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J Bacteriol. Jun 2011; 193(12): 3146.
PMCID: PMC3133198

Complete Genome Sequence of a Beneficial Plant Root-Associated Bacterium, Pseudomonas brassicacearum [down-pointing small open triangle]

Abstract

To shed light on the genetic equipment of the beneficial plant-associated bacterium Pseudomonas brassicacearum, we sequenced the whole genome of the strain NFM421. Its genome consists of one chromosome equipped with a repertoire of factors beneficial for plant growth. In addition, a complete type III secretion system and two complete type VI secretion systems were identified. We report here the first genome sequence of this species.

TEXT

P. brassicacearum has been described as the major root-associated bacteria of Arabidopsis thaliana and Brassica napus plants (1, 2, 5, 7). It has the ability to suppress plant pathogens (10) by producing antifungal compounds, such as 2,4-diacetyl-phloroglucinol and cyanide.

To gain more knowledge on the genetic equipment of this highly competitive bacterium in the rhizosphere, we sequenced the genome of the laboratory strain of P. brassicacearum NFM421, using a two-step DNA shotgun sequencing strategy that comprises Sanger and pyrosequencing-based approaches, conducted at the Genoscope (8).

The circular chromosome of P. brassicacearum NFM421 has 6,843,248 bp and an average G+C content of 60.8%. The genome was submitted to the Genobrowser annotation platform for automated annotation and gene prediction using the annotation tools GeneMark (4), Glimmer (6), and MedP (11). The whole genome was reannotated manually. The chromosome contains 6,097 protein-coding sequences with an average length of 989 bp, 65 tRNAs, and 16 rRNAs. A total of 4,686 proteins (76.9%) were assigned a biological function, while 324 orphan proteins were identified. Protein-coding genes represent 88.2% of the genome. Regulatory genes, including those encoding two-component signal transduction proteins (TCSs) and transcription factors (TFs), were analyzed using P2CS (3) and P2TF (http://www.p2tf.org) systems, which identified 178 TCSs and 501 TFs. The genome analysis revealed clusters of hitherto-unknown secondary metabolites, which may contribute to bacterial fitness and competitiveness in the rhizosphere. In addition, the P. brassicacearum genome contains a complete type III secretion system and two complete type VI secretion systems.

The large size of P. brassicacearum genome is attributable mainly to lateral gene transfer, as acquired genes represent up to 12% of the whole genome. From acquired genes, three prophage regions, at least one confirmed ICE (integrative conjugative element) (9), and many genes relevant to plant-bacterium interaction and survival under saprophytic conditions were identified.

A further and deep exploration of the P. brassicacearum genome will provide new insights on this bacterium's lifestyle and the molecular mechanism underlying the molecular dialogue with other microorganisms and with plants.

Nucleotide sequence accession number.

The complete genome sequence of P. brassicacearum NFM421 is available in GenBank under accession number CP002585.

Acknowledgments

This work was supported by ECCOREV and the GENOSCOPE.

Footnotes

[down-pointing small open triangle]Published ahead of print on 22 April 2011.

REFERENCES

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