Research Article: Computational prediction of microRNAs in marine bacteria of the genus Thalassospira

Date Published: March 12, 2019

Publisher: Public Library of Science

Author(s): Thi Hoang Yen Dang, Sonika Tyagi, Glenn D’Cunha, Mrinal Bhave, Russell Crawford, Elena P. Ivanova, Patrick Jon Biggs.

http://doi.org/10.1371/journal.pone.0212996

Abstract

MicroRNAs (miRNAs) are key players in regulation of gene expression at post-transcription level in eukaryotic cells. MiRNAs have been intensively studied in plants, animals and viruses. The investigations of bacterial miRNAs have gained less attention, except for the recent studies on miRNAs derived from Streptococcus mutans ATCC 25175 and Escherichia coli DH10B. In this study, high-throughput sequencing approach was employed to investigate the miRNA population in bacteria of the genus Thalassospira using both the miRDeep2 and CID-miRNA methods. A total of 984 putative miRNAs were identified in 9 species of the genus Thalassospira using both miRDeep and CID-miRNA analyses. Fifty seven conserved putative miRNAs were found in different species of the genus Thalassospira, and up to 6 miRNAs were found to be present at different locations in the T. alkalitolerans JCM 18968T, T. lucentensis QMT2T and T. xianhensis P-4T. None of the putative miRNAs was found to share sequence to the reported miRNAs in E. coli DH10B and S. mutans ATCC 25175. The findings provide a comprehensive list of computationally identified miRNAs in 9 bacterial species of the genus Thalassospira and addressed the existing knowledge gap on the presence of miRNAs in the Thalassospira genomes.

Partial Text

MicroRNA (miRNA) is a class of small, non-coding RNA molecules containing 19–22 nucleotides. Since the discovery of miRNA in Caenorhabditis elegans [1], a large number of predicted miRNA molecules has been reported in animals, plants and viruses as key players in regulation of gene expression networks [2–5]. In bacteria, the small non-coding RNAs (sRNAs) have been demonstrated to have a similar function to eukaryotic miRNA, in modulating the target mRNAs in various ways at a post-transcriptional level [6]. A number of sRNAs have been identified in bacteria, some of which were identified in marine bacteria such as Vibrio spp. and Synechococcus spp. that are functional analogues to plant miRNAs in response to environmental changes [7, 8]. The investigations of bacterial miRNAs, however, have gained little attention, except for the recent studies on miRNAs derived from Streptococcus mutans ATCC 25175 and Escherichia coli DH10B [9, 10].

Over 242 million reads of 18 to 33 nucleotides length were generated from nine bacterial species using high-throughput sequencing technology. Using miRDeep2 and CID-miRNA analyses, a total of 984 putative miRNAs were eventually identified, with typical miRNA length of 19–25 nucleotides. Compared to other species, these detected putative miRNAs were not conserved to those reported in E. coli DH10B and S. mutans ATCC 25175. This study presents the first comprehensive list of computationally identified miRNAs in 9 bacterial species of the genus Thalassospira without experimental verification. The further work, however, is needed to validate these candidates experimentally. In addition, further identification of miRNA targets will provide insights into the fundamental functions of miRNAs in the physiology of these bacteria.

 

Source:

http://doi.org/10.1371/journal.pone.0212996

 

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