1
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Nguyen LD, LeBlanc H, Berry KE. Improved constructs for bait RNA display in a bacterial three-hybrid assay. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.23.604302. [PMID: 39091812 PMCID: PMC11291032 DOI: 10.1101/2024.07.23.604302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
We have previously developed a transcription-based bacterial three-hybrid (B3H) assay as a genetic approach to probe RNA-protein interactions inside of E. coli cells. This system offers a straightforward path to identify and assess the consequences of mutations in RBPs with molecular phenotypes of interest. One limiting factor in detecting RNA-protein interactions in the B3H assay is RNA misfolding arising from incorrect base-pair interactions with neighboring RNA sequences in a hybrid RNA. To support correct folding of hybrid bait RNAs, we have explored the use of a highly stable stem ("GC clamp") to isolate regions of a hybrid RNA as discrete folding units. In this work, we introduce new bait RNA constructs to 1) insulate the folding of individual components of the hybrid RNA with GC clamps and 2) express bait RNAs that do not encode their own intrinsic terminator. We find that short GC clamps (5 or 7 bp long) are more effective than a longer 13bp GC clamp in the B3H assay. These new constructs increase the number of Hfq-sRNA and -5'UTR interactions that are detectable in the B3H system and improve the signal-to-noise ratio of many of these interactions. We therefore recommend the use of constructs containing short GC clamps for the expression of future B3H bait RNAs. With these new constructs, a broader range of RNA-protein interactions are detectable in the B3H assay, expanding the utility and impact of this genetic tool as a platform to search for and interrogate mechanisms of additional RNA-protein interactions.
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Affiliation(s)
- Linh D. Nguyen
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA, 01075, USA
| | - Hannah LeBlanc
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA, 01075, USA
| | - Katherine E. Berry
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA, 01075, USA
- Department of Chemistry, Mount Holyoke College, South Hadley, MA, 01075, USA
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2
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Washington HS, Wang S, Berry KE. Generation of single-cysteine E. coli ProQ variants to study RNA-protein interaction mechanisms. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001188. [PMID: 38660567 PMCID: PMC11040395 DOI: 10.17912/micropub.biology.001188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 04/26/2024]
Abstract
ProQ is a FinO-domain protein found in E. coli and other proteobacteria that has a global RNA-binding profile. In order to probe the detailed mechanism of RNA interactions, we have developed a collection of 13 E. coli ProQ variants that possess single-cysteine residues at varied positions on the surface of the N-terminal FinO domain and retain the ability to bind well to RNA. This set of variant ProQ proteins will support future biochemical and biophysical studies to map the orientation of bound RNAs to different sites around the ProQ protein, shedding light on the mechanism of ProQ-RNA interactions.
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Affiliation(s)
- Helen S. Washington
- Program in Biochemistry, Mount Holyoke College, South Hadley, Massachusetts, United States
| | - Shiying Wang
- Program in Biochemistry, Mount Holyoke College, South Hadley, Massachusetts, United States
| | - Katherine E. Berry
- Program in Biochemistry and Department of Chemistry, Mount Holyoke College, South Hadley, Massachusetts, United States
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3
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Stein EM, Wang S, Dailey KG, Gravel CM, Wang S, Olejniczak M, Berry KE. Biochemical and genetic dissection of the RNA-binding surface of the FinO domain of Escherichia coli ProQ. RNA (NEW YORK, N.Y.) 2023; 29:1772-1791. [PMID: 37607742 PMCID: PMC10578477 DOI: 10.1261/rna.079697.123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/03/2023] [Indexed: 08/24/2023]
Abstract
RNA-binding proteins play important roles in bacterial gene regulation through interactions with both coding and noncoding RNAs. ProQ is a FinO-domain protein that binds a large set of RNAs in Escherichia coli, though the details of how ProQ binds these RNAs remain unclear. In this study, we used a combination of in vivo and in vitro binding assays to confirm key structural features of E. coli ProQ's FinO domain and explore its mechanism of RNA interactions. Using a bacterial three-hybrid assay, we performed forward genetic screens to confirm the importance of the concave face of ProQ in RNA binding. Using gel shift assays, we directly probed the contributions of ten amino acids on ProQ binding to seven RNA targets. Certain residues (R58, Y70, and R80) were found to be essential for binding of all seven RNAs, while substitutions of other residues (K54 and R62) caused more moderate binding defects. Interestingly, substitutions of two amino acids (K35, R69), which are evolutionarily variable but adjacent to conserved residues, showed varied effects on the binding of different RNAs; these may arise from the differing sequence context around each RNA's terminator hairpin. Together, this work confirms many of the essential RNA-binding residues in ProQ initially identified in vivo and supports a model in which residues on the conserved concave face of the FinO domain such as R58, Y70, and R80 form the main RNA-binding site of E. coli ProQ, while additional contacts contribute to the binding of certain RNAs.
