Abstract
The facultatively sulfur-oxidizing chemolithoautotrophic alphaproteobacterium Pseudaminobacter salicylatoxidans KCT001 (MTCC 7265) belongs to the family Phyllobacteriaceae of the order Rhizobiales. Analysis of its genome offers valuable insight into the adaptive specializations and evolution of free-living soil bacteria that are phylogenetically closely related to symbiotic and invasive rhizobacteria.
GENOME ANNOUNCEMENT
Taxonomically diverse bacteria can use sulfur as an inorganic substrate (lithotrophy) by apparently distinct biochemical pathways (5). This mechanistic multiplicity notwithstanding, sox (sulfur oxidation) genes are omnipresent in members of the domain Bacteria (4, 6). However, functional essentiality of the Sox complex is proven only in facultatively lithotrophic alphaproteobacteria (5). The soil-dwelling alphaproteobacterium Pseudaminobacter salicylatoxidans KCT001 (family Phyllobacteriaceae, order Rhizobiales [2]) is a well-studied Sox model (9, 10), but unlike the prototypical Paracoccus pantotrophus (4), it can utilize tetrathionate as a substrate (10) and produces distinct 34S fractionation during thiosulfate oxidation (M. Alam et al., unpublished data). Evidently, there is more to sulfur lithotrophy even within members of the class Alphaproteobacteria than what is explained by the Sox system alone. As such, whole-genome information on strain KCT001 would not only help us understand sulfur lithotrophy better but would also help in elucidating adaptations and evolution of free-living soil bacteria vis-à-vis their symbiotic and invasive relatives.
Genome sequencing was performed on the Ion PGM sequencer (12) using a 316 chip. MIRA 3.4.0 was used to assemble 1,640,570 reads (mean length of 226 nucleotides) into 53 contigs at 66× overall coverage. The genome was annotated by compiling results obtained from the RAST server (1) with those derived from manual analyses. In the estimated 4,612,407-bp genome of P. salicylatoxidans KCT001, 4,553 potential coding sequences (CDSs) could be identified, out of which ∼800 were hypothetical genes. The G+C content of the genome was 62.8%. One copy each of the 16S, 23S, and 5S rRNA genes were identified together with 48 tRNA genes. Though the rRNA operon was distributed over five contigs, careful scrutiny revealed 200- to 250-nucleotide overlaps among them (viz., PROY_52, PROY_44, reverse complementary [RC] of PROY_45, RC of PROY_50 and PROY_46, in that order), thereby suggesting their merger into one. Again, the 125,589-bp contig PROY_16 could be part of a large plasmid, since it harbored a repABC operon alongside a parB gene, four integrases/recombinases, and 11 transposon/IS-related genes. Notably, the putative chromosome replicating and partitioning genes were found located elsewhere.
Corroborating the phylogenetic proximity of the KCT001 strain with the nodule-forming and nitrogen-fixing mesorhizobia, its genome revealed at least one homolog each of nodB (involved in nodulation signal synthesis) (7) and of nodF and nodE (which define the host range of rhizobia) (3). Additionally, several exo genes, attributed to succinoglycan biosynthesis for infection thread formation (8, 11), plus one ntrYX-ntrBC global nitrogen regulatory system were also identified.
Neither a pathogenicity island nor a gene coding for a toxin or superantigen or for a protein involved in quorum sensing, biofilm formation, or adhesion was detected. The genome, however, encompassed 14 constituents of the mycobacterial virulence operon, six genes coding for colicin V and bacteriocin, 53 flagellar motility and chemotaxis genes, 56 genes for resistance to antibiotics and toxic compounds, and 12 genes encoding components of a type II protein secretion system.
Salient genomic features reflecting KCT001's adaptation to tropical soil include the following: tetrathionate respiration and use of anaerobic respiratory reductases; oxidation of carbon monoxide and sulfur, dehydrogenation of succinate, formate, etc.; nitrate and nitrite ammonification and ammonia assimilation; methanogenesis; CO2 fixation and photorespiration; di- and oligosaccharide biosynthesis; glycerate metabolism; lactate utilization; butanol biosynthesis; glycerol and glycerol-3-phosphate utilization; use of acetone as a carbon and energy source; and monosaccharide metabolism.
