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Yeter-Alat H, Belgareh-Touzé N, Le Saux A, Huvelle E, Mokdadi M, Banroques J, Tanner NK. The RNA Helicase Ded1 from Yeast Is Associated with the Signal Recognition Particle and Is Regulated by SRP21. Molecules 2024; 29:2944. [PMID: 38931009 PMCID: PMC11206880 DOI: 10.3390/molecules29122944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/12/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
The DEAD-box RNA helicase Ded1 is an essential yeast protein involved in translation initiation that belongs to the DDX3 subfamily. The purified Ded1 protein is an ATP-dependent RNA-binding protein and an RNA-dependent ATPase, but it was previously found to lack substrate specificity and enzymatic regulation. Here we demonstrate through yeast genetics, yeast extract pull-down experiments, in situ localization, and in vitro biochemical approaches that Ded1 is associated with, and regulated by, the signal recognition particle (SRP), which is a universally conserved ribonucleoprotein complex required for the co-translational translocation of polypeptides into the endoplasmic reticulum lumen and membrane. Ded1 is physically associated with SRP components in vivo and in vitro. Ded1 is genetically linked with SRP proteins. Finally, the enzymatic activity of Ded1 is inhibited by SRP21 in the presence of SCR1 RNA. We propose a model where Ded1 actively participates in the translocation of proteins during translation. Our results provide a new understanding of the role of Ded1 during translation.
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Affiliation(s)
- Hilal Yeter-Alat
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France; (H.Y.-A.); (A.L.S.); (E.H.); (M.M.); (J.B.)
- Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, 75005 Paris, France
| | - Naïma Belgareh-Touzé
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, UMR8226 CNRS, Sorbonne Université, 13 rue Pierre et Marie Curie, 75005 Paris, France;
| | - Agnès Le Saux
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France; (H.Y.-A.); (A.L.S.); (E.H.); (M.M.); (J.B.)
- Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, 75005 Paris, France
| | - Emmeline Huvelle
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France; (H.Y.-A.); (A.L.S.); (E.H.); (M.M.); (J.B.)
- Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, 75005 Paris, France
| | - Molka Mokdadi
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France; (H.Y.-A.); (A.L.S.); (E.H.); (M.M.); (J.B.)
- Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, 75005 Paris, France
- Laboratory of Molecular Epidemiology and Experimental Pathology, LR16IPT04, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis 1002, Tunisia
- Institut National des Sciences Appliquées et Technologies, Université de Carthage, Tunis 1080, Tunisia
| | - Josette Banroques
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France; (H.Y.-A.); (A.L.S.); (E.H.); (M.M.); (J.B.)
- Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, 75005 Paris, France
| | - N. Kyle Tanner
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France; (H.Y.-A.); (A.L.S.); (E.H.); (M.M.); (J.B.)
- Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, 75005 Paris, France
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2
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Massenet S. In vivo assembly of eukaryotic signal recognition particle: A still enigmatic process involving the SMN complex. Biochimie 2019; 164:99-104. [PMID: 30978374 DOI: 10.1016/j.biochi.2019.04.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/07/2019] [Indexed: 12/29/2022]
Abstract
The signal recognition particle (SRP) is a universally conserved non-coding ribonucleoprotein complex that is essential for targeting transmembrane and secretory proteins to the endoplasmic reticulum. Its composition and size varied during evolution. In mammals, SRP contains one RNA molecule, 7SL RNA, and six proteins: SRP9, 14, 19, 54, 68 and 72. Despite a very good understanding of the SRP structure and of the SRP assembly in vitro, how SRP is assembled in vivo remains largely enigmatic. Here we review current knowledge on how the 7SL RNA is assembled with core proteins to form functional RNP particles in cells. SRP biogenesis is believed to take place both in the nucleolus and in the cytoplasm and to rely on the survival of motor neuron complex, whose defect leads to spinal muscular atrophy.
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Affiliation(s)
- Séverine Massenet
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-University of Lorraine, Biopôle de l'Université de Lorraine, Campus Brabois-Santé, 9 avenue de la forêt de Haye, BP 20199, 54505 Vandoeuvre-les-Nancy, France.
