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

BACKGROUND: 6S RNA is a regulator of cellular transcription that tunes the metabolism of cells. This small non-coding RNA is found in nearly all bacteria and among the most abundant transcripts. Lactic acid bacteria (LAB) constitute a group of microorganisms with strong biotechnological relevance, o...

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Autores principales: Cataldo, Pablo Gabriel, Klemm, Paul, Thüring, Marietta, Saavedra, Lucila, Hebert, Elvira Maria, Hartmann, Roland K., Lechner, Marcus
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8414754/
https://www.ncbi.nlm.nih.gov/pubmed/34479493
http://dx.doi.org/10.1186/s12863-021-00983-2
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author Cataldo, Pablo Gabriel
Klemm, Paul
Thüring, Marietta
Saavedra, Lucila
Hebert, Elvira Maria
Hartmann, Roland K.
Lechner, Marcus
author_facet Cataldo, Pablo Gabriel
Klemm, Paul
Thüring, Marietta
Saavedra, Lucila
Hebert, Elvira Maria
Hartmann, Roland K.
Lechner, Marcus
author_sort Cataldo, Pablo Gabriel
collection PubMed
description BACKGROUND: 6S RNA is a regulator of cellular transcription that tunes the metabolism of cells. This small non-coding RNA is found in nearly all bacteria and among the most abundant transcripts. Lactic acid bacteria (LAB) constitute a group of microorganisms with strong biotechnological relevance, often exploited as starter cultures for industrial products 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 is that LAB with 6S RNA defects may metabolize nutrients faster, as inferred from studies of Echerichia coli. This may accelerate fermentation processes with the potential to reduce production costs. Similarly, elevated levels of secondary metabolites might be produced. Evidence for this possibility comes from preliminary findings regarding the production of surfactin in Bacillus subtilis, which has functions similar to those of bacteriocins. The prerequisite for its 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 for a 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 a template site for product RNA synthesis. 6S RNA exhibits strong syntenic conservation. It is usually flanked by the replication-associated recombination protein A and the universal stress protein A. A catabolite responsive element was identified in over a third of all 6S RNA genes. It is known to modulate gene expression based on the available carbon 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 is well-conserved both from a structural as well as a syntenic perspective. This is the first approach to describe 6S RNAs and short 6S RNA-derived transcripts beyond a single species, spanning a large taxonomic group covering multiple families. It yields universal insights into this regulator and complements the findings derived from other bacterial model organisms. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at (10.1186/s12863-021-00983-2).
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spelling pubmed-84147542021-09-09 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 Genom Data Research Article BACKGROUND: 6S RNA is a regulator of cellular transcription that tunes the metabolism of cells. This small non-coding RNA is found in nearly all bacteria and among the most abundant transcripts. Lactic acid bacteria (LAB) constitute a group of microorganisms with strong biotechnological relevance, often exploited as starter cultures for industrial products 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 is that LAB with 6S RNA defects may metabolize nutrients faster, as inferred from studies of Echerichia coli. This may accelerate fermentation processes with the potential to reduce production costs. Similarly, elevated levels of secondary metabolites might be produced. Evidence for this possibility comes from preliminary findings regarding the production of surfactin in Bacillus subtilis, which has functions similar to those of bacteriocins. The prerequisite for its 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 for a 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 a template site for product RNA synthesis. 6S RNA exhibits strong syntenic conservation. It is usually flanked by the replication-associated recombination protein A and the universal stress protein A. A catabolite responsive element was identified in over a third of all 6S RNA genes. It is known to modulate gene expression based on the available carbon 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 is well-conserved both from a structural as well as a syntenic perspective. This is the first approach to describe 6S RNAs and short 6S RNA-derived transcripts beyond a single species, spanning a large taxonomic group covering multiple families. It yields universal insights into this regulator and complements the findings derived from other bacterial model organisms. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at (10.1186/s12863-021-00983-2). BioMed Central 2021-09-03 /pmc/articles/PMC8414754/ /pubmed/34479493 http://dx.doi.org/10.1186/s12863-021-00983-2 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research Article
Cataldo, Pablo Gabriel
Klemm, Paul
Thüring, Marietta
Saavedra, Lucila
Hebert, Elvira Maria
Hartmann, Roland K.
Lechner, Marcus
Insights into 6S RNA in lactic acid bacteria (LAB)
title Insights into 6S RNA in lactic acid bacteria (LAB)
title_full Insights into 6S RNA in lactic acid bacteria (LAB)
title_fullStr Insights into 6S RNA in lactic acid bacteria (LAB)
title_full_unstemmed Insights into 6S RNA in lactic acid bacteria (LAB)
title_short Insights into 6S RNA in lactic acid bacteria (LAB)
title_sort insights into 6s rna in lactic acid bacteria (lab)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8414754/
https://www.ncbi.nlm.nih.gov/pubmed/34479493
http://dx.doi.org/10.1186/s12863-021-00983-2
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