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Affiliation(s)
- Ewa M Stein
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Suxuan Wang
- Program in Biochemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
| | - Katherine G Dailey
- Program in Biochemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
| | - Chandra M Gravel
- Program in Biochemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
- Department of Chemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
| | - Shiying Wang
- Program in Biochemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
| | - Mikołaj Olejniczak
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Katherine E Berry
- Program in Biochemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
- Department of Chemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
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4
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Stein EM, Wang S, Dailey K, Gravel CM, Wang S, Olejniczak M, Berry KE. Biochemical and genetic dissection of the RNA-binding surface of the FinO domain of Escherichia coli ProQ. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.25.538249. [PMID: 37163069 PMCID: PMC10168233 DOI: 10.1101/2023.04.25.538249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
RNA-binding proteins play important roles in bacterial gene regulation through interactions with both coding and non-coding RNAs. ProQ is a FinO-domain protein that binds a large set of RNAs in Escherichia coli , though the details of how ProQ binds these RNAs remain unclear. In this study, we used a combination of in vivo and in vitro binding assays to confirm key structural features of E. coli ProQ's FinO domain and explore its mechanism of RNA interactions. Using a bacterial three-hybrid assay, we performed forward genetic screens to confirm the importance of the concave face of ProQ in RNA binding. Using gel shift assays, we directly probed the contributions of ten amino acids on ProQ binding to seven RNA targets. Certain residues (R58, Y70, and R80) were found to be essential for binding of all seven RNAs, while substitutions of other residues (K54 and R62) caused more moderate binding defects. Interestingly, substitutions of two amino acids (K35, R69), which are evolutionarily variable but adjacent to conserved residues, showed varied effects on the binding of different RNAs; these may arise from the differing sequence context around each RNA's terminator hairpin. Together, this work confirms many of the essential RNA-binding residues in ProQ initially identified in vivo and supports a model in which residues on the conserved concave face of the FinO domain such as R58, Y70 and R80 form the main RNA-binding site of E. coli ProQ, while additional contacts contribute to the binding of certain RNAs.
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Affiliation(s)
- Ewa M. Stein
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Suxuan Wang
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA, 01075, USA
| | - Katherine Dailey
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA, 01075, USA
| | - Chandra M Gravel
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA, 01075, USA
- Department of Chemistry, Mount Holyoke College, South Hadley, MA, 01075, USA
| | - Shiying Wang
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA, 01075, USA
| | - Mikołaj Olejniczak
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Katherine E Berry
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA, 01075, USA
- Department of Chemistry, Mount Holyoke College, South Hadley, MA, 01075, USA
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5
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Nowacki J, Malenica M, Schmeing S, Schiller D, Buchmuller B, Amrahova G, 't Hart P. A translational repression reporter assay for the analysis of RNA-binding protein consensus sites. RNA Biol 2023; 20:85-94. [PMID: 36946649 PMCID: PMC10038052 DOI: 10.1080/15476286.2023.2192553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
RNA-binding proteins are essential regulators of RNA processing and function. Translational repression assays can be used to study how they interact with specific RNA sequences by insertion of such a consensus sequence into the 5' untranslated region of a reporter mRNA and measuring reporter protein translation. The straightforward set-up of these translational repression assays avoids the need for the isolation of the protein or the RNA providing speed, robustness and a low-cost method. Here, we report the optimization of the assay to function with linear RNA sequences instead of the previously reported hairpin type sequences to allow the study of a wider variety of RNA-binding proteins. Multiplication of a consensus sequence strongly improves the signal allowing analysis by both fluorescence intensity measurements and flow cytometry.
