Identification and characterization of the nitrate assimilation genes in the isolate of Streptomyces griseorubens JSD-1

Microbial Cell Factories

Research

Yujing Sun¹  Haiwei Feng²  Liang Mao²  Pei Zhou²  Yuee Zhi²  Xing Wei²  Yanqing Luo² 

[1] School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, China;School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, China;Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai Jiao Tong University, 200240, Shanghai, China;Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, 200240, Shanghai, China;

关键词: Streptomyces griseorubens;    Genome sequencing;    Nitrogen metabolism;    Nitrate reductase;    Nitrite reductase;    Glutamine synthetase;    Glutamate synthase;    Glutamate dehydrogenase;   

DOI  :  10.1186/s12934-014-0174-4

 received in 2014-08-22, accepted in 2014-11-24,  发布年份 2014

来源: Springer

【 摘 要 】

BackgroundStreptomyces griseorubens JSD-1 is a novel actinomycete isolated from soil that can utilize nitrate as its sole nitrogen source for growth and these nitrate assimilation genes active in this biotransformation are expected to be crucial. However, little is known about its genomic or genetic background related to nitrogen metabolism in this isolate. Thus, this study concentrates on identification and characterization of genes involved in nitrate assimilation.ResultsTo investigate the molecular mechanism of nitrate metabolism, genome sequencing was performed by Illumina Miseq platform. Then the draft genome of a single linear chromosome with 8,463,223 bp and an average G+C content of 72.42% was obtained, which has been deposited at GenBank under the accession number JJMG00000000. Sequences of nitrate assimilation proteins such as nitrate reductase (EC 1.7.99.4), nitrite reductase (EC 1.7.1.4), glutamine synthetase (EC 6.3.1.2), glutamate synthase (EC 1.4.1.13) and glutamate dehydrogenase (EC 1.4.1.2) were acquired. All proteins were predicted to be intracellular enzymes and their sequences were highly identical to those from their similar species owing to the conservative character. Putative 3D structures of these proteins were also modeled based on the templates with the most identities in the PDB database. Through KEGG annotated map, these proteins proved to be located on the key positions of nitrogen metabolic signaling pathway. Finally, quantitative RT-PCR indicated that expression responses of all genes were up-regulated generally and significantly when stimulated with nitrate.ConclusionIn this manuscript, we describe the genome features of an isolate of S. griseorubens JSD-1 following with identification and characterization of these nitrate assimilation proteins such as nitrate reductase, nitrite reductase, glutamine synthetase, glutamate synthase and glutamate dehydrogenase accounts for the ability to utilize nitrate as its sole nitrogen source for growth through cellular localization, multiple sequence alignment, putative 3D modeling and quantitative RT-PCR. In summary, our findings provide the genomic and genetic background of utilizing nitrate of this strain.

【 授权许可】

Unknown   
© Feng et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.