1
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Reislöhner S, Schermann G, Kilian M, Santamaría-Muñoz D, Zimmerli C, Kellner N, Baßler J, Brunner M, Hurt E. Identification and characterization of sugar-regulated promoters in Chaetomium thermophilum. BMC Biotechnol 2023; 23:19. [PMID: 37422618 PMCID: PMC10329369 DOI: 10.1186/s12896-023-00791-9] [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: 08/11/2022] [Accepted: 06/20/2023] [Indexed: 07/10/2023] Open
Abstract
The thermophilic fungus Chaetomium thermophilum has been used extensively for biochemical and high-resolution structural studies of protein complexes. However, subsequent functional analyses of these assemblies have been hindered owing to the lack of genetic tools compatible with this thermophile, which are typically suited to other mesophilic eukaryotic model organisms, in particular the yeast Saccharomyces cerevisiae. Hence, we aimed to find genes from C. thermophilum that are expressed under the control of different sugars and examine their associated 5' untranslated regions as promoters responsible for sugar-regulated gene expression. To identify sugar-regulated promoters in C. thermophilum, we performed comparative xylose- versus glucose-dependent gene expression studies, which uncovered a number of enzymes with induced expression in the presence of xylose but repressed expression in glucose-supplemented media. Subsequently, we cloned the promoters of the two most stringently regulated genes, the xylosidase-like gene (XYL) and xylitol dehydrogenase (XDH), obtained from this genome-wide analysis in front of a thermostable yellow fluorescent protein (YFP) reporter. With this, we demonstrated xylose-dependent YFP expression by both Western blotting and live-cell imaging fluorescence microscopy. Prompted by these results, we expressed the C. thermophilum orthologue of a well-characterized dominant-negative ribosome assembly factor mutant, under the control of the XDH promoter, which allowed us to induce a nuclear export defect on the pre-60S subunit when C. thermophilum cells were grown in xylose- but not glucose-containing medium. Altogether, our study identified xylose-regulatable promoters in C. thermophilum, which might facilitate functional studies of genes of interest in this thermophilic eukaryotic model organism.
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Affiliation(s)
- Sven Reislöhner
- Biochemistry Center (BZH), University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Geza Schermann
- Institute for Neurovascular Cell Biology, University Hospital Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Max Kilian
- Max-Planck-Institute für terrestrische Mikrobiologie, Marburg, Germany
| | | | - Christian Zimmerli
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-Von-Laue-Straße 3, Frankfurt Am Main, 60438 Germany
| | - Nikola Kellner
- Biochemistry Center (BZH), University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Jochen Baßler
- Biochemistry Center (BZH), University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Michael Brunner
- Biochemistry Center (BZH), University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Ed Hurt
- Biochemistry Center (BZH), University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
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2
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Kišonaitė M, Wild K, Lapouge K, Gesé GV, Kellner N, Hurt E, Sinning I. Structural inventory of cotranslational protein folding by the eukaryotic RAC complex. Nat Struct Mol Biol 2023; 30:670-677. [PMID: 37081320 DOI: 10.1038/s41594-023-00973-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 03/20/2023] [Indexed: 04/22/2023]
Abstract
The challenge of nascent chain folding at the ribosome is met by the conserved ribosome-associated complex (RAC), which forms a chaperone triad with the Hsp70 protein Ssb in fungi, and consists of the non-canonical Hsp70 Ssz1 and the J domain protein Zuotin (Zuo1). Here we determine cryo-EM structures of Chaetomium thermophilum RAC bound to 80S ribosomes. RAC adopts two distinct conformations accommodating continuous ribosomal rotation by a flexible lever arm. It is held together by a tight interaction between the Ssz1 substrate-binding domain and the Zuo1 N terminus, and additional contacts between the Ssz1 nucleotide-binding domain and Zuo1 J- and Zuo1 homology domains, which form a rigid unit. The Zuo1 HPD motif conserved in J-proteins is masked in a non-canonical interaction by the Ssz1 nucleotide-binding domain, and allows the positioning of Ssb for activation by Zuo1. Overall, we provide the basis for understanding how RAC cooperates with Ssb in a dynamic nascent chain interaction and protein folding.
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Affiliation(s)
- Miglė Kišonaitė
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Klemens Wild
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | | | - Nikola Kellner
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Ed Hurt
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany.
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3
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Dörner K, Ruggeri C, Zemp I, Kutay U. Ribosome biogenesis factors-from names to functions. EMBO J 2023; 42:e112699. [PMID: 36762427 PMCID: PMC10068337 DOI: 10.15252/embj.2022112699] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/13/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
The assembly of ribosomal subunits is a highly orchestrated process that involves a huge cohort of accessory factors. Most eukaryotic ribosome biogenesis factors were first identified by genetic screens and proteomic approaches of pre-ribosomal particles in Saccharomyces cerevisiae. Later, research on human ribosome synthesis not only demonstrated that the requirement for many of these factors is conserved in evolution, but also revealed the involvement of additional players, reflecting a more complex assembly pathway in mammalian cells. Yet, it remained a challenge for the field to assign a function to many of the identified factors and to reveal their molecular mode of action. Over the past decade, structural, biochemical, and cellular studies have largely filled this gap in knowledge and led to a detailed understanding of the molecular role that many of the players have during the stepwise process of ribosome maturation. Such detailed knowledge of the function of ribosome biogenesis factors will be key to further understand and better treat diseases linked to disturbed ribosome assembly, including ribosomopathies, as well as different types of cancer.
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Affiliation(s)
- Kerstin Dörner
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.,Molecular Life Sciences Ph.D. Program, Zurich, Switzerland
| | - Chiara Ruggeri
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.,RNA Biology Ph.D. Program, Zurich, Switzerland
| | - Ivo Zemp
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Ulrike Kutay
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
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4
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Fiedler M, Franco-Echevarría E, Schulten A, Nielsen M, Rutherford TJ, Yeates A, Ahsan B, Dean C, Bienz M. Head-to-tail polymerization by VEL proteins underpins cold-induced Polycomb silencing in flowering control. Cell Rep 2022; 41:111607. [PMID: 36351412 PMCID: PMC7614096 DOI: 10.1016/j.celrep.2022.111607] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/30/2022] [Accepted: 10/14/2022] [Indexed: 11/09/2022] Open
Abstract
Transcriptional silencing through the Polycomb silencing machinery utilizes a "read-write" mechanism involving histone tail modifications. However, nucleation of silencing and long-term stable transmission of the silenced state also requires P-olycomb Repressive Complex 2 (PRC2) accessory proteins, whose molecular role is poorly understood. The Arabidopsis VEL proteins are accessory proteins that interact with PRC2 to nucleate and propagate silencing at the FLOWERING LOCUS C (FLC) locus, enabling early flowering in spring. Here, we report that VEL proteins contain a domain related to an atypical four-helix bundle that engages in spontaneous concentration-dependent head-to-tail polymerization to assemble dynamic biomolecular condensates. Mutations blocking polymerization of this VEL domain prevent Polycomb silencing at FLC. Plant VEL proteins thus facilitate assembly of dynamic multivalent Polycomb complexes required for inheritance of the silenced state.
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Affiliation(s)
- Marc Fiedler
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | | | - Anna Schulten
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Mathias Nielsen
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Trevor J Rutherford
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Anna Yeates
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Bilal Ahsan
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Caroline Dean
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Mariann Bienz
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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5
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Prattes M, Grishkovskaya I, Hodirnau VV, Hetzmannseder C, Zisser G, Sailer C, Kargas V, Loibl M, Gerhalter M, Kofler L, Warren AJ, Stengel F, Haselbach D, Bergler H. Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. Nat Struct Mol Biol 2022; 29:942-953. [PMID: 36097293 PMCID: PMC9507969 DOI: 10.1038/s41594-022-00832-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 08/03/2022] [Indexed: 11/23/2022]
Abstract
The AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis that initiates cytoplasmic maturation of the large ribosomal subunit. Drg1 releases the shuttling maturation factor Rlp24 from pre-60S particles shortly after nuclear export, a strict requirement for downstream maturation. The molecular mechanism of release remained elusive. Here, we report a series of cryo-EM structures that captured the extraction of Rlp24 from pre-60S particles by Saccharomyces cerevisiae Drg1. These structures reveal that Arx1 and the eukaryote-specific rRNA expansion segment ES27 form a joint docking platform that positions Drg1 for efficient extraction of Rlp24 from the pre-ribosome. The tips of the Drg1 N domains thereby guide the Rlp24 C terminus into the central pore of the Drg1 hexamer, enabling extraction by a hand-over-hand translocation mechanism. Our results uncover substrate recognition and processing by Drg1 step by step and provide a comprehensive mechanistic picture of the conserved modus operandi of AAA-ATPases.
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Affiliation(s)
- Michael Prattes
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Irina Grishkovskaya
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
| | | | | | - Gertrude Zisser
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Carolin Sailer
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Vasileios Kargas
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Cambridge, UK
- Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge School of Clinical Medicine, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Mathias Loibl
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | | | - Lisa Kofler
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Alan J Warren
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Cambridge, UK
- Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge School of Clinical Medicine, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Florian Stengel
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - David Haselbach
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria.
| | - Helmut Bergler
- Institute of Molecular Biosciences, University of Graz, Graz, Austria.
- BioTechMed-Graz, Graz, Austria.
- Field of Excellence BioHealth - University of Graz, Graz, Austria.
