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Willems P, Van Ruyskensvelde V, Maruta T, Pottie R, Fernández-Fernández ÁD, Pauwels J, Hannah MA, Gevaert K, Van Breusegem F, Van der Kelen K. Mutation of Arabidopsis SME1 and Sm core assembly improves oxidative stress resilience. Free Radic Biol Med 2023; 200:117-129. [PMID: 36870374 DOI: 10.1016/j.freeradbiomed.2023.02.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/18/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
Alternative splicing is a key posttranscriptional gene regulatory process, acting in diverse adaptive and basal plant processes. Splicing of precursor-messenger RNA (pre-mRNA) is catalyzed by a dynamic ribonucleoprotein complex, designated the spliceosome. In a suppressor screen, we identified a nonsense mutation in the Smith (Sm) antigen protein SME1 to alleviate photorespiratory H2O2-dependent cell death in catalase deficient plants. Similar attenuation of cell death was observed upon chemical inhibition of the spliceosome, suggesting pre-mRNA splicing inhibition to be responsible for the observed cell death alleviation. Furthermore, the sme1-2 mutants showed increased tolerance to the reactive oxygen species inducing herbicide methyl viologen. Both an mRNA-seq and shotgun proteomic analysis in sme1-2 mutants displayed a constitutive molecular stress response, together with extensive alterations in pre-mRNA splicing of transcripts encoding metabolic enzymes and RNA binding proteins, even under unstressed conditions. Using SME1 as a bait to identify protein interactors, we provide experimental evidence for almost 50 homologs of the mammalian spliceosome-associated protein to reside in the Arabidopsis thaliana spliceosome complexes and propose roles in pre-mRNA splicing for four uncharacterized plant proteins. Furthermore, as for sme1-2, a mutant in the Sm core assembly protein ICLN resulted in a decreased sensitivity to methyl viologen. Taken together, these data show that both a perturbed Sm core composition and assembly results in the activation of a defense response and in enhanced resilience to oxidative stress.
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Affiliation(s)
- Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Technologiepark 75, 9052, Ghent, Belgium; Center for Medical Biotechnology, VIB, Technologiepark 75, 9052, Ghent, Belgium.
| | - Valerie Van Ruyskensvelde
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Ghent, Belgium.
| | - Takanori Maruta
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Ghent, Belgium; Department of Life Sciences, Faculty of Life and Environmental Sciences, Shimane University, 1060 Nishikawatsu-cho, Matsue, Shimane, 690-8504, Japan.
| | - Robin Pottie
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Ghent, Belgium.
| | - Álvaro D Fernández-Fernández
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Ghent, Belgium.
| | - Jarne Pauwels
- Department of Biomolecular Medicine, Ghent University, Technologiepark 75, 9052, Ghent, Belgium; Center for Medical Biotechnology, VIB, Technologiepark 75, 9052, Ghent, Belgium.
| | - Matthew A Hannah
- BASF Belgium Coordination Center, Innovation Center Gent, Technologiepark 101, 9052, Ghent, Belgium.
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, Technologiepark 75, 9052, Ghent, Belgium; Center for Medical Biotechnology, VIB, Technologiepark 75, 9052, Ghent, Belgium.
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Ghent, Belgium.
| | - Katrien Van der Kelen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Ghent, Belgium.
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Cai H, Roca J, Zhao YF, Woodson SA. Dynamic Refolding of OxyS sRNA by the Hfq RNA Chaperone. J Mol Biol 2022; 434:167776. [PMID: 35934049 PMCID: PMC10044511 DOI: 10.1016/j.jmb.2022.167776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/19/2022] [Accepted: 08/01/2022] [Indexed: 10/16/2022]
Abstract
The Sm protein Hfq chaperones small non-coding RNAs (sRNAs) in bacteria, facilitating sRNA regulation of target mRNAs. Hfq acts in part by remodeling the sRNA and mRNA structures, yet the basis for this remodeling activity is not understood. To understand how Hfq remodels RNA, we used single-molecule Förster resonance energy transfer (smFRET) to monitor conformational changes in OxyS sRNA upon Hfq binding. The results show that E. coli Hfq first compacts OxyS, bringing its 5' and 3 ends together. Next, Hfq destabilizes an internal stem-loop in OxyS, allowing the RNA to adopt a more open conformation that is stabilized by a conserved arginine on the rim of Hfq. The frequency of transitions between compact and open conformations depend on interactions with Hfqs flexible C-terminal domain (CTD), being more rapid when the CTD is deleted, and slower when OxyS is bound to Caulobacter crescentus Hfq, which has a shorter and more stable CTD than E. coli Hfq. We propose that the CTDs gate transitions between OxyS conformations that are stabilized by interaction with one or more arginines. These results suggest a general model for how basic residues and intrinsically disordered regions of RNA chaperones act together to refold RNA.
