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J Bacteriol. Dec 2012; 194(24): 7001–7002.
PMCID: PMC3510573
Genome Sequence of the Protease-Producing Bacterium Rheinheimera nanhaiensis E407-8T, Isolated from Deep-Sea Sediment of the South China Sea
Xi-Ying Zhang, Yan-Jiao Zhang, Qi-Long Qin, Bin-Bin Xie,corresponding author Xiu-Lan Chen, Bai-Cheng Zhou, and Yu-Zhong Zhang
State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, China
corresponding authorCorresponding author.
Address correspondence to Bin-Bin Xie, xbb/at/sdu.edu.cn.
X.-Y.Z. and Y.-J.Z. contributed equally to this article.
Received September 29, 2012; Accepted October 4, 2012.
Abstract
The protease-producing bacterium E407-8T was isolated from deep-sea sediment of the South China Sea and has been identified recently as representing a new species, Rheinheimera nanhaiensis. The draft genome of R. nanhaiensis E407-8T consists of 3,987,205 bp and contains 3,730 predicated protein-coding genes, including 82 extracellular peptidase genes.
Protease-producing bacteria are considered to be key players for the degradation of organic nitrogen in marine environments (3, 11, 17). They secrete extracellular proteases with particular catalytic properties to effectively hydrolyze complex, high-molecular-weight organic substances (3, 15, 16), releasing smaller molecules available for bacterial utilization in response to their surroundings, which represents the initial step of transformation of organic nitrogen in marine ecosystem (1, 6, 11, 14, 17). A protease-producing marine bacterium, designated strain E407-8T, was isolated (at a water depth of 1,800 m) from deep-sea sediment of the South China Sea and was found to represent a new species: Rheinheimera nanhaiensis sp. nov. (7, 17). It is a Gram-negative, polarly flagellated, rod-shaped bacterium that is able to hydrolyze gelatin, casein, and elastin. We sequenced the genome of R. nanhaiensis E407-8T to provide a better understanding of the ecological roles of protease-producing bacterial strains and the mechanisms of bacterial degradation of organic nitrogen in deep-sea sediments.
The genome of strain E407-8T was sequenced using Illumina Solexa technology (2). A 500-bp paired-end library was constructed, and a total of 5,666,668 clean reads (totaling 510 Mb) were generated from the library. The reads were further assembled into 55 contigs (>500 bp) using SOAPdenovo version 1.05 (8). The protein-coding open reading frames (ORFs) were predicted using Glimmer version 3.02 (4) and were annotated using the Swiss-Prot, NCBI nr, and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases (9). The tRNA genes were predicted using the tRNAScan-SE search server (13). Signal peptide prediction was performed using SignalP 4.0 (10).
The draft genome of R. nanhaiensis E407-8T consists of 3,987,205 bp with a G+C content of 51.3%. It contains 3,730 protein-coding ORFs and 68 tRNA genes. A total of 82 peptidases with signal peptides were identified from the genome. These predicted extracellular peptidases belong to different families in the MEROPS peptidase database (12), suggesting that the bacterium has the capacity to hydrolyze various peptides or proteins. The R. nanhaiensis E407-8T genome represents the second reported genome of a Rheinheimera strain (5), providing valuable information on the role of strain E407-8T in degradation of deep-sea sedimentary organic nitrogen and the adaption mechanism of the bacterium to the deep-sea sedimentary environment. It also facilitates the functional and structural studies of the proteases produced by the bacterium.
Nucleotide sequence accession numbers.
The sequence from this Whole Genome Shotgun project has been deposited in DDBJ/EMBL/GenBank under accession no. BAFK00000000. The version described in this article is the first version, BAFK01000000.
ACKNOWLEDGMENTS
This work was supported by the National Natural Science Foundation of China (31025001, 31070061, 31170055, 41106161, 41176130, and 41276149), the Hi-Tech Research and Development Program of China (2011AA090703 and 2012AA092103), the Special Fund of China for Marine-Scientific Research in the Public Interest (201005032-6), the Natural Science Foundation of Shandong Province, China (JQ200910, ZR2009DZ002), the Foundation for Young Excellent Scientists in Shandong Province, China (BS2010SW015), and the China Ocean Mineral Resources R & D Association (COMRA) Special Foundation (DY125-15-T-05).
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