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6
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Structural remodeling of ribosome associated Hsp40-Hsp70 chaperones during co-translational folding. Nat Commun 2022; 13:3410. [PMID: 35701497 PMCID: PMC9197937 DOI: 10.1038/s41467-022-31127-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 06/02/2022] [Indexed: 11/16/2022] Open
Abstract
Ribosome associated complex (RAC), an obligate heterodimer of HSP40 and HSP70 (Zuo1 and Ssz1 in yeast), is conserved in eukaryotes and functions as co-chaperone for another HSP70 (Ssb1/2 in yeast) to facilitate co-translational folding of nascent polypeptides. Many mechanistic details, such as the coordination of one HSP40 with two HSP70s and the dynamic interplay between RAC-Ssb and growing nascent chains, remain unclear. Here, we report three sets of structures of RAC-containing ribosomal complexes isolated from Saccharomyces cerevisiae. Structural analyses indicate that RAC on the nascent-chain-free ribosome is in an autoinhibited conformation, and in the presence of a nascent chain at the peptide tunnel exit (PTE), RAC undergoes large-scale structural remodeling to make Zuo1 J-Domain more accessible to Ssb. Our data also suggest a role of Zuo1 in orienting Ssb-SBD proximal to the PTE for easy capture of the substrate. Altogether, in accordance with previous data, our work suggests a sequence of structural remodeling events for RAC-Ssb during co-translational folding, triggered by the binding and passage of growing nascent chain from one to another. Ribosome associated complex (RAC)- HSP70 (Ssb in yeast) is a eukaryotic chaperone system involved in co-translational folding. Here, authors report structures of RAC-containing ribosomal complexes, which suggest a working model for the dynamic actions of RAC-Ssb during the process.
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7
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Mo C, Xie C, Wang G, Tian T, Liu J, Zhu C, Xiao X, Xiao Y. Cyclophilin acts as a ribosome biogenesis factor by chaperoning the ribosomal protein (PlRPS15) in filamentous fungi. Nucleic Acids Res 2021; 49:12358-12376. [PMID: 34792171 PMCID: PMC8643696 DOI: 10.1093/nar/gkab1102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 10/18/2021] [Accepted: 10/22/2021] [Indexed: 11/14/2022] Open
Abstract
The rapid transport of ribosomal proteins (RPs) into the nucleus and their efficient assembly into pre-ribosomal particles are prerequisites for ribosome biogenesis. Proteins that act as dedicated chaperones for RPs to maintain their stability and facilitate their assembly have not been identified in filamentous fungi. PlCYP5 is a nuclear cyclophilin in the nematophagous fungus Purpureocillium lilacinum, whose expression is up-regulated during abiotic stress and nematode egg-parasitism. Here, we found that PlCYP5 co-translationally interacted with the unassembled small ribosomal subunit protein, PlRPS15 (uS19). PlRPS15 contained an eukaryote-specific N-terminal extension that mediated the interaction with PlCYP5. PlCYP5 increased the solubility of PlRPS15 independent of its catalytic peptide-prolyl isomerase function and supported the integration of PlRPS15 into pre-ribosomes. Consistently, the phenotypes of the PlCYP5 loss-of-function mutant were similar to those of the PlRPS15 knockdown mutant (e.g. growth and ribosome biogenesis defects). PlCYP5 homologs in Arabidopsis thaliana, Homo sapiens, Schizosaccharomyces pombe, Sclerotinia sclerotiorum, Botrytis cinerea and Metarhizium anisopliae were identified. Notably, PlCYP5-PlRPS15 homologs from three filamentous fungi interacted with each other but not those from other species. In summary, our data disclosed a unique dedicated chaperone system for RPs by cyclophilin in filamentous fungi.
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Affiliation(s)
- Chenmi Mo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.,Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Chong Xie
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Gaofeng Wang
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Tian Tian
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Juan Liu
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Chunxiao Zhu
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Xueqiong Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.,Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Yannong Xiao
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
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8
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Singh A, Schermann G, Reislöhner S, Kellner N, Hurt E, Brunner M. Global Transcriptome Characterization and Assembly of the Thermophilic Ascomycete Chaetomium thermophilum. Genes (Basel) 2021; 12:1549. [PMID: 34680944 PMCID: PMC8535861 DOI: 10.3390/genes12101549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/24/2021] [Accepted: 09/26/2021] [Indexed: 12/30/2022] Open
Abstract
A correct genome annotation is fundamental for research in the field of molecular and structural biology. The annotation of the reference genome of Chaetomium thermophilum has been reported previously, but it is essentially limited to open reading frames (ORFs) of protein coding genes and contains only a few noncoding transcripts. In this study, we identified and annotated full-length transcripts of C. thermophilum by deep RNA sequencing. We annotated 7044 coding genes and 4567 noncoding genes. Astonishingly, 23% of the coding genes are alternatively spliced. We identified 679 novel coding genes as well as 2878 novel noncoding genes and corrected the structural organization of more than 50% of the previously annotated genes. Furthermore, we substantially extended the Gene Ontology (GO) and Enzyme Commission (EC) lists, which provide comprehensive search tools for potential industrial applications and basic research. The identified novel transcripts and improved annotation will help to understand the gene regulatory landscape in C. thermophilum. The analysis pipeline developed here can be used to build transcriptome assemblies and identify coding and noncoding RNAs of other species.
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Affiliation(s)
| | | | | | | | | | - Michael Brunner
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany; (A.S.); (G.S.); (S.R.); (N.K.); (E.H.)
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9
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Lee K, Ziegelhoffer T, Delewski W, Berger SE, Sabat G, Craig EA. Pathway of Hsp70 interactions at the ribosome. Nat Commun 2021; 12:5666. [PMID: 34580293 PMCID: PMC8476630 DOI: 10.1038/s41467-021-25930-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 09/08/2021] [Indexed: 11/09/2022] Open
Abstract
In eukaryotes, an Hsp70 molecular chaperone triad assists folding of nascent chains emerging from the ribosome tunnel. In fungi, the triad consists of canonical Hsp70 Ssb, atypical Hsp70 Ssz1 and J-domain protein cochaperone Zuo1. Zuo1 binds the ribosome at the tunnel exit. Zuo1 also binds Ssz1, tethering it to the ribosome, while its J-domain stimulates Ssb’s ATPase activity to drive efficient nascent chain interaction. But the function of Ssz1 and how Ssb engages at the ribosome are not well understood. Employing in vivo site-specific crosslinking, we found that Ssb(ATP) heterodimerizes with Ssz1. Ssb, in a manner consistent with the ADP conformation, also crosslinks to ribosomal proteins across the tunnel exit from Zuo1. These two modes of Hsp70 Ssb interaction at the ribosome suggest a functionally efficient interaction pathway: first, Ssb(ATP) with Ssz1, allowing optimal J-domain and nascent chain engagement; then, after ATP hydrolysis, Ssb(ADP) directly with the ribosome. Here, the authors use in vivo site-specific crosslinking to provide molecular-level insight into how the fungal Hsp70 chaperone system — the Ssb:Ssz1:Zuo1 triad — assists the folding process for the nascent peptide chain emerging from the ribosome tunnel.
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Affiliation(s)
- Kanghyun Lee
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.,Department of Biochemistry and Biophysics, Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, 94158, USA
| | - Thomas Ziegelhoffer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Wojciech Delewski
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Scott E Berger
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.,Department of Chemistry, Lafayette College, Easton, PA, 18042, USA.,Biophysics Program, Stanford University, Stanford, CA, 94305, USA
| | - Grzegorz Sabat
- Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Elizabeth A Craig
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.
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10
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A role for the ribosome-associated complex in activation of the IRE1 branch of UPR. Cell Rep 2021; 35:109217. [PMID: 34107246 DOI: 10.1016/j.celrep.2021.109217] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 03/31/2021] [Accepted: 05/13/2021] [Indexed: 12/11/2022] Open
Abstract
The ubiquitous ribosome-associated complex (RAC) is a chaperone that spans ribosomes, making contacts near both the polypeptide exit tunnel and the decoding center, a position prime for sensing and coordinating translation and folding. Loss of RAC is known to result in growth defects and sensitization to translational and osmotic stresses. However, the physiological substrates of RAC and the mechanism(s) by which RAC is involved in responding to specific stresses in higher eukaryotes remain obscure. The data presented here uncover an essential function of mammalian RAC in the unfolded protein response (UPR). Knockdown of RAC sensitizes mammalian cells to endoplasmic reticulum (ER) stress and selectively interferes with IRE1 branch activation. Higher-order oligomerization of the inositol-requiring enzyme 1α (IRE1α) kinase/endoribonuclease depends upon RAC. These results reveal a surveillance function for RAC in the UPR, as follows: modulating IRE1α clustering as required for endonuclease activation and splicing of the substrate Xbp1 mRNA.
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11
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Fries SJ, Braun TS, Globisch C, Peter C, Drescher M, Deuerling E. Deciphering molecular details of the RAC-ribosome interaction by EPR spectroscopy. Sci Rep 2021; 11:8681. [PMID: 33883604 PMCID: PMC8060413 DOI: 10.1038/s41598-021-87847-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/25/2021] [Indexed: 11/09/2022] Open
Abstract
The eukaryotic ribosome-associated complex (RAC) plays a significant role in de novo protein folding. Its unique interaction with the ribosome, comprising contacts to both ribosomal subunits, suggests a RAC-mediated coordination between translation elongation and co-translational protein folding. Here, we apply electron paramagnetic resonance (EPR) spectroscopy combined with site-directed spin labeling (SDSL) to gain deeper insights into a RAC-ribosome contact affecting translational accuracy. We identified a local contact point of RAC to the ribosome. The data provide the first experimental evidence for the existence of a four-helix bundle as well as a long α-helix in full-length RAC, in solution as well as on the ribosome. Additionally, we complemented the structural picture of the region mediating this functionally important contact on the 40S ribosomal subunit. In sum, this study constitutes the first application of SDSL-EPR spectroscopy to elucidate the molecular details of the interaction between the 3.3 MDa translation machinery and a chaperone complex.
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Affiliation(s)
- Sandra J Fries
- Department of Biology, Molecular Microbiology, University of Konstanz, 78457, Konstanz, Germany.,Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, 78457, Konstanz, Germany
| | - Theresa S Braun
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, 78457, Konstanz, Germany.,Department of Chemistry, Physical and Biophysical Chemistry, University of Konstanz, 78457, Konstanz, Germany
| | - Christoph Globisch
- Department of Chemistry, Computational and Theoretical Chemistry, University of Konstanz, 78457, Konstanz, Germany
| | - Christine Peter
- Department of Chemistry, Computational and Theoretical Chemistry, University of Konstanz, 78457, Konstanz, Germany
| | - Malte Drescher
- Department of Chemistry, Physical and Biophysical Chemistry, University of Konstanz, 78457, Konstanz, Germany.
| | - Elke Deuerling
- Department of Biology, Molecular Microbiology, University of Konstanz, 78457, Konstanz, Germany.
