Protease-producing bacteria are considered to be key players for the degradation of organic nitrogen in marine environments (3
). They secrete extracellular proteases with particular catalytic properties to effectively hydrolyze complex, high-molecular-weight organic substances (3
), 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
). 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
). 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
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
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
genome represents the second reported genome of a Rheinheimera
), 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.