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Affiliation(s)
- Jessica Nowacki
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Mateo Malenica
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Stefan Schmeing
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Damian Schiller
- Faculty of Chemistry and Chemical Biology, Technical University of Dortmund, Dortmund, Germany
| | - Benjamin Buchmuller
- Faculty of Chemistry and Chemical Biology, Technical University of Dortmund, Dortmund, Germany
| | - Gulshan Amrahova
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Peter 't Hart
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology, Dortmund, Germany
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6
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Stockert OM, Gravel CM, Berry KE. A bacterial three-hybrid assay for forward and reverse genetic analysis of RNA-protein interactions. Nat Protoc 2022; 17:941-961. [PMID: 35197605 DOI: 10.1038/s41596-021-00657-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/03/2021] [Indexed: 11/09/2022]
Abstract
This protocol describes a bacterial three-hybrid (B3H) assay, an in vivo system that reports on RNA-protein interactions and can be implemented in both forward and reverse genetic experiments. The B3H assay connects the strength of an RNA-protein interaction inside of living Escherichia coli cells to the transcription of a reporter gene (here, lacZ). We present protocols to (1) insert RNA and protein sequences into appropriate vectors for B3H experiments, (2) detect putative RNA-protein interactions with both qualitative and quantitative readouts and (3) carry out forward genetic mutagenesis screens. The B3H assay builds on a well-established bacterial two-hybrid system for genetic analyses. As a result, protein-protein interactions can be assessed in tandem with RNA interactions with a bacterial two-hybrid assay to ensure that protein variants maintain their functionality. The B3H system is a powerful complement to traditional biochemical methods for dissecting RNA-protein interaction mechanisms: RNAs and proteins of interest do not need to be purified, and their interactions can be assessed under native conditions inside of a living bacterial cell. Once cloning has been completed, an assay can be completed in under a week and a screen in 1-2 weeks.
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Affiliation(s)
- Oliver M Stockert
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA, USA.,Medical Scientist Training Program, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Chandra M Gravel
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA, USA.,Department of Chemistry, Mount Holyoke College, South Hadley, MA, USA
| | - Katherine E Berry
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA, USA. .,Department of Chemistry, Mount Holyoke College, South Hadley, MA, USA.
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7
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Jansen S, Smlatic E, Copmans D, Debaveye S, Tangy F, Vidalain PO, Neyts J, Dallmeier K. Identification of host factors binding to dengue and Zika virus subgenomic RNA by efficient yeast three-hybrid screens of the human ORFeome. RNA Biol 2021; 18:732-744. [PMID: 33459164 PMCID: PMC8086697 DOI: 10.1080/15476286.2020.1868754] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 10/26/2022] Open
Abstract
Flaviviruses such as the dengue (DENV) and the Zika virus (ZIKV) are important human pathogens causing around 100 million symptomatic infections each year. During infection, small subgenomic flavivirus RNAs (sfRNAs) are formed inside the infected host cell as a result of incomplete degradation of the viral RNA genome by cellular exoribonuclease XRN1. Although the full extent of sfRNA functions is to be revealed, these non-coding RNAs are key virulence factors and their detrimental effects on multiple cellular processes seem to consistently involve molecular interactions with RNA-binding proteins (RBPs). Discovery of such sfRNA-binding host-factors has followed established biochemical pull-down approaches skewed towards highly abundant proteins hampering proteome-wide coverage. Yeast three-hybrid (Y3H) systems represent an attractive alternative approach. To facilitate proteome-wide screens for RBP, we revisited and improved existing RNA-Y3H methodology by (1) implementing full-length ORF libraries in combination with (2) efficient yeast mating to increase screening depth and sensitivity, and (3) stringent negative controls to eliminate over-representation of non-specific RNA-binders. These improvements were validated employing the well-characterized interaction between DDX6 (DEAD-box helicase 6) and sfRNA of DENV as paradigm. Our advanced Y3H system was used to screen for human proteins binding to DENV and ZIKV sfRNA, resulting in a list of 69 putative sfRNA-binders, including several previously reported as well as numerous novel RBP host factors. Our methodology requiring no sophisticated infrastructure or analytic pipeline may be employed for the discovery of meaningful RNA-protein interactions at large scale in other fields.