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12
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Ghosh A, Shcherbik N. Cooperativity between the Ribosome-Associated Chaperone Ssb/RAC and the Ubiquitin Ligase Ltn1 in Ubiquitination of Nascent Polypeptides. Int J Mol Sci 2020; 21:ijms21186815. [PMID: 32957466 PMCID: PMC7554835 DOI: 10.3390/ijms21186815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/12/2020] [Accepted: 09/14/2020] [Indexed: 11/25/2022] Open
Abstract
Eukaryotic cells have evolved multiple mechanisms to detect and eliminate aberrant polypeptides. Co-translational protein surveillance systems play an important role in these mechanisms. These systems include ribosome-associated protein quality control (RQC) that detects aberrant nascent chains stalled on ribosomes and promotes their ubiquitination and degradation by the proteasome, and ribosome-associated chaperone Ssb/RAC, which ensures correct nascent chain folding. Despite the known function of RQC and Ssb/ribosome-associated complex (RAC) in monitoring the quality of newly generated polypeptides, whether they cooperate during initial stages of protein synthesis remains unexplored. Here, we provide evidence that Ssb/RAC and the ubiquitin ligase Ltn1, the major component of RQC, display genetic and functional cooperativity. Overexpression of Ltn1 rescues growth suppression of the yeast strain-bearing deletions of SSB genes during proteotoxic stress. Moreover, Ssb/RAC promotes Ltn1-dependent ubiquitination of nascent chains associated with 80S ribosomal particles but not with translating ribosomes. Consistent with this finding, quantitative western blot analysis revealed lower levels of Ltn1 associated with 80S ribosomes and with free 60S ribosomal subunits in the absence of Ssb/RAC. We propose a mechanism in which Ssb/RAC facilitates recruitment of Ltn1 to ribosomes, likely by detecting aberrations in nascent chains and leading to their ubiquitination and degradation.
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13
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The ribosome-associated complex RAC serves in a relay that directs nascent chains to Ssb. Nat Commun 2020; 11:1504. [PMID: 32198371 PMCID: PMC7083937 DOI: 10.1038/s41467-020-15313-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 03/03/2020] [Indexed: 11/21/2022] Open
Abstract
The conserved ribosome-associated complex (RAC) consisting of Zuo1 (Hsp40) and Ssz1 (non-canonical Hsp70) acts together with the ribosome-bound Hsp70 chaperone Ssb in de novo protein folding at the ribosomal tunnel exit. Current models suggest that the function of Ssz1 is confined to the support of Zuo1, however, it is not known whether RAC by itself serves as a chaperone for nascent chains. Here we show that, via its rudimentary substrate binding domain (SBD), Ssz1 directly binds to emerging nascent chains prior to Ssb. Structural and biochemical analyses identify a conserved LP-motif at the Zuo1 N-terminus forming a polyproline-II helix, which binds to the Ssz1-SBD as a pseudo-substrate. The LP-motif competes with nascent chain binding to the Ssz1-SBD and modulates nascent chain transfer. The combined data indicate that Ssz1 is an active chaperone optimized for transient, low-affinity substrate binding, which ensures the flux of nascent chains through RAC/Ssb. The ribosome-associated complex (RAC), which contains the Hsp40 protein Zuo1 and the non-canonical Hsp70 protein Ssz1 forms a chaperone triad with the fungal-specific Hsp70 protein Ssb. Here the authors combine X-ray crystallography, crosslinking and biochemical experiments and present the structure of the Zuo1 N-terminus bound to Ssz1 and demonstrate that Ssz1 is an active chaperone for nascent chains.
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14
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Deuerling E, Gamerdinger M, Kreft SG. Chaperone Interactions at the Ribosome. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a033977. [PMID: 30833456 DOI: 10.1101/cshperspect.a033977] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The continuous refreshment of the proteome is critical to maintain protein homeostasis and to adapt cells to changing conditions. Thus, de novo protein biogenesis by ribosomes is vitally important to every cellular system. This process is delicate and error-prone and requires, besides cytosolic chaperones, the guidance by a specialized set of molecular chaperones that bind transiently to the translation machinery and the nascent protein to support early folding events and to regulate cotranslational protein transport. These chaperones include the bacterial trigger factor (TF), the archaeal and eukaryotic nascent polypeptide-associated complex (NAC), and the eukaryotic ribosome-associated complex (RAC). This review focuses on the structures, functions, and substrates of these ribosome-associated chaperones and highlights the most recent findings about their potential mechanisms of action.
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Affiliation(s)
- Elke Deuerling
- Molecular Microbiology, Department of Biology, University of Konstanz, 78464 Konstanz, Germany
| | - Martin Gamerdinger
- Molecular Microbiology, Department of Biology, University of Konstanz, 78464 Konstanz, Germany
| | - Stefan G Kreft
- Molecular Microbiology, Department of Biology, University of Konstanz, 78464 Konstanz, Germany
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15
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The Link That Binds: The Linker of Hsp70 as a Helm of the Protein's Function. Biomolecules 2019; 9:biom9100543. [PMID: 31569820 PMCID: PMC6843406 DOI: 10.3390/biom9100543] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 09/13/2019] [Accepted: 09/21/2019] [Indexed: 12/26/2022] Open
Abstract
The heat shock 70 (Hsp70) family of molecular chaperones plays a central role in maintaining cellular proteostasis. Structurally, Hsp70s are composed of an N-terminal nucleotide binding domain (NBD) which exhibits ATPase activity, and a C-terminal substrate binding domain (SBD). The binding of ATP at the NBD and its subsequent hydrolysis influences the substrate binding affinity of the SBD through allostery. Similarly, peptide binding at the C-terminal SBD stimulates ATP hydrolysis by the N-terminal NBD. Interdomain communication between the NBD and SBD is facilitated by a conserved linker segment. Hsp70s form two main subgroups. Canonical Hsp70 members generally suppress protein aggregation and are also capable of refolding misfolded proteins. Hsp110 members are characterized by an extended lid segment and their function tends to be largely restricted to suppression of protein aggregation. In addition, the latter serve as nucleotide exchange factors (NEFs) of canonical Hsp70s. The linker of the Hsp110 family is less conserved compared to that of the canonical Hsp70 group. In addition, the linker plays a crucial role in defining the functional features of these two groups of Hsp70. Generally, the linker of Hsp70 is quite small and varies in size from seven to thirteen residues. Due to its small size, any sequence variation that Hsp70 exhibits in this motif has a major and unique influence on the function of the protein. Based on sequence data, we observed that canonical Hsp70s possess a linker that is distinct from similar segments present in Hsp110 proteins. In addition, Hsp110 linker motifs from various genera are distinct suggesting that their unique features regulate the flexibility with which the NBD and SBD of these proteins communicate via allostery. The Hsp70 linker modulates various structure-function features of Hsp70 such as its global conformation, affinity for peptide substrate and interaction with co-chaperones. The current review discusses how the unique features of the Hsp70 linker accounts for the functional specialization of this group of molecular chaperones.
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16
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Structure and evolution of the 4-helix bundle domain of Zuotin, a J-domain protein co-chaperone of Hsp70. PLoS One 2019; 14:e0217098. [PMID: 31091298 PMCID: PMC6519820 DOI: 10.1371/journal.pone.0217098] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 05/03/2019] [Indexed: 11/28/2022] Open
Abstract
The J-domain protein Zuotin is a multi-domain eukaryotic Hsp70 co-chaperone. Though it is primarily ribosome-associated, positioned at the exit of the 60S subunit tunnel where it promotes folding of nascent polypeptide chains, Zuotin also has off-ribosome functions. Domains of Zuotin needed for 60S association and interaction with Hsp70 are conserved in eukaryotes. However, whether the 4-helix bundle (4HB) domain is conserved remains an open question. We undertook evolutionary and structural approaches to clarify this issue. We found that the 4HB segment of human Zuotin also forms a bundle of 4 helices. The positive charge of Helix I, which in Saccharomyces cerevisiae is responsible for interaction with the 40S subunit, is particularly conserved. However, the C-termini of fungal and human 4HBs are not similar. In fungi the C-terminal segment forms a plug that folds back into the bundle; in S. cerevisiae it plays an important role in bundle stability and, off the ribosome, in transcriptional activation. In human, C-terminal helix IV of the 4HB is extended, protruding from the bundle. This extension serves as a linker to the regulatory SANT domains, which are present in animals, plants and protists, but not fungi. Further analysis of Zuotin sequences revealed that the plug likely arose as a result of genomic rearrangement upon SANT domain loss early in the fungal lineage. In the lineage leading to S. cerevisiae, the 4HB was subjected to positive selection with the plug becoming increasingly hydrophobic. Eventually, these hydrophobic plug residues were coopted for a novel regulatory function—activation of a recently emerged transcription factor, Pdr1. Our data suggests that Zuotin evolved off-ribosome functions twice—once involving SANT domains, then later in fungi, after SANT domain loss, by coopting the hydrophobic plug. Zuotin serves as an example of complex intertwining of molecular chaperone function and cell regulation.
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17
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G-Quadruplexes in Human Ribosomal RNA. J Mol Biol 2019; 431:1940-1955. [PMID: 30885721 DOI: 10.1016/j.jmb.2019.03.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 11/20/2022]
Abstract
rRNA is the single most abundant polymer in most cells. Mammalian rRNAs are nearly twice as large as those of prokaryotes. Differences in rRNA size are due to expansion segments, which contain extended tentacles in metazoans. Here we show that the terminus of an rRNA tentacle of Homo sapiens contains 10 tandem G-tracts that form highly stable G-quadruplexes in vitro. We characterized rRNA of the H. sapiens large ribosomal subunit by computation, circular dichroism, UV melting, fluorescent probes, nuclease accessibility, electrophoretic mobility shifts, and blotting. We investigated Expansion Segment 7 (ES7), oligomers derived from ES7, intact 28S rRNA, 80S ribosomes, and polysomes. We used mass spectrometry to identify proteins that bind to rRNA G-quadruplexes in cell lysates. These proteins include helicases (DDX3, CNBP, DDX21, DDX17) and heterogeneous nuclear ribonucleoproteins. Finally, by multiple sequence alignments, we observe that G-quadruplex-forming sequences are a general feature of LSU rRNA of Chordata but not, as far as we can tell, of other species. Chordata ribosomes present polymorphic tentacles with the potential to switch between inter- and intramolecular G-quadruplexes. To our knowledge, G-quadruplexes have not been reported previously in ribosomes.