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Affiliation(s)
- Huahuan Cai
- Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., MD 21218, USA; Department of Chemistry, College of Chemistry and Chemical Engineering, and Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, Fujian 361005, China
| | - Jorjethe Roca
- Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., MD 21218, USA
| | - Yu-Fen Zhao
- Department of Chemistry, College of Chemistry and Chemical Engineering, and Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, Fujian 361005, China; Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Sarah A Woodson
- Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., MD 21218, USA.
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3
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Wang Z, Hong Y, Yao J, Huang H, Qian B, Liu X, Chen Y, Pang J, Zhan X, Zhu JK, Zhu J. Modulation of plant development and chilling stress responses by alternative splicing events under control of the spliceosome protein SmEb in Arabidopsis. Plant Cell Environ 2022; 45:2762-2779. [PMID: 35770732 DOI: 10.1111/pce.14386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/20/2022] [Accepted: 06/26/2022] [Indexed: 06/15/2023]
Abstract
Cold stress resulting from chilling and freezing temperatures substantially inhibits plant growth and reduces crop production worldwide. Tremendous research efforts have been focused on elucidating the molecular mechanisms of freezing tolerance in plants. However, little is known about the molecular nature of chilling stress responses in plants. Here we found that two allelic mutants in a spliceosome component gene SmEb (smeb-1 and smeb-2) are defective in development and responses to chilling stress. RNA-seq analysis revealed that SmEb controls the splicing of many pre-messenger RNAs (mRNAs) under chilling stress. Our results suggest that SmEb is important to maintain proper ratio of the two COP1 splicing variants (COP1a/COP1b) to fine tune the level of HY5. In addition, the transcription factor BES1 shows a dramatic defect in pre-mRNA splicing in the smeb mutants. Ectopic expression of the two BES1 splicing variants enhances the chilling sensitivity of the smeb-1 mutant. Furthermore, biochemical and genetic analysis showed that CBFs act as negative upstream regulators of SmEb by directly suppressing its transcription. Together, our results demonstrate that proper alternative splicing of pre-mRNAs controlled by the spliceosome component SmEb is critical for plant development and chilling stress responses.
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Affiliation(s)
- Zhen Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui, China
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yechun Hong
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Juanjuan Yao
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Huan Huang
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Bilian Qian
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland, USA
| | - Xue Liu
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yunjuan Chen
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Jia Pang
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Xiangqiang Zhan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jianhua Zhu
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui, China
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland, USA
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Mulvaney KM, Blomquist C, Acharya N, Li R, Ranaghan MJ, O'Keefe M, Rodriguez DJ, Young MJ, Kesar D, Pal D, Stokes M, Nelson AJ, Jain SS, Yang A, Mullin-Bernstein Z, Columbus J, Bozal FK, Skepner A, Raymond D, LaRussa S, McKinney DC, Freyzon Y, Baidi Y, Porter D, Aguirre AJ, Ianari A, McMillan B, Sellers WR. Molecular basis for substrate recruitment to the PRMT5 methylosome. Mol Cell 2021; 81:3481-3495.e7. [PMID: 34358446 DOI: 10.1016/j.molcel.2021.07.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/07/2021] [Accepted: 07/14/2021] [Indexed: 12/15/2022]
Abstract
PRMT5 is an essential arginine methyltransferase and a therapeutic target in MTAP-null cancers. PRMT5 uses adaptor proteins for substrate recruitment through a previously undefined mechanism. Here, we identify an evolutionarily conserved peptide sequence shared among the three known substrate adaptors (CLNS1A, RIOK1, and COPR5) and show that it is necessary and sufficient for interaction with PRMT5. We demonstrate that PRMT5 uses modular adaptor proteins containing a common binding motif for substrate recruitment, comparable with other enzyme classes such as kinases and E3 ligases. We structurally resolve the interface with PRMT5 and show via genetic perturbation that it is required for methylation of adaptor-recruited substrates including the spliceosome, histones, and ribosomal complexes. Furthermore, disruption of this site affects Sm spliceosome activity, leading to intron retention. Genetic disruption of the PRMT5-substrate adaptor interface impairs growth of MTAP-null tumor cells and is thus a site for development of therapeutic inhibitors of PRMT5.
