Abstract
We report the draft genome sequence of Achromobacter arsenitoxydans SY8, the first reported arsenite-oxidizing bacterium belonging to the genus Achromobacter and containing a genomic arsenic island, an intact type III secretion system, and multiple metal(loid) transporters. The genome may be helpful to explore the mechanisms intertwining metal(loid) resistance and pathogenicity.
GENOME ANNOUNCEMENT
Achromobacter bacteria are Gram-negative, strictly aerobic, rod-shaped cells that do not produce pigment on agar and can use xylose and glucose as the sole carbon sources. Some members of the genus Achromobacter are common inhabitants of the human intestinal tract, and these bacteria may become opportunistic pathogens (e.g., causing bacteremia, meningitis, and urinary tract infection) (7, 10). Four Achromobacter members have been sequenced, including one strain isolated from polychlorinated biphenyl-contaminated soil (A. xylosoxidans A8, GenBank accession number CP002287) (16) and three clinical isolates (A. xylosoxidans AXX-A [GenBank accession number AFRQ00000000], A. xylosoxidans C54 [GenBank accession number ACRC00000000], and A. piechaudii ATCC 43553 [GenBank accession number ADMS00000000]).
Achromobacter arsenitoxydans SY8 was isolated from arsenic-contaminated soil of a pig farm (5, 6) and assigned to the Achromobacter genus based on 16S rRNA gene similarity and physiological/biochemical analyses. The MIC for arsenite was 18 mM in CDM medium (5). It could oxidize arsenite to arsenate with efficiencies of up to 721.1 μM h−1 OD600 (optical density at 600 nm)−1 (6).
Whole-genome shotgun sequencing was performed using Roche 454 GS-FLXTM (11). The NCBI Prokaryotic Genomes Automatic Annotation Pipeline (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html) was used for genome annotation. The automatic outputs were modified manually based on Blastp/rps-BLAST and COG analyses through Artemis software (15) and the Cognitor tool, respectively (17). Genome comparative analysis was performed using the SEED Viewer (4) and Local BLAST (3). GC content was analyzed using CLC Sequence Viewer version 5.6.4 (CLCbio).
The draft genome was assembled into 105 contigs with a genome size of 6,156,664 bp and a genome coverage of 24-fold using GS De Novo Assembler (Newbler) version 2.5.3. It had a GC content of 66.0%, 5,655 putative coding sequences (CDS), 57 tRNA genes, and 5 scattered rRNA genes. The genome of A. arsenitoxydans SY8 was most similar to that of A. piechaudii ATCC 43553 (78.9% identity), followed by those of A. xylosoxidans A8 (78.2%), A. xylosoxidans C54 (78.0%), and A. xylosoxidans AXX-A (76.2%), based on ortholog CDS analysis.
Genome analysis indicated that A. arsenitoxydans SY8 possessed a genomic “arsenic island” with 37 genes on contig 00053 (GenBank accession number AGUF01000052), including three arsenic resistance operons (arsR-arsC1-arsD-arsA-arsB, arsR-arsO-arsC2-mfs-arsH1, and arsR-acr3-mfs-arsC3-arsH2) (1, 6, 12), an arsenite oxidation operon (aioX-aioS-aioR-aioA-aioB-aioC-aioD) (6, 8, 9, 12, 13), and an operon encoding proteins putatively involved in phosphate uptake (pstS-pstC-pstB-pstA). Such an extensive arsenic island was absent in the other four sequenced Achromobacter genomes. In addition, many genes encoding putative metal (copper, mercury, chromate, and zinc) transporters were also identified on the genome.