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18
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Pobre KFR, Poet GJ, Hendershot LM. The endoplasmic reticulum (ER) chaperone BiP is a master regulator of ER functions: Getting by with a little help from ERdj friends. J Biol Chem 2018; 294:2098-2108. [PMID: 30563838 DOI: 10.1074/jbc.rev118.002804] [Citation(s) in RCA: 247] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The endoplasmic reticulum (ER) represents the entry point into the secretory pathway where nascent proteins encounter a specialized environment for their folding and maturation. Inherent to these processes is a dedicated quality-control system that detects proteins that fail to mature properly and targets them for cytosolic degradation. An imbalance in protein folding and degradation can result in the accumulation of unfolded proteins in the ER, resulting in the activation of a signaling cascade that restores proper homeostasis in this organelle. The ER heat shock protein 70 (Hsp70) family member BiP is an ATP-dependent chaperone that plays a critical role in these processes. BiP interacts with specific ER-localized DnaJ family members (ERdjs), which stimulate BiP's ATP-dependent substrate interactions, with several ERdjs also binding directly to unfolded protein clients. Recent structural and biochemical studies have provided detailed insights into the allosteric regulation of client binding by BiP and have enhanced our understanding of how specific ERdjs enable BiP to perform its many functions in the ER. In this review, we discuss how BiP's functional cycle and interactions with ERdjs enable it to regulate protein homeostasis in the ER and ensure protein quality control.
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Affiliation(s)
- Kristine Faye R Pobre
- From the Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Greg J Poet
- From the Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Linda M Hendershot
- From the Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
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19
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Parker MS, Balasubramaniam A, Sallee FR, Parker SL. The Expansion Segments of 28S Ribosomal RNA Extensively Match Human Messenger RNAs. Front Genet 2018; 9:66. [PMID: 29563925 PMCID: PMC5850279 DOI: 10.3389/fgene.2018.00066] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 02/15/2018] [Indexed: 11/26/2022] Open
Abstract
Eukaryote ribosomal RNAs (rRNAs) have expanded in the course of phylogeny by addition of nucleotides in specific insertion areas, the expansion segments. These number about 40 in the larger (25–28S) rRNA (up to 2,400 nucleotides), and about 12 in the smaller (18S) rRNA (<700 nucleotides). Expansion of the larger rRNA shows a clear phylogenetic increase, with a dramatic rise in mammals and especially in hominids. Substantial portions of expansion segments in this RNA are not bound to ribosomal proteins, and may engage extraneous interactants, including messenger RNAs (mRNAs). Studies on the ribosome-mRNA interaction have focused on proteins of the smaller ribosomal subunit, with some examination of 18S rRNA. However, the expansion segments of human 28S rRNA show much higher density and numbers of mRNA matches than those of 18S rRNA, and also a higher density and match numbers than its own core parts. We have studied that with frequent and potentially stable matches containing 7–15 nucleotides. The expansion segments of 28S rRNA average more than 50 matches per mRNA even assuming only 5% of their sequence as available for such interaction. Large expansion segments 7, 15, and 27 of 28S rRNA also have copious long (≥10-nucleotide) matches to most human mRNAs, with frequencies much higher than in other 28S rRNA parts. Expansion segments 7 and 27 and especially segment 15 of 28S rRNA show large size increase in mammals compared to other metazoans, which could reflect a gain of function related to interaction with non-ribosomal partners. The 28S rRNA expansion segment 15 shows very high increments in size, guanosine, and cytidine nucleotide content and mRNA matching in mammals, and especially in hominids. With these segments (but not with other 28S rRNA or any 18S rRNA expansion segments) the density and number of matches are much higher in 5′-terminal than in 3′-terminal untranslated mRNA regions, which may relate to mRNA mobilization via 5′ termini. Matches in the expansion segments 7, 15, and 27 of human 28S rRNA appear as candidates for general interaction with mRNAs, especially those associated with intracellular matrices such as the endoplasmic reticulum.
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Affiliation(s)
- Michael S Parker
- Department of Microbiology and Molecular Cell Sciences, University of Memphis, Memphis, TN, United States
| | | | - Floyd R Sallee
- Department of Psychiatry, University of Cincinnati School of Medicine, Cincinnati, OH, United States
| | - Steven L Parker
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, TN, United States
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20
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Parks MM, Kurylo CM, Dass RA, Bojmar L, Lyden D, Vincent CT, Blanchard SC. Variant ribosomal RNA alleles are conserved and exhibit tissue-specific expression. SCIENCE ADVANCES 2018; 4:eaao0665. [PMID: 29503865 PMCID: PMC5829973 DOI: 10.1126/sciadv.aao0665] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 01/08/2018] [Indexed: 05/25/2023]
Abstract
The ribosome, the integration point for protein synthesis in the cell, is conventionally considered a homogeneous molecular assembly that only passively contributes to gene expression. Yet, epigenetic features of the ribosomal DNA (rDNA) operon and changes in the ribosome's molecular composition have been associated with disease phenotypes, suggesting that the ribosome itself may possess inherent regulatory capacity. Analyzing whole-genome sequencing data from the 1000 Genomes Project and the Mouse Genomes Project, we find that rDNA copy number varies widely across individuals, and we identify pervasive intra- and interindividual nucleotide variation in the 5S, 5.8S, 18S, and 28S ribosomal RNA (rRNA) genes of both human and mouse. Conserved rRNA sequence heterogeneities map to functional centers of the assembled ribosome, variant rRNA alleles exhibit tissue-specific expression, and ribosomes bearing variant rRNA alleles are present in the actively translating ribosome pool. These findings provide a critical framework for exploring the possibility that the expression of genomically encoded variant rRNA alleles gives rise to physically and functionally heterogeneous ribosomes that contribute to mammalian physiology and human disease.
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Affiliation(s)
- Matthew M. Parks
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Chad M. Kurylo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Randall A. Dass
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Linda Bojmar
- Children’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children’s Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
- Department of Surgery, County Council of Östergötland, and Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, 58185 Linköping, Sweden
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - David Lyden
- Children’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children’s Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - C. Theresa Vincent
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Scott C. Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- Tri-Institutional Training Program in Chemical Biology, Weill Cornell Medicine, New York, NY 10065, USA
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21
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Ferrer M, Sorokin DY, Wolf YI, Ciordia S, Mena MC, Bargiela R, Koonin EV, Makarova KS. Proteomic Analysis of Methanonatronarchaeum thermophilum AMET1, a Representative of a Putative New Class of Euryarchaeota, "Methanonatronarchaeia". Genes (Basel) 2018; 9:E28. [PMID: 29360740 PMCID: PMC5852551 DOI: 10.3390/genes9020028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 01/09/2018] [Accepted: 01/10/2018] [Indexed: 01/22/2023] Open
Abstract
The recently discovered Methanonatronarchaeia are extremely halophilic and moderately thermophilic methyl-reducing methanogens representing a novel class-level lineage in the phylum Euryarchaeota related to the class Halobacteria. Here we present a detailed analysis of 1D-nano liquid chromatography-electrospray ionization tandem mass spectrometry data obtained for "Methanonatronarchaeum thermophilum" AMET1 grown in different physiological conditions, including variation of the growth temperature and substrates. Analysis of these data allows us to refine the current understanding of the key biosynthetic pathways of this triple extremophilic methanogenic euryarchaeon and identify proteins that are likely to be involved in its response to growth condition changes.
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Affiliation(s)
| | - Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre for Biotechnology, Russian Academy of Sciences, Prospect 60-let Octyabrya 7/2, 117312 Moscow, Russia.
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Sergio Ciordia
- Proteomics Facility, Centro Nacional de Biotecnología, CSIC, 28049 Madrid, Spain.
| | - María C Mena
- Proteomics Facility, Centro Nacional de Biotecnología, CSIC, 28049 Madrid, Spain.
| | | | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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22
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Li Z, Guo Q, Zheng L, Ji Y, Xie YT, Lai DH, Lun ZR, Suo X, Gao N. Cryo-EM structures of the 80S ribosomes from human parasites Trichomonas vaginalis and Toxoplasma gondii. Cell Res 2017; 27:1275-1288. [PMID: 28809395 DOI: 10.1038/cr.2017.104] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 05/27/2017] [Accepted: 06/27/2017] [Indexed: 12/20/2022] Open
Abstract
As an indispensable molecular machine universal in all living organisms, the ribosome has been selected by evolution to be the natural target of many antibiotics and small-molecule inhibitors. High-resolution structures of pathogen ribosomes are crucial for understanding the general and unique aspects of translation control in disease-causing microbes. With cryo-electron microscopy technique, we have determined structures of the cytosolic ribosomes from two human parasites, Trichomonas vaginalis and Toxoplasma gondii, at resolution of 3.2-3.4 Å. Although the ribosomal proteins from both pathogens are typical members of eukaryotic families, with a co-evolution pattern between certain species-specific insertions/extensions and neighboring ribosomal RNA (rRNA) expansion segments, the sizes of their rRNAs are sharply different. Very interestingly, rRNAs of T. vaginalis are in size comparable to prokaryotic counterparts, with nearly all the eukaryote-specific rRNA expansion segments missing. These structures facilitate the dissection of evolution path for ribosomal proteins and RNAs, and may aid in design of novel translation inhibitors.
