Insights into 6S RNA in lactic acid bacteria (LAB)

CATALDO, PABLO GABRIEL; KLEMM, PAUL; THÜRING, MARIETTA; SAAVEDRA, LUCILA; HEBERT, ELVIRA MARIA; HARTMANN, ROLAND K.; LECHNER, MARCUS

BMC Genomic Data

Springer Nature

Año: 2021 vol. 22

AbstractBackground: 6S RNA is a regulator of cellular transcription that tunes the metabolism of cells. This small non-codingRNA is found in nearly all bacteria and among the most abundant transcripts. Lactic acid bacteria (LAB) constitute agroup of microorganisms with strong biotechnological relevance, often exploited as starter cultures for industrialproducts through fermentation. Some strains are used as probiotics while others represent potential pathogens.Occasional reports of 6S RNA within this group already indicate striking metabolic implications. A conceivable idea isthat LAB with 6S RNA defects may metabolize nutrients faster, as inferred from studies of Echerichia coli. This mayaccelerate fermentation processes with the potential to reduce production costs. Similarly, elevated levels ofsecondary metabolites might be produced. Evidence for this possibility comes from preliminary findings regardingthe production of surfactin in Bacillus subtilis, which has functions similar to those of bacteriocins. The prerequisite forits potential biotechnological utility is a general characterization of 6S RNA in LAB.Results: We provide a genomic annotation of 6S RNA throughout the Lactobacillales order. It laid the foundation fora bioinformatic characterization of common 6S RNA features. This covers secondary structures, synteny, phylogeny,and product RNA start sites. The canonical 6S RNA structure is formed by a central bulge flanked by helical arms and atemplate site for product RNA synthesis. 6S RNA exhibits strong syntenic conservation. It is usually flanked by thereplication-associated recombination protein A and the universal stress protein A. A catabolite responsive elementwas identified in over a third of all 6S RNA genes. It is known to modulate gene expression based on the availablecarbon sources. The presence of antisense transcripts could not be verified as a general trait of LAB 6S RNAs.Conclusions: Despite a large number of species and the heterogeneity of LAB, the stress regulator 6S RNA iswell-conserved both from a structural as well as a syntenic perspective. This is the first approach to describe 6S RNAsand short 6S RNA-derived transcripts beyond a single species, spanning a large taxonomic group covering multiplefamilies. It yields universal insights into this regulator and complements the findings derived from other bacterialmodel organisms.Keywords: 6S RNA, SsrS, ncRNA, CcpA, cre site, Lactic acid bacteria, LAB