Complete Genome Sequence of the Representative γ-Hexachlorocyclohexane-Degrading Bacterium Sphingobium japonicum UT26

Abstract

Sphingobium japonicum strain UT26 utilizes γ-hexachlorocyclohexane (γ-HCH), a man-made chlorinated pesticide that causes serious environmental problems due to its toxicity and long persistence, as a sole source of carbon and energy. Here, we report the complete genome sequence of UT26, which consists of two chromosomes and three plasmids. The 15 lin genes involved in γ-HCH degradation are dispersed on the two chromosomes and one of the three plasmids.

γ-Hexachlorocylohexane (γ-HCH) is a man-made insecticide that has caused serious environmental problems worldwide (9). Although only several decades have passed since the initial release of γ-HCH into the environment, many γ-HCH-degrading bacterial strains have been isolated (9), suggesting that γ-HCH-degrading ability was acquired by such strains within a short period (14). Sphingobium japonicum UT26 was isolated from upland γ-HCH-contaminated soil in Japan and utilizes γ-HCH as its sole source of carbon and energy (8, 16). In UT26, 15 lin genes are involved in γ-HCH utilization (2, 11, 12). Our clarification of the complete genome sequence of this strain is expected to provide insights into the mechanisms by which bacteria adapt to xenobiotics.

One S. japonicum UT26 colony was designated UT26S (NBRC 101211), and its complete genome sequence was determined by a whole-genome shotgun sequencing strategy using the Sanger method (10, 15, 17). The sequences of ca. 92,400 reads were assembled by the Phrap and CONSED assembly tools (4, 5, 7), and the gaps between contigs were closed by sequencing PCR products which were amplified from genomic DNA using the appropriate primers. The prediction and annotation of open reading frames (ORFs) were performed using Glimmer3 (1), BLASTP, the In Silico Molecular Cloning software suite (In Silico Biology, Inc.), and the GenomeMatcher software (13). Nontranslating genes were predicted using the Rfam, tRNAscan-SE, and ARAGORN programs.

The genome of S. japonicum UT26S consists of two circular chromosomes (Chr), Chr 1 (3,514,822 bp, 64.8% G+C, 3,529 ORFs) and Chr 2 (681,892 bp, 65.9% G+C, 589 ORFs), and three circular plasmids, pCHQ1 (190,974 bp, 63.0% G+C, 224 ORFs), pUT1 (31,776 bp, 63.7% G+C, 44 ORFs), and pUT2 (5,398 bp, 61.0% G+C, 8 ORFs). Chr 1 and Chr 2 have one and two copies, respectively, of rRNA operons. Fifty-one and 4 tRNA genes were located on Chr 1 and Chr 2, respectively. One hundred ninety-six out of 206 bacterial essential genes proposed by Gil et al. (6) were all located on Chr 1, indicating that this is clearly a “main” chromosome. The 15 lin genes for γ-HCH degradation are dispersed on Chr 1, Chr 2, and pCHQ1. Comparison of the UT26S genome with those of five other sphingomonad (TM1) strains revealed that the lin genes (linA, linB, linC, linRED, and linF) specific for the conversion of γ-HCH to β-ketoadipate are located in the DNA regions unique to the UT26S genome. On the other hand, linGHIJ for the β-ketoadipate pathway (12) and linKLMN for the ABC transporter system (3) are located in conserved genomic regions of these sphingomonads. Based on these results, we propose a model in which UT26S was established by recruiting the specific lin genes into an ancestral strain having core functions of sphingomonads.

Nucleotide sequence accession numbers.

The nucleotide sequences of the S. japonicum UT26S chromosomes and plasmids were deposited in the DDBJ/EMBL/GenBank databases under accession numbers AP010803 to AP010806. The annotated genome sequence is also available in the genome database DOGAN (http://www.bio.nite.go.jp/dogan/Top).