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Affiliation(s)
- Zhifei Li
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiang Guo
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lvqin Zheng
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yongsheng Ji
- Anhui Provincial Laboratory of Pathogen Biology, Anhui Key Laboratory of Zoonoses, Department of Microbiology and Parasitology, Anhui Medical University, Hefei, Anhui 230022, China
| | - Yi-Ting Xie
- Center for Parasitic Organisms, State Key Laboratory of Biocontrol, Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China
| | - De-Hua Lai
- Center for Parasitic Organisms, State Key Laboratory of Biocontrol, Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China
| | - Zhao-Rong Lun
- Center for Parasitic Organisms, State Key Laboratory of Biocontrol, Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China
| | - Xun Suo
- State Key Laboratory of Agrobiotechnology &National Animal Protozoa Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
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23
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Two chaperones locked in an embrace: structure and function of the ribosome-associated complex RAC. Nat Struct Mol Biol 2017; 24:611-619. [PMID: 28771464 DOI: 10.1038/nsmb.3435] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/14/2017] [Indexed: 12/26/2022]
Abstract
Chaperones, which assist protein folding are essential components of every living cell. The yeast ribosome-associated complex (RAC) is a chaperone that is highly conserved in eukaryotic cells. The RAC consists of the J protein Zuo1 and the unconventional Hsp70 homolog Ssz1. The RAC heterodimer stimulates the ATPase activity of the ribosome-bound Hsp70 homolog Ssb, which interacts with nascent polypeptide chains to facilitate de novo protein folding. In addition, the RAC-Ssb system is required to maintain the fidelity of protein translation. Recent work reveals important details of the unique structures of RAC and Ssb and identifies how the chaperones interact with the ribosome. The new findings start to uncover how the exceptional chaperone triad cooperates in protein folding and maintenance of translational fidelity and its connection to extraribosomal functions.
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24
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Döring K, Ahmed N, Riemer T, Suresh HG, Vainshtein Y, Habich M, Riemer J, Mayer MP, O'Brien EP, Kramer G, Bukau B. Profiling Ssb-Nascent Chain Interactions Reveals Principles of Hsp70-Assisted Folding. Cell 2017; 170:298-311.e20. [PMID: 28708998 DOI: 10.1016/j.cell.2017.06.038] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 04/04/2017] [Accepted: 06/23/2017] [Indexed: 12/21/2022]
Abstract
The yeast Hsp70 chaperone Ssb interacts with ribosomes and nascent polypeptides to assist protein folding. To reveal its working principle, we determined the nascent chain-binding pattern of Ssb at near-residue resolution by in vivo selective ribosome profiling. Ssb associates broadly with cytosolic, nuclear, and hitherto unknown substrate classes of mitochondrial and endoplasmic reticulum (ER) nascent proteins, supporting its general chaperone function. Ssb engages most substrates by multiple binding-release cycles to a degenerate sequence enriched in positively charged and aromatic amino acids. Timely association with this motif upon emergence at the ribosomal tunnel exit requires ribosome-associated complex (RAC) but not nascent polypeptide-associated complex (NAC). Ribosome footprint densities along orfs reveal faster translation at times of Ssb binding, mainly imposed by biases in mRNA secondary structure, codon usage, and Ssb action. Ssb thus employs substrate-tailored dynamic nascent chain associations to coordinate co-translational protein folding, facilitate accelerated translation, and support membrane targeting of organellar proteins.
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Affiliation(s)
- Kristina Döring
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg, Germany; German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - Nabeel Ahmed
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Trine Riemer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg, Germany; German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - Harsha Garadi Suresh
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg, Germany; German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany; The Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, Canada
| | - Yevhen Vainshtein
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg, Germany
| | - Markus Habich
- Institute of Biochemistry, University of Cologne, Zuelpicher Str. 47, Cologne, Germany
| | - Jan Riemer
- Institute of Biochemistry, University of Cologne, Zuelpicher Str. 47, Cologne, Germany
| | - Matthias P Mayer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg, Germany
| | - Edward P O'Brien
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA; Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Günter Kramer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg, Germany; German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany.
| | - Bernd Bukau
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg, Germany; German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany.
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25
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Protein quality control at the ribosome: focus on RAC, NAC and RQC. Essays Biochem 2017; 60:203-212. [PMID: 27744336 DOI: 10.1042/ebc20160011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 05/09/2016] [Indexed: 11/17/2022]
Abstract
The biogenesis of new polypeptides by ribosomes and their subsequent correct folding and localization to the appropriate cellular compartments are essential key processes to maintain protein homoeostasis. These complex mechanisms are governed by a repertoire of protein biogenesis factors that directly bind to the ribosome and chaperone nascent polypeptide chains as soon as they emerge from the ribosomal tunnel exit. This nascent chain 'welcoming committee' regulates multiple co-translational processes including protein modifications, folding, targeting and degradation. Acting at the front of the protein production line, these ribosome-associated protein biogenesis factors lead the way in the cellular proteostasis network to ensure proteome integrity. In this article, I focus on three different systems in eukaryotes that are critical for the maintenance of protein homoeostasis by controlling the birth, life and death of nascent polypeptide chains.
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26
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Weyer FA, Gumiero A, Lapouge K, Bange G, Kopp J, Sinning I. Structural basis of HypK regulating N-terminal acetylation by the NatA complex. Nat Commun 2017; 8:15726. [PMID: 28585574 PMCID: PMC5467210 DOI: 10.1038/ncomms15726] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 04/21/2017] [Indexed: 11/09/2022] Open
Abstract
In eukaryotes, N-terminal acetylation is one of the most common protein modifications involved in a wide range of biological processes. Most N-acetyltransferase complexes (NATs) act co-translationally, with the heterodimeric NatA complex modifying the majority of substrate proteins. Here we show that the Huntingtin yeast two-hybrid protein K (HypK) binds tightly to the NatA complex comprising the auxiliary subunit Naa15 and the catalytic subunit Naa10. The crystal structures of NatA bound to HypK or to a N-terminal deletion variant of HypK were determined without or with a bi-substrate analogue, respectively. The HypK C-terminal region is responsible for high-affinity interaction with the C-terminal part of Naa15. In combination with acetylation assays, the HypK N-terminal region is identified as a negative regulator of the NatA acetylation activity. Our study provides mechanistic insights into the regulation of this pivotal protein modification. N-terminal acetylation is a common eukaryotic protein modification that is primarily catalysed by the N-acetyl transferase complex A (NatA). Here, the authors present the crystal structure of NatA bound to Huntingtin yeast two-hybrid protein K (HypK) and show that HypK is a negative regulator of NatA.
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Affiliation(s)
- Felix Alexander Weyer
- Heidelberg University Biochemistry Center (BZH), INF328, D-69120 Heidelberg, Germany
| | - Andrea Gumiero
- Heidelberg University Biochemistry Center (BZH), INF328, D-69120 Heidelberg, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Center (BZH), INF328, D-69120 Heidelberg, Germany
| | - Gert Bange
- Heidelberg University Biochemistry Center (BZH), INF328, D-69120 Heidelberg, Germany
| | - Jürgen Kopp
- Heidelberg University Biochemistry Center (BZH), INF328, D-69120 Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), INF328, D-69120 Heidelberg, Germany
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27
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Ponce-Rojas JC, Avendaño-Monsalve MC, Yañez-Falcón AR, Jaimes-Miranda F, Garay E, Torres-Quiroz F, DeLuna A, Funes S. αβ'-NAC cooperates with Sam37 to mediate early stages of mitochondrial protein import. FEBS J 2017; 284:814-830. [PMID: 28109174 DOI: 10.1111/febs.14024] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 12/20/2016] [Accepted: 01/18/2017] [Indexed: 11/30/2022]
Abstract
The mitochondrial proteome is mostly composed of nuclear-encoded proteins. Such polypeptides are synthesized with signals that guide their intracellular transport to the surface of the organelle and later within the different mitochondrial subcompartments until they reach their functional destination. It has been suggested that the nascent-polypeptide associated complex (NAC) - a cytosolic chaperone that recognizes nascent chains on translationally active ribosomes - has a role in the import of nuclear-encoded mitochondrial proteins. However, the molecular mechanisms that regulate the NAC-mediated cotranslational import are still not clear. Here, we show that a particular NAC heterodimer formed by subunits α and β' in Saccharomyces cerevisiae is specifically involved in the process of mitochondrial import and functionally cooperates with Sam37, an outer membrane protein subunit of the sorting and assembly machinery complex. Mutants in both components display growth defects, incorrectly accumulate precursor forms of mitochondrial proteins in the cytosol, and have an altered mitochondrial protein content. We propose that αβ'-NAC and Sam37 are members of the system that recognizes mitochondrial proteins at early stages of their synthesis, escorting them to the import machinery of mitochondria.
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Affiliation(s)
- José Carlos Ponce-Rojas
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico
| | - Maria Clara Avendaño-Monsalve
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico
| | - Armando Roberto Yañez-Falcón
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico
| | - Fabiola Jaimes-Miranda
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico
| | - Erika Garay
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Mexico
| | - Francisco Torres-Quiroz
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico
| | - Alexander DeLuna
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Mexico
| | - Soledad Funes
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico
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28
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Baßler J, Ahmed YL, Kallas M, Kornprobst M, Calviño FR, Gnädig M, Thoms M, Stier G, Ismail S, Kharde S, Castillo N, Griesel S, Bastuck S, Bradatsch B, Thomson E, Flemming D, Sinning I, Hurt E. Interaction network of the ribosome assembly machinery from a eukaryotic thermophile. Protein Sci 2017; 26:327-342. [PMID: 27863450 DOI: 10.1002/pro.3085] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 10/24/2016] [Accepted: 11/08/2016] [Indexed: 12/30/2022]
Abstract
Ribosome biogenesis in eukaryotic cells is a highly dynamic and complex process innately linked to cell proliferation. The assembly of ribosomes is driven by a myriad of biogenesis factors that shape pre-ribosomal particles by processing and folding the ribosomal RNA and incorporating ribosomal proteins. Biochemical approaches allowed the isolation and characterization of pre-ribosomal particles from Saccharomyces cerevisiae, which lead to a spatiotemporal map of biogenesis intermediates along the path from the nucleolus to the cytoplasm. Here, we cloned almost the entire set (∼180) of ribosome biogenesis factors from the thermophilic fungus Chaetomium thermophilum in order to perform an in-depth analysis of their protein-protein interaction network as well as exploring the suitability of these thermostable proteins for structural studies. First, we performed a systematic screen, testing about 80 factors for crystallization and structure determination. Next, we performed a yeast 2-hybrid analysis and tested about 32,000 binary combinations, which identified more than 1000 protein-protein contacts between the thermophilic ribosome assembly factors. To exemplary verify several of these interactions, we performed biochemical reconstitution with the focus on the interaction network between 90S pre-ribosome factors forming the ctUTP-A and ctUTP-B modules, and the Brix-domain containing assembly factors of the pre-60S subunit. Our work provides a rich resource for biochemical reconstitution and structural analyses of the conserved ribosome assembly machinery from a eukaryotic thermophile.
