Complete Genome Sequence of Clostridium acetobutylicum DSM 1731, a Solvent-Producing Strain with Multireplicon Genome Architecture

Abstract

Clostridium acetobutylicum is an important microorganism for solvent production. We report the complete genome sequence of C. acetobutylicum DSM 1731, a genome with multireplicon architecture. Comparison with the sequenced type strain C. acetobutylicum ATCC 824, the genome of strain DSM1731 harbors a 1.7-kb insertion and a novel 11.1-kb plasmid, which might have been acquired during evolution.

GENOME ANNOUNCEMENT

Acetone butanol ethanol (ABE) fermentation by Clostridium acetobutylicum is one of the oldest industrial fermentations ever known, and it was historically ranked second to ethanol fermentation by yeast in terms of scale of production. C. acetobutylicum is a low-GC-content, Gram-positive, spore-forming obligate anaerobe (2). Recent “-omics” studies, including genomics (4), transcriptomics (12, 13), proteomics (9, 10), and metabolomics (1), have greatly improved our understanding of the physiology of this species. Here we report the complete genome sequence of Clostridium acetobutylicum DSM 1731, which was obtained from the German Collection of Microorganisms and Cell Cultures (DSMZ, Braunschweig, Germany).

The genome was sequenced at the Department of Human Genetics at the University of California, Los Angeles, utilizing Solexa technology according to Illumina's recommendations. A total of 6,043,147 reads, comprising 217,553,292 bases, were obtained, providing 52× coverage. Assembly was performed by AMOScmp (5) and Velvet (14), using comparative genome assembly and de novo assembly. The gaps were filled by sequencing PCR fragments using ABI 3730. The complete genome of C. acetobutylicum DSM 1731 consists of a single circular chromosome of 3,942,462 bp (30.9% GC content) and two plasmids, pSMBa (191,996 bp, 30.9% GC content) and pSMBb (11,123 bp, 25.9% GC content).

Putative protein-coding sequences were identified by GeneMark.hmm (8) and Glimmer (3). tRNAscan-SE (7) was used to predict tRNA genes, and the RNAmmer 1.2 server (6) was employed to detect rRNA genes. BLASTP were applied to perform annotation, followed by manual curation. The chromosome of C. acetobutylicum DSM 1731 contains 3,765 predicated protein-coding genes, 11 rRNA operons, and 73 tRNA genes, while the two plasmids contain 176 (pSMBa) and 9 (pSMBb) protein-coding genes. Functional classification of all proteins was conducted using NCBI clusters of orthologous groups (COG); 3,072, 126, and 2 COG-classified genes are located on the chromosome, pSMBa, and pSMBb, respectively.

Compared with the genome sequences of C. acetobutylicum strains ATCC 824 (11) and EA 2018 (4), the most remarkable feature of strain DSM 1731 is the presence of a 11.1-kb plasmid, pSMBb, which has not been previously reported in this species. In addition, 7 of the 9 predicted genes of pSMBb are hypothetical proteins, suggesting that pSMBb plays an unknown role in clostridial physiology. In addition, 345 single nucleotide variations (SNVs) were identified between the chromosomes of strains DSM 1731 and ATCC 824. The largest insertion is 1,753 bp in the position of 1,278,525 to 1,280,278, located within a hypothetical protein gene. Consistent with strain EA 2018, the megaplasmid in strain DSM 1731 (pSMBa) is 4 bp smaller than that in strain ATCC 824.

Nucleotide sequence accession numbers.

The complete genome sequence of Clostridium acetobutylicum DSM 1731 has been deposited in GenBank under the accession numbers CP002660 to CP002662.