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.
Highlights
Microbes are often exposed to the changing environmental conditions such as low temperature, oxidative stress and heavy metal stress, etc [1]–[6]
Before predicting the sRNAs based on the transcription site it is necessary to identify different sigma factors that are being encoded by respective genomes [29]
Verification of the predicted sRNA regions with target Intergenic Regions (IGR) We have overlapped the predicted sRNA locations with the intergenic region coordinates retrieved from the genome microarray by using the In-house developed awk script
Summary
Microbes are often exposed to the changing environmental conditions such as low temperature, oxidative stress and heavy metal stress, etc [1]–[6] To adapt in such drastic environments, it modulates the physiological and metabolic networks. Stress response may be exhibited through changes in the metabolic activities by producing specific regulatory molecules to activate or suppress the synthesis of particular protein to maintain the physiological conditions. The result of these changes will show as temporary slowdown or stoppage of the cell division, morphological changes, etc. First one is intracellular synthesis, where the nano particles synthesized by the microbes accumulates within the cell after the transportation of metal ions. Silver nano particles are synthesized by ISSN 0973-2063 (online) 0973-8894 (print)
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