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Affiliation(s)
- Sander Jansen
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Enisa Smlatic
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
- Division of Paediatric Infectious Diseases, Ludwig-Maximilians-University Munich, Dr. Von Hauner Children’s Hospital, Munich, Germany
| | - Daniëlle Copmans
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
- KU Leuven Department of Pharmaceutical and Pharmacological Sciences, Laboratory for Molecular Biodiscovery, Leuven, Belgium
| | - Sarah Debaveye
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Frédéric Tangy
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS, Paris, France
| | - Pierre-Olivier Vidalain
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS, Paris, France
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, Lyon, France
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Kai Dallmeier
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
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8
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Wang CD, Mansky R, LeBlanc H, Gravel CM, Berry KE. Optimization of a bacterial three-hybrid assay through in vivo titration of an RNA-DNA adapter protein. RNA (NEW YORK, N.Y.) 2021; 27:513-526. [PMID: 33500316 PMCID: PMC7962490 DOI: 10.1261/rna.077404.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/19/2021] [Indexed: 05/25/2023]
Abstract
Noncoding RNAs regulate gene expression in every domain of life. In bacteria, small RNAs (sRNAs) regulate gene expression in response to stress and are often assisted by RNA-chaperone proteins, such as Hfq. We have recently developed a bacterial three-hybrid (B3H) assay that detects the strong binding interactions of certain E. coli sRNAs with proteins Hfq and ProQ. Despite the promise of this system, the signal-to-noise has made it challenging to detect weaker interactions. In this work, we use Hfq-sRNA interactions as a model system to optimize the B3H assay, so that weaker RNA-protein interactions can be more reliably detected. We find that the concentration of the RNA-DNA adapter is an important parameter in determining the signal in the system and have modified the plasmid expressing this component to tune its concentration to optimal levels. In addition, we have systematically perturbed the binding affinity of Hfq-RNA interactions to define, for the first time, the relationship between B3H signal and in vitro binding energetics. The new pAdapter construct presented here substantially expands the range of detectable interactions in the B3H assay, broadening its utility. This improved assay will increase the likelihood of identifying novel protein-RNA interactions with the B3H system and will facilitate exploration of the binding mechanisms of these interactions.
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Affiliation(s)
- Clara D Wang
- Department of Biological Sciences, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
| | - Rachel Mansky
- Department of Biological Sciences, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
| | - Hannah LeBlanc
- Program in Biochemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
| | - Chandra M Gravel
- Program in Biochemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
| | - Katherine E Berry
- Program in Biochemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
- Department of Chemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
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9
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Stein EM, Kwiatkowska J, Basczok MM, Gravel CM, Berry KE, Olejniczak M. Determinants of RNA recognition by the FinO domain of the Escherichia coli ProQ protein. Nucleic Acids Res 2020; 48:7502-7519. [PMID: 32542384 PMCID: PMC7367173 DOI: 10.1093/nar/gkaa497] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 05/27/2020] [Accepted: 06/01/2020] [Indexed: 11/13/2022] Open
Abstract
The regulation of gene expression by small RNAs in Escherichia coli depends on RNA binding proteins Hfq and ProQ, which bind mostly distinct RNA pools. To understand how ProQ discriminates between RNA substrates, we compared its binding to six different RNA molecules. Full-length ProQ bound all six RNAs similarly, while the isolated N-terminal FinO domain (NTD) of ProQ specifically recognized RNAs with Rho-independent terminators. Analysis of malM 3′-UTR mutants showed that tight RNA binding by the ProQ NTD required a terminator hairpin of at least 2 bp preceding an 3′ oligoU tail of at least four uridine residues. Substitution of an A-rich sequence on the 5′ side of the terminator to uridines strengthened the binding of several ProQ-specific RNAs to the Hfq protein, but not to the ProQ NTD. Substitution of the motif in the malM-3′ and cspE-3′ RNAs also conferred the ability to bind Hfq in E. coli cells, as measured using a three-hybrid assay. In summary, these data suggest that the ProQ NTD specifically recognizes 3′ intrinsic terminators of RNA substrates, and that the discrimination between RNA ligands by E. coli ProQ and Hfq depends both on positive determinants for binding to ProQ and negative determinants against binding to Hfq.
