Global Transcriptional Regulators Involved in Carbon, Nitrogen, Phosphorus, and Sulfur Metabolisms in Corynebacterium glutamicum

Toyoda, K.; Inui, Masayuki

doi:10.1007/978-3-030-39267-3_5

Cited by 4 publications

(6 citation statements)

References 138 publications

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“…Some aspects of the transcriptional regulatory mechanism of C. glutamicum have also been found to be different from those in other model organisms [3]. In contrast to E. coli, repression is the most common regulatory mechanism in C. glutamicum [4], and unlike B. subtilis and E. coli that have diauxic growth due to the preferential consumption of one carbon source over the others, C. glutamicum cometabolizes glucose with several other carbon sources [3]. In terms of σ factors, E. coli and C. glutamicum have seven, while B. subtilis has 17, and over 60 σ factors have been found in Streptomyces species [5].…”

Section: Introductionmentioning

confidence: 96%

“…These model organisms are usually compared and diverse differences have been found (e.g., while C. glutamicum grows by apical elongation, B. subtilis and E. coli grow by lateral elongation [2]). Some aspects of the transcriptional regulatory mechanism of C. glutamicum have also been found to be different from those in other model organisms [3]. In contrast to E. coli, repression is the most common regulatory mechanism in C. glutamicum [4], and unlike B. subtilis and E. coli that have diauxic growth due to the preferential consumption of one carbon source over the others, C. glutamicum cometabolizes glucose with several other carbon sources [3].…”

Section: Introductionmentioning

confidence: 99%

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Corynebacterium glutamicumregulation beyond transcription: Organizing principles and reconstruction of an extended regulatory network incorporating regulations mediated by small RNA and protein-protein interactions

Escorcia-Rodríguez

Tauch

Freyre-González

2021

Preprint

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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 non-directed experiments, and protein-protein interactions with a direct effect on gene transcription; and 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 sRNAs 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.

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Section: Introductionmentioning

confidence: 96%

Section: Introductionmentioning

confidence: 99%

Corynebacterium glutamicumregulation beyond transcription: Organizing principles and reconstruction of an extended regulatory network incorporating regulations mediated by small RNA and protein-protein interactions

Escorcia-Rodríguez

Tauch

Freyre-González

2021

Preprint

View full text Add to dashboard Cite

show abstract

“…These model organisms are usually compared, and diverse differences have been found (e.g., while C. glutamicum grows by apical elongation, B. subtilis and E. coli grow by lateral elongation [ 2 ]). Some aspects of the transcriptional regulatory mechanism of C. glutamicum have also been found to be different from those in other model organisms [ 3 ]. In contrast to E. coli , repression is the most common regulatory mechanism in C. glutamicum [ 4 ], and unlike B. subtilis and E. coli , which have diauxic growth due to the preferential consumption of one carbon source over others, C. glutamicum cometabolizes glucose with several other carbon sources [ 3 ].…”

Section: Introductionmentioning

confidence: 99%

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

2021

View full text Add to dashboard Cite

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.

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“…However, like S. coelicolor, C. glutamicum also tethers oriCs to the cell poles [2]. The transcriptional regulatory mechanism of C. glutamicum has also been found to be different from those in other model organisms [3]. In contrast to E. coli, repression is the most common regulatory mechanism in C. glutamicum [4].…”

Section: Introductionmentioning

confidence: 99%

“…In contrast to E. coli, repression is the most common regulatory mechanism in C. glutamicum [4]. And unlike B. subtilis and E. coli that have diauxic growth due to the preferential consumption of one carbon source over the others, C. glutamicum co-metabolizes glucose with several other carbon sources [3]. In terms of σ factors, E. coli and C. glutamicum have seven, while B. subtilis has 17, and over 60 σ factors have been found in Streptomyces species [5].…”

Section: Introductionmentioning

confidence: 99%

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

Tauch²,

Freyre-González

2020

Preprint

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Corynebacterium glutamicum is a Gram-positive bacterium found in soil where the condition changes demand plasticity of the regulatory interactions, which study at the global scale has been challenged by the lack of data integration. Here, we update the manually-curated C. glutamicum transcriptional regulatory network, now including protein-protein interactions having a direct effect on gene transcription. The network model with regulations supported by any experimental evidence increased by 557 interactions regarding the previous (2018) version. 73 interactions supported by directed experiments were also included in a second model. We included 545 sRNA-mediated regulations in a third model with a total of 5164 interactions. We deposited the three network models in Abasy Atlas v2.4. We study the C. glutamicum regulatory structure by comparing it against the networks for more than 40 species, finding it to contrast in several global structural properties. We analyze the system-level components of the networks, finding that the inclusion of the sRNAs regulations changes their proportions, transferring part of the basal machinery to the modular class and increasing the number of modules while decreasing their size. Finally, we use strong networks of three model organisms to provide insights in future directions of the C. glutamicum network characterization.

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Global Transcriptional Regulators Involved in Carbon, Nitrogen, Phosphorus, and Sulfur Metabolisms in Corynebacterium glutamicum

Cited by 4 publications

References 138 publications

Corynebacterium glutamicumregulation beyond transcription: Organizing principles and reconstruction of an extended regulatory network incorporating regulations mediated by small RNA and protein-protein interactions

Corynebacterium glutamicumregulation beyond transcription: Organizing principles and reconstruction of an extended regulatory network incorporating regulations mediated by small RNA and protein-protein interactions

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

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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