Experimental promoter identification of a foodborne pathogen Salmonella enterica subsp. enterica serovar Typhimurium with near single base-pair resolution
Salmonella enterica serovar Typhimurium (S. Typhimurium) is a common foodborne pathogen which is frequently used as the reference strain for Salmonella. Investigating the sigma factor network and protomers is crucial to understand the genomic and transcriptomic properties of the bacterium. Its promo...
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Frontiers Media S.A.
2024-01-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1271121/full |
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| author | Sang-Mok Lee Hoa Thi Le Assiya Taizhanova Linh Khanh Nong Joon Young Park Eun-Jin Lee Bernhard O. Palsson Donghyuk Kim |
| author_facet | Sang-Mok Lee Hoa Thi Le Assiya Taizhanova Linh Khanh Nong Joon Young Park Eun-Jin Lee Bernhard O. Palsson Donghyuk Kim |
| author_sort | Sang-Mok Lee |
| collection | DOAJ |
| description | Salmonella enterica serovar Typhimurium (S. Typhimurium) is a common foodborne pathogen which is frequently used as the reference strain for Salmonella. Investigating the sigma factor network and protomers is crucial to understand the genomic and transcriptomic properties of the bacterium. Its promoters were identified using various methods such as dRNA-seq, ChIP-chip, or ChIP-Seq. However, validation using ChIP-exo, which exhibits higher-resolution performance compared to conventional ChIP, has not been conducted to date. In this study, using the representative strain S. Typhimurium LT2 (LT2), the ChIP-exo experiment was conducted to accurately determine the binding sites of catalytic RNA polymerase subunit RpoB and major sigma factors (RpoD, RpoN, RpoS, and RpoE) during exponential phase. Integrated with the results of RNA-Seq, promoters and sigmulons for the sigma factors and their association with RpoB have been discovered. Notably, the overlapping regions among binding sites of each alternative sigma factor were found. Furthermore, comparative analysis with Escherichia coli str. K-12 substr. MG1655 (MG1655) revealed conserved binding sites of RpoD and RpoN across different species. In the case of small RNAs (sRNAs), 50 sRNAs observed their expression during the exponential growth of LT2. Collectively, the integration of ChIP-exo and RNA-Seq enables genome-scale promoter mapping with high resolution and facilitates the characterization of binding events of alternative sigma factors, enabling a comprehensive understanding of the bacterial sigma factor network and condition-specific active promoters. |
| first_indexed | 2024-03-08T17:06:54Z |
| format | Article |
| id | doaj.art-6e86eb6319e94b2ea40bfc0c8f85438d |
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| issn | 1664-302X |
| language | English |
| last_indexed | 2024-03-08T17:06:54Z |
| publishDate | 2024-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-6e86eb6319e94b2ea40bfc0c8f85438d2024-01-04T04:37:31ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2024-01-011410.3389/fmicb.2023.12711211271121Experimental promoter identification of a foodborne pathogen Salmonella enterica subsp. enterica serovar Typhimurium with near single base-pair resolutionSang-Mok Lee0Hoa Thi Le1Assiya Taizhanova2Linh Khanh Nong3Joon Young Park4Eun-Jin Lee5Bernhard O. Palsson6Donghyuk Kim7School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of KoreaSchool of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of KoreaDepartment of Genetic Engineering and Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, Republic of KoreaSchool of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of KoreaSchool of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of KoreaDepartment of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of KoreaDepartment of Bioengineering, University of California San Diego, La Jolla, CA, United StatesSchool of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of KoreaSalmonella enterica serovar Typhimurium (S. Typhimurium) is a common foodborne pathogen which is frequently used as the reference strain for Salmonella. Investigating the sigma factor network and protomers is crucial to understand the genomic and transcriptomic properties of the bacterium. Its promoters were identified using various methods such as dRNA-seq, ChIP-chip, or ChIP-Seq. However, validation using ChIP-exo, which exhibits higher-resolution performance compared to conventional ChIP, has not been conducted to date. In this study, using the representative strain S. Typhimurium LT2 (LT2), the ChIP-exo experiment was conducted to accurately determine the binding sites of catalytic RNA polymerase subunit RpoB and major sigma factors (RpoD, RpoN, RpoS, and RpoE) during exponential phase. Integrated with the results of RNA-Seq, promoters and sigmulons for the sigma factors and their association with RpoB have been discovered. Notably, the overlapping regions among binding sites of each alternative sigma factor were found. Furthermore, comparative analysis with Escherichia coli str. K-12 substr. MG1655 (MG1655) revealed conserved binding sites of RpoD and RpoN across different species. In the case of small RNAs (sRNAs), 50 sRNAs observed their expression during the exponential growth of LT2. Collectively, the integration of ChIP-exo and RNA-Seq enables genome-scale promoter mapping with high resolution and facilitates the characterization of binding events of alternative sigma factors, enabling a comprehensive understanding of the bacterial sigma factor network and condition-specific active promoters.https://www.frontiersin.org/articles/10.3389/fmicb.2023.1271121/fullSalmonella enterica serovar Typhimurium LT2promotersigma factor networkChIP-exoRNA-seq |
| spellingShingle | Sang-Mok Lee Hoa Thi Le Assiya Taizhanova Linh Khanh Nong Joon Young Park Eun-Jin Lee Bernhard O. Palsson Donghyuk Kim Experimental promoter identification of a foodborne pathogen Salmonella enterica subsp. enterica serovar Typhimurium with near single base-pair resolution Frontiers in Microbiology Salmonella enterica serovar Typhimurium LT2 promoter sigma factor network ChIP-exo RNA-seq |
| title | Experimental promoter identification of a foodborne pathogen Salmonella enterica subsp. enterica serovar Typhimurium with near single base-pair resolution |
| title_full | Experimental promoter identification of a foodborne pathogen Salmonella enterica subsp. enterica serovar Typhimurium with near single base-pair resolution |
| title_fullStr | Experimental promoter identification of a foodborne pathogen Salmonella enterica subsp. enterica serovar Typhimurium with near single base-pair resolution |
| title_full_unstemmed | Experimental promoter identification of a foodborne pathogen Salmonella enterica subsp. enterica serovar Typhimurium with near single base-pair resolution |
| title_short | Experimental promoter identification of a foodborne pathogen Salmonella enterica subsp. enterica serovar Typhimurium with near single base-pair resolution |
| title_sort | experimental promoter identification of a foodborne pathogen salmonella enterica subsp enterica serovar typhimurium with near single base pair resolution |
| topic | Salmonella enterica serovar Typhimurium LT2 promoter sigma factor network ChIP-exo RNA-seq |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1271121/full |
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