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

• Published in: BMC ecology and evolution Vol. 19; no. 1; p. 124
• Main Authors: Behra, Phani Rama Krishna, Pettersson, B M Fredrik, Das, Sarbashis, Dasgupta, Santanu, Kirsebom, Leif A
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 18.06.2019; BioMed Central; BMC
• Subjects: Amino Acyl-tRNA Synthetases - genetics; Annotations; Antisense RNA; Bacteria; Bacteriophages - genetics; Binding sites; Biological evolution; Comparative mycobacterial genomics; Deoxyribonucleic acid; DNA; Drinking water; Ecological niches; Evolution; Evolution (Biology); Expression of tRNA and non-coding RNA; Gene clusters; Gene expression; Gene sequencing; Gene transfer; Genes; Genetic aspects; Genome Size; Genome, Bacterial; Genomes; Genomics; Groundwater; Health aspects; Homology; Horizontal transfer; Molecular Sequence Annotation; Mycobacteria; Mycobacterial genomes; Mycobacterium; Mycobacterium - classification; Mycobacterium - genetics; Mycobacterium - growth & development; Mycobacterium neoaurum; Niches (Ecology); Non-coding RNA; Non-coding RNA in mycobacteria; Noncoding DNA; Novels; Phages; Phylogenetics; Phylogeny; Plasmids; Plasmids - genetics; Ribonuclease; Ribonuclease P; Ribonuclease P - genetics; Ribonucleic acid; RNA; RNA phages; RNA processing; RNA, Bacterial - genetics; RNA, Transfer - genetics; RNA, Untranslated - chemistry; RNA, Untranslated - genetics; Salmonella; Salmonella typhimurium; Sequence Inversion; Software; Soil water; Stationary phase; TmRNA; Transfer RNA; tRNA; tRNA genes; Tuberculosis; Water; Water utilities; Expression of tRNA and non-coding RNA; Mycobacterial genomes; Non-coding RNA in mycobacteria; Comparative mycobacterial genomics; tRNA genes
• ISSN: 1471-2148; 1471-2148; 2730-7182
• DOI: 10.1186/s12862-019-1447-7

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. Genome sizes for Mmuc- and Mneo-clade members vary between 5.4 and 6.5 Mbps with the complete Mmuc (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 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. 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.