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Affiliation(s)
| | | | | | | | - Matthew J Ranaghan
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | - Meghan O'Keefe
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Adam Skepner
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | - Donald Raymond
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | - Salvatore LaRussa
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | - David C McKinney
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | | | | | - Dale Porter
- Broad Institute, Cambridge, MA, USA; Cedilla Therapeutics, Cambridge, MA, USA
| | - Andrew J Aguirre
- Broad Institute, Cambridge, MA, USA; Medical Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | | | - Brian McMillan
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA; Tango Therapeutics, Cambridge, MA, USA
| | - William R Sellers
- Broad Institute, Cambridge, MA, USA; Medical Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
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5
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Wien F, Martinez D, Le Brun E, Jones NC, Vrønning Hoffmann S, Waeytens J, Berbon M, Habenstein B, Arluison V. The Bacterial Amyloid-Like Hfq Promotes In Vitro DNA Alignment. Microorganisms 2019; 7:microorganisms7120639. [PMID: 31816864 PMCID: PMC6956100 DOI: 10.3390/microorganisms7120639] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 11/25/2019] [Accepted: 11/28/2019] [Indexed: 12/14/2022] Open
Abstract
The Hfq protein is reported to be involved in environmental adaptation and virulence of several bacteria. In Gram-negative bacteria, Hfq mediates the interaction between regulatory noncoding RNAs and their target mRNAs. Besides these RNA-related functions, Hfq is also associated with DNA and is a part of the bacterial chromatin. Its precise role in DNA structuration is, however, unclear and whether Hfq plays a direct role in DNA-related processes such as replication or recombination is controversial. In previous works, we showed that Escherichia coli Hfq, or more precisely its amyloid-like C-terminal region (CTR), induces DNA compaction into a condensed form. In this paper, we evidence a new property for Hfq; precisely we show that its CTR influences double helix structure and base tilting, resulting in a strong local alignment of nucleoprotein Hfq:DNA fibers. The significance of this alignment is discussed in terms of chromatin structuration and possible functional consequences on evolutionary processes and adaptation to environment.
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Affiliation(s)
- Frank Wien
- Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France
- Correspondence: (F.W.); (V.A.); Tel.: +33-(0)1-69-35-96-65 (F.W.); +33-(0)1-69-08-32-82 (V.A.)
| | - Denis Martinez
- Institute of Chemistry and Biology of Membranes and Nano-objects, CBMN UMR5248 CNRS Université de Bordeaux INP, 33607 Pessac, France; (D.M.); (M.B.); (B.H.)
| | - Etienne Le Brun
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France;
| | - Nykola C. Jones
- ISA, Department of Physics and Astronomy, Aarhus University, 8000 Aarhus C, Denmark; (N.C.J.); (S.V.H.)
| | - Søren Vrønning Hoffmann
- ISA, Department of Physics and Astronomy, Aarhus University, 8000 Aarhus C, Denmark; (N.C.J.); (S.V.H.)
| | - Jehan Waeytens
- Structure et Fonction des Membranes Biologiques, Université libre de Bruxelles, B1050 Bruxelles, Belgique;
- Laboratoire de Chimie Physique d’Orsay, CNRS UMR8000, Université Paris-Sud, Université Paris-Saclay 91400 Orsay, France
| | - Melanie Berbon
- Institute of Chemistry and Biology of Membranes and Nano-objects, CBMN UMR5248 CNRS Université de Bordeaux INP, 33607 Pessac, France; (D.M.); (M.B.); (B.H.)
| | - Birgit Habenstein
- Institute of Chemistry and Biology of Membranes and Nano-objects, CBMN UMR5248 CNRS Université de Bordeaux INP, 33607 Pessac, France; (D.M.); (M.B.); (B.H.)
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France;
- Université de Paris, UFR Sciences du vivant, 35 rue Hélène Brion, 75205 Paris cedex, France
- Correspondence: (F.W.); (V.A.); Tel.: +33-(0)1-69-35-96-65 (F.W.); +33-(0)1-69-08-32-82 (V.A.)
