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Lacoux C, Fouquier d'Hérouël A, Wessner-Le Bohec F, Innocenti N, Bohn C, Kennedy SP, Rochat T, Bonnin RA, Serror P, Aurell E, Bouloc P, Repoila F. Dynamic insights on transcription initiation and RNA processing during bacterial adaptation. RNA 2020; 26:382-395. [PMID: 31992590 PMCID: PMC7075262 DOI: 10.1261/rna.073288.119] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/20/2020] [Indexed: 05/04/2023]
Abstract
Transcription initiation and RNA processing govern gene expression and enable bacterial adaptation by reshaping the RNA landscape. The aim of this study was to simultaneously observe these two fundamental processes in a transcriptome responding to an environmental signal. A controlled σE system in E. coli was coupled to our previously described tagRNA-seq method to yield process kinetics information. Changes in transcription initiation frequencies (TIF) and RNA processing frequencies (PF) were followed using 5' RNA tags. Changes in TIF showed a binary increased/decreased pattern that alternated between transcriptionally activated and repressed promoters, providing the bacterial population with transcriptional oscillation. PF variation fell into three categories of cleavage activity: (i) constant and independent of RNA levels, (ii) increased once RNA has accumulated, and (iii) positively correlated to changes in TIF. This work provides a comprehensive and dynamic view of major events leading to transcriptomic reshaping during bacterial adaptation. It unveils an interplay between transcription initiation and the activity of specific RNA cleavage sites. This study utilized a well-known genetic system to analyze fundamental processes and can serve as a blueprint for comprehensive studies that exploit the RNA metabolism to decipher and understand bacterial gene expression control.
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Affiliation(s)
- Caroline Lacoux
- Université Paris-Saclay, INRAE, AgroParisTech, MIcalis Institute, 78350, Jouy-en-Josas, France
| | | | | | - Nicolas Innocenti
- Université Paris-Saclay, INRAE, AgroParisTech, MIcalis Institute, 78350, Jouy-en-Josas, France
- Department of Computational Biology, Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden
| | - Chantal Bohn
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Sean P Kennedy
- Department of Computational Biology, USR3756 CNRS, Institut Pasteur, 75 015 Paris, France
| | - Tatiana Rochat
- VIM, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Rémy A Bonnin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Pascale Serror
- Université Paris-Saclay, INRAE, AgroParisTech, MIcalis Institute, 78350, Jouy-en-Josas, France
| | - Erik Aurell
- Department of Computational Biology, Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden
| | - Philippe Bouloc
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Francis Repoila
- Université Paris-Saclay, INRAE, AgroParisTech, MIcalis Institute, 78350, Jouy-en-Josas, France
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