Assignment of sigma factors of RNA polymerase to promoters in Corynebacterium glutamicum
Abstract Corynebacterium glutamicum is an important industrial producer of various amino acids and other metabolites. The C. glutamicum genome encodes seven sigma subunits (factors) of RNA polymerase: the primary sigma factor SigA (σA), the primary-like σB and five alternative sigma factors (σC, σD,...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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SpringerOpen
2017-06-01
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| Series: | AMB Express |
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| Online Access: | http://link.springer.com/article/10.1186/s13568-017-0436-8 |
| _version_ | 1811239751931396096 |
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| author | Hana Dostálová Jiří Holátko Tobias Busche Lenka Rucká Andrey Rapoport Petr Halada Jan Nešvera Jörn Kalinowski Miroslav Pátek |
| author_facet | Hana Dostálová Jiří Holátko Tobias Busche Lenka Rucká Andrey Rapoport Petr Halada Jan Nešvera Jörn Kalinowski Miroslav Pátek |
| author_sort | Hana Dostálová |
| collection | DOAJ |
| description | Abstract Corynebacterium glutamicum is an important industrial producer of various amino acids and other metabolites. The C. glutamicum genome encodes seven sigma subunits (factors) of RNA polymerase: the primary sigma factor SigA (σA), the primary-like σB and five alternative sigma factors (σC, σD, σE, σH and σM). We have developed in vitro and in vivo methods to assign particular sigma factors to individual promoters of different classes. In vitro transcription assays and measurements of promoter activity using the overexpression of a single sigma factor gene and the transcriptional fusion of the promoter to the gfpuv reporter gene enabled us to reliably define the sigma factor dependency of promoters. To document the strengths of these methods, we tested examples of respective promoters for each C. glutamicum sigma factor. Promoters of the rshA (anti-sigma for σH) and trxB1 (thioredoxin) genes were found to be σH-dependent, whereas the promoter of the sigB gene (sigma factor σB) was σE- and σH-dependent. It was confirmed that the promoter of the cg2556 gene (iron-regulated membrane protein) is σC-dependent as suggested recently by other authors. The promoter of cmt1 (trehalose corynemycolyl transferase) was found to be clearly σD-dependent. No σM-dependent promoter was identified. The typical housekeeping promoter P2sigA (sigma factor σA) was proven to be σA-dependent but also recognized by σB. Similarly, the promoter of fba (fructose-1,6-bisphosphate aldolase) was confirmed to be σB-dependent but also functional with σA. The study provided demonstrations of the broad applicability of the developed methods and produced original data on the analyzed promoters. |
| first_indexed | 2024-04-12T13:06:40Z |
| format | Article |
| id | doaj.art-17a4bdb7158545bfaf72cdf127ed497f |
| institution | Directory Open Access Journal |
| issn | 2191-0855 |
| language | English |
| last_indexed | 2024-04-12T13:06:40Z |
| publishDate | 2017-06-01 |
| publisher | SpringerOpen |
| record_format | Article |
| series | AMB Express |
| spelling | doaj.art-17a4bdb7158545bfaf72cdf127ed497f2022-12-22T03:32:00ZengSpringerOpenAMB Express2191-08552017-06-017111310.1186/s13568-017-0436-8Assignment of sigma factors of RNA polymerase to promoters in Corynebacterium glutamicumHana Dostálová0Jiří Holátko1Tobias Busche2Lenka Rucká3Andrey Rapoport4Petr Halada5Jan Nešvera6Jörn Kalinowski7Miroslav Pátek8Institute of Microbiology of the CAS, v. v. i.Institute of Microbiology of the CAS, v. v. i.Center for Biotechnology, Bielefeld UniversityInstitute of Microbiology of the CAS, v. v. i.Institute of Microbiology of the CAS, v. v. i.Institute of Microbiology of the CAS, v. v. i.Institute of Microbiology of the CAS, v. v. i.Center for Biotechnology, Bielefeld UniversityInstitute of Microbiology of the CAS, v. v. i.Abstract Corynebacterium glutamicum is an important industrial producer of various amino acids and other metabolites. The C. glutamicum genome encodes seven sigma subunits (factors) of RNA polymerase: the primary sigma factor SigA (σA), the primary-like σB and five alternative sigma factors (σC, σD, σE, σH and σM). We have developed in vitro and in vivo methods to assign particular sigma factors to individual promoters of different classes. In vitro transcription assays and measurements of promoter activity using the overexpression of a single sigma factor gene and the transcriptional fusion of the promoter to the gfpuv reporter gene enabled us to reliably define the sigma factor dependency of promoters. To document the strengths of these methods, we tested examples of respective promoters for each C. glutamicum sigma factor. Promoters of the rshA (anti-sigma for σH) and trxB1 (thioredoxin) genes were found to be σH-dependent, whereas the promoter of the sigB gene (sigma factor σB) was σE- and σH-dependent. It was confirmed that the promoter of the cg2556 gene (iron-regulated membrane protein) is σC-dependent as suggested recently by other authors. The promoter of cmt1 (trehalose corynemycolyl transferase) was found to be clearly σD-dependent. No σM-dependent promoter was identified. The typical housekeeping promoter P2sigA (sigma factor σA) was proven to be σA-dependent but also recognized by σB. Similarly, the promoter of fba (fructose-1,6-bisphosphate aldolase) was confirmed to be σB-dependent but also functional with σA. The study provided demonstrations of the broad applicability of the developed methods and produced original data on the analyzed promoters.http://link.springer.com/article/10.1186/s13568-017-0436-8Corynebacterium glutamicumPromoterSigma factorIn vitro transcriptionRNA polymerase |
| spellingShingle | Hana Dostálová Jiří Holátko Tobias Busche Lenka Rucká Andrey Rapoport Petr Halada Jan Nešvera Jörn Kalinowski Miroslav Pátek Assignment of sigma factors of RNA polymerase to promoters in Corynebacterium glutamicum AMB Express Corynebacterium glutamicum Promoter Sigma factor In vitro transcription RNA polymerase |
| title | Assignment of sigma factors of RNA polymerase to promoters in Corynebacterium glutamicum |
| title_full | Assignment of sigma factors of RNA polymerase to promoters in Corynebacterium glutamicum |
| title_fullStr | Assignment of sigma factors of RNA polymerase to promoters in Corynebacterium glutamicum |
| title_full_unstemmed | Assignment of sigma factors of RNA polymerase to promoters in Corynebacterium glutamicum |
| title_short | Assignment of sigma factors of RNA polymerase to promoters in Corynebacterium glutamicum |
| title_sort | assignment of sigma factors of rna polymerase to promoters in corynebacterium glutamicum |
| topic | Corynebacterium glutamicum Promoter Sigma factor In vitro transcription RNA polymerase |
| url | http://link.springer.com/article/10.1186/s13568-017-0436-8 |
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