Beyond the Limits: tRNA Array Units in Mycobacterium Genomes

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.

Exploring tRNA gene cluster in archaea

“…Similarly to what was found in bacteria (Talla et al 2013;Morgado and Vicente, 2018), archaea tRNA gene clusters favor tRNA isotype redundancy, just increasing the number of tRNA gene copies. Another common trait between archaea and bacteria is the presence of protein coding genes within some tRNA gene clusters.…”

“…Indeed, there are evidence showing the association of the tRNA gene clusters with mobile genetic elements. In several bacteria species there are plasmids carrying tRNA gene clusters (Talla et al 2013;Morgado and Vicente, 2018), and in archaea we have evidences that some contigs harboring tRNA gene clusters are associated with homologous sequences of archaea plasmids (this work). Interestingly, one of these contigs presented a relaxase gene, which is rare in archaeal plasmids (Smillie et al, 2010;Guglielmini et al, 2013), but a common trait of conjugative bacterial plasmids.…”

“…The tRNA gene prediction of the data set was performed by tRNAscan-SE 2.0 (Lowe &Chan, 2016). Here we surveyed tRNA gene clusters with a minimum of 10 tRNA genes and used the approach described in a previous study (Morgado and Vicente, 2018) to identify them. tRNA genes were considered clustered if presented a tRNA gene density ≥ 2 tRNA/kb (Bermudez-Santana et al, 2010).…”

“…In order to identify the presence of tRNA gene clusters in archaea genomes we used the methodology described in a previous study (Morgado and Vicente, 2018). The analysis identified tRNA gene clusters in 29/2481 archaea genomes from GenBank (Table 1).…”

“…Besides mitogenomes, tRNA gene clusters have been shown to be abundant in Eukarya (Tawari et al, 2008;Bermudez-Santana et al, 2010). In prokaryotes, tRNA gene clusters were characterized in some bacteria, being prevalent in Firmicutes phylum and Mycobacterium genus (Tran et al, 2016;Morgado and Vicente, 2018), while in archaea, the presence of one tRNA gene cluster was only identified in the Methanobrevibacter M1 strain genome (Tran et al, 2016). Considering the common features among the three domains of life we hypothesized the prevalence of tRNA gene cluster also in archaea.…”