome (6.1 Mb) contains a circular chromosome and no plasmid, whereas the Pst DC3000 genome is 6.5 mbp in size, composed of a circular chromosome and two plasmids. Although a high degree of similarity exists between the two sequenced Pseudomonads, 976 protein-encoding genes are unique to Pss B728a when compared with Pst DC3000, including large genomic islands likely to contribute to virulence and host specificity. Over 375 repetitive extragenic palindromic sequences unique to Pss B728a when compared with Pst DC3000 are widely distributed throughout the chromosome except in 14 genomic islands, which generally had lower GC content than the genome as a whole. Content of the genomic islands varies, with one containing a prophage and another the plasmid pKLC102 of Pseudomonas aeruginosa PAO1. Among the 976 genes of Pss B728a with no counterpart in Pst DC3000 are those encoding for syringopeptin, syringomycin, indole acetic acid biosynthesis, arginine degradation, and production of ice nuclei. The genomic comparison suggests that several unique genes for Pss B728a such as ectoine synthase, DNA repair, and antibiotic production may contribute to the epiphytic fitness and stress tolerance of this organism.virulence genes ͉ epiphyte ͉ plant pathogen

Complete genome sequence of the entomopathogenic and metabolically versatile soil bacterium Pseudomonas entomophila

“…The P. entomophila genome is smaller than the six other Pseudomonas genomes that have been published (Table 1): the human opportunistic pathogen P. aeruginosa PAO1 (ref. 4), the three P. syringae pathovars [5][6][7] , the plant commensal P. fluorescens Pf-5 (ref. 8) and the saprophytic soil bacterium P. putida KT2440 (ref.…”

“…The P. entomophila genome harbors several genes that encode hydrolytic activities such as chitinases, lipases and proteases as well as a set of 19 uncharacterized hydrolases, which are potentially involved in the degradation of polymers found in the soil. However, contrary to phytopathogenic strains such as P. syringae [5][6][7] , the genome of P. entomophila is devoid of genes encoding enzymes capable of degrading plant cell walls. This is consistent with the observation that this species is not pathogenic for plants (M. Arlat, Institut National de la Recherche Agronomique, Castanet, France, personal communication).…”

Genetic analysis of genes involved in dipeptide metabolism and cytotoxicity in Pseudomonas aeruginosa PAO1

“…Most clinical strains of P. aeruginosa produce elastase, a zinc metalloprotease that is implicated in the pathogenesis of infections related to these organisms. Indeed, numerous other examples of proteases and aminopeptidases that are linked to virulence have been highlighted (Coffey et al, 2000;Corbett et al, 2003;Feil et al, 2005;Hidalgo-Grass et al, 2006;Kooi et al, 2006;Song et al, 2004;Spratt et al, 1995). Dipeptidyl aminopeptidase activity has previously been implicated in the virulence of Porphyromonas gingivalis (Kumagai et al, 2000).…”

“…tomato DC3000 (Buell et al, 2003), P. syringae pv. syringae B728a (Feil et al, 2005) and P. syringae pv. phaseolicola 1448A (Joardar et al, 2005).…”

Mining ancient microbiomes using selective enrichment of damaged DNA molecules

“…Specifically, the references of Streptosporangium roseum [37], Pseudomonas syringae pv. syringae B728a [38], Pseudomonas rhizosphaerae [39] and Pantoea vagans [23] were used. Since mapping metagenomic libraries to bacterial reference genomes is very prone to false alignments, we used a different mapping strategy for these genomes.…”