Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis
Abstract
Outside In Acquisition and analysis of large data sets promises to move us toward a greater understanding of the mechanisms by which biological systems are dynamically regulated to respond to external cues. Now, two papers explore the responses of a bacterium to changing nutritional conditions (see the Perspective by Chalancon et al. ). Nicolas et al. (p. 1103 ) measured transcriptional regulation for more than 100 different conditions. Greater amounts of antisense RNA were generated than expected and appeared to be produced by alternative RNA polymerase targeting subunits called sigma factors. One transition, from malate to glucose as the primary nutrient, was studied in more detail by Buescher et al. (p. 1099 ) who monitored RNA abundance, promoter activity in live cells, protein abundance, and absolute concentrations of intracellular and extracellular metabolites. In this case, the bacteria responded rapidly and largely without transcriptional changes to life on malate, but only slowly adapted to use glucose, a shift that required changes in nearly half the transcription network. These data offer an initial understanding of why certain regulatory strategies may be favored during evolution of dynamic control systems.
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A previous study observed that opuB expression is strongly enhanced while opuC transcription was seemingly not induced by sustained high salinity.
“It was observed in a previous study that, while opuB expression is strongly enhanced, opuC transcription was seemingly not induced by sustained high salinity (Nicolas et al., 2012).”
From Two MarR-Type Repressors Balance Precursor Uptake and Glycine Betaine Synthesis in Bacillus subtilis to Provide Cytoprotection Against Sustained Osmotic Stress (2020) · cites this paper as Nicolas et al., 2012
A shortcoming of the tiling array data reported by Nicolas et al. (2012) is that only a single salt concentration was used to assess transcriptome changes in continuously osmotically stressed B. subtilis cells.
“However, a shortcoming of the tiling array data reported by Nicolas et al. (2012) is that only a single salt concentration was used to assess changes in the transcriptome of continuously osmotically stressed B. subtilis cells.”
From Two MarR-Type Repressors Balance Precursor Uptake and Glycine Betaine Synthesis in Bacillus subtilis to Provide Cytoprotection Against Sustained Osmotic Stress (2020) · cites this paper as Nicolas et al., 2012
B. subtilis encodes four MpfA paralogs, all with salt-responsive transcriptional regulation.
“Interestingly, B. subtilis encodes four MpfA paralogs (5), all with salt-responsive transcriptional regulation (64).”
From A Central Role for Magnesium Homeostasis during Adaptation to Osmotic Stress (2022) · cites this paper as [64]
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- Authors
- Nicolas, P., Mäder, U., Dervyn, E., Rochat, T., Leduc, A., Pigeonneau, N., Bidnenko, E., Marchadier, E., Hoebeke, M., Aymerich, S., Becher, D., Bisicchia, P., Botella, E., Delumeau, O., Doherty, G., Denham, E. L., Fogg, M. J., Fromion, V., Goelzer, A., Hansen, A., Härtig, E., Harwood, C. R., Homuth, G., Jarmer, H., Jules, M., Klipp, E., Le Chat, L., Lecointe, F., Lewis, P., Liebermeister, W., March, A., Mars, R. A. T., Nannapaneni, P., Noone, D., Pohl, S., Rinn, B., Rügheimer, F., Sappa, P. K., Samson, F., Schaffer, M., Schwikowski, B., Steil, L., Stülke, J., Wiegert, T., Devine, K. M., Wilkinson, A. J., Maarten van Dijl, J., Hecker, M., Völker, U., Bessières, P., & Noirot, P.
- Affiliations
- Institut National de la Recherche Agronomique (FR)
- Universität Greifswald (DE)
- Microbiologie de l’alimentation au service de la santé (FR)
- Trinity College Dublin (IE)
- University of Newcastle Australia (AU)
- University Medical Center Groningen (NL)
- University of York (GB)
- Technische Universität Braunschweig (DE)
- Newcastle University (GB)
- Technical University of Denmark (DK)
- Humboldt-Universität zu Berlin (DE)
- INRA, UMR1319 Micalis, F-78350 Jouy-en-Josas, France.
- ETH Zurich (CH)
- Centre National de la Recherche Scientifique (FR)
- University of Göttingen (DE)
- Zittau/Görlitz University of Applied Sciences (DE)
- Department of Medical Microbiology, University of Groningen and University Medical Center Groningen, 9700 RB Groningen, Netherlands.
- Corresponding author
- Nicolas, Pierre
- Mäder, Ulrike
- Dervyn, Etienne
- Noirot, Philippe
- ORCID
- Mäder, Ulrike
- Dervyn, Etienne
- Rochat, Tatiana
- Leduc, Aurélie
- Bidnenko, Elena
- Marchadier, Elodie
- Hoebeke, Mark
- Aymerich, Stéphane
- Becher, Dörte
- Delumeau, Olivier
- Denham, Emma L.
- Fogg, Mark J.
- Fromion, Vincent
- Goelzer, Anne
- Härtig, Elisabeth
- Harwood, Colin R.
- Homuth, Georg
- Jarmer, Hanne
- Jules, Matthieu
- Klipp, Edda
- Lecointe, François
- Lewis, Peter
- Liebermeister, Wolfram
- Mars, Ruben A. T.
- Nannapaneni, Priyanka
- Noone, David
- Schwikowski, Benno
- Steil, Leif
- Stülke, Jörg
- Wiegert, Thomas
- Devine, Kevin M.
- Wilkinson, Anthony J.
- Völker, Uwe
- Venue
- Science
- Published
- 2012-03-02
- Volume
- 335
- Issue
- 6072
- Pages
- 1103-1106
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2077460182
- Cited by
- 910
- References
- 3
- Citations by year
- 2026: 30 · 2025: 55 · 2024: 55 · 2023: 73 · 2022: 52 · 2021: 66 · 2020: 69 · 2019: 63 · 2018: 55 · 2017: 81 · 2016: 84 · 2015: 73 · 2014: 56 · 2013: 61 · 2012: 37
- FWCI
- 43.43
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (publishedVersion)
- HAL (submittedVersion)
- GRO (submittedVersion)
- Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (submittedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion)
- NOVA (University of Newcastle Australia) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Keywords
- Bacillus subtilis, transcriptional regulation, antisense RNA, sigma factor, promoter activity, metabolite concentrations, gene expression regulation
- MeSH terms
- Adaptation, Physiological, Algorithms, Bacillus subtilis, Binding Sites, Promoter Regions, Genetic, RNA, Bacterial, RNA, Messenger, Sigma Factor, Terminator Regions, Genetic, Transcription, Genetic, Gene Expression Regulation, Bacterial, RNA, Antisense, Regulon, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Gene Regulatory Networks, Transcriptome
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