Abstract
Microbial transformations of arsenic influence its mobility and toxicity. We report the draft genome sequence of the arsenite-oxidizing strain Agrobacterium tumefaciens 5A isolated from an As-contaminated soil in the Madison River Valley, MT. A large number of metal (or metalloid) resistance genes, especially contributing to arsenite oxidation, were identified.
GENOME ANNOUNCEMENT
The alphaproteobacterium Agrobacterium tumefaciens is best known as a soilborne phytopathogen and is widely used in plant transgenics (3). A. tumefaciens is also reported to be metal resistant because it is commonly exposed to high levels of metal ions for agricultural pathogen management (6). We report the draft genome of the arsenite [As(III)]-oxidizing A. tumefaciens strain 5A isolated from an As-enriched Typic Calciaquoll soil collected from an irrigated pasture in the Madison River Valley, MT (9). Complex regulation of arsenite oxidation, including As(III)-sensing, three-component signal transduction, and quorum sensing are involved (7, 8). Prior to this genome report, only a single A. tumefaciens whole-genome sequence (strain C58) had been published (4).
The A. tumefaciens strain 5A genome was sequenced using the 454 GS FLX sequencer (10) and assembled with GS de novo assembler (Newbler), version 2.3. The Rapid Annotation Subsystem Technology (RAST) server (1) was used for functional annotation. The NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) was employed for submission (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html). The draft genome consists of 59 contigs (5,743,748 bp) with an 18-fold genome coverage (58.58% G+C). At least two copies of 5S, one copy of 23S, and three copies of 16S rRNAs and 49 tRNA genes were predicted by RAST. A total of 5,580 protein-coding sequences (CDSs) were annotated, and an additional 1,440 did not match annotated proteins. Based on BLASTp with KEGG Orthology (KO) (http://www.genome.jp/kegg), strain 5A contains 2,390 orthologs (bit score, >60) to A. tumefaciens C58, and 4,524 proteins were assigned to COG families by PGAAP.
The strain 5A genome carries genes involved in As(III) oxidation. Transposon mutagenesis and reverse transcriptase PCR data identified an aio operon (aioX-aioS-aioR-aioA-aioB-cytc2) involved in As(III) oxidation (7). The expression of aioS was reduced by the interruption of aioR, and expression of aioAB was induced by As(III). AioR appears to be autoregulatory and partially controls the expression of the aio operon. Complementation of an aioR::Tn5B22 mutant [As(III) oxidation minus] required the entire aio region, indicating genes in the aio operon are part of a common transcriptional unit (7). Thus far, it appears that there are at least two separate regulatory circuits controlling the expression of the aio operon: (i) a two-component signal transduction system, AioS and AioR, which recently has been shown to include AioX as a putative periplasmic signal receptor (8); and (ii) quorum sensing, which is normally involved in virulence of plants (2, 5), is also involved in regulating As(III) oxidation in A. tumefaciens 5A (7).
Nucleotide sequence accession numbers.
The draft genome sequence has been deposited in GenBank under accession no. AGVZ00000000. The version described in this paper is the first version, AGVZ01000000.
ACKNOWLEDGMENTS
This work was supported by projects from National Science Foundation of China (31125007, 30970003, and 30900215), the 973 Project of China (2010CB126502), and U.S. National Science Foundation grants MCB-0817170 and EAR-0745956 to T.R.M.
Sequencing was performed at the University of Arizona Genetics Core facility.
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