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Weaver JW, Proshkin S, Duan W, Epshtein V, Gowder M, Bharati BK, Afanaseva E, Mironov A, Serganov A, Nudler E. Control of transcription elongation and DNA repair by alarmone ppGpp. Nat Struct Mol Biol 2023; 30:600-607. [PMID: 36997761 PMCID: PMC10191844 DOI: 10.1038/s41594-023-00948-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/27/2023] [Indexed: 04/01/2023]
Abstract
Second messenger (p)ppGpp (collectively guanosine tetraphosphate and guanosine pentaphosphate) mediates bacterial adaptation to nutritional stress by modulating transcription initiation. More recently, ppGpp has been implicated in coupling transcription and DNA repair; however, the mechanism of ppGpp engagement remained elusive. Here we present structural, biochemical and genetic evidence that ppGpp controls Escherichia coli RNA polymerase (RNAP) during elongation via a specific site that is nonfunctional during initiation. Structure-guided mutagenesis renders the elongation (but not initiation) complex unresponsive to ppGpp and increases bacterial sensitivity to genotoxic agents and ultraviolet radiation. Thus, ppGpp binds RNAP at sites with distinct functions in initiation and elongation, with the latter being important for promoting DNA repair. Our data provide insights on the molecular mechanism of ppGpp-mediated adaptation during stress, and further highlight the intricate relationships between genome stability, stress responses and transcription.
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Affiliation(s)
- Jacob W Weaver
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Sergey Proshkin
- Engelhardt Institute of Molecular Biology, Russian Academy of Science, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Moscow, Russia
| | - Wenqian Duan
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Vitaly Epshtein
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Manjunath Gowder
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA
| | - Binod K Bharati
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA
| | - Elena Afanaseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Science, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Moscow, Russia
| | - Alexander Mironov
- Engelhardt Institute of Molecular Biology, Russian Academy of Science, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Moscow, Russia
| | - Alexander Serganov
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA.
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Mahalik S, Sharma A, Das DR, Mittra D, Mukherjee KJ. Co-expressing Leucine Responsive Regulatory protein (Lrp) enhances Recombinant L-Asparaginase-II production in Escherichia coli. J Biotechnol 2022; 351:99-108. [DOI: 10.1016/j.jbiotec.2022.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 11/27/2022]
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