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Goodson JR, Zhang C, Trettel D, Ailinger HE, Lee PE, Spirito CM, Winkler WC. An autoinhibitory mechanism controls RNA-binding activity of the nitrate-sensing protein NasR. Mol Microbiol 2020; 114:348-360. [PMID: 32314426 PMCID: PMC7496416 DOI: 10.1111/mmi.14517] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 01/04/2023]
Abstract
The ANTAR domain harnesses RNA‐binding activity to promote transcription attenuation. Although several ANTAR proteins have been analyzed by high‐resolution structural analyses, the residues involved in RNA‐recognition and transcription attenuation have not been identified. Nor is it clear how signal‐responsive domains are allosterically coupled with ANTAR domains for control of gene expression. Herein, we examined the sequence conservation of ANTAR domains to find residues that may associate with RNA. We subjected the corresponding positions of Klebsiella oxytoca NasR to site‐directed alanine substitutions and measured RNA‐binding activity. This revealed a functionally important patch of residues that forms amino acid pairing interactions with residues from NasR’s nitrate‐sensing NIT domain. We hypothesize these amino acid pairing interactions are part of an autoinhibitory mechanism that holds the structure in an “off” state in the absence of nitrate signal. Indeed, mutational disruption of these interactions resulted in constitutively active proteins, freed from autoinhibition and no longer influenced by nitrate. Moreover, sequence analyses suggested the autoinhibitory mechanism has been evolutionarily maintained by NasR proteins. These data reveal a molecular mechanism for how NasR couples its nitrate signal to RNA‐binding activity, and generally show how signal‐responsive domains of one‐component regulatory proteins have evolved to exert control over RNA‐binding ANTAR domains.
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Affiliation(s)
- Jonathan R Goodson
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD, USA
| | - Christopher Zhang
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD, USA
| | - Daniel Trettel
- Department of Chemistry and Biochemistry, The University of Maryland, College Park, MD, USA
| | - Heather E Ailinger
- FIRE: The First-Year Innovation & Research Experience Program, The University of Maryland, College Park, MD, USA
| | - Priscilla E Lee
- FIRE: The First-Year Innovation & Research Experience Program, The University of Maryland, College Park, MD, USA
| | - Catherine M Spirito
- FIRE: The First-Year Innovation & Research Experience Program, The University of Maryland, College Park, MD, USA
| | - Wade C Winkler
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD, USA.,Department of Chemistry and Biochemistry, The University of Maryland, College Park, MD, USA.,FIRE: The First-Year Innovation & Research Experience Program, The University of Maryland, College Park, MD, USA
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Maunder HE, Wright J, Kolli BR, Vieira CR, Mkandawire TT, Tatoris S, Kennedy V, Iqball S, Devarajan G, Ellis S, Lad Y, Clarkson NG, Mitrophanous KA, Farley DC. Enhancing titres of therapeutic viral vectors using the transgene repression in vector production (TRiP) system. Nat Commun 2017; 8:14834. [PMID: 28345582 PMCID: PMC5378976 DOI: 10.1038/ncomms14834] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 02/03/2017] [Indexed: 12/28/2022] Open
Abstract
A key challenge in the field of therapeutic viral vector/vaccine manufacturing is maximizing production. For most vector platforms, the ‘benchmark' vector titres are achieved with inert reporter genes. However, expression of therapeutic transgenes can often adversely affect vector titres due to biological effects on cell metabolism and/or on the vector virion itself. Here, we exemplify the novel ‘Transgene Repression In vector Production' (TRiP) system for the production of both RNA- and DNA-based viral vectors. The TRiP system utilizes a translational block of one or more transgenes by employing the bacterial tryptophan RNA-binding attenuation protein (TRAP), which binds its target RNA sequence close to the transgene initiation codon. We report enhancement of titres of lentiviral vectors expressing Cyclo-oxygenase-2 by 600-fold, and adenoviral vectors expressing the pro-apoptotic gene Bax by >150,000-fold. The TRiP system is transgene-independent and will be a particularly useful platform in the clinical development of viral vectors expressing problematic transgenes. The maximum titre of therapeutic viral vectors can be adversely affected by the encoded transgene. Here the authors repress transgene expression in producing cells by employing the tryptophan RNA-binding attenuation protein and show that it improves titre of RNA- and DNA-based viral vectors expressing toxic transgenes.
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Affiliation(s)
- H E Maunder
- Research Department, Oxford BioMedica Ltd., Windrush Court, Transport Way, Oxford OX4 6LT, UK
| | - J Wright
- Research Department, Oxford BioMedica Ltd., Windrush Court, Transport Way, Oxford OX4 6LT, UK
| | - B R Kolli
- Research Department, Oxford BioMedica Ltd., Windrush Court, Transport Way, Oxford OX4 6LT, UK
| | - C R Vieira
- Research Department, Oxford BioMedica Ltd., Windrush Court, Transport Way, Oxford OX4 6LT, UK
| | - T T Mkandawire
- Research Department, Oxford BioMedica Ltd., Windrush Court, Transport Way, Oxford OX4 6LT, UK
| | - S Tatoris
- Research Department, Oxford BioMedica Ltd., Windrush Court, Transport Way, Oxford OX4 6LT, UK
| | - V Kennedy
- Research Department, Oxford BioMedica Ltd., Windrush Court, Transport Way, Oxford OX4 6LT, UK
| | - S Iqball
- Research Department, Oxford BioMedica Ltd., Windrush Court, Transport Way, Oxford OX4 6LT, UK
| | - G Devarajan
- Research Department, Oxford BioMedica Ltd., Windrush Court, Transport Way, Oxford OX4 6LT, UK
| | - S Ellis
- Research Department, Oxford BioMedica Ltd., Windrush Court, Transport Way, Oxford OX4 6LT, UK
| | - Y Lad
- Research Department, Oxford BioMedica Ltd., Windrush Court, Transport Way, Oxford OX4 6LT, UK
| | - N G Clarkson
- Research Department, Oxford BioMedica Ltd., Windrush Court, Transport Way, Oxford OX4 6LT, UK
| | - K A Mitrophanous
- Research Department, Oxford BioMedica Ltd., Windrush Court, Transport Way, Oxford OX4 6LT, UK
| | - D C Farley
- Research Department, Oxford BioMedica Ltd., Windrush Court, Transport Way, Oxford OX4 6LT, UK
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