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6
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Santiago-Frangos A, Woodson SA. Hfq chaperone brings speed dating to bacterial sRNA. Wiley Interdiscip Rev RNA 2018; 9:e1475. [PMID: 29633565 PMCID: PMC6002925 DOI: 10.1002/wrna.1475] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 02/22/2018] [Accepted: 02/26/2018] [Indexed: 11/11/2022]
Abstract
Hfq is a ubiquitous, Sm-like RNA binding protein found in most bacteria and some archaea. Hfq binds small regulatory RNAs (sRNAs), facilitates base pairing between sRNAs and their mRNA targets, and directly binds and regulates translation of certain mRNAs. Because sRNAs regulate many stress response pathways in bacteria, Hfq is essential for adaptation to different environments and growth conditions. The chaperone activities of Hfq arise from multipronged RNA binding by three different surfaces of the Hfq hexamer. The manner in which the structured Sm core of Hfq binds RNA has been well studied, but recent work shows that the intrinsically disordered C-terminal domain of Hfq modulates sRNA binding, creating a kinetic hierarchy of RNA competition for Hfq and ensuring the release of double-stranded sRNA-mRNA complexes. A combination of structural, biophysical, and genetic experiments reveals how Hfq recognizes its RNA substrates and plays matchmaker for sRNAs and mRNAs in the cell. The interplay between structured and disordered domains of Hfq optimizes sRNA-mediated post-transcriptional regulation, and is a common theme in RNA chaperones. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry.
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Affiliation(s)
- Andrew Santiago-Frangos
- Program in Cellular, Molecular and Developmental Biology and Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Sarah A Woodson
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
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Thompson LW, Morrison KD, Shirran SL, Groen EJN, Gillingwater TH, Botting CH, Sleeman JE. Neurochondrin interacts with the SMN protein suggesting a novel mechanism for spinal muscular atrophy pathology. J Cell Sci 2018; 131:jcs.211482. [PMID: 29507115 PMCID: PMC5963842 DOI: 10.1242/jcs.211482] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 02/16/2018] [Indexed: 12/15/2022] Open
Abstract
Spinal muscular atrophy (SMA) is an inherited neurodegenerative condition caused by a reduction in the amount of functional survival motor neuron (SMN) protein. SMN has been implicated in transport of mRNA in neural cells for local translation. We previously identified microtubule-dependent mobile vesicles rich in SMN and SNRPB, a member of the Sm family of small nuclear ribonucleoprotein (snRNP)-associated proteins, in neural cells. By comparing the interactomes of SNRPB and SNRPN, a neural-specific Sm protein, we now show that the essential neural protein neurochondrin (NCDN) interacts with Sm proteins and SMN in the context of mobile vesicles in neurites. NCDN has roles in protein localisation in neural cells and in maintenance of cell polarity. NCDN is required for the correct localisation of SMN, suggesting they may both be required for formation and transport of trafficking vesicles. NCDN may have potential as a therapeutic target for SMA together with, or in place of the targeting of SMN expression. This article has an associated First Person interview with the first author of the paper. Highlighted Article: The essential neural protein neurochondrin interacts with the spinal muscular atrophy (SMA) protein SMN in cell lines and in mice. This might be relevant to the molecular pathology of SMA.
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Affiliation(s)
- Luke W Thompson
- School of Biology, University of St Andrews, BSRC Complex, North Haugh St Andrews, KY16 9ST, UK
| | - Kim D Morrison
- School of Biology, University of St Andrews, BSRC Complex, North Haugh St Andrews, KY16 9ST, UK
| | - Sally L Shirran
- School of Biology, University of St Andrews, BSRC Complex, North Haugh St Andrews, KY16 9ST, UK
| | - Ewout J N Groen
- Edinburgh Medical School, Biomedical Sciences and Euan MacDonald Centre for Motor Neuron Disease Research, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh, EH8 9XD, UK
| | - Thomas H Gillingwater
- Edinburgh Medical School, Biomedical Sciences and Euan MacDonald Centre for Motor Neuron Disease Research, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh, EH8 9XD, UK
| | - Catherine H Botting
- School of Biology, University of St Andrews, BSRC Complex, North Haugh St Andrews, KY16 9ST, UK
| | - Judith E Sleeman
- School of Biology, University of St Andrews, BSRC Complex, North Haugh St Andrews, KY16 9ST, UK
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8
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Santiago-Frangos A, Jeliazkov JR, Gray JJ, Woodson SA. Acidic C-terminal domains autoregulate the RNA chaperone Hfq. eLife 2017; 6:27049. [PMID: 28826489 PMCID: PMC5606850 DOI: 10.7554/elife.27049] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/03/2017] [Indexed: 11/15/2022] Open
Abstract
The RNA chaperone Hfq is an Sm protein that facilitates base pairing between bacterial small RNAs (sRNAs) and mRNAs involved in stress response and pathogenesis. Hfq possesses an intrinsically disordered C-terminal domain (CTD) that may tune the function of the Sm domain in different organisms. In Escherichia coli, the Hfq CTD increases kinetic competition between sRNAs and recycles Hfq from the sRNA-mRNA duplex. Here, de novo Rosetta modeling and competitive binding experiments show that the acidic tip of the E. coli Hfq CTD transiently binds the basic Sm core residues necessary for RNA annealing. The CTD tip competes against non-specific RNA binding, facilitates dsRNA release, and prevents indiscriminate DNA aggregation, suggesting that this acidic peptide mimics nucleic acid to auto-regulate RNA binding to the Sm ring. The mechanism of CTD auto-inhibition predicts the chaperone function of Hfq in bacterial genera and illuminates how Sm proteins may evolve new functions.