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Affiliation(s)
- Ewa M Stein
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Joanna Kwiatkowska
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Maciej M Basczok
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Chandra M Gravel
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA 01075, USA
| | - Katherine E Berry
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA 01075, USA.,Department of Chemistry, Mount Holyoke College, South Hadley, MA 01075, USA
| | - Mikołaj Olejniczak
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
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10
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Pandey S, Gravel CM, Stockert OM, Wang CD, Hegner CL, LeBlanc H, Berry KE. Genetic identification of the functional surface for RNA binding by Escherichia coli ProQ. Nucleic Acids Res 2020; 48:4507-4520. [PMID: 32170306 PMCID: PMC7192607 DOI: 10.1093/nar/gkaa144] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/20/2020] [Accepted: 02/24/2020] [Indexed: 12/17/2022] Open
Abstract
The FinO-domain-protein ProQ is an RNA-binding protein that has been known to play a role in osmoregulation in proteobacteria. Recently, ProQ has been shown to act as a global RNA-binding protein in Salmonella and Escherichia coli, binding to dozens of small RNAs (sRNAs) and messenger RNAs (mRNAs) to regulate mRNA-expression levels through interactions with both 5′ and 3′ untranslated regions (UTRs). Despite excitement around ProQ as a novel global RNA-binding protein, and its potential to serve as a matchmaking RNA chaperone, significant gaps remain in our understanding of the molecular mechanisms ProQ uses to interact with RNA. In order to apply the tools of molecular genetics to this question, we have adapted a bacterial three-hybrid (B3H) assay to detect ProQ’s interactions with target RNAs. Using domain truncations, site-directed mutagenesis and an unbiased forward genetic screen, we have identified a group of highly conserved residues on ProQ’s NTD as the primary face for in vivo recognition of two RNAs, and propose that the NTD structure serves as an electrostatic scaffold to recognize the shape of an RNA duplex.
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Affiliation(s)
- Smriti Pandey
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA 01075, USA
| | - Chandra M Gravel
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA 01075, USA
| | - Oliver M Stockert
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA 01075, USA
| | - Clara D Wang
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA 01075, USA
| | - Courtney L Hegner
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA 01075, USA
| | - Hannah LeBlanc
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA 01075, USA
| | - Katherine E Berry
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA 01075, USA.,Department of Chemistry, Mount Holyoke College, South Hadley, MA 01075, USA
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11
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Lemmens I, Jansen S, de Rouck S, de Smet AS, Defever D, Neyts J, Dallmeier K, Tavernier J. The Development of RNA-KISS, a Mammalian Three-Hybrid Method to Detect RNA-Protein Interactions in Living Mammalian Cells. J Proteome Res 2020; 19:2529-2538. [PMID: 32216351 DOI: 10.1021/acs.jproteome.0c00068] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
RNA-protein interactions are essential for the regulation of mRNA and noncoding RNA functions and are implicated in many diseases, such as cancer and neurodegenerative disorders. A method that can detect RNA-protein interactions in living mammalian cells on a proteome-wide scale will be an important asset to identify and study these interactions. Here we show that a combination of the mammalian two-hybrid protein-protein detection method KISS (kinase substrate sensor) and the yeast RNA three-hybrid method, utilizing the specific interaction between the MS2 RNA and MS2 coat protein, is capable of detecting RNA-protein interactions in living mammalian cells. For conceptional proof we used the subgenomic flavivirus RNA (sfRNA) of the dengue virus (DENV), a highly structured noncoding RNA derived from the DENV genome known to target host cell proteins involved in innate immunity and antiviral defense, as bait. Using RNA-KISS, we could confirm the previously established interaction between the RNA-binding domain of DDX6 and the DENV sfRNA. Finally, we performed a human proteome-wide screen for DENV sfRNA-binding host factors, identifying several known flavivirus host factors such as DDX6 and PACT, further validating the RNA-KISS method as a robust and high-throughput cell-based RNA-protein interaction screening tool.
