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J Bacteriol. Mar 2012; 194(5): 1266.
PMCID: PMC3294771
Genome Sequence of Paenibacillus terrae HPL-003, a Xylanase-Producing Bacterium Isolated from Soil Found in Forest Residue
Sang Heum Shin,a Sewhan Kim,a Jae Young Kim,a Ha Young Song,b Soo Jin Cho,b Dal Rye Kim,b Kee-In Lee,b Hee Kyung Lim,b No-Joong Park,b In Taek Hwang,b and Kap-Seok Yangcorresponding authora
aMacrogen Inc., Gasan-dong, Seoul, Republic of Korea
bBiorefinery Research Center, Green Chemistry Division, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
corresponding authorCorresponding author.
Address correspondence to Kap-Seok Yang, ksyang/at/macrogen.com.
S.H.S. and S.K. contributed equally to this article.
Received December 13, 2011; Accepted December 20, 2011.
Abstract
This article reports on the full genome sequence of Paenibacillus terrae HPL-003, which is a Gram-positive, endospore-forming, xylanase-producing bacterium isolated from soil found in forest residue on Gara Mountain. The strain HPL-003 contains 6,083,395 bp with a G+C content of 46.77 mol%, 2,633 protein-coding genes, and 117 structural RNAs.
Recently, research on the conversion from petrochemical industry to biobased industry has begun to receive attention (1, 3, 7). Degradable xylanase as well as cellulase biomass is being recognized as an important enzyme, as xylanase is an indispensable enzyme in biobased industries (4, 6, 9). Various strains isolated from soil in a variety of locations have been screened to detect bacteria with high xylanase activities. Of all of them, strain HPL-003, isolated from soil found in forest residue on Gara Mountain, is considered the best producer (4a). This strain was identified as Paenibacillus terrae by 16S rRNA gene sequencing and physiological analysis (2), showing the highest 16S rRNA gene sequence identity, 99.4%, to strain AM141T (NCBI accession number AF391124) (10). P. terrae HPL-003 is a Gram-positive, endospore-forming, xylanase-producing bacterium, and whole-genome sequencing was carried out in order to facilitate understanding of the unique properties of P. terrae HPL-003 at the genomic level.
Genomic DNA isolated from an overnight culture of strain P. terrae HPL-003 using a DNeasy blood and tissue kit (Qiagen) was sequenced by 454 GS FLX Titanium pyrosequencing (Roche), following the manufacturer's instructions, with 25× coverage (5). Then, the 529,514 reads generated, with a length of 112,887,195 bp, were assembled using a GS De Novo assembler (version 2.3; Roche), and 506,076 reads (95.57% of the total) were assembled into 11 scaffolds, with a length of 6,039,623 bp.
The order of scaffolds was determined by a similarity search among published references and confirmed by a PCR size check. Gaps both within and between scaffolds can be closed by long-range PCR (using MG Taq-HF DNA polymerase; Macrogen, Seoul, South Korea) and subsequent Sanger sequencing using a ABI 3730 capillary sequencer. The sequences from ABI 3730 sequencing and scaffolds can be completely assembled into one circular genome using Phred/Phrap/Consed software and annotated with the Prokaryote Genomes Automatic Annotation Pipeline (PGAAP) (8).
The complete genome is composed of a circular chromosome of 6,083,395 bp (46.77% GC content), which includes 5,845 coding genes, 89 tRNAs, and 28 rRNAs. A total of 2,633 coding genes (45.1% of the total) have putative functions assigned on the basis of annotation.
A detailed analysis of a full genome comparison of this and other available Paenibacillus strains will be included in a future publication on transcriptome analysis. As the first genome sequence study of P. terrae, the present study will provide the basis for a better understanding of its genetic background, which in turn will aid future studies.
Nucleotide sequence accession number.
The complete genome sequence of Paenibacillus terrae HPL-003 has been deposited in GenBank under accession number CP003107.
ACKNOWLEDGMENT
This study was conducted by a research fund supported by the Agricultural R&D Promotion Center (ARPC) in the Republic of Korea (grant 109192-03-0-HD110).
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