1
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Carmody P, Roushar FJ, Tedman A, Wang W, Herwig M, Kim M, McDonald EF, Noguera K, Wong-Roushar J, Poirier JL, Zelt NB, Pockrass BT, McKee AG, Kuntz CP, Raju SV, Plate L, Penn WD, Schlebach JP. Ribosomal Frameshifting Selectively Modulates the Assembly, Function, and Pharmacological Rescue of a Misfolded CFTR Variant. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.02.539166. [PMID: 39091758 PMCID: PMC11290997 DOI: 10.1101/2023.05.02.539166] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
The cotranslational misfolding of the cystic fibrosis transmembrane conductance regulator chloride channel (CFTR) plays a central role in the molecular basis of cystic fibrosis (CF). The misfolding of the most common CF variant (ΔF508) remodels both the translational regulation and quality control of CFTR. Nevertheless, it is unclear how the misassembly of the nascent polypeptide may directly influence the activity of the translation machinery. In this work, we identify a structural motif within the CFTR transcript that stimulates efficient -1 ribosomal frameshifting and triggers the premature termination of translation. Though this motif does not appear to impact the interactome of wild-type CFTR, silent mutations that disrupt this RNA structure alter the association of nascent ΔF508 CFTR with numerous translation and quality control proteins. Moreover, disrupting this RNA structure enhances the functional gating of the ΔF508 CFTR channel at the plasma membrane and its pharmacological rescue by the CFTR modulators contained in the CF drug Trikafta. The effects of the RNA structure on ΔF508 CFTR appear to be attenuated in the absence of the ER membrane protein complex (EMC), which was previously found to modulate ribosome collisions during preemptive quality control of a misfolded CFTR homolog. Together, our results reveal that ribosomal frameshifting selectively modulates the assembly, function, and pharmacological rescue of a misfolded CFTR variant. These findings suggest interactions between the nascent chain, quality control machinery, and ribosome may dynamically modulate ribosomal frameshifting in order to tune the processivity of translation in response to cotranslational misfolding.
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Affiliation(s)
- Patrick Carmody
- Department of Chemistry, Indiana University Bloomington, Bloomington, IN, USA 47401
| | - Francis J. Roushar
- Department of Chemistry, Indiana University Bloomington, Bloomington, IN, USA 47401
| | - Austin Tedman
- The James Tarpo Jr. and Margaret Tarpo Department of Chemistry, Purdue University, West Lafayette, IN, USA 47907
| | - Wei Wang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA 35233
| | - Madeline Herwig
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA 37240
| | - Minsoo Kim
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA 37240
- Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN, USA 37240
| | - Eli F. McDonald
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA 37240
| | - Karen Noguera
- Department of Chemistry, Indiana University Bloomington, Bloomington, IN, USA 47401
| | | | - Jon-Luc Poirier
- Department of Chemistry, Indiana University Bloomington, Bloomington, IN, USA 47401
| | - Nathan B. Zelt
- Department of Chemistry, Indiana University Bloomington, Bloomington, IN, USA 47401
| | - Ben T. Pockrass
- Department of Chemistry, Indiana University Bloomington, Bloomington, IN, USA 47401
| | - Andrew G. McKee
- Department of Chemistry, Indiana University Bloomington, Bloomington, IN, USA 47401
| | - Charles P. Kuntz
- The James Tarpo Jr. and Margaret Tarpo Department of Chemistry, Purdue University, West Lafayette, IN, USA 47907
| | - S. Vamsee Raju
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA 35233
| | - Lars Plate
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA 37240
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA 37240
| | - Wesley D. Penn
- Department of Chemistry, Indiana University Bloomington, Bloomington, IN, USA 47401
| | - Jonathan P. Schlebach
- The James Tarpo Jr. and Margaret Tarpo Department of Chemistry, Purdue University, West Lafayette, IN, USA 47907
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2
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van der Sluijs P, Hoelen H, Schmidt A, Braakman I. The Folding Pathway of ABC Transporter CFTR: Effective and Robust. J Mol Biol 2024; 436:168591. [PMID: 38677493 DOI: 10.1016/j.jmb.2024.168591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/16/2024] [Accepted: 04/23/2024] [Indexed: 04/29/2024]
Abstract
De novo protein folding into a native three-dimensional structure is indispensable for biological function, is instructed by its amino acid sequence, and occurs along a vectorial trajectory. The human proteome contains thousands of membrane-spanning proteins, whose biosynthesis begins on endoplasmic reticulum-associated ribosomes. Nearly half of all membrane proteins traverse the membrane more than once, including therapeutically important protein families such as solute carriers, G-protein-coupled receptors, and ABC transporters. These mediate a variety of functions like signal transduction and solute transport and are often of vital importance for cell function and tissue homeostasis. Missense mutations in multispan membrane proteins can lead to misfolding and cause disease; an example is the ABC transporter Cystic Fibrosis Transmembrane Conductance Regulator (CFTR). Even though our understanding of multispan membrane-protein folding still is rather rudimental, the cumulative knowledge of 20 years of basic research on CFTR folding has led to development of drugs that modulate the misfolded protein. This has provided the prospect of a life without CF to the vast majority of patients. In this review we describe our understanding of the folding pathway of CFTR in cells, which is modular and tolerates many defects, making it effective and robust. We address how modulator drugs affect folding and function of CFTR, and distinguish protein stability from its folding process. Since the domain architecture of (mammalian) ABC transporters are highly conserved, we anticipate that the insights we discuss here for folding of CFTR may lay the groundwork for understanding the general rules of ABC-transporter folding.
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Affiliation(s)
- Peter van der Sluijs
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands.
| | - Hanneke Hoelen
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands; Present address: GenDx, Yalelaan 48, 3584 CM Utrecht, The Netherlands
| | - Andre Schmidt
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands; 3D-Pharmxchange, Tilburg, the Netherlands
| | - Ineke Braakman
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
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3
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Chen S, Collart MA. Membrane-associated mRNAs: A Post-transcriptional Pathway for Fine-turning Gene Expression. J Mol Biol 2024; 436:168579. [PMID: 38648968 DOI: 10.1016/j.jmb.2024.168579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
Gene expression is a fundamental and highly regulated process involving a series of tightly coordinated steps, including transcription, post-transcriptional processing, translation, and post-translational modifications. A growing number of studies have revealed an additional layer of complexity in gene expression through the phenomenon of mRNA subcellular localization. mRNAs can be organized into membraneless subcellular structures within both the cytoplasm and the nucleus, but they can also targeted to membranes. In this review, we will summarize in particular our knowledge on localization of mRNAs to organelles, focusing on important regulators and available techniques for studying organellar localization, and significance of this localization in the broader context of gene expression regulation.
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Affiliation(s)
- Siyu Chen
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Institute of Genetics and Genomics of Geneva, Geneva, Switzerland.
| | - Martine A Collart
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Institute of Genetics and Genomics of Geneva, Geneva, Switzerland.
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4
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Kim M, McDonald EF, Sabusap CMP, Timalsina B, Joshi D, Hong JS, Rab A, Sorscher EJ, Plate L. Elexacaftor/VX-445