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Zhao J, Sun X, Mao Z, Zheng Y, Geng Z, Zhang Y, Ma H, Wang Z. Independent component analysis of Corynebacterium glutamicum transcriptomes reveals its transcriptional regulatory network. Microbiol Res 2023; 276:127485. [PMID: 37683565 DOI: 10.1016/j.micres.2023.127485] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023]
Abstract
Gene expression in bacteria is regulated by multiple transcription factors. Clarifying the regulation mechanism of gene expression is necessary to understand bacterial physiological activities. To further understand the structure of the transcriptional regulatory network of Corynebacterium glutamicum, we applied independent component analysis, an unsupervised machine learning algorithm, to the high-quality C. glutamicum gene expression profile which includes 263 samples from 29 independent projects. We obtained 87 robust independent regulatory modules (iModulons). These iModulons explain 76.7% of the variance in the expression profile and constitute the quantitative transcriptional regulatory network of C. glutamicum. By analyzing the constituent genes in iModulons, we identified potential targets for 20 transcription factors. We also captured the changes in iModulon activities under different growth rates and dissolved oxygen concentrations, demonstrating the ability of iModulons to comprehensively interpret transcriptional responses to environmental changes. In summary, this study provides a genome-scale quantitative transcriptional regulatory network for C. glutamicum and informs future research on complex changes in the transcriptome.
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Affiliation(s)
- Jianxiao Zhao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Xi Sun
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Zhitao Mao
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Yangyang Zheng
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Zhouxiao Geng
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yuhan Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Hongwu Ma
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China.
| | - Zhiwen Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
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4
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Kranz A, Polen T, Kotulla C, Arndt A, Bosco G, Bussmann M, Chattopadhyay A, Cramer A, Davoudi CF, Degner U, Diesveld R, Freiherr von Boeselager R, Gärtner K, Gätgens C, Georgi T, Geraths C, Haas S, Heyer A, Hünnefeld M, Ishige T, Kabus A, Kallscheuer N, Kever L, Klaffl S, Kleine B, Kočan M, Koch-Koerfges A, Kraxner KJ, Krug A, Krüger A, Küberl A, Labib M, Lange C, Mack C, Maeda T, Mahr R, Majda S, Michel A, Morosov X, Müller O, Nanda AM, Nickel J, Pahlke J, Pfeifer E, Platzen L, Ramp P, Rittmann D, Schaffer S, Scheele S, Spelberg S, Schulte J, Schweitzer JE, Sindelar G, Sorger-Herrmann U, Spelberg M, Stansen C, Tharmasothirajan A, Ooyen JV, van Summeren-Wesenhagen P, Vogt M, Witthoff S, Zhu L, Eikmanns BJ, Oldiges M, Schaumann G, Baumgart M, Brocker M, Eggeling L, Freudl R, Frunzke J, Marienhagen J, Wendisch VF, Bott M. A manually curated compendium of expression profiles for the microbial cell factory Corynebacterium glutamicum. Sci Data 2022; 9:594. [PMID: 36182956 PMCID: PMC9526701 DOI: 10.1038/s41597-022-01706-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 08/18/2022] [Indexed: 11/12/2022] Open
Abstract
Corynebacterium glutamicum is the major host for the industrial production of amino acids and has become one of the best studied model organisms in microbial biotechnology. Rational strain construction has led to an improvement of producer strains and to a variety of novel producer strains with a broad substrate and product spectrum. A key factor for the success of these approaches is detailed knowledge of transcriptional regulation in C. glutamicum. Here, we present a large compendium of 927 manually curated microarray-based transcriptional profiles for wild-type and engineered strains detecting genome-wide expression changes of the 3,047 annotated genes in response to various environmental conditions or in response to genetic modifications. The replicates within the 927 experiments were combined to 304 microarray sets ordered into six categories that were used for differential gene expression analysis. Hierarchical clustering confirmed that no outliers were present in the sets. The compendium provides a valuable resource for future fundamental and applied research with C. glutamicum and contributes to a systemic understanding of this microbial cell factory. Measurement(s) Gene Expression Analysis Technology Type(s) Two Color Microarray Factor Type(s) WT condition A vs. WT condition B • Plasmid-based gene overexpression in parental strain vs. parental strain with empty vector control • Deletion mutant vs. parental strain Sample Characteristic - Organism Corynebacterium glutamicum Sample Characteristic - Environment laboratory environment Sample Characteristic - Location Germany.
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Affiliation(s)
- Angela Kranz
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany.
