Draft Genome Sequence of Shewanella sp. Strain HN-41, Which Produces Arsenic-Sulfide Nanotubes

Abstract

The dissimilatory metal reducing bacterium Shewanella sp. strain HN-41 was first reported to produce novel photoactive As-S nanotubes via reduction of As(V) and S₂O₃²⁻ under anaerobic conditions. Here we report the draft genome sequence and annotation of strain HN-41.

GENOME ANNOUNCEMENT

Dissimilatory iron-reducing bacteria appear to play important roles in the cycling of iron and carbon in subsurface environments (9). Shewanella spp. are known for their versatile electron-accepting capacities, which allow them to couple the decomposition of organic matter to the reduction of various terminal electron acceptors, such as As(V), Fe(III), Mn(IV), Se(IV), Te(IV), and U(VI), under anaerobic conditions (4, 5, 7–9, 12). Previously, we reported that strain HN-41 produces an extensive extracellular network of filamentous arsenic-sulfide (As-S) nanotubes via the reduction of As(V) and S₂O₃²⁻ under anaerobic conditions (5, 8). In addition, strain HN-41 could be used to produce diverse structures of nanomaterials through the reduction of metal(loid)s (4, 7, 9, 12).

The draft genome sequence of strain HN-41 was obtained using a whole-genome shotgun strategy (1) with Roche 454 pyrosequencing technology on a GS FLX Titanium system (Roche Diagnostics, Branford, CT), consisting of single-end reads (188,333 reads, totaling ∼64.6 Mb) with approximately 15.6-fold coverage of the entire genome. Additional sequencing was carried out by with an Illumina GA IIx sequencer (San Diego, CA), resulting in paired-end reads (34,036,718 reads, totaling ∼ 2,918 Mb) to reach a depth of 704-fold coverage. All reads were assembled using Newbler Assembler 2.3 (454 Life Sciences, Branford, CT) and CLC Genomics Workbench 4.5.1 (CLC Bio, Denmark). The functional annotation of predicted genes was achieved using the RAST server (http://rast.nmpdr.org/) and in-house comparison with the KEGG (6) and COG (13) databases.

The draft genome includes 4,414,027 bp with a G+C content of 46.5% and is composed of 4,131 putative protein-coding genes or open reading frames (ORFs). Furthermore, the strain HN-41 genome contains 4 rRNA operons and total of 72 tRNA genes.

The genus Shewanella has been shown to contain highly conserved membrane transport respiratory systems to utilize diverse inorganic compounds (2, 11). The genome of strain HN-41 also contained a gene cluster similar to those coding for the multiheme c-type cytochromes of Shewanella oneidensis MR-1 (2, 3). Among these genes, omcA-mtrCAB encode a set of outer membrane-associated proteins that are essential for the reduction of iron, manganese, and other metals in strain MR-1. Strain HN-41 does not contain genes (arrB and arrA) for an arsenate respiratory reduction pathway (arr) to utilize As(V) as the electron acceptor, which is known to be conserved in the arsenate-reducing bacteria Shewanella sp. strain ANA-3 (10) and Shewanella putrefaciens CN-32. However, strain HN-41 contains arsBC, which are among the genes (arsDABC) involved in an arsenate detoxification pathway (ars).

Nucleotide sequence accession numbers.

The draft genome sequence of Shewanella sp. strain HN-41 has been deposited in DDBJ/EMBL/GenBank under the accession number AFOZ00000000. The version described in this paper is the first version, AFOZ01000000.