Draft Genome Sequence of Paenibacillus sp. Strain OSY-SE, a Bacterium Producing the Novel Broad-Spectrum Lipopeptide Antibiotic Paenibacterin

Abstract

A strain of Paenibacillus sp., OSY-SE, was isolated from soil and found to produce a novel lipopeptide antibiotic. The antibiotic, paenibacterin, is active against Gram-negative and Gram-positive bacterial pathogens. Paenibacterin is biosynthesized by a nonribosomal peptide synthetase pathway. Here we report the draft genome sequence of Paenibacillus sp. OSY-SE.

GENOME ANNOUNCEMENT

Resistance of pathogens to antibiotics is a rapidly evolving phenomenon with serious public health implications. Methicillin-resistant Staphylococcus aureus (MRSA) exemplifies the emergence of multidrug resistance among Gram-positive bacterial pathogens. Similarly, some Gram-negative pathogens have become resistant to β-lactams, fluoroquinolones, and aminoglycosides, threatening the therapeutic choices for treating these pathogens (2). Antimicrobial lipopeptides may combat antibiotic-resistant pathogens, but some of these compounds have limitations. Polymyxin, for example, has strong activity against Gram-negative bacteria (5, 9), but concerns on nephrotoxicity and neurotoxicity have limited its broad use as a therapeutic agent. Therefore, new and effective antimicrobials are urgently needed to combat these emerging drug-resistant pathogens. Paenibacterin is a newly discovered cyclic lipopeptide produced by Paenibacillus sp. OSY-SE. The lipopeptide comprises 13 amino acids and a C₁₅ fatty acyl moiety (3). Paenibacterin is active against Gram-negative and Gram-positive pathogens, including Escherichia coli O157:H7, Salmonella enterica serovar Typhimurium, Listeria monocytogenes, and methicillin-resistant Staphylococcus aureus. To understand the biosynthesis of paenibacterin, we determined the whole-genome sequence of the producer strain, Paenibacillus sp. OSY-SE.

Genomic DNA of Paenibacillus sp. OSY-SE was isolated using a DNA extraction kit (DNeasy blood and tissue kit; Qiagen, Valencia, CA). RNase-treated genomic DNA in Tris-Cl buffer (pH 8.5) was used for construction of a paired-end library with a TruSeq DNA sample preparation kit (Illumina, San Diego, CA) according to the manufacturer's instruction. The constructed library was sequenced (76-cycle paired-end runs) in a flow cell lane using Illumina Genome Analyzer II. De novo assembly of the short reads with commercial software (CLC Genomics Workbench 4.7.2; CLCBio, Cambridge, MA) yielded 205 contigs (>200 bp each), with a maximum contig size of 359,285 bp. The resulting draft genome of Paenibacillus sp. OSY-SE consists of 6,931,767 bases; the overall GC content of the genome was calculated as 48.66% by the software Artemis (8). Automatic genome annotation was performed using the rapid annotations using subsystems technology (RAST) server (1). Among the 6,475 protein-coding sequences (CDSs), 65.79% have been assigned a putative function by RAST. The chromosome has one rRNA operon and 38 tRNA genes, as predicted by RNAmmer (4) and tRNAscan-SE (6), respectively.

The average nucleotide identities (ANI) between Paenibacillus sp. OSY-SE and 20 genomes of Paenibacillus species that are available in GenBank were determined using the in silico DNA-DNA hybridization method implemented in the software JSpecies (7). The results indicated that Paenibacillus sp. OSY-SE has the closest genetic relatedness with Paenibacillus lactis strain 154 (ANI, 77.21%). The gene cluster responsible for paenibacterin biosynthesis was identified in a 52-kb region encoding three nonribosomal peptide synthetases and two ABC-like transporters.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number ALKF00000000. The version described in this paper is the first version, ALKF01000000.