Comparative genomics of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members emphasizing tRNA and non-coding RNA

Abstract

Background Mycobacteria occupy various ecological niches and can be isolated from soil, tap water and ground water. Several cause diseases in humans and animals. To get deeper insight into our understanding of mycobacterial evolution focusing on tRNA and non-coding (nc)RNA, we conducted a comparative genome analysis of Mycobacterium mucogenicum ( Mmuc ) and Mycobacterium neoaurum ( Mneo ) clade members. Results Genome sizes for Mmuc- and Mneo -clade members vary between 5.4 and 6.5 Mbps with the complete Mmuc T (type strain) genome encompassing 6.1 Mbp. The number of tRNA genes range between 46 and 79 (including one pseudo tRNA gene) with 39 tRNA genes common among the members of these clades, while additional tRNA genes were probably acquired through horizontal gene transfer. Selected tRNAs and ncRNAs (RNase P RNA, tmRNA, 4.5S RNA, Ms1 RNA and 6C RNA) are expressed, and the levels for several of these are higher in stationary phase compared to exponentially growing cells. The rare tRNA Ile TAT isoacceptor and two for mycobacteria novel ncRNAs: the Lactobacillales -derived GOLLD RNA and a homolog to the antisense Salmonella typhimurium phage Sar RNA, were shown to be present and expressed in certain Mmuc -clade members. Conclusions Phages, IS elements, horizontally transferred tRNA gene clusters, and phage-derived ncRNAs appears to have influenced the evolution of the Mmuc - and Mneo -clades. While the number of predicted coding sequences correlates with genome size, the number of tRNA coding genes does not. The majority of the tRNA genes in mycobacteria are transcribed mainly from single genes and the levels of certain ncRNAs, including RNase P RNA (essential for the processing of tRNAs), are higher at stationary phase compared to exponentially growing cells. We provide supporting evidence that Ms1 RNA represents a mycobacterial 6S RNA variant. The evolutionary routes for the ncRNAs RNase P RNA, tmRNA and Ms1 RNA are different from that of the core genes. Electronic supplementary material The online version of this article (10.1186/s12862-019-1447-7) contains supplementary material, which is available to authorized users.

Insight into the biology of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members

“…S1; Pettersson et al . unpublished) 7,11 . We first discuss the overall functional classification of common and unique genes in Mmuc - and Mneo -members focusing on the type strains Mmuc T , Mpho T , and Maub T belonging to the Mmuc -clade, and Mneo T and Mcos T members of the Mneo -clade (see Methods).…”

“…Following this, our analysis focuses on virulence and regulatory genes with a specific emphasis on mammalian cell entry factors ( mce ), type VII secretion (ESX systems) factors, transcription sigma/anti-sigma factors and serine threonine protein kinases (STPK). Finally, we discuss transcription of selected genes in Mmuc T (for which the complete genome is available 7 ) under different in vitro growth phases focusing on virulence genes. In this context, we compare the transcription patterns in Mmuc T and in the SGM pathogen M. marinum CCUG 20998 (a derivative carrying the gene coding for the red fluorescent protein, rfp , and referred to as Mmar rfp while Mmar T lacks rfp ) 18 .…”

“…So far, this is the highest number of σ-factor genes predicted in any mycobacteria. Compared to the other mycobacteria, its genome is larger (≈7.5 Mbp) and it does not belong to either the Mmuc - or the Mneo -clade 7 .…”

“…In addition to Mmuc , the Mmuc -clade includes Mycobacterium phocaicum ( Mpho ), Mycobacterium aubagnense ( Maub ) and Mycobacterium llatzerense ( Mlla ) while Mneo and Mcos belong to the Mneo -clade 7 . These rapid growing NTM are associated with various infections and they show high tolerance against the first-line anti-tuberculosis drugs isoniazid, rifampin and pyrazinamide 3,5,7–12 (and Refs therein) and can also show unusual patterns of antibiotic susceptibility 13 . Together this emphasizes the importance of this group of NTMs and provided an incentive for a comparative genomic analysis focusing on virulence and selected regulatory genes.…”

“…Moreover, information about transcription of genes in NTM, other than Msmeg are limited (but see the recent Mneo transcriptome and proteome study 14 ). Hence, we decided to focus on Mmuc T , for which the complete genome is available 7 , and study mRNA levels at different in vitro growth conditions of selected genes suggested to be involved in gene expression and virulence.…”