Abstract
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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12934-014-0174-4) contains supplementary material, which is available to authorized users.
Highlights
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
Identification and characterization of the isolate A novel strain, designated as JSD-1, was isolated on the basal medium owing to its ability to grow efficiently upon the medium with the addition of nitrate as the unique nitrogen source
The same conclusion could be drawn from their 3D structure modelings, both indicating the conservative character from their primary and secondary structures. Since these analyzed proteins were determined to be located on the key positions of nitrogen signaling pathway, nitrate metabolism was inferred and summarized as: nitrate extracellular was transported into cells by membrane transporters
Summary
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. Physically and biologically, soil is a complex and variable environment, of which the indispensable component is inorganic salts. Among these numerous elements, nitrogen is crucial as it supplies essential nutrient for plants and microorganisms. The most important stages of nitrogen recycle in nature, has various functions as follows: (1) as a source of nitrogen by utilization of NO3− (nitrate assimilation); (2) as terminal acceptor of electrons by producing metabolic energy during NO3− utilization (nitrate respiration); (3) maintain oxidation reduction balance by dissipating excessed energy (nitrate dissimilation). Membrane-bounded nitrate reductases (Nar) are mainly involved in anaerobic nitrate respiration and denitrification. Periplasmic dissimilatory reductases (Nap) contribute to redox balancing and aerobic or anaerobic denitrification
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