Abstract
Herein we report the draft genome sequence of a phototrophic bacterium, Rubrivivax benzoatilyticus strain JA2T, which apparently is the first genome sequence report of a phototrophic member belonging to the class Betaproteobacteria. The unique feature of this strain is its capability to synthesize carotenoids through both spirilloxanthin and spheroidenone pathways. Strain JA2T produces several novel secondary metabolites, and the genome insights help in understanding the unique machinery that the strain adapted.
TEXT
Rubrivivax benzoatilyticus JA2T was isolated from a flooded paddy field in South India and was found to be closely related to Rubrivivax gelatinosus ATCC 17011T based on 16S rRNA gene sequence similarity (6). Extended growth modes (photo-/chemoheterotrophy and photoautotrophy) coupled with utilization of a variety of organic compounds make the strain highly metabolically flexible. Rubrivivax benzoatilyticus JA2T can fix N2 and also produces H2. Rubrivivax benzoatilyticus JA2T produces polyhydroxyalkanoates and secondary metabolites such as phenolic compounds (8) and indole derivatives (4, 5, 7). Here, we report the draft genome sequence of this bacterium, which may provide insights into the molecular aspects of its metabolic versatility.
Rubrivivax benzoatilyticus JA2T (= ATCC BBA-35T = JCM13220T = MTTC7087T) was grown photoheterotrophically on mineral medium (1) with malate (22 mM) and ammonium chloride (7 mM) as carbon and nitrogen sources, respectively. DNA was isolated with the QIAamp minikit (Qiagen), and the authenticity of the genome was confirmed by 16S rRNA gene sequencing. The genome of Rubrivivax benzoatilyticus JA2T was sequenced by using the Roche 454 GS (FLX titanium) pyrosequencing platform. Sequencing resulted in a total of 262,346 high-quality reads with approximately 24× coverage of the entire genome. All of the reads were assembled by using a Newbler assembler (Roche Life Sciences), which generated 165 contigs. Functional annotation was carried out by using the BLAST tool (NCBI), identification of tRNA genes was carried out by using tRNAscan-SE (3), and identification of rRNA genes was carried out by using RNammer (2). GC content was estimated from the genome sequence.
The Rubrivivax benzoatilyticus JA2T draft genome consists of a single circular chromosome of 4,130,132 bp with an average GC content of 72.77%. A total of 3,762 open reading frames (ORFs) were found in the genome where 3,210 (85.32%) are functionally annotated, 382 (10.15%) are hypothetical, and 170 (4.51%) are unknown. The numbers of genes transcribed were 1,926 from the positive strand and 1,836 from the negative strand. The coding density of the genome is 87.5%, with an average gene length of 961 bp, and the average intergenic length is 136 bp. The Rubrivivax benzoatilyticus JA2T genome contains a single 16S-23S-5S operon, 46 tRNA genes, and 25 aminoacyl-tRNA synthetase genes for all 20 amino acids. The genome consisted of 56 predicted ABC transporters, 17 putative transposases, and 29 methyl-accepting chemosensory transducer genes. The Rubrivivax benzoatilyticus JA2T genome has a complete set of genes for bacterial chlorophyll, carotenoid, quinone, and vitamin biosynthesis. Light-harvesting complex and reaction center-encoding genes along with Calvin-Benson cycle-dependent autotrophic CO2 fixation genes were also located in the genome. Nitrogenase regulatory and nitrogen molybdenum-iron protein- and nitrogenase iron protein-encoding genes were predicted. Many multidrug-resistant transporter, organic solvent resistance, and aromatic compound metabolism genes were also revealed in the genome. A detailed analysis of the R. benzoatilyticus JA2T genome and comparative genome analysis with other photosynthetic members will provide insights into the unique biochemical and molecular characteristics of this strain.
Nucleotide sequence accession number.
The complete genome sequence was deposited in GenBank under accession number AEWG00000000.
Acknowledgments
The Department of Biotechnology, the Department of Science and Technology, the Ministry of Earth Sciences, the Council for Scientific and Industrial Research, and the Government of India are acknowledged for financial support. M.M. thanks the CSIR (India) for the Senior Research Fellowship.
We acknowledge the help of Xcelris Labs for genome sequence deposition. We thank Niyaz Ahmed, Department of Biotechnology, University of Hyderabad, for his critical suggestions.
Footnotes
Published ahead of print on 8 April 2011.
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