Identification of sigma factor 54-regulated small non-coding RNAs by employing genome-wide and transcriptome-based methods in rhizobium strains

Autor: Ilamathi Raja, K. Rajendran, Vikram Kumar, Jebasingh Tennyson, Manoharan Kumariah
Rok vydání: 2022
Předmět:
Zdroj: 3 Biotech. 12
ISSN: 2190-5738
2190-572X
DOI: 10.1007/s13205-022-03394-x
Popis: Rhizobium-legume symbiosis is considered as the major contributor of biological nitrogen fixation. In the present study, we have identified sigma factor 54-regulated sRNAs from the genome of five Rhizobium strains and integrated with the free-living and symbiotic specific transcriptome data to identify the novel putative sRNAs that are over expressed during the regulation of nitrogen fixation. A total of 1059 sRNAs were predicted from each genome of the select set of Rhizobium strains and 1,375 sRNAs were predicted from the transcriptome data of Bradyrhizobium japonicum. Target mRNA analysis revealed the functional role of putative novel sRNAs from different free-living and symbiotic strains. Those novel sRNAs were inferred to target several nodulation and nitrogen fixation genes including nodC, nodJ, nodY, nodJ, nodM, nodW, nodZ, nifD, nifN, nifQ, fixK, fixL, Fdx, nolB, and several cytochrome proteins. Further, sRNAs of Bradyrhizobium japonicum which targeted the regulatory genes of nitrogen fixation were experimentally confirmed with semi-quantitative reverse transcription polymerase chain reaction. Predicted target mRNAs were functionally classified based on the COG analysis and GO annotations. Studies on this sigma factor 54-regulated sRNA identification could be a better method to relate the role of sRNAs in nitrogen metabolism during free-living and symbiotic association with legumes.
Databáze: OpenAIRE
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