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Affiliation(s)
- Andrew Santiago-Frangos
- Cell, Molecular and Developmental Biology and Biophysics Program, Johns Hopkins University, Baltimore, United States
| | - Jeliazko R Jeliazkov
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, United States
| | - Jeffrey J Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, United States
| | - Sarah A Woodson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
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9
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Stanek KA, Patterson-West J, Randolph PS, Mura C. Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode. Acta Crystallogr D Struct Biol 2017; 73:294-315. [PMID: 28375142 PMCID: PMC5379935 DOI: 10.1107/s2059798317000031] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 01/02/2017] [Indexed: 11/10/2022] Open
Abstract
The host factor Hfq, as the bacterial branch of the Sm family, is an RNA-binding protein involved in the post-transcriptional regulation of mRNA expression and turnover. Hfq facilitates pairing between small regulatory RNAs (sRNAs) and their corresponding mRNA targets by binding both RNAs and bringing them into close proximity. Hfq homologs self-assemble into homo-hexameric rings with at least two distinct surfaces that bind RNA. Recently, another binding site, dubbed the `lateral rim', has been implicated in sRNA·mRNA annealing; the RNA-binding properties of this site appear to be rather subtle, and its degree of evolutionary conservation is unknown. An Hfq homolog has been identified in the phylogenetically deep-branching thermophile Aquifex aeolicus (Aae), but little is known about the structure and function of Hfq from basal bacterial lineages such as the Aquificae. Therefore, Aae Hfq was cloned, overexpressed, purified, crystallized and biochemically characterized. Structures of Aae Hfq were determined in space groups P1 and P6, both to 1.5 Å resolution, and nanomolar-scale binding affinities for uridine- and adenosine-rich RNAs were discovered. Co-crystallization with U6 RNA reveals that the outer rim of the Aae Hfq hexamer features a well defined binding pocket that is selective for uracil. This Aae Hfq structure, combined with biochemical and biophysical characterization of the homolog, reveals deep evolutionary conservation of the lateral RNA-binding mode, and lays a foundation for further studies of Hfq-associated RNA biology in ancient bacterial phyla.
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Affiliation(s)
- Kimberly A. Stanek
- Department of Chemistry, University of Virginia, 409 McCormick Road, Charlottesville, VA 22904, USA
| | - Jennifer Patterson-West
- Department of Chemistry, University of Virginia, 409 McCormick Road, Charlottesville, VA 22904, USA
| | - Peter S. Randolph
- Department of Chemistry, University of Virginia, 409 McCormick Road, Charlottesville, VA 22904, USA
| | - Cameron Mura
- Department of Chemistry, University of Virginia, 409 McCormick Road, Charlottesville, VA 22904, USA
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10
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Zheng A, Panja S, Woodson SA. Arginine Patch Predicts the RNA Annealing Activity of Hfq from Gram-Negative and Gram-Positive Bacteria. J Mol Biol 2016; 428:2259-2264. [PMID: 27049793 DOI: 10.1016/j.jmb.2016.03.027] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/24/2016] [Accepted: 03/25/2016] [Indexed: 12/20/2022]
Abstract
The Sm-protein Hfq facilitates interactions between small non-coding RNA (sRNA) and target mRNAs. In enteric Gram-negative bacteria, Hfq is required for sRNA regulation, and hfq deletion results in stress intolerance and reduced virulence. By contrast, the role of Hfq in Gram-positive is less established and varies among species. The RNA binding and RNA annealing activity of Hfq from Escherichia coli, Pseudomonas aeruginosa, Listeria monocytogenes, Bacillus subtilis, and Staphylococcus aureus were compared using minimal RNAs and fluorescence spectroscopy. The results show that RNA annealing activity increases with the number of arginines in a semi-conserved patch on the rim of the Hfq hexamer and correlates with the previously reported requirement for Hfq in sRNA regulation. Thus, the amino acid sequence of the arginine patch can predict the chaperone function of Hfq in sRNA regulation in different organisms.
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Affiliation(s)
- Amy Zheng
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Subrata Panja
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA.
| | - Sarah A Woodson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA.
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