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Maeda T, Tanaka Y, Wachi M, Inui M. Polynucleotide Phosphorylase, RNase E/G, and YbeY Are Involved in the Maturation of 4.5S RNA in Corynebacterium glutamicum. J Bacteriol 2017; 199:e00798-16. [PMID: 28031281 PMCID: PMC5309912 DOI: 10.1128/jb.00798-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 12/20/2016] [Indexed: 12/13/2022] Open
Abstract
Corynebacterium glutamicum has been applied for the industrial production of various metabolites, such as amino acids. To understand the biosynthesis of the membrane protein in this bacterium, we investigated the process of signal recognition particle (SRP) assembly. SRP is found in all three domains of life and plays an important role in the membrane insertion of proteins. SRP RNA is initially transcribed as precursor molecules; however, relatively little is known about its maturation. In C. glutamicum, SRP consists of the Ffh protein and 4.5S RNA lacking an Alu domain. In this study, we found that 3'-to-5' exoribonuclease, polynucleotide phosphorylase (PNPase), and two endo-type RNases, RNase E/G and YbeY, are involved in the 3' maturation of 4.5S RNA in C. glutamicum The mature form of 4.5S RNA was inefficiently formed in ΔrneG Δpnp mutant cells, suggesting the existence of an alternative pathway for the 3' maturation of 4.5S RNA. Primer extension analysis also revealed that the 5' mature end of 4.5S RNA corresponds to that of the transcriptional start site. Immunoprecipitated Ffh protein contained immature 4.5S RNA in Δpnp, ΔrneG, and ΔybeY mutants, suggesting that 4.5S RNA precursors can interact with Ffh. These results imply that the maturation of 4.5S RNA can be performed in the 4.5S RNA-Ffh complex.IMPORTANCE Overproduction of a membrane protein, such as a transporter, is useful for engineering of strains of Corynebacterium glutamicum, which is a workhorse of amino acid production. To understand membrane protein biogenesis in this bacterium, we investigated the process of signal recognition particle (SRP) assembly. SRP contains the Ffh protein and SRP RNA and plays an important role in the membrane insertion of proteins. Although SRP RNA is highly conserved among the three domains of life, relatively little is known about its maturation. We show that PNPase, RNase E/G, and YbeY are involved in the 3' maturation of the SRP RNA (4.5S RNA) in this bacterium. This indicates that 3' end processing in this organism is different from that in other bacteria, such as Escherichia coli.
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Affiliation(s)
- Tomoya Maeda
- Research Institute of Innovative Technology for the Earth, Kyoto, Japan
- Department of Bioengineering, Tokyo Institute of Technology, Yokohama, Japan
| | - Yuya Tanaka
- Research Institute of Innovative Technology for the Earth, Kyoto, Japan
| | - Masaaki Wachi
- Department of Bioengineering, Tokyo Institute of Technology, Yokohama, Japan
| | - Masayuki Inui
- Research Institute of Innovative Technology for the Earth, Kyoto, Japan
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
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4
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Russo J, Lee JE, López CM, Anderson J, Nguyen TMP, Heck AM, Wilusz J, Wilusz CJ. The CELF1 RNA-Binding Protein Regulates Decay of Signal Recognition Particle mRNAs and Limits Secretion in Mouse Myoblasts. PLoS One 2017; 12:e0170680. [PMID: 28129347 PMCID: PMC5271678 DOI: 10.1371/journal.pone.0170680] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 01/09/2017] [Indexed: 02/06/2023] Open
Abstract
We previously identified several mRNAs encoding components of the secretory pathway, including signal recognition particle (SRP) subunit mRNAs, among transcripts associated with the RNA-binding protein CELF1. Through immunoprecipitation of RNAs crosslinked to CELF1 in myoblasts and in vitro binding assays using recombinant CELF1, we now provide evidence that CELF1 directly binds the mRNAs encoding each of the subunits of the SRP. Furthermore, we determined the half-lives of the Srp transcripts in control and CELF1 knockdown myoblasts. Our results indicate CELF1 is a destabilizer of at least five of the six Srp transcripts and that the relative abundance of the SRP proteins is out of balance when CELF1 is depleted. CELF1 knockdown myoblasts exhibit altered secretion of a luciferase reporter protein and are impaired in their ability to migrate and close a wound, consistent with a defect in the secreted extracellular matrix. Importantly, similar defects in wound healing are observed when SRP subunit imbalance is induced by over-expression of SRP68. Our studies support the existence of an RNA regulon containing Srp mRNAs that is controlled by CELF1. One implication is that altered function of CELF1 in myotonic dystrophy may contribute to changes in the extracellular matrix of affected muscle through defects in secretion.
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Affiliation(s)
- Joseph Russo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Jerome E. Lee
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Carolina M. López
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - John Anderson
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Thuy-mi P. Nguyen
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Adam M. Heck
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Carol J. Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail:
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5
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Weyer FA, Gumiero A, Gesé GV, Lapouge K, Sinning I. Structural insights into a unique Hsp70-Hsp40 interaction in the eukaryotic ribosome-associated complex. Nat Struct Mol Biol 2017; 24:144-151. [PMID: 28067917 DOI: 10.1038/nsmb.3349] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 12/01/2016] [Indexed: 01/19/2023]
Abstract
Cotranslational chaperones assist de novo folding of nascent polypeptides, prevent them from aggregating and modulate translation. The ribosome-associated complex (RAC) is unique in that the Hsp40 protein Zuo1 and the atypical Hsp70 chaperone Ssz1 form a stable heterodimer, which acts as a cochaperone for the Hsp70 chaperone Ssb. Here we present the structure of the Chaetomium thermophilum RAC core comprising Ssz1 and the Zuo1 N terminus. We show how the conserved allostery of Hsp70 proteins is abolished and this Hsp70-Hsp40 pair is molded into a functional unit. Zuo1 stabilizes Ssz1 in trans through interactions that in canonical Hsp70s occur in cis. Ssz1 is catalytically inert and cannot adopt the closed conformation, but the substrate binding domain β is completed by Zuo1. Our study offers insights into the coupling of a special Hsp70-Hsp40 pair, which evolved to link protein folding and translation.