Nucleotide sequence accession numbers.
This Whole Genome Shotgun project has been deposited at EMBL/DDBJ/GenBank under the accession number CAIU00000000. The version described in this paper is the first version, CAIU01000000.
ACKNOWLEDGMENTS
This work was financed by the Council of Scientific and Industrial Research (CSIR), Government of India, through a grant-in-aid research scheme. M.A. and P.P. were endowed with a fellowship by the CSIR, Government of India. C.R. received a fellowship from the UGC, Government of India.
We were inspired by the visionary thinking of Sujoy Kumar Das Gupta.
REFERENCES
- 1. Aziz RK, et al. 2008. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75 doi:10.1186/1471-2164-9-75 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2. Deb C, Stackebrandt E, Pradella S, Saha A, Roy P. 2004. Phylogenetically diverse new sulfur chemolithotrophs of alpha-proteobacteria isolated from Indian soils. Curr. Microbiol. 48:452–458 [DOI] [PubMed] [Google Scholar]
- 3. Demont N, Debelle F, Aurelle H, Denarie J, Prome JC. 1993. Role of the Rhizobium meliloti nodF and nodE genes in the biosynthesis of lipo-oligosaccharidic nodulation factors. J. Biol. Chem. 268:20134–20142 [PubMed] [Google Scholar]
- 4. Friedrich CG, Rother D, Bardischewsky F, Quentmeier A, Fischer J. 2001. Oxidation of reduced inorganic sulfur compounds by bacteria: emergence of a common mechanism? Appl. Environ. Microbiol. 67:2873–2882 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5. Ghosh W, Dam B. 2009. Biochemistry and molecular biology of lithotrophic sulfur-oxidation by taxonomically and ecologically diverse bacteria and archaea. FEMS Microbiol. Rev. 33:999–1043 [DOI] [PubMed] [Google Scholar]
- 6. Ghosh W, Mallick S, DasGupta SK. 2009. Origin of the Sox multienzyme complex system in ancient thermophilic bacteria and coevolution of its constituent proteins. Res. Microbiol. 160:409–420 [DOI] [PubMed] [Google Scholar]
- 7. John M, Rohrig H, Schmidt J, Wieneke U, Schell J. 1993. Rhizobium NodB protein involved in nodulation signal synthesis is a chitooligosaccharide deacetylase. Proc. Natl. Acad. Sci. U. S. A. 90:625–629 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. Jones KM, Kobayashi H, Davies BW, Taga ME, Walker GC. 2007. How rhizobial symbionts invade plants: the Sinorhizobium-Medicago model. Nat. Rev. Microbiol. 5:619–633 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9. Lahiri C, Mandal S, Ghosh W, Dam B, Roy P. 2006. A novel gene cluster soxSRT is essential for the chemolithotrophic oxidation of thiosulfate and tetrathionate by Pseudaminobacter salicylatoxidans KCT001. Curr. Microbiol. 52:267–273 [DOI] [PubMed] [Google Scholar]
- 10. Mukhopadhyaya PN, Deb C, Lahiri C, Roy P. 2000. A soxA gene, encoding a diheme cytochrome c, and a sox locus, essential for sulfur oxidation in a new sulfur lithotrophic bacterium. J. Bacteriol. 182:4278–4287 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11. Reuber TL, Walker GC. 1993. Biosynthesis of succinoglycan, a symbiotically important exopolysaccharide of Rhizobium meliloti. Cell 74:269–280 [DOI] [PubMed] [Google Scholar]
- 12. Rothberg JM, et al. 2011. An integrated semiconductor device enabling non-optical genome sequencing. Nature 475:348–352 [DOI] [PubMed] [Google Scholar]