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Open Access Research article

The genome of the versatile nitrogen fixer Azorhizobium caulinodans ORS571

Kyung-Bum Lee12, Philippe De Backer34, Toshihiro Aono1, Chi-Te Liu1, Shino Suzuki1, Tadahiro Suzuki1, Takakazu Kaneko5, Manabu Yamada5, Satoshi Tabata5, Doris M Kupfer6, Fares Z Najar6, Graham B Wiley6, Bruce Roe6, Tim T Binnewies7, David W Ussery7, Wim D'Haeze4, Jeroen Den Herder34, Dirk Gevers348, Danny Vereecke34, Marcelle Holsters34 and Hiroshi Oyaizu1*

Author Affiliations

1 Laboratory of Plant Biotechnology, Biotechnology Research Center, University of Tokyo, Tokyo 113-8657, Japan

2 Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima 411-8540, Japan

3 Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), 9052 Gent, Belgium

4 Department of Molecular Genetics, Ghent University, 9052 Gent, Belgium

5 Kazusa DNA Research Institute, Chiba 292-0818, Japan

6 Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019-3051, USA

7 Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark

8 Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA

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BMC Genomics 2008, 9:271  doi:10.1186/1471-2164-9-271

Published: 4 June 2008

Abstract

Background

Biological nitrogen fixation is a prokaryotic process that plays an essential role in the global nitrogen cycle. Azorhizobium caulinodans ORS571 has the dual capacity to fix nitrogen both as free-living organism and in a symbiotic interaction with Sesbania rostrata. The host is a fast-growing, submergence-tolerant tropical legume on which A. caulinodans can efficiently induce nodule formation on the root system and on adventitious rootlets located on the stem.

Results

The 5.37-Mb genome consists of a single circular chromosome with an overall average GC of 67% and numerous islands with varying GC contents. Most nodulation functions as well as a putative type-IV secretion system are found in a distinct symbiosis region. The genome contains a plethora of regulatory and transporter genes and many functions possibly involved in contacting a host. It potentially encodes 4717 proteins of which 96.3% have homologs and 3.7% are unique for A. caulinodans. Phylogenetic analyses show that the diazotroph Xanthobacter autotrophicus is the closest relative among the sequenced genomes, but the synteny between both genomes is very poor.

Conclusion

The genome analysis reveals that A. caulinodans is a diazotroph that acquired the capacity to nodulate most probably through horizontal gene transfer of a complex symbiosis island. The genome contains numerous genes that reflect a strong adaptive and metabolic potential. These combined features and the availability of the annotated genome make A. caulinodans an attractive organism to explore symbiotic biological nitrogen fixation beyond leguminous plants.