Abstract
Geobacillus thermoglucosidasius strain W-2 is a thermophilic bacterium isolated from a deep-subsurface oil reservoir in northern China, which is capable of degrading organosulfur compounds. Here, we report the draft genome sequence of G. thermoglucosidasius strain W-2, which may help to elucidate the genetic basis of biodegradation of organosulfur pollutants under heated conditions.
GENOME ANNOUNCEMENT
Geobacillus thermoglucosidasius strain W-2 was isolated from a deep-subsurface oil reservoir in northern China, which can degrade organosulfur compounds. Sulfur presenting in fuels leads to SO2 emission during combustion, which causes not only serious air pollution, but also metal catalysts poisoning. Benzothiophene (BT) and dibenzothiophene (DBT) are the most widely studied heterocyclic sulfur compounds with respect to its susceptibility to microbial desulfurization (1, 2). To date, two major DBT biodesulfurization pathways (“Kodama” and “4S”) have been widely characterized (3–5), and a BT biodesulfurization pathway has been newly identified in a Gordonia terrae strain C-6 (6). In addition, alkanesulfonates are the major alkyl sulfur-containing compounds and the desulfonation mechanism has been investigated (7). However, the previously reported pathways for degrading BT, DBT and alkanesulfonates were all found in mesophilic bacteria. We report the draft genome sequence of strain W-2, which may provide further insights into genetic information of a thermophilic mechanism of biodesulfurization.
The genome sequencing of strain W-2 was carried out using the Illumina HiSeq 2500 platform at the Majorbio Bio-Pharm Technology Co., Ltd. (Shanghai, China), and Illumina paired-end (PE) libraries were constructed. de novo assembly was performed by using SOAPdenovo (version 2.04) and GapCloser (version 1.12). The final genome draft of strain W-2 contains 51 contigs, with a total size of 3,894,555 bp and an average G+C content of 43.34%. The average contig length was 76,664 bp, with the largest contig being 560,848 bp. Gene prediction and annotation were performed as described previously (8). As a result, 3,935 protein-encoding genes, one rRNA operon, and 76 tRNA genes for all 20 amino acids were predicted.
Genes encoding for three putative alkanesulfonate monooxygenases, seven putative sulfonate ABC transporters, and two putative sulfate permeases were identified in the draft genome. They were hypothesized to be responsible for organosulfur compounds degradation (9–11). In addition, we also found some genes that encode nitronate monooxygenases, which catalyze oxidative denitrification of nitroalkanes to carbonyl compounds and nitrites (12). It may be the first time that the two groups of enzymes responsible for biodesulfurization and biodenitrification pathways have been found in thermophilic bacteria. The functions and mechanisms of the two biodegradation pathways in strain W-2 are under investigation. As thermophilic enzymes offer major biotechnological advantages over mesophilic enzymes (13), the draft genome of strain W-2 may provide an excellent platform for further improvement of this organism for bioremediation and other biotechnological applications at elevated temperature.
Accession number(s).
The whole-genome shotgun project of G. thermoglucosidasius strain W-2 has been deposited at DDBJ/EMBL/GenBank under the accession number LXMA00000000. The version described in this paper is the first version, LXMA01000000.
ACKNOWLEDGMENTS
This work was supported by the National Natural Science Foundation of China (grants 31570119, 31370121, and 31070078) and by the Tianjin Municipal Science and Technology Committee (grants 15JCZDJC32400 and 11JCZDJC16100).
Footnotes
Citation Zhu L, Li M, Guo S, Wang W. 2016. Draft genome sequence of a thermophilic desulfurization bacterium, Geobacillus thermoglucosidasius strain W-2. Genome Announc 4(4):e00793-16. doi:10.1128/genomeA.00793-16.
REFERENCES
- 1.McFarland BL, Boron DJ, Deever W, Meyer JA, Johnson AR, Atlas RM. 1998. Biocatalytic sulfur removal from fuels: applicability for producing low sulfur gasoline. Crit Rev Microbiol 24:99–147. doi: 10.1080/10408419891294208. [DOI] [PubMed] [Google Scholar]
- 2.Kurita S, Endo T, Nakamura H, Yagi T, Tamiya N. 1971. Decomposition of some organic sulfur compounds in petroleum by anaerobic bacteria. J Gen Appl Microbiol 17:185–198. doi: 10.2323/jgam.17.185. [DOI] [Google Scholar]
- 3.Denome SA, Olson ES, Young KD. 1993. Identification and cloning of genes involved in specific desulfurization of dibenzothiophene by Rhodococcus sp. strain IGTS8. Appl Environ Microbiol 59:2837–2843. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Denome SA, Oldfield C, Nash LJ, Young KD. 1994. Characterization of the desulfurization genes from Rhodococcus sp. strain IGTS8. J Bacteriol 176:6707–6716. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Kodama K, Umehara K, Shimizu K, Nakatani S, Minoda Y, Yamada K. 1973. Identification of microbial products from dibenzothiophene and its proposed oxidation pathway. Agric Biol Chem 37:45–50. [Google Scholar]
- 6.Wang W, Ma T, Lian K, Zhang Y, Tian H, Ji K, Li G. 2013. Genetic analysis of benzothiophene biodesulfurization pathway of Gordonia terrae strain C-6. PLoS One 8:e84386. doi: 10.1371/journal.pone.0084386. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Van der Ploeg JR, Iwanicka-Nowicka R, Bykowski T, Hryniewicz MM, Leisinger T. 1999. The Escherichia coli ssuEADCB gene cluster is required for the utilization of sulfur from aliphatic sulfonates and is regulated by the transcriptional activator Cbl. J Biol Chem 274:29358–29365. doi: 10.1074/jbc.274.41.29358. [DOI] [PubMed] [Google Scholar]
- 8.Yao N, Ren Y, Wang W. 2013. Genome sequence of a thermophilic Bacillus, Geobacillus thermodenitrificans DSM465. Genome Announc 1(6):e01046-13. doi: 10.1128/genomeA.01046-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Van Hamme JD, Bottos EM, Bilbey NJ, Brewer SE. 2013. Genomic and proteomic characterization of Gordonia sp. NB4-1Y in relation to 6:2 fluorotelomer sulfonate biodegradation. Microbiology 159:1618–1628. doi: 10.1099/mic.0.068932-0. [DOI] [PubMed] [Google Scholar]
- 10.Erwin KN, Nakano S, Zuber P. 2005. Sulfate-dependent repression of genes that function in organosulfur metabolism in Bacillus subtilis requires Spx. J Bacteriol 187:4042–4049. doi: 10.1128/JB.187.12.4042-4049.2005. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Ellis HR. 2011. Mechanism for sulfur acquisition by the alkanesulfonate monooxygenase system. Bioorg Chem 39:178–184. doi: 10.1016/j.bioorg.2011.08.001. [DOI] [PubMed] [Google Scholar]
- 12.Ha JY, Min JY, Lee SK, Kim HS, Kim DJ, Kim KH, Lee HH, Kim HK, Yoon HJ, Suh SW. 2006. Crystal structure of 2-nitropropane dioxygenase complexed with FMN and substrate. Identification of the catalytic base. J Biol Chem 281:18660–18667. doi: 10.1074/jbc.M601658200. [DOI] [PubMed] [Google Scholar]
- 13.Feng L, Wang W, Cheng J, Ren Y, Zhao G, Gao C, Tang Y, Liu X, Han W, Peng X, Liu R, Wang L. 2007. Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir. Proc Natl Acad Sci U S A 104:5602–5607. doi: 10.1073/pnas.0609650104. [DOI] [PMC free article] [PubMed] [Google Scholar]