Corynebacterium glutamicum Regulation beyond Transcription: Organizing Principles and Reconstruction of an Extended Regulatory Network Incorporating Regulations Mediated by Small RNA and Protein–Protein Interactions

Escorcia-Rodríguez, Juan M.; Tauch, Andreas; Freyre-González, Julio A.

doi:10.3390/microorganisms9071395

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Corynebacterium glutamicum Regulation beyond Transcription: Organizing Principles and Reconstruction of an Extended Regulatory Network Incorporating Regulations Mediated by Small RNA and Protein–Protein Interactions

Juan M. Escorcia-Rodríguez

Andreas Tauch

² and

Julio A. Freyre-González

^1,*

Regulatory Systems Biology Research Group, Laboratory of Systems and Synthetic Biology, Center for Genomic Sciences, Universidad Nacional Autónoma de México, Av. Universidad s/n, Col. Chamilpa, Cuernavaca 62210, Morelos, Mexico

Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany

Author to whom correspondence should be addressed.

Academic Editor: Hiroya Yurimoto

Microorganisms 2021, 9(7), 1395; https://doi.org/10.3390/microorganisms9071395

Received: 20 December 2020 / Revised: 8 January 2021 / Accepted: 12 January 2021 / Published: 28 June 2021

(This article belongs to the Special Issue Genetics and Physiology of Corynebacteria)

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Abstract

Corynebacterium glutamicum is a Gram-positive bacterium found in soil where the condition changes demand plasticity of the regulatory machinery. The study of such machinery at the global scale has been challenged by the lack of data integration. Here, we report three regulatory network models for C. glutamicum: strong (3040 interactions) constructed solely with regulations previously supported by directed experiments; all evidence (4665 interactions) containing the strong network, regulations previously supported by nondirected experiments, and protein–protein interactions with a direct effect on gene transcription; sRNA (5222 interactions) containing the all evidence network and sRNA-mediated regulations. Compared to the previous version (2018), the strong and all evidence networks increased by 75 and 1225 interactions, respectively. We analyzed the system-level components of the three networks to identify how they differ and compared their structures against those for the networks of more than 40 species. The inclusion of the sRNA-mediated regulations changed the proportions of the system-level components and increased the number of modules but decreased their size. The C. glutamicum regulatory structure contrasted with other bacterial regulatory networks. Finally, we used the strong networks of three model organisms to provide insights and future directions of the C.glutamicum regulatory network characterization. View Full-Text

Keywords: Corynebacterium glutamicum; regulatory interactions; regulatory network; curation; network inference; systems; modules; NDA; regulogs

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Escorcia-Rodríguez, J.M.; Tauch, A.; Freyre-González, J.A. Corynebacterium glutamicum Regulation beyond Transcription: Organizing Principles and Reconstruction of an Extended Regulatory Network Incorporating Regulations Mediated by Small RNA and Protein–Protein Interactions. Microorganisms 2021, 9, 1395. https://doi.org/10.3390/microorganisms9071395

AMA Style

Escorcia-Rodríguez JM, Tauch A, Freyre-González JA. Corynebacterium glutamicum Regulation beyond Transcription: Organizing Principles and Reconstruction of an Extended Regulatory Network Incorporating Regulations Mediated by Small RNA and Protein–Protein Interactions. Microorganisms. 2021; 9(7):1395. https://doi.org/10.3390/microorganisms9071395

Chicago/Turabian Style

Escorcia-Rodríguez, Juan M., Andreas Tauch, and Julio A. Freyre-González. 2021. "Corynebacterium glutamicum Regulation beyond Transcription: Organizing Principles and Reconstruction of an Extended Regulatory Network Incorporating Regulations Mediated by Small RNA and Protein–Protein Interactions" Microorganisms 9, no. 7: 1395. https://doi.org/10.3390/microorganisms9071395

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Corynebacterium glutamicum Regulation beyond Transcription: Organizing Principles and Reconstruction of an Extended Regulatory Network Incorporating Regulations Mediated by Small RNA and Protein–Protein Interactions

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