Genome Sequence of the Thermophilic Strain Bacillus coagulans ...

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Sep 9, 2011 - L-lactic acid, 2,3-butanediol, and acetoin. Here we present a 2.8-Mb assembly of its genome. Simple and efficient carbohydrate metabolism ...

JOURNAL OF BACTERIOLOGY, Nov. 2011, p. 6398–6399 0021-9193/11/$12.00 doi:10.1128/JB.06157-11 Copyright © 2011, American Society for Microbiology. All Rights Reserved.

Vol. 193, No. 22

Genome Sequence of the Thermophilic Strain Bacillus coagulans XZL4, an Efficient Pentose-Utilizing Producer of Chemicals Fei Su,† Ke Xu,† Bo Zhao,† Cui Tai, Fei Tao, Hongzhi Tang, and Ping Xu* State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China Received 9 September 2011/Accepted 9 September 2011

Bacillus coagulans XZL4 is an efficient pentose-utilizing producer of important platform compounds, such as acid, 2,3-butanediol, and acetoin. Here we present a 2.8-Mb assembly of its genome. Simple and efficient carbohydrate metabolism systems, especially the transketolase/transaldolase pathway, make it possible to convert pentose sugars to products at high levels.

L-lactic

in the genome, and this information was used to construct the metabolic network by the RAST system. The absence of pyruvate decarboxylase and D-lactate hydrogenase might be responsible for the high-yield production of high-opticalpurity L-lactic acid. Based on carbohydrate metabolism analysis, the key enzymes (xylose/arabinose isomerase, ribulokinase, and ribulose-5-phosphate 4-epimerase) involved in the pentose metabolite were found in the genome (6). The transketolase/transaldolase pathway, instead of phosphoketolase, was predicted in the genome, implying that strain XZL4 could utilize pentose more efficiently. In addition, there is a complete metabolite pathway for 2,3-butanediol and acetoin biosynthesis, suggesting that this strain is a good producer of platform compounds. Finally, we identified a large number of insertion sequences, transposons, and phage-like elements in the draft genome sequence, implying that the genome of B. coagulans XZL4 has hardly been shaped by horizontal gene transfer. Further intraspecies analysis may provide important genetic insights into the functional capability of B. coagulans, especially in carbohydrate metabolism. Nucleotide sequence accession numbers. This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under accession no. AFWM00000000. The version described in this paper is the first version, with accession no. AFWM01000000.

Lignocellulose-derived sugars are considered an economically attractive carbohydrate feedstock for the large-scale fermentation of important platform chemicals such as lactic acid, 2,3-butanediol, and acetoin, which are characterized by interesting properties and a wide range of applications (2, 4, 11). Pentose sugars, xylose, and arabinose are the major components of hemicellulose (10), and few organisms can effectively convert pentose sugars to products at high levels (3). The phosphoketolase pathway used by pentose-utilizing organisms produces 1 mol lactic acid with equimolar acetate. On the other hand, most pentose-utilizing organisms lack thermal tolerance, which limits their fermentation activity at temperatures above 43°C (9). Bacillus coagulans is a Gram-positive, endospore-forming, heat-resistant, facultatively anaerobic bacterium (7). B. coagulans XZL4, isolated by our group, can produce high concentrations of L-lactic acid (130 g/liter) from xylose with a high optical purity of ⬎99% and a high yield of ⬎98% at a temperature of 50°C (data not shown). The results suggest that strain XZL4 is a good pentose-utilizing producer of L-lactic acid. Here we report the draft genome sequence of B. coagulans XZL4, which was obtained using the Illumina Genome Analyzer IIx system at the Shenzhen Huada Genomics Institute with a paired-end library. A total of 5,555,556 filtered reads were generated, to reach a depth of 180-fold coverage, and assembled into 123 scaffolds by using Velvet (13). The genome sequence of strain XZL4 was annotated using the RAST system (1), and functional description was determined using Clusters of Orthologous Genes (12) and KEGG (8). Genes encoding rRNA were identified by RNAmmer (5). The draft genome sequence of B. coagulans XZL4 comprises 2,854,991 bases with a G⫹C content of 47.5%. According to the annotation of the RAST system, there are 3,297 coding sequence (CDS) and 64 tRNAs in the genome, among which 2,185 CDS (66.3%) were assigned putative biological functions. There are 247 subsystems represented

This work was partly supported by the Chinese National Programs for High Technology Research and Development (2011AA02A202 and 2011AA02A207) and the National Natural Science Foundation of China (30821005). REFERENCES 1. Aziz, R., et al. 8 February 2008, posting date. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. 2. Gao, C., C. Ma, and P. Xu. 6 August 2011, posting date. Biotechnological routes based on lactic acid production from biomass. Biotechnol. Adv. [Epub ahead of print.] doi:10.1016/j.biotechadv.2011.07.022. 3. Hofvendahl, K., and B. Hahn-Hagerdal. 2000. Factors affecting the fermentative lactic acid production from renewable resources. Enzyme Microb. Technol. 26:87–107. 4. Ji, X. J., H. Huang, and P. K. Ouyang. 2011. Microbial 2,3-butanediol production: a state-of-the-art review. Biotechnol. Adv. 29:351–364. 5. Lagesen, K., et al. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35:3100. 6. Mota, L. J., P. Tavares, and I. Sa-Nogueira. 1999. Mode of action of AraR, the key regulator of L-arabinose metabolism in Bacillus subtilis. Mol. Microbiol. 33:476–489. 7. Nakamura, L. K., I. Blumenstock, and D. Claus. 1988. Taxonomic study of

* Corresponding author. Mailing address: School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China. Phone: 86 21 34206647. Fax: 86 21 34206723. E-mail: [email protected] † These authors contributed equally to this work. 6398

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