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Affiliation(s)
- Jochen Baßler
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Yasar Luqman Ahmed
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Martina Kallas
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Markus Kornprobst
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Fabiola R Calviño
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Marén Gnädig
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Matthias Thoms
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Gunter Stier
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Sherif Ismail
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Satyavati Kharde
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Nestor Castillo
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Sabine Griesel
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Sonja Bastuck
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Bettina Bradatsch
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Emma Thomson
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Dirk Flemming
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Irmgard Sinning
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
| | - Ed Hurt
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, 69120, Germany
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29
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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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30
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Inada T. The Ribosome as a Platform for mRNA and Nascent Polypeptide Quality Control. Trends Biochem Sci 2017; 42:5-15. [DOI: 10.1016/j.tibs.2016.09.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 09/05/2016] [Accepted: 09/13/2016] [Indexed: 11/28/2022]
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31
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Multivalent contacts of the Hsp70 Ssb contribute to its architecture on ribosomes and nascent chain interaction. Nat Commun 2016; 7:13695. [PMID: 27917864 PMCID: PMC5150220 DOI: 10.1038/ncomms13695] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 10/25/2016] [Indexed: 01/11/2023] Open
Abstract
Hsp70 chaperones assist de novo folding of newly synthesized proteins in all cells. In yeast, the specialized Hsp70 Ssb directly binds to ribosomes. The structural basis and functional mode of recruitment of Ssb to ribosomes is not understood. Here, we present the molecular details underlying ribosome binding of Ssb in Saccharomyces cerevisiae. This interaction is multifaceted, involving the co-chaperone RAC and two specific regions within Ssb characterized by positive charges. The C-terminus of Ssb mediates the key contact and a second attachment point is provided by a KRR-motif in the substrate binding domain. Strikingly, ribosome binding of Ssb is not essential. Autonomous ribosome attachment becomes necessary if RAC is absent, suggesting a dual mode of Ssb recruitment to nascent chains. We propose, that the multilayered ribosomal interaction allows positioning of Ssb in an optimal orientation to the tunnel exit guaranteeing an efficient nascent polypeptide interaction. The correct folding of proteins often requires the intervention molecular chaperones, which can occur co-translationally. Here the authors identify elements of yeast Ssb (Hsp70) that mediate ribosomal binding, and suggest a mechanism that directs efficient interaction of Ssb with the nascent chain.
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32
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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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33
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Pillet B, Mitterer V, Kressler D, Pertschy B. Hold on to your friends: Dedicated chaperones of ribosomal proteins: Dedicated chaperones mediate the safe transfer of ribosomal proteins to their site of pre-ribosome incorporation. Bioessays 2016; 39:1-12. [PMID: 27859409 DOI: 10.1002/bies.201600153] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Eukaryotic ribosomes are assembled from their components, the ribosomal RNAs and ribosomal proteins, in a tremendously complex, multi-step process, which primarily takes place in the nuclear compartment. Therefore, most ribosomal proteins have to travel from the cytoplasm to their incorporation site on pre-ribosomes within the nucleus. However, due to their particular characteristics, such as a highly basic amino acid composition and the presence of unstructured extensions, ribosomal proteins are especially prone to aggregation and degradation in their unassembled state, hence specific mechanisms must operate to ensure their safe delivery. Recent studies have uncovered a group of proteins, termed dedicated chaperones, specialized in accompanying and guarding individual ribosomal proteins. In this essay, we review how these dedicated chaperones utilize different folds to interact with their ribosomal protein clients and how they ensure their soluble expression and interconnect their intracellular transport with their efficient assembly into pre-ribosomes.
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Affiliation(s)
- Benjamin Pillet
- Unit of Biochemistry, Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Valentin Mitterer
- Institut für Molekulare Biowissenschaften, Universität Graz, Graz, Austria
| | - Dieter Kressler
- Unit of Biochemistry, Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Brigitte Pertschy
- Institut für Molekulare Biowissenschaften, Universität Graz, Graz, Austria
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34
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Greber BJ. Mechanistic insight into eukaryotic 60S ribosomal subunit biogenesis by cryo-electron microscopy. RNA (NEW YORK, N.Y.) 2016; 22:1643-1662. [PMID: 27875256 PMCID: PMC5066618 DOI: 10.1261/rna.057927.116] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Eukaryotic ribosomes, the protein-producing factories of the cell, are composed of four ribosomal RNA molecules and roughly 80 proteins. Their biogenesis is a complex process that involves more than 200 biogenesis factors that facilitate the production, modification, and assembly of ribosomal components and the structural transitions along the maturation pathways of the pre-ribosomal particles. Here, I review recent structural and mechanistic insights into the biogenesis of the large ribosomal subunit that were furthered by cryo-electron microscopy of natively purified pre-60S particles and in vitro reconstituted ribosome assembly factor complexes. Combined with biochemical, genetic, and previous structural data, these structures have provided detailed insights into the assembly and maturation of the central protuberance of the 60S subunit, the network of biogenesis factors near the ribosomal tunnel exit, and the functional activation of the large ribosomal subunit during cytoplasmic maturation.
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Affiliation(s)
- Basil J Greber
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720-3220, USA
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35
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Lee K, Sharma R, Shrestha OK, Bingman CA, Craig EA. Dual interaction of the Hsp70 J-protein cochaperone Zuotin with the 40S and 60S ribosomal subunits. Nat Struct Mol Biol 2016; 23:1003-1010. [PMID: 27669034 PMCID: PMC5097012 DOI: 10.1038/nsmb.3299] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 08/31/2016] [Indexed: 12/30/2022]
Abstract
Ribosome-associated J protein-Hsp70 chaperones promote nascent polypeptide folding and normal translational fidelity. Though known to span the ribosome subunits, understanding of J protein Zuo1 function is limited. New structural and crosslinking data allow more precise positioning of Saccharomyces cerevisiae Zuo1 near the 60S polypeptide exit site, pointing to interactions with ribosomal protein eL31 and 25S rRNA helix 24. The junction between the 60S-interacting and subunit-spanning helices is a hinge, positioning Zuo1 on the 40S, yet accommodating subunit rotation. Interaction between C-terminus of Zuo1 and 40S occurs via 18S rRNA expansion segment 12 (ES12) of helix 44, which originates at the decoding site. Deletions in either ES12 or C-terminus of Zuo1 alter stop codon readthrough and −1 frameshifting. Our study offers insight into how this cotranslational chaperone system may monitor decoding site activity and nascent polypeptide transit, thereby coordinating protein translation and folding.
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Affiliation(s)
- Kanghyun Lee
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ruchika Sharma
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Om Kumar Shrestha
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Elizabeth A Craig
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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36
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Dynamic Behavior of Trigger Factor on the Ribosome. J Mol Biol 2016; 428:3588-602. [DOI: 10.1016/j.jmb.2016.06.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 06/10/2016] [Accepted: 06/10/2016] [Indexed: 11/22/2022]
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37
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Wang J, Ying SH, Hu Y, Feng MG. Vital role for the J-domain protein Mdj1 in asexual development, multiple stress tolerance, and virulence of Beauveria bassiana. Appl Microbiol Biotechnol 2016; 101:185-195. [DOI: 10.1007/s00253-016-7757-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/07/2016] [Accepted: 07/19/2016] [Indexed: 12/24/2022]
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38
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Pfeffer S, Dudek J, Zimmermann R, Förster F. Organization of the native ribosome-translocon complex at the mammalian endoplasmic reticulum membrane. Biochim Biophys Acta Gen Subj 2016; 1860:2122-9. [PMID: 27373685 DOI: 10.1016/j.bbagen.2016.06.024] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 06/24/2016] [Accepted: 06/28/2016] [Indexed: 11/17/2022]
Abstract
BACKGROUND In eukaryotic cells, many proteins have to be transported across or inserted into the endoplasmic reticulum membrane during their biogenesis on the ribosome. This process is facilitated by the protein translocon, a highly dynamic multi-subunit membrane protein complex. SCOPE OF REVIEW The aim of this review is to summarize the current structural knowledge about protein translocon components in mammals. MAJOR CONCLUSIONS Various structural biology approaches have been used in synergy to characterize the translocon in recent years. X-ray crystallography and cryoelectron microscopy single particle analysis have yielded highly detailed insights into the structure and functional mechanism of the protein-conducting channel Sec61, which constitutes the functional core of the translocon. Cryoelectron tomography and subtomogram analysis have advanced our understanding of the overall structure, molecular organization and compositional heterogeneity of the translocon in a native membrane environment. Tomography densities at subnanometer resolution revealed an intricate network of interactions between the ribosome, Sec61 and accessory translocon components that assist in protein transport, membrane insertion and maturation. GENERAL SIGNIFICANCE The protein translocon is a gateway for approximately one third of all synthesized proteins and numerous human diseases are associated with malfunctioning of its components. Thus, detailed insights into the structure and molecular organization of the translocon will not only advance our understanding of membrane protein biogenesis in general, but they can potentially pave the way for novel therapeutic approaches against human diseases.
