Abstract
tRNA array unit, a genomic region presenting an intriguing high tRNA gene number and density, was supposed to occur only in few bacteria phyla, particularly Firmicutes. Here, we identified and characterized an abundance and diversity of tRNA array units in Mycobacterium associated genomes. These genomes comprised chromosome, bacteriophages and plasmids from mycobacteria. Firstly, we had identified 32 tRNA genes organized in an array unit within a mycobacteria plasmid genome and therefore, we hypothesized the presence of such structures in Mycobacterium genus. However, at the time, bioinformatics tools only predict tRNA genes, not characterizing their arrangement as arrays. In order to test our hypothesis, we developed and applied an in-house Perl script that identified tRNA genes organization as an array unit. This survey included a total of 7,670 complete and drafts genomes of Mycobacterium genus, 4312 mycobacteriophage genomes and 40 mycobacteria plasmids. We showed that tRNA array units are abundant in genomes associated to the Mycobacterium genus, mainly in Mycobacterium abscessus complex species, being spread in chromosome, prophage, and plasmid genomes. Moreover, other non-coding RNA species (tmRNA and structured RNA) were also identified in these regions. Our results revealed that tRNA array units are not restrict, as previously assumed, to few bacteria phyla and genomes being present in one of the most diverse bacteria genus. We also provide a bioinformatics tool that allows further exploration of this issue in huge genomic databases. The presence of tRNA array units in plasmids and bacteriophages, associated with horizontal gene transfer, and in a bacteria genus that explores diverse niches, are indicatives that tRNA array units have impact in the bacteria biology.
Highlights
Transfer RNAs are smalls non-coding RNAs with the main function associated to the translation machinery and, essential for all living organism
Our findings suggest that Transfer RNAs (tRNAs) array units are abundant in genomes associated to the Mycobacterium genus, being spread in chromosome, prophage and plasmid genomes
A total of 7,670 complete and drafts genomes of Mycobacterium genus, 4312 mycobacteriophage genomes and 40 plasmids were surveyed for the presence of tRNA gene
Summary
Transfer RNAs (tRNAs) are smalls non-coding RNAs with the main function associated to the translation machinery and, essential for all living organism. In order to test our hypothesis, we developed a Perl script to identify tRNA array units and applied it in a large-scale complete/draft genome survey associated to the Mycobacterium genus. This strategy allowed accessing a large data set encompassing a broad mycobacteria genomes spectrum (chromosomes, mycobacteriophages, and plasmids). Our findings suggest that tRNA array units are abundant in genomes associated to the Mycobacterium genus, being spread in chromosome, prophage and plasmid genomes These arrays could be characterized in multiple groups according to their tRNA gene isotype organization and besides, RNA species other than tRNA were identified in such structures
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