title: Identification and characterization of the nitrate assimilation genes in the isolate of Streptomyces griseorubens JSD-1.
abstract: BACKGROUND
  Streptomyces 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.
  
  
  RESULTS
  To 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.
  
  
  CONCLUSIONS
  In 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.
authors.affiliation: School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China. fhwsjtu@163.com.|Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai Jiao Tong University, Shanghai, 200240, China. fhwsjtu@163.com.|Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, China. fhwsjtu@163.com.
authors.forename: Haiwei
authors.initials: H
authors.lastname: Feng
authors.affiliation: School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China. shuaijing008@163.com.
authors.forename: Yujing
authors.initials: Y
authors.lastname: Sun
authors.affiliation: School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China. yueezhi@sjtu.edu.cn.|Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai Jiao Tong University, Shanghai, 200240, China. yueezhi@sjtu.edu.cn.|Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, China. yueezhi@sjtu.edu.cn.
authors.forename: Yuee
authors.initials: Y
authors.lastname: Zhi
authors.affiliation: School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China. 11weixing11@163.com.|Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai Jiao Tong University, Shanghai, 200240, China. 11weixing11@163.com.|Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, China. 11weixing11@163.com.
authors.forename: Xing
authors.initials: X
authors.lastname: Wei
authors.affiliation: School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China. lyq88dream@163.com.|Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai Jiao Tong University, Shanghai, 200240, China. lyq88dream@163.com.|Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, China. lyq88dream@163.com.
authors.forename: Yanqing
authors.initials: Y
authors.lastname: Luo
authors.affiliation: School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China. lightxiaofang@163.com.|Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai Jiao Tong University, Shanghai, 200240, China. lightxiaofang@163.com.|Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, China. lightxiaofang@163.com.
authors.forename: Liang
authors.initials: L
authors.lastname: Mao
authors.affiliation: School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China. peizhousjtu@163.com.|Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai Jiao Tong University, Shanghai, 200240, China. peizhousjtu@163.com.|Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, China. peizhousjtu@163.com.
authors.forename: Pei
authors.initials: P
authors.lastname: Zhou
mesh_terms: D000595:Amino Acid Sequence; D005798:Genes, Bacterial; D008969:Molecular Sequence Data; D009584:Nitrogen; D058458:Nitrogen Cycle / Q000235:genetics*; D013302:Streptomyces / Q000235:genetics*
chemical_list: D009584:Nitrogen