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Affiliation(s)
- Stefan Pfeffer
- Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, D-82152 Martinsried, Germany
| | - Johanna Dudek
- Saarland University, Medical Biochemistry and Molecular Biology, D-66421 Homburg, Germany
| | - Richard Zimmermann
- Saarland University, Medical Biochemistry and Molecular Biology, D-66421 Homburg, Germany.
| | - Friedrich Förster
- Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, D-82152 Martinsried, Germany; Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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39
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HSP70L1-mediated intracellular priming of dendritic cell vaccination induces more potent CTL response against cancer. Cell Mol Immunol 2016; 15:135-145. [PMID: 27345726 DOI: 10.1038/cmi.2016.33] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 05/11/2016] [Accepted: 05/11/2016] [Indexed: 12/21/2022] Open
Abstract
Heat-shock protein (HSP)-based immunotherapy is established on its adjuvant effects when applied via an extracellular approach to pulse and activate dendritic cells (DCs). Our previous studies indicate that DCs pulsed with recombinant fusion proteins of antigenic fragment and HSP70-like protein 1 (HSP70L1) are potent in stimulating antigen-specific Th1 responses. We herein evaluated the cytotoxic T cell (CTL) response by an intracellular approach of priming DCs with transfection of recombinant adenovirus-expressing the fusion gene of the 576-699 fragment of carcinoembryonic antigen (CEA) and HSP70L1. As compared with DCs pulsed with extracellular fusion protein, the DCs transfected with recombinant adenovirus expressing the fusion gene displayed equivalent mature phenotypes but less inflammatory appearance. However, the transfected DCs were superior to the pulsed DCs in inducing CEA-specific CTLs. Consistently, immunization of HLA-A2.1/H-2Kb transgene mice with the transfected DCs could induce more quantities of HLA-A2.1-restricted CEA-specific CTLs, protecting nude mice more significantly from human CEA-expressing colon tumor challenge when adoptively transferred. Mechanistic investigation indicated that intracellular expression of the fusion protein empowered the transfected DCs by activation of STAT1 possibly via inducing IFN-β and ERK pathways. Therefore, the more potent ability to induce anti-CEA CTL responses enables the DCs, which transfected with recombinant adenovirus expressing the fusion gene of antigenic CEA fragment and Th1 adjuvant, as an alternative promising approach for the immunotherapy of CEA-positive tumors.
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40
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Nyathi Y, Pool MR. Analysis of the interplay of protein biogenesis factors at the ribosome exit site reveals new role for NAC. J Cell Biol 2016. [PMID: 26195668 PMCID: PMC4508901 DOI: 10.1083/jcb.201410086] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The protein biogenesis factor NAC regulates the access of the enzyme MetAP and the signal recognition particle (SRP) to the ribosome, functions in SRP-dependent targeting, and can act to protect substrates from aggregation before translocation The ribosome exit site is a focal point for the interaction of protein-biogenesis factors that guide the fate of nascent polypeptides. These factors include chaperones such as NAC, N-terminal-modifying enzymes like Methionine aminopeptidase (MetAP), and the signal recognition particle (SRP), which targets secretory and membrane proteins to the ER. These factors potentially compete with one another in the short time-window when the nascent chain first emerges at the exit site, suggesting a need for regulation. Here, we show that MetAP contacts the ribosome at the universal adaptor site where it is adjacent to the α subunit of NAC. SRP is also known to contact the ribosome at this site. In the absence of NAC, MetAP and SRP antagonize each other, indicating a novel role for NAC in regulating the access of MetAP and SRP to the ribosome. NAC also functions in SRP-dependent targeting and helps to protect substrates from aggregation before translocation.
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Affiliation(s)
- Yvonne Nyathi
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, England, UK
| | - Martin R Pool
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, England, UK
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Kellner N, Schwarz J, Sturm M, Fernandez-Martinez J, Griesel S, Zhang W, Chait BT, Rout MP, Kück U, Hurt E. Developing genetic tools to exploit Chaetomium thermophilum for biochemical analyses of eukaryotic macromolecular assemblies. Sci Rep 2016; 6:20937. [PMID: 26864114 PMCID: PMC4750058 DOI: 10.1038/srep20937] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 01/14/2016] [Indexed: 11/09/2022] Open
Abstract
We describe a method to genetically manipulate Chaetomium thermophilum, a eukaryotic thermophile, along with various biochemical applications. The transformation method depends on a thermostable endogenous selection marker operating at high temperatures combined with chromosomal integration of target genes. Our technique allows exploiting eukaryotic thermophiles as source for purifying thermostable native macromolecular complexes with an emphasis on the nuclear pore complex, holding great potential for applications in basic science and biotechnology.
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Affiliation(s)
- Nikola Kellner
- Biochemistry Center, University of Heidelberg, Heidelberg, Germany
| | - Johannes Schwarz
- Biochemistry Center, University of Heidelberg, Heidelberg, Germany
| | - Miriam Sturm
- Biochemistry Center, University of Heidelberg, Heidelberg, Germany
| | - Javier Fernandez-Martinez
- Laboratory of Cellular and Structural Biology and Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, USA
| | - Sabine Griesel
- Biochemistry Center, University of Heidelberg, Heidelberg, Germany
| | - Wenzhu Zhang
- Laboratory of Cellular and Structural Biology and Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, USA
| | - Brian T Chait
- Laboratory of Cellular and Structural Biology and Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, USA
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology and Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, USA
| | - Ulrich Kück
- Department for General and Molecular Botany, Ruhr-University Bochum, Bochum, Germany
| | - Ed Hurt
- Biochemistry Center, University of Heidelberg, Heidelberg, Germany
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Amor AJ, Castanzo DT, Delany SP, Selechnik DM, van Ooy A, Cameron DM. The ribosome-associated complex antagonizes prion formation in yeast. Prion 2016; 9:144-64. [PMID: 25739058 PMCID: PMC4601405 DOI: 10.1080/19336896.2015.1022022] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The number of known fungal proteins capable of switching between alternative stable conformations is steadily increasing, suggesting that a prion-like mechanism may be broadly utilized as a means to propagate altered cellular states. To gain insight into the mechanisms by which cells regulate prion formation and toxicity we examined the role of the yeast ribosome-associated complex (RAC) in modulating both the formation of the [PSI(+)] prion - an alternative conformer of Sup35 protein - and the toxicity of aggregation-prone polypeptides. The Hsp40 RAC chaperone Zuo1 anchors the RAC to ribosomes and stimulates the ATPase activity of the Hsp70 chaperone Ssb. We found that cells lacking Zuo1 are sensitive to over-expression of some aggregation-prone proteins, including the Sup35 prion domain, suggesting that co-translational protein misfolding increases in Δzuo1 strains. Consistent with this finding, Δzuo1 cells exhibit higher frequencies of spontaneous and induced prion formation. Cells expressing mutant forms of Zuo1 lacking either a C-terminal charged region required for ribosome association, or the J-domain responsible for Ssb ATPase stimulation, exhibit similarly high frequencies of prion formation. Our findings are consistent with a role for the RAC in chaperoning nascent Sup35 to regulate folding of the N-terminal prion domain as it emerges from the ribosome.
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Affiliation(s)
- Alvaro J Amor
- a Biology Department ; Ursinus College ; Collegeville , PA USA
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43
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Greber BJ, Gerhardy S, Leitner A, Leibundgut M, Salem M, Boehringer D, Leulliot N, Aebersold R, Panse VG, Ban N. Insertion of the Biogenesis Factor Rei1 Probes the Ribosomal Tunnel during 60S Maturation. Cell 2015; 164:91-102. [PMID: 26709046 DOI: 10.1016/j.cell.2015.11.027] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 10/08/2015] [Accepted: 11/05/2015] [Indexed: 10/22/2022]
Abstract
Eukaryotic ribosome biogenesis depends on several hundred assembly factors to produce functional 40S and 60S ribosomal subunits. The final phase of 60S subunit biogenesis is cytoplasmic maturation, which includes the proofreading of functional centers of the 60S subunit and the release of several ribosome biogenesis factors. We report the cryo-electron microscopy (cryo-EM) structure of the yeast 60S subunit in complex with the biogenesis factors Rei1, Arx1, and Alb1 at 3.4 Å resolution. In addition to the network of interactions formed by Alb1, the structure reveals a mechanism for ensuring the integrity of the ribosomal polypeptide exit tunnel. Arx1 probes the entire set of inner-ring proteins surrounding the tunnel exit, and the C terminus of Rei1 is deeply inserted into the ribosomal tunnel, where it forms specific contacts along almost its entire length. We provide genetic and biochemical evidence that failure to insert the C terminus of Rei1 precludes subsequent steps of 60S maturation.
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Affiliation(s)
- Basil Johannes Greber
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Stefan Gerhardy
- Institute of Biochemistry, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Marc Leibundgut
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Michèle Salem
- Laboratoire de Cristallographie et RMN Biologiques, UMR CNRS 8015, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, 75006 Paris, France
| | - Daniel Boehringer
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Nicolas Leulliot
- Laboratoire de Cristallographie et RMN Biologiques, UMR CNRS 8015, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, 75006 Paris, France
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland; Faculty of Science, University of Zurich, CH-8057 Zurich, Switzerland
| | - Vikram Govind Panse
- Institute of Biochemistry, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland.
| | - Nenad Ban
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland.
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Mammalian SRP receptor switches the Sec61 translocase from Sec62 to SRP-dependent translocation. Nat Commun 2015; 6:10133. [PMID: 26634806 PMCID: PMC4686813 DOI: 10.1038/ncomms10133] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 11/05/2015] [Indexed: 02/07/2023] Open
Abstract
Two distinct pathways deliver secretory proteins to the Sec61 protein translocase in the endoplasmic reticulum membrane. The canonical pathway requires the signal recognition particle (SRP) and its cognate receptor (SR), and targets ribosome-associated proteins to the Sec translocase. The SRP-independent pathway requires the Sec translocase-associated ER membrane protein Sec62 and can be uncoupled from translation. Here we show that SR switches translocons to SRP-dependent translocation by displacing Sec62. This activity localizes to the charged linker region between the longin and GTPase domains of SRα. Using truncation variants, crosslinking and translocation assays reveals two elements with distinct functions as follows: one rearranges the translocon, displacing Sec62 from Sec61. A second promotes ribosome binding and is conserved between all eukaryotes. These specific regions in SRα reprogramme the Sec translocon and facilitate recruitment of ribosome-nascent chain complexes. Overall, our study identifies an important function of SR, which mechanistically links two seemingly independent modes of translocation.
