The rare lncRNA GOLLD is widespread and structurally conserved among <i>Mycobacterium</i> tRNA arrays

Noncoding RNA (ncRNA) genes produce transcripts involved in a wide range of functions, including catalytic and regulatory functions. Besides, some transcripts have highly complex structures that may impact their activities. Among the largest bacterial ncRNAs, there is the rare GOLLD RNA, which is associated with tRNA genes and supposed to be chromosome- and phage-encoded in specialized groups of bacteria, including those from <i>Lactobacillales</i> and <i>Actinomycetales</i> orders. The only GOLLD structure was inferred from a variety of sequences, including many marine metagenomes. To explore GOLLD RNA in bacterial genomes, we mined the GOLLD gene in thousands of <i>Mycobacterium</i> and virus genomes using Infernal software. We identified this gene in 350 mycobacteria, including megaplasmids, and 39 bacteriophages, mainly in the genomic context of tRNA arrays. <i>Mycobacterium</i> GOLLD genes presented a high diversity and were distributed in three phylogenetic groups: (i) <i>Mycobacterium</i> exclusive; (ii) <i>Mycobacterium</i> and mycobacteriophages; and (iii) mycobacteriophage exclusive. We also determined the GOLLD secondary structure of each group using R2 R software based on GOLLD alignments generated by Infernal software. All GOLLD groups displayed a 3ʹ half conserved structure, including utter E-loops pseudoknots substructures, also shared by non<i>-Mycobacterium</i> GOLLD while the 5ʹ half motif was different among the groups. Here, we showed that the lncRNA GOLLD is widespread in <i>Mycobacterium</i> within tRNA arrays and corroborated the previously predicted GOLLD secondary structure.