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Affiliation(s)
- Irma Lemmens
- Cytokine Receptor Laboratory, Faculty of Medicine and Health Sciences, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Center for Medical Biotechnology, VIB, B-9000 Ghent, Belgium
| | - Sander Jansen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | - Steffi de Rouck
- Cytokine Receptor Laboratory, Faculty of Medicine and Health Sciences, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Center for Medical Biotechnology, VIB, B-9000 Ghent, Belgium
| | - Anne-Sophie de Smet
- Cytokine Receptor Laboratory, Faculty of Medicine and Health Sciences, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Center for Medical Biotechnology, VIB, B-9000 Ghent, Belgium
| | - Dieter Defever
- Cytokine Receptor Laboratory, Faculty of Medicine and Health Sciences, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Center for Medical Biotechnology, VIB, B-9000 Ghent, Belgium
| | - Johan Neyts
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | - Kai Dallmeier
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | - Jan Tavernier
- Cytokine Receptor Laboratory, Faculty of Medicine and Health Sciences, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Center for Medical Biotechnology, VIB, B-9000 Ghent, Belgium.,Orionis Biosciences, B-9052 Ghent, Belgium
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Kwiatkowska J, Wroblewska Z, Johnson KA, Olejniczak M. The binding of Class II sRNA MgrR to two different sites on matchmaker protein Hfq enables efficient competition for Hfq and annealing to regulated mRNAs. RNA (NEW YORK, N.Y.) 2018; 24:1761-1784. [PMID: 30217864 PMCID: PMC6239178 DOI: 10.1261/rna.067777.118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 09/07/2018] [Indexed: 05/08/2023]
Abstract
MgrR is an Hfq-dependent sRNA, whose transcription is controlled by the level of Mg2+ ions in Escherichia coli MgrR belongs to Class II sRNAs because its stability in the cell is affected by mutations in Hfq differently than canonical, Class I sRNAs. Here, we examined the effect of mutations in RNA binding sites of Hfq on the kinetics of the annealing of MgrR to two different target mRNAs, eptB and ygdQ, by global data fitting of the reaction kinetics monitored by gel electrophoresis of intermediates and products. The data showed that the mutation on the rim of the Hfq ring trapped MgrR on Hfq preventing the annealing of MgrR to either mRNA. The mutation in the distal face slowed the ternary complex formation and affected the release of MgrR-mRNA complexes from Hfq, while the mutation in the proximal face weakened the MgrR binding to Hfq and in this way affected the annealing. Moreover, competition assays established that MgrR bound to both faces of Hfq and competed against other sRNAs. Further studies showed that uridine-rich sequences located in less structurally stable regions served as Hfq binding sites in each mRNA. Overall, the data show that the binding of MgrR sRNA to both faces of the Hfq ring enables it to efficiently anneal to target mRNAs. It also confers on MgrR a competitive advantage over other sRNAs, which could contribute to efficient cellular response to changes in magnesium homeostasis.
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Affiliation(s)
- Joanna Kwiatkowska
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Zuzanna Wroblewska
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Kenneth A Johnson
- Institute of Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA
| | - Mikolaj Olejniczak
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
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