1
|
Wang F, Feng Y, Shang Z, Lin W. A unique binding between SspA and RNAP β 'NTH across low-GC Gram-negative bacteria facilitates SspA-mediated transcription regulation. Biochem Biophys Res Commun 2021; 583:86-92. [PMID: 34735884 DOI: 10.1016/j.bbrc.2021.10.048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 10/18/2021] [Accepted: 10/18/2021] [Indexed: 11/19/2022]
Abstract
Stringent starvation protein A (SspA) involved in nucleotide metabolism, acid tolerance and virulence of bacteria has been demonstrated to function as a transcription factor to regulate σ70-dependent gene transcription through interacting with σ70 region 4 and the zinc binding domain (ZBD) of E. coli RNA polymerase (EcoRNAP) β' subunit simultaneously. Despite extensive biochemical and structural analyses were reported recently, the interactions of SspA with RNAP are not comprehensively understood. Here, we reprocessed our previous cryo-EM dataset of EcoRNAP-promoter open complex with SspA (SspA-RPo) and obtained a significantly improved density map. Unexpectedly, the new map showed that SspA interacts with both N-terminal helix of β' subunit (β'ΝΤΗ) and ω subunit, which contributes to stabilize the SspA-EcoRNAP σ70 holoenzyme complex. Sequence alignments and phylogenetic tree analyses of N-terminal sequences of β' subunit from different classes of bacteria revealed that β'ΝΤΗ is highly conserved and exclusively found in low-GC-content Gram-negative bacteria that harbor SspA, implying a co-evolution of β'ΝΤΗ and SspA. The transcription assays of wild-type SspA and its mutants demonstrated the interaction between SspA and β'ΝΤΗ facilitates the transcription regulation of SspA. Together, our results provide a more comprehensive insight into the interactions between SspA and RNAP and their roles in bacterial transcription regulation.
Collapse
Affiliation(s)
- Fulin Wang
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, 210023, China
| | - Yu Feng
- Department of Biophysics, And Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Zhejiang Provincial Key Laboratory of Immunity and Inflammatory Diseases, Hangzhou, China.
| | - Zhuo Shang
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Wei Lin
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, 210023, China.
| |
Collapse
|
2
|
Zhan J, Tan X, Wang X. Null mutation in sspA of Cronobacter sakazakii influences its tolerance to environmental stress. Can J Microbiol 2021; 67:902-918. [PMID: 34379995 DOI: 10.1139/cjm-2021-0114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cronobacter sakazakii is a known foodborne opportunistic pathogen that can affect the intestinal health of infants. Despite undergoing complex manufacturing processes and low water concentration in the finished product, infant formula has been associated with Cronobacter infections, suggesting that C. sakazakii's pathogenicity may be related to its tolerance to stress. In this study, the effect of the stringent starvation protein A (SspA), which plays an important role in E. coli cellular survival under environmental stresses, on the stress tolerance of C. sakazakii BAA894 was investigated by creating an sspA-knockout mutant. The effects of this mutation on the acid, desiccation and drug tolerance were assessed, and results showed that acid tolerance decreased, while desiccation tolerance increased in LB and decreased in M9. Moreover, the MICs of 10 antibiotics in LB medium and 8 antibiotics in M9 medium were determined and compared of the wild-type and ΔsspA. Transcriptome analysis showed that 27.21% or 37.78% of the genes in ΔsspA were significantly differentially expressed in LB or M9 media, the genes relevant to microbial metabolism in diverse environments and bacterial chemotaxis were detailed analyzed. The current study contributes towards an improved understanding of the role of SspA in C. sakazakii BAA894 stress tolerance.