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Breiman A, Fieulaine S, Meinnel T, Giglione C. The intriguing realm of protein biogenesis: Facing the green co-translational protein maturation networks. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:531-50. [PMID: 26555180 DOI: 10.1016/j.bbapap.2015.11.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/05/2015] [Indexed: 01/13/2023]
Abstract
The ribosome is the cell's protein-making factory, a huge protein-RNA complex, that is essential to life. Determining the high-resolution structures of the stable "core" of this factory was among the major breakthroughs of the past decades, and was awarded the Nobel Prize in 2009. Now that the mysteries of the ribosome appear to be more traceable, detailed understanding of the mechanisms that regulate protein synthesis includes not only the well-known steps of initiation, elongation, and termination but also the less comprehended features of the co-translational events associated with the maturation of the nascent chains. The ribosome is a platform for co-translational events affecting the nascent polypeptide, including protein modifications, folding, targeting to various cellular compartments for integration into membrane or translocation, and proteolysis. These events are orchestrated by ribosome-associated protein biogenesis factors (RPBs), a group of a dozen or more factors that act as the "welcoming committee" for the nascent chain as it emerges from the ribosome. In plants these factors have evolved to fit the specificity of different cellular compartments: cytoplasm, mitochondria and chloroplast. This review focuses on the current state of knowledge of these factors and their interaction around the exit tunnel of dedicated ribosomes. Particular attention has been accorded to the plant system, highlighting the similarities and differences with other organisms.
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Affiliation(s)
- Adina Breiman
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay 91198 Gif-sur-Yvette cedex, France; Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
| | - Sonia Fieulaine
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay 91198 Gif-sur-Yvette cedex, France
| | - Thierry Meinnel
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay 91198 Gif-sur-Yvette cedex, France
| | - Carmela Giglione
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay 91198 Gif-sur-Yvette cedex, France.
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Structure and Switch Cycle of SRβ as Ancestral Eukaryotic GTPase Associated with Secretory Membranes. Structure 2015; 23:1838-1847. [PMID: 26299945 DOI: 10.1016/j.str.2015.07.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 07/15/2015] [Accepted: 07/19/2015] [Indexed: 11/22/2022]
Abstract
G proteins of the Ras-family of small GTPases trace the evolution of eukaryotes. The earliest branching involves the closely related Arf, Sar1, and SRβ GTPases associated with secretory membranes. SRβ is an integral membrane component of the signal recognition particle (SRP) receptor that targets ribosome-nascent chain complexes to the ER. How SRβ integrates into the regulation of SRP-dependent membrane protein biogenesis is not known. Here we show that SRβ-GTP interacts with ribosomes only in presence of SRα and present crystal structures of SRβ in complex with the SRX domain of SRα in the GTP-bound state at 3.2 Å, and of GDP- and GDP · Mg(2+)-bound SRβ at 1.9 Å and 2.4 Å, respectively. We define the GTPase switch cycle of SRβ and identify specific differences to the Arf and Sar1 families with implications for GTPase regulation. Our data allow a better integration of SRβ into the scheme of protein targeting.
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47
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Aibara S, Valkov E, Lamers MH, Dimitrova L, Hurt E, Stewart M. Structural characterization of the principal mRNA-export factor Mex67-Mtr2 from Chaetomium thermophilum. Acta Crystallogr F Struct Biol Commun 2015; 71:876-88. [PMID: 26144233 PMCID: PMC4498709 DOI: 10.1107/s2053230x15008766] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/05/2015] [Indexed: 12/11/2022] Open
Abstract
Members of the Mex67-Mtr2/NXF-NXT1 family are the principal mediators of the nuclear export of mRNA. Mex67/NXF1 has a modular structure based on four domains (RRM, LRR, NTF2-like and UBA) that are thought to be present across species, although the level of sequence conservation between organisms, especially in lower eukaryotes, is low. Here, the crystal structures of these domains from the thermophilic fungus Chaetomium thermophilum are presented together with small-angle X-ray scattering (SAXS) and in vitro RNA-binding data that indicate that, not withstanding the limited sequence conservation between different NXF family members, the molecules retain similar structural and RNA-binding properties. Moreover, the resolution of crystal structures obtained with the C. thermophilum domains was often higher than that obtained previously and, when combined with solution and biochemical studies, provided insight into the structural organization, self-association and RNA-binding properties of Mex67-Mtr2 that facilitate mRNA nuclear export.
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Affiliation(s)
- Shintaro Aibara
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England
| | - Eugene Valkov
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England
| | - Meindert H. Lamers
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England
| | - Lyudmila Dimitrova
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Ed Hurt
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Murray Stewart
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England
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48
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Regulation by a chaperone improves substrate selectivity during cotranslational protein targeting. Proc Natl Acad Sci U S A 2015; 112:E3169-78. [PMID: 26056263 DOI: 10.1073/pnas.1422594112] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ribosome exit site is a crowded environment where numerous factors contact nascent polypeptides to influence their folding, localization, and quality control. Timely and accurate selection of nascent polypeptides into the correct pathway is essential for proper protein biogenesis. To understand how this is accomplished, we probe the mechanism by which nascent polypeptides are accurately sorted between the major cotranslational chaperone trigger factor (TF) and the essential cotranslational targeting machinery, signal recognition particle (SRP). We show that TF regulates SRP function at three distinct stages, including binding of the translating ribosome, membrane targeting via recruitment of the SRP receptor, and rejection of ribosome-bound nascent polypeptides beyond a critical length. Together, these mechanisms enhance the specificity of substrate selection into both pathways. Our results reveal a multilayered mechanism of molecular interplay at the ribosome exit site, and provide a conceptual framework to understand how proteins are selected among distinct biogenesis machineries in this crowded environment.
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49
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Kaschner LA, Sharma R, Shrestha OK, Meyer AE, Craig EA. A conserved domain important for association of eukaryotic J-protein co-chaperones Jjj1 and Zuo1 with the ribosome. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1035-45. [PMID: 25639645 DOI: 10.1016/j.bbamcr.2015.01.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 01/20/2015] [Accepted: 01/22/2015] [Indexed: 11/28/2022]
Abstract
J-proteins, obligate co-chaperones, provide specialization for Hsp70 function in a variety of cellular processes. Two of the 13 J-proteins of the yeast cytosol/nucleus, Zuo1 and Jjj1, are associated with 60S ribosomal subunits. Abundant Zuo1 facilitates folding of nascent polypeptides; Jjj1, of much lower abundance, functions in ribosome biogenesis. However, overexpression of Jjj1 substantially rescues growth defects of cells lacking Zuo1. We analyzed a region held in common by Zuo1 and Jjj1, outside the signature J-domain found in all J-proteins. This shared "zuotin homology domain" (ZHD) is important for ribosome association of both proteins. An N-terminal segment of Jjj1, containing the J-domain and ZHD, is ribosome-associated and, like full-length Jjj1, is competent to rescue both the cold- and cation-sensitivity of ∆zuo1. However, this fragment, when expressed at normal levels, cannot rescue the cytosolic ribosome biogenesis defect of ∆jjj1. Our results are consistent with a model in which the primary functions of Zuo1 and Jjj1 occur in the cytosol. In addition, our data suggest that Zuo1 and Jjj1 bind overlapping sites on ribosomes due to an interaction via their common ZHDs, but Jjj1 binds primarily to pre-60S particles and Zuo1 to mature subunits. We hypothesize that ZUO1 and JJJ1, which are conserved throughout eukaryotes, arose from an ancient duplication of a progenitor J-protein gene that encoded the ZHD ribosome-binding region; subsequently, specialized roles and additional ribosome interaction sites evolved.
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Affiliation(s)
- Lindsey A Kaschner
- Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison, USA; Department of Biochemistry, University of Wisconsin-Madison, USA
| | - Ruchika Sharma
- Department of Biochemistry, University of Wisconsin-Madison, USA
| | | | - Alison E Meyer
- Department of Biochemistry, University of Wisconsin-Madison, USA
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50
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Tenge VR, Zuehlke AD, Shrestha N, Johnson JL. The Hsp90 cochaperones Cpr6, Cpr7, and Cns1 interact with the intact ribosome. EUKARYOTIC CELL 2015; 14:55-63. [PMID: 25380751 PMCID: PMC4279014 DOI: 10.1128/ec.00170-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 11/05/2014] [Indexed: 01/02/2023]
Abstract
The abundant molecular chaperone Hsp90 is essential for the folding and stabilization of hundreds of distinct client proteins. Hsp90 is assisted by multiple cochaperones that modulate Hsp90's ATPase activity and/or promote client interaction, but the in vivo functions of many of these cochaperones are largely unknown. We found that Cpr6, Cpr7, and Cns1 interact with the intact ribosome and that Saccharomyces cerevisiae lacking CPR7 or containing mutations in CNS1 exhibited sensitivity to the translation inhibitor hygromycin. Cpr6 contains a peptidyl-prolyl isomerase (PPIase) domain and a tetratricopeptide repeat (TPR) domain flanked by charged regions. Truncation or alteration of basic residues near the carboxy terminus of Cpr6 disrupted ribosome interaction. Cns1 contains an amino-terminal TPR domain and a poorly characterized carboxy-terminal domain. The isolated carboxy-terminal domain was able to interact with the ribosome. Although loss of CPR6 does not cause noticeable growth defects, overexpression of CPR6 results in enhanced growth defects in cells expressing the temperature-sensitive cns1-G90D mutation (the G-to-D change at position 90 encoded by cns1). Cpr6 mutants that exhibit reduced ribosome interaction failed to cause growth defects, indicating that ribosome interaction is required for in vivo functions of Cpr6. Together, these results represent a novel link between the Hsp90 molecular-chaperone machine and protein synthesis.
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Affiliation(s)
- Victoria R Tenge
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Abbey D Zuehlke
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Neelima Shrestha
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Jill L Johnson
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
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