Revealing systematic changes in the transcriptome during the transition from exponential growth to stationary phase
Nutrient limitations are critical environmental perturbations in bacterial physiology. Despite its importance, a detailed understanding of how bacterial transcriptomes are adjusted has been limited. By utilizing independent component analysis (ICA) to decompose transcriptome data, this study reveals key regulatory events that enable bacteria to adapt to nutrient limitations. The findings not only highlight common responses, such as the stringent response, but also condition-specific regulatory shifts associated with carbon, nitrogen, and sulfur starvation. The insights gained from this work advance our knowledge of bacterial physiology, gene regulation, and metabolic adaptation.
Authors
- Cameron Lamoureux
- Hyun Gyu Lim (ORCID: https://orcid.org/0000-0002-0469-2388)
- Ye Gao (ORCID: https://orcid.org/0000-0001-8519-1392)
- Bernhard Ø. Palsson (ORCID: https://orcid.org/0000-0003-2357-6785)
- Kevin Rychel (ORCID: https://orcid.org/0000-0002-4769-2804)
- Xiaoying Lou (ORCID: https://orcid.org/0000-0003-4847-5649)
Institutions
- Inha University (KR)
- Novo Nordisk Foundation (DK)
- Second Hospital of Shandong University (CN)
- Joint BioEnergy Institute (US)
Publication Details
- Journal
- mSystems
- Published
- 2024-12-23
- DOI
- https://doi.org/10.1128/msystems.01315-24
- Citations
- 10
- Primary Topic
- RNA and protein synthesis mechanisms
- Type
- article
- Field-Weighted Citation Impact
- 2.34
Funders
- U.S. Department of Energy
- National Research Foundation
- National Research Foundation of Korea
- Ministry of Science and ICT, South Korea
- Office of Science
- Biological and Environmental Research