Collapse
Affiliation(s)
- Jie Zhan
- Jiangnan University, 66374, State Key Laboratory of Food Science and Technology, Wuxi, China;
| | - Xin Tan
- Jiangnan University, 66374, Wuxi, China.,Jiangnan University, 66374, Wuxi, China;
| | - Xiaoyuan Wang
- Jiangnan University, 66374, Wuxi, China, 214122.,Jiangnan University, 66374, Wuxi, China, 214122.,Jiangnan University, 66374, Wuxi, China, 214122;
| |
Collapse
|
3
|
Wang F, Shi J, He D, Tong B, Zhang C, Wen A, Zhang Y, Feng Y, Lin W. Structural basis for transcription inhibition by E. coli SspA. Nucleic Acids Res 2020; 48:9931-9942. [PMID: 32785630 PMCID: PMC7515715 DOI: 10.1093/nar/gkaa672] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/30/2020] [Accepted: 08/01/2020] [Indexed: 12/18/2022] Open
Abstract
Stringent starvation protein A (SspA) is an RNA polymerase (RNAP)-associated protein involved in nucleotide metabolism, acid tolerance and virulence of bacteria. Despite extensive biochemical and genetic analyses, the precise regulatory role of SspA in transcription is still unknown, in part, because of a lack of structural information for bacterial RNAP in complex with SspA. Here, we report a 3.68 Å cryo-EM structure of an Escherichia coli RNAP-promoter open complex (RPo) with SspA. Unexpectedly, the structure reveals that SspA binds to the E. coli σ70-RNAP holoenzyme as a homodimer, interacting with σ70 region 4 and the zinc binding domain of EcoRNAP β′ subunit simultaneously. Results from fluorescent polarization assays indicate the specific interactions between SspA and σ70 region 4 confer its σ selectivity, thereby avoiding its interactions with σs or other alternative σ factors. In addition, results from in vitro transcription assays verify that SspA inhibits transcription probably through suppressing promoter escape. Together, the results here provide a foundation for understanding the unique physiological function of SspA in transcription regulation in bacteria.
Collapse
Affiliation(s)
- Fulin Wang
- Department of Microbiology and Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.,Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing 210023, China
| | - Jing Shi
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, China.,Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Dingwei He
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bei Tong
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Chao Zhang
- Department of Microbiology and Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Aijia Wen
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, China.,Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu Feng
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, China.,Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Lin
- Department of Microbiology and Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.,Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing 210023, China
| |
Collapse
|
4
|
Elkina D, Weber L, Lechner M, Burenina O, Weisert A, Kubareva E, Hartmann RK, Klug G. 6S RNA in Rhodobacter sphaeroides: 6S RNA and pRNA transcript levels peak in late exponential phase and gene deletion causes a high salt stress phenotype. RNA Biol 2017; 14:1627-1637. [PMID: 28692405 DOI: 10.1080/15476286.2017.1342933] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
The function of 6S RNA, a global regulator of transcription, was studied in the photosynthetic α-proteobacterium Rhodobacter sphaeroides. The cellular levels of R. sphaeroides 6S RNA peak toward the transition to stationary phase and strongly decrease during extended stationary phase. The synthesis of so-called product RNA transcripts (mainly 12-16-mers) on 6S RNA as template by RNA polymerase was found to be highest in late exponential phase. Product RNA ≥ 13-mers are expected to trigger the dissociation of 6S RNA:RNA polymerase complexes. A 6S RNA deletion in R. sphaeroides had no impact on growth under various metabolic and oxidative stress conditions (with the possible exception of tert-butyl hydroperoxide stress). However, the 6S RNA knockout resulted in a robust growth defect under high salt stress (0.25 M NaCl). Remarkably, the sspA gene encoding the putative salt stress-induced membrane protein SspA and located immediately downstream of the 6S RNA (ssrS) gene on the antisense strand was expressed at elevated levels in the ΔssrS strain when grown in the presence of 250 mM NaCl.
Collapse
Affiliation(s)
- Daria Elkina
- a Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology , M.V. Lomonosov Moscow State University , Leninskie Gory 1, Moscow , Russia
| | - Lennart Weber
- b Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-University-Gießen, Heinrich-Buff-Ring 26-32 , Gießen , Germany
| | - Marcus Lechner
- c Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6 , Marburg , Germany ; Skolkovo Institute for Science and Technology , Skoltech, Moscow
| | - Olga Burenina
- a Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology , M.V. Lomonosov Moscow State University , Leninskie Gory 1, Moscow , Russia
| | - Andrea Weisert
- b Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-University-Gießen, Heinrich-Buff-Ring 26-32 , Gießen , Germany
| | - Elena Kubareva
- a Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology , M.V. Lomonosov Moscow State University , Leninskie Gory 1, Moscow , Russia
| | - Roland K Hartmann
- c Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6 , Marburg , Germany ; Skolkovo Institute for Science and Technology , Skoltech, Moscow
| | - Gabriele Klug
- b Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-University-Gießen, Heinrich-Buff-Ring 26-32 , Gießen , Germany
| |
Collapse
|