- IBG-4: Bioinformatics, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany.
| | - Tino Polen
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Christian Kotulla
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Annette Arndt
- Institute of Microbiology and Biotechnology, University of Ulm, D-89069, Ulm, Germany
| | - Graziella Bosco
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Michael Bussmann
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Ava Chattopadhyay
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Annette Cramer
- Institute of Microbiology and Biotechnology, University of Ulm, D-89069, Ulm, Germany
| | - Cedric-Farhad Davoudi
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Ursula Degner
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Ramon Diesveld
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | | | - Kim Gärtner
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Cornelia Gätgens
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Tobias Georgi
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Christian Geraths
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Sabine Haas
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Antonia Heyer
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Max Hünnefeld
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Takeru Ishige
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Armin Kabus
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Nicolai Kallscheuer
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Larissa Kever
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Simon Klaffl
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Britta Kleine
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Martina Kočan
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Abigail Koch-Koerfges
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Kim J Kraxner
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Andreas Krug
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Aileen Krüger
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Andreas Küberl
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Mohamed Labib
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Christian Lange
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Christina Mack
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Tomoya Maeda
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Regina Mahr
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Stephan Majda
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Andrea Michel
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Xenia Morosov
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Olga Müller
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Arun M Nanda
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Jens Nickel
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Jennifer Pahlke
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Eugen Pfeifer
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Laura Platzen
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Paul Ramp
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Doris Rittmann
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Steffen Schaffer
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Sandra Scheele
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Stephanie Spelberg
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Julia Schulte
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Jens-Eric Schweitzer
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Georg Sindelar
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Ulrike Sorger-Herrmann
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Markus Spelberg
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Corinna Stansen
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Apilaasha Tharmasothirajan
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Jan van Ooyen
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | | | - Michael Vogt
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Sabrina Witthoff
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Lingfeng Zhu
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Bernhard J Eikmanns
- Institute of Microbiology and Biotechnology, University of Ulm, D-89069, Ulm, Germany
| | - Marco Oldiges
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Georg Schaumann
- SenseUp GmbH, c/o Campus Forschungszentrum, Wilhelm-Johnen-Strasse, D-52425, Jülich, Germany
| | - Meike Baumgart
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Melanie Brocker
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Lothar Eggeling
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Roland Freudl
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Julia Frunzke
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Jan Marienhagen
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Volker F Wendisch
- Genetics of Prokaryotes, Biology & CeBiTec, Bielefeld University, Universitaetsstr. 25, D-33615, Bielefeld, Germany
| | - Michael Bott
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany.
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6
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Parise MTD, Parise D, Aburjaile FF, Pinto Gomide AC, Kato RB, Raden M, Backofen R, Azevedo VADC, Baumbach J. An Integrated Database of Small RNAs and Their Interplay With Transcriptional Gene Regulatory Networks in Corynebacteria. Front Microbiol 2021; 12:656435. [PMID: 34220744 PMCID: PMC8247434 DOI: 10.3389/fmicb.2021.656435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/19/2021] [Indexed: 12/02/2022] Open
Abstract
Small RNAs (sRNAs) are one of the key players in the post-transcriptional regulation of bacterial gene expression. These molecules, together with transcription factors, form regulatory networks and greatly influence the bacterial regulatory landscape. Little is known concerning sRNAs and their influence on the regulatory machinery in the genus Corynebacterium, despite its medical, veterinary and biotechnological importance. Here, we expand corynebacterial regulatory knowledge by integrating sRNAs and their regulatory interactions into the transcriptional regulatory networks of six corynebacterial species, covering four human and animal pathogens, and integrate this data into the CoryneRegNet database. To this end, we predicted sRNAs to regulate 754 genes, including 206 transcription factors, in corynebacterial gene regulatory networks. Amongst them, the sRNA Cd-NCTC13129-sRNA-2 is predicted to directly regulate ydfH, which indirectly regulates 66 genes, including the global regulator glxR in C. diphtheriae. All of the sRNA-enriched regulatory networks of the genus Corynebacterium have been made publicly available in the newest release of CoryneRegNet(www.exbio.wzw.tum.de/coryneregnet/) to aid in providing valuable insights and to guide future experiments.
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Affiliation(s)
- Mariana Teixeira Dornelles Parise
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany.,Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Doglas Parise
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany.,Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Rodrigo Bentes Kato
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Martin Raden
- Bioinformatics, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | | | - Jan Baumbach
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany.,Computational Biomedicine Lab, Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark.,Chair of Computational Systems Biology, University of Hamburg, Hamburg, Germany
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