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Kinetic Modeling and Meta-Analysis of the Bacillus subtilis SigB Regulon during Spore Germination and Outgrowth

The exponential increase in the number of conducted studies combined with the development of sequencing methods have led to an enormous accumulation of partially processed experimental data in the past two decades. Here, we present an approach using literature-mined data complemented with gene expre...

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Autores principales: Vohradsky, Jiri, Schwarz, Marek, Ramaniuk, Olga, Ruiz-Larrabeiti, Olatz, Vaňková Hausnerová, Viola, Šanderová, Hana, Krásný, Libor
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7824861/
https://www.ncbi.nlm.nih.gov/pubmed/33466511
http://dx.doi.org/10.3390/microorganisms9010112
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author Vohradsky, Jiri
Schwarz, Marek
Ramaniuk, Olga
Ruiz-Larrabeiti, Olatz
Vaňková Hausnerová, Viola
Šanderová, Hana
Krásný, Libor
author_facet Vohradsky, Jiri
Schwarz, Marek
Ramaniuk, Olga
Ruiz-Larrabeiti, Olatz
Vaňková Hausnerová, Viola
Šanderová, Hana
Krásný, Libor
author_sort Vohradsky, Jiri
collection PubMed
description The exponential increase in the number of conducted studies combined with the development of sequencing methods have led to an enormous accumulation of partially processed experimental data in the past two decades. Here, we present an approach using literature-mined data complemented with gene expression kinetic modeling and promoter sequence analysis. This approach allowed us to identify the regulon of Bacillus subtilis sigma factor SigB of RNA polymerase (RNAP) specifically expressed during germination and outgrowth. SigB is critical for the cell’s response to general stress but is also expressed during spore germination and outgrowth, and this specific regulon is not known. This approach allowed us to (i) define a subset of the known SigB regulon controlled by SigB specifically during spore germination and outgrowth, (ii) identify the influence of the promoter sequence binding motif organization on the expression of the SigB-regulated genes, and (iii) suggest additional sigma factors co-controlling other SigB-dependent genes. Experiments then validated promoter sequence characteristics necessary for direct RNAP–SigB binding. In summary, this work documents the potential of computational approaches to unravel new information even for a well-studied system; moreover, the study specifically identifies the subset of the SigB regulon, which is activated during germination and outgrowth.
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spelling pubmed-78248612021-01-24 Kinetic Modeling and Meta-Analysis of the Bacillus subtilis SigB Regulon during Spore Germination and Outgrowth Vohradsky, Jiri Schwarz, Marek Ramaniuk, Olga Ruiz-Larrabeiti, Olatz Vaňková Hausnerová, Viola Šanderová, Hana Krásný, Libor Microorganisms Article The exponential increase in the number of conducted studies combined with the development of sequencing methods have led to an enormous accumulation of partially processed experimental data in the past two decades. Here, we present an approach using literature-mined data complemented with gene expression kinetic modeling and promoter sequence analysis. This approach allowed us to identify the regulon of Bacillus subtilis sigma factor SigB of RNA polymerase (RNAP) specifically expressed during germination and outgrowth. SigB is critical for the cell’s response to general stress but is also expressed during spore germination and outgrowth, and this specific regulon is not known. This approach allowed us to (i) define a subset of the known SigB regulon controlled by SigB specifically during spore germination and outgrowth, (ii) identify the influence of the promoter sequence binding motif organization on the expression of the SigB-regulated genes, and (iii) suggest additional sigma factors co-controlling other SigB-dependent genes. Experiments then validated promoter sequence characteristics necessary for direct RNAP–SigB binding. In summary, this work documents the potential of computational approaches to unravel new information even for a well-studied system; moreover, the study specifically identifies the subset of the SigB regulon, which is activated during germination and outgrowth. MDPI 2021-01-05 /pmc/articles/PMC7824861/ /pubmed/33466511 http://dx.doi.org/10.3390/microorganisms9010112 Text en © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Vohradsky, Jiri
Schwarz, Marek
Ramaniuk, Olga
Ruiz-Larrabeiti, Olatz
Vaňková Hausnerová, Viola
Šanderová, Hana
Krásný, Libor
Kinetic Modeling and Meta-Analysis of the Bacillus subtilis SigB Regulon during Spore Germination and Outgrowth
title Kinetic Modeling and Meta-Analysis of the Bacillus subtilis SigB Regulon during Spore Germination and Outgrowth
title_full Kinetic Modeling and Meta-Analysis of the Bacillus subtilis SigB Regulon during Spore Germination and Outgrowth
title_fullStr Kinetic Modeling and Meta-Analysis of the Bacillus subtilis SigB Regulon during Spore Germination and Outgrowth
title_full_unstemmed Kinetic Modeling and Meta-Analysis of the Bacillus subtilis SigB Regulon during Spore Germination and Outgrowth
title_short Kinetic Modeling and Meta-Analysis of the Bacillus subtilis SigB Regulon during Spore Germination and Outgrowth
title_sort kinetic modeling and meta-analysis of the bacillus subtilis sigb regulon during spore germination and outgrowth
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7824861/
https://www.ncbi.nlm.nih.gov/pubmed/33466511
http://dx.doi.org/10.3390/microorganisms9010112
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