AUTHOR=Nawaz Muhammad Z. , Jian Huahua , He Ying , Xiong Lei , Xiao Xiang , Wang Fengping 

TITLE=Genome-Wide Detection of Small Regulatory RNAs in Deep-Sea Bacterium Shewanella piezotolerans WP3

JOURNAL=Frontiers in Microbiology

VOLUME=8

YEAR=2017

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2017.01093

DOI=10.3389/fmicb.2017.01093

ISSN=1664-302X

ABSTRACT=<p><italic>Shewanella</italic> are one of the most abundant Proteobacteria in the deep-sea and are renowned for their versatile electron accepting capacities. The molecular mechanisms involved in their adaptation to diverse and extreme environments are not well understood. Small non-coding RNAs (sRNAs) are known for modulating the gene expression at transcriptional and posttranscriptional levels, subsequently playing a key role in microbial adaptation. To understand the potential roles of sRNAs in the adaptation of <italic>Shewanella</italic> toward deep-sea environments, here an <italic>in silico</italic> approach was utilized to detect the sRNAs in the genome of <italic>Shewanella piezotolerans</italic> WP3, a piezotolerant and psychrotolerant deep-sea iron reducing bacterium. After scanning 3673 sets of 5′ and 3′ UTRs of orthologous genes, 209 sRNA candidates were identified with high confidence in <italic>S. piezotolerans</italic> WP3. About 92% (193 out of 209) of these putative sRNAs belong to the class <italic>trans</italic>-encoded RNAs, suggesting that <italic>trans</italic>-regulatory RNAs are the dominant class of sRNAs in <italic>S. piezotolerans</italic> WP3. The remaining 16 <italic>cis</italic>-regulatory RNAs were validated through quantitative polymerase chain reaction. Five <italic>cis</italic>-sRNAs were further shown to act as cold regulated sRNAs. Our study provided additional evidence at the transcriptional level to decipher the microbial adaptation mechanisms to extreme environmental conditions.</p>