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Affiliation(s)
| | - Andrea Gumiero
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | | | - Karine Lapouge
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
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6
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Gumiero A, Conz C, Gesé GV, Zhang Y, Weyer FA, Lapouge K, Kappes J, von Plehwe U, Schermann G, Fitzke E, Wölfle T, Fischer T, Rospert S, Sinning I. Interaction of the cotranslational Hsp70 Ssb with ribosomal proteins and rRNA depends on its lid domain. Nat Commun 2016; 7:13563. [PMID: 27882919 PMCID: PMC5123055 DOI: 10.1038/ncomms13563] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 10/13/2016] [Indexed: 12/22/2022] Open
Abstract
Cotranslational chaperones assist in de novo folding of nascent polypeptides in all organisms. In yeast, the heterodimeric ribosome-associated complex (RAC) forms a unique chaperone triad with the Hsp70 homologue Ssb. We report the X-ray structure of full length Ssb in the ATP-bound open conformation at 2.6 Å resolution and identify a positively charged region in the α-helical lid domain (SBDα), which is present in all members of the Ssb-subfamily of Hsp70s. Mutational analysis demonstrates that this region is strictly required for ribosome binding. Crosslinking shows that Ssb binds close to the tunnel exit via contacts with both, ribosomal proteins and rRNA, and that specific contacts can be correlated with switching between the open (ATP-bound) and closed (ADP-bound) conformation. Taken together, our data reveal how Ssb dynamics on the ribosome allows for the efficient interaction with nascent chains upon RAC-mediated activation of ATP hydrolysis. In yeast, the heterodimeric ribosome-associated complex (RAC) acts in concert with the Hsp70 protein Ssb, forming a unique chaperone triad. Here the authors use structural and biochemical approaches to shed light on how translation and folding are coupled in eukaryotes.
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Affiliation(s)
- Andrea Gumiero
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Charlotte Conz
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104 Freiburg, Germany
| | - Genís Valentín Gesé
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Ying Zhang
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104 Freiburg, Germany
| | - Felix Alexander Weyer
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Julia Kappes
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany
| | - Ulrike von Plehwe
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany
| | - Géza Schermann
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Edith Fitzke
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104 Freiburg, Germany
| | - Tina Wölfle
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104 Freiburg, Germany
| | - Tamás Fischer
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Sabine Rospert
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104 Freiburg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
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7
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Dumesic PA, Rosenblad MA, Samuelsson T, Nguyen T, Moresco JJ, Yates JR, Madhani HD. Noncanoncial signal recognition particle RNAs in a major eukaryotic phylum revealed by purification of SRP from the human pathogen Cryptococcus neoformans. Nucleic Acids Res 2015; 43:9017-27. [PMID: 26275773 PMCID: PMC4605306 DOI: 10.1093/nar/gkv819] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 08/01/2015] [Indexed: 12/21/2022] Open
Abstract
Despite conservation of the signal recognition particle (SRP) from bacteria to man, computational approaches have failed to identify SRP components from genomes of many lower eukaryotes, raising the possibility that they have been lost or altered in those lineages. We report purification and analysis of SRP in the human pathogen Cryptococcus neoformans, providing the first description of SRP in basidiomycetous yeast. The C. neoformans SRP RNA displays a predicted structure in which the universally conserved helix 8 contains an unprecedented stem-loop insertion. Guided by this sequence, we computationally identified 152 SRP RNAs throughout the phylum Basidiomycota. This analysis revealed additional helix 8 alterations including single and double stem-loop insertions as well as loop diminutions affecting RNA structural elements that are otherwise conserved from bacteria to man. Strikingly, these SRP RNA features in Basidiomycota are accompanied by phylum-specific alterations in the RNA-binding domain of Srp54, the SRP protein subunit that directly interacts with helix 8. Our findings reveal unexpected fungal SRP diversity and suggest coevolution of the two most conserved SRP features-SRP RNA helix 8 and Srp54-in basidiomycetes. Because members of this phylum include important human and plant pathogens, these noncanonical features provide new targets for antifungal compound development.
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Affiliation(s)
- Phillip A Dumesic
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Magnus A Rosenblad
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, SE-405 30, Sweden
| | - Tore Samuelsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, SE-405 30, Sweden
| | - Tiffany Nguyen
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - James J Moresco
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
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