SY8's genome harbored an intact type III secretion system (30 genes) in contig 00052 (GenBank accession number AGUF01000051) and displayed synthetic conservation with amino acid identities of 74.2%, 51.2%, and 50.9% to A. xylosoxidans AXX-A, Bordetella bronchiseptica RB50 (2, 14), and A. xylosoxidans C54, respectively. Such an intact type III secretion system was absent in A. piechaudii ATCC 43553 and A. xylosoxidans A8. Furthermore, strain SY8 contained several virulence factors, implicating cell adhesion and endotoxin, exotoxin, and serum resistance (2, 14), indicating the possibility that it could be an opportunistic pathogen. The draft genome of strain SY8 provides information to explore the metal(loid) resistance mechanisms, as well as pathogenic analysis.
Nucleotide sequence accession numbers.
The draft genome sequence of strain SY8 has been deposited at DDBJ/EMBL/GenBank under accession number AGUF00000000. The version described in this paper is the first version, AGUF01000000.
ACKNOWLEDGMENTS
This work was supported by the National Natural Science Foundation of China (grant 30970075).
Sequencing was performed at the University of Arizona Genetics Core.
REFERENCES
- 1. Achour AR, Bauda P, Billard P. 2007. Diversity of arsenite transporter genes from arsenic-resistant soil bacteria. Res. Microbiol. 158:128–137 [DOI] [PubMed] [Google Scholar]
- 2. Aizawa SI. 2001. Bacterial flagella and type III secretion systems. FEMS Microbiol. Lett. 202:157–164 [DOI] [PubMed] [Google Scholar]
- 3. Altschul SF, et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389–3402 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4. Aziz RK, et al. 2008. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5. Cai L, Liu G, Rensing C, Wang G. 2009. Genes involved in arsenic transformation and resistance associated with different levels of arsenic-contaminated soils. BMC Microbiol. 9:4. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6. Cai L, Rensing C, Li X, Wang G. 2009. Novel gene clusters involved in arsenite oxidation and resistance in two arsenite oxidizers: Achromobacter sp. SY8 and Pseudomonas sp. TS44. Appl. Microbiol. Biotechnol. 83:715–725 [DOI] [PubMed] [Google Scholar]
- 7. Gomez-Cerezo J, et al. 2003. Achromobacter xylosoxidans bacteremia: a 10-year analysis of 54 cases. Eur. J. Clin. Microbiol. Infect. Dis. 22:360–363 [DOI] [PubMed] [Google Scholar]
- 8. Kashyap DR, Botero LM, Franck WL, Hassett DJ, McDermott TR. 2006. Complex regulation of arsenite oxidation in Agrobacterium tumefaciens. J. Bacteriol. 188:1081–1088 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9. Lebrun E, et al. 2003. Arsenite oxidase, an ancient bioenergetic enzyme. Mol. Biol. Evol. 20:686–693 [DOI] [PubMed] [Google Scholar]
- 10. Mandell WF, Garvey GJ, Neu HC. 1987. Achromobacter xylosoxidans bacteremia. Rev. Infect. Dis. 9:1001–1005 [DOI] [PubMed] [Google Scholar]
- 11. Margulies M, et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12. Mukhopadhyay R, Rosen BP, Phung LT, Silver S. 2002. Microbial arsenic: from geocycles to genes and enzymes. FEMS Microbiol. Rev. 26:311–325 [DOI] [PubMed] [Google Scholar]
- 13. Muller D, et al. 2007. A tale of two oxidation states: bacterial colonization of arsenic-rich environments. PLoS Genet. 3:e53. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14. Parkhill J, et al. 2003. Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nat. Genet. 35:32–40 [DOI] [PubMed] [Google Scholar]
- 15. Rutherford K, et al. 2000. Artemis: sequence visualization and annotation. Bioinformatics 16:944–945 [DOI] [PubMed] [Google Scholar]
- 16. Strnad H, et al. 2011. Complete genome sequence of the haloaromatic acid-degrading bacterium Achromobacter xylosoxidans A8. J. Bacteriol. 193:791–792 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 17. Tatusov RL, Galperin MY, Natale DA, Koonin EV. 2000. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28:33–36 [DOI] [PMC free article] [PubMed] [Google Scholar]