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. 2013 Feb 21;1(1):e00232-12. doi: 10.1128/genomeA.00232-12

Draft Genome Sequence of Type Strain Clostridium pasteurianum DSM 525 (ATCC 6013), a Promising Producer of Chemicals and Fuels

Sugima Rappert 1, Lifu Song 1, Wael Sabra 1, Wei Wang 1, An-Ping Zeng 1,✉
PMCID: PMC3587944  PMID: 23469350

Abstract

Clostridium pasteurianum, an anaerobic bacterium able to utilize atmospheric free nitrogen for biosynthesis, has recently been proven to be a promising producer of chemicals and fuels, such as 1,3-propanediol and n-butanol. Here, we report the high-quality draft genome sequence of DSM 525, a type strain of C. pasteurianum.

GENOME ANNOUNCEMENT

Clostridium pasteurianum is an anaerobic bacterium that can utilize free nitrogen from the atmosphere for biosynthesis. The nitrogen-fixing mechanism of C. pasteurianum has been widely investigated since the 1950s (1–9). The production of n-butanol (10–15) and 1,3-propanediol (11, 13, 16–18) using strains of C. pasteurianum has been studied mainly in recent years, showing promising potential applications for C. pasteurianum in industrial biotechnology.

Here, we present the first draft genome sequence of the C. pasteurianum type strain DSM 525, obtained using the high-throughput Illumina sequencing technology, which was performed by the Beijing Genomics Institute (BGI) in Shenzhen, China, with a paired-end library. The sequence reads were assembled with Short Oligonucleotide Analysis Package 2 (SOAP2) (19) with a k-mer setting of 63, which was determined by the optimal assembly result. The assembled genome sequence was annotated using the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html). Open reading frames (ORFs) were predicted with Glimmer (20), GeneMark (21), and Prodigal (22); tRNAs were predicted using tRNAscan-SE (23); and ribosomal RNAs were predicted by sequence similarity search using BLAST against an RNA sequence database and/or using Infernal and Rfam models. The G+C content was calculated using the genome sequence. Prophage analysis was performed by a BLAST search against the prophage protein database derived from the prediction results of the Prophinder software and A Classification of Mobile Genetic Elements (ACLAME) database (http://aclame.ulb.ac.be/Tools/Prophinder/).

The final genome sequence of the strain DSM 525 comprises 4,285,687 bases, which are assembled into 37 contigs. It has a G+C content of 29.75%. In total, 3,964 genes were predicted using the PGAAP, including 3,887 protein-coding sequences (CDSs), 74 tRNAs, and 3 rRNA genes. According to the annotation, C. pasteurianum is predicted to possess a complete glycolysis pathway, while the tricarboxylic acid cycle and the pentose phosphate pathways are incomplete. Of special importance is the ability of this bacterium to produce n-butanol and 1,3-propanediol as major byproducts of glycerol in a minimal medium with low concentration of yeast extract (1 g/liter). Interestingly, unlike the traditional acetone-butanol-ethanol fermentation, acetone is not a byproduct of glycerol fermentation. No prophage elements were detected.

Nucleotide sequence accession numbers.

This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. ANZB00000000. The version described in this paper is the first version, ANZB01000000.

ACKNOWLEDGMENTS

This work was supported by the Seventh Framework Programme of the European Union through the project EUROpean multilevel integrated BIOREFinery design for sustainable biomass processing (EuroBioRef, contract no. 241718) in the area Cooperation Sustainable Biorefinerie FP7-ENERGY.2009.3.3.1.

Footnotes

Citation Rappert S, Song L, Sabra W, Wang W, Zeng A-P. 2013. Draft genome sequence of type strain Clostridium pasteurianum DSM 525 (ATCC 6013), a promising producer of chemicals and fuels. Genome Announc. 1(1):e00232-12. doi:10.1128/genomeA.00232-12.

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