Identification of non-coding RNAs in the hyper thermophilic bacterium Thermotoga maritima MSB8 through comparative genomics and in-silico analyses
Rahma Alshamrani1, Muhammad Huzaifa Arshad2, Munazza Gull3, Muhammad Zohaib Nawaz4, Sana Malik2*
1Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
2Bioenergy Research Centre, Department of Bioinformatics & Biotechnology, Government College University, Faisalabad, Pakistan
3Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
4State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
Abstract
Thermotoga maritima is a hyperthermophile with the potential to produce thermostable commercial enzymes which can be used for saccharification of plant biomass for subsequent fermentation to bioproducts. The molecular mechanism involved in the hyper thermostability in this bacterium is still not well-understood. It is known that small non-coding RNAs (ncRNAs) regulate and modulate the gene expression of various biological processes at transcriptional and post-transcriptional levels, hence coordinate the adaptation processes in response to environmental stimuli in both prokaryotes and eukaryotes. To understand the role of small ncRNAs in the hyper thermostability of T. maritima, an in silico-based approach was employed involving the identification of the ncRNAs in this bacterium on a genome-wide scale. A novel pipeline was constructed which involved a combination of various bioinformatics algorithms. In total, 20804 orthologous groups were predicted on the genome of T. maritima and 20 other bacteria (reference genomes) by the OrthoMCL tool. By using the “Perl” and “Bash” languages 258 orthologous IGR datasets were created. Among these datasets, small ncRNAs were identified by employing RNAz and RNA Infernal tools. Total 28 ncRNA candidates were predicted by the RNAz tool and 9 candidates were confirmed as novel cis-regulatory small ncRNAs in T. maritima MSB8 by Infernal tool and were named as Tmn (T. maritima ncRNAs). This work provides novel insights into the role of ncRNAs in the stress adaptability of MSB8 and can give a much better understanding of the lifestyle of this bacterium after validation of the data through wet-lab approaches. Having a clear understanding of the thermo-tolerance mechanism, the MSB8 can be exploited in the future for the commercial production of thermostable compounds and biohydrogen.
