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Bioinformation. 2019 Jul 31;15(7):474-479. doi: 10.6026/97320630015474. eCollection 2019.

Transcriptome based Identification of silver stress responsive sRNAs from Bacillus cereus ATCC14579.

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1
Department of Biotechnology (DDE), Madurai Kamaraj University, Madurai-625021, Tamil Nadu, India.

Abstract

Microbes modulate their metabolic and physiological mechanisms in response to changing environmental conditions. It is our interest to identify small regulatory RNAs using microarray expression data (GSE26043) obtained from B. cereus ATCC 14579 in AgNO3 stress. By definition, expression of transcripts from the Intergenic Regions (IGR) with >=2 fold under silver stress is predicted as novel small RNAs. Computational analysis of the IGR expression levels extracted from the available microarray data help in the identification of stress responsive sRNAs with rare promoters (Sigma 24, 28, 32, 54 and 70) followed by terminator signals predicted using the sRNAscanner tool. We predicted 1512 sRNA specific regions on both positive and negative strands collectively. Thus, a non-redundant high scoring unique 860 sRNAs with distinct promoter (S24: 83, S28: 86, S32: 31, S54: 57, S70: 223, sRNA_specific_S70: 380) and terminator signals are reported. These unique computationally predicted sRNA regions were verified with the highly expressing IGRs from the microarray data. It should be noted that 14 sRNAs reported in earlier studies were also found in this dataset. This study has reported 71 additional sRNAs from the transcriptome under metal stress response. Hence, we use global transcriptomics data for the identification of novel sRNAs in B. cereus. We described a general model using a procedure for the identification of small regulatory RNAs using microarray expression data with appropriate cross validation modules. It is found that some sRNAs reported in this study were found to have multiple rare promoters. This opens the possibility of sRNA activation under multiple stress condition. These sRNA data reported in this study should be characterized for their mRNA targets and molecular functional networks in future investigations.

KEYWORDS:

Bacillus cereus ATCC 14579; Silver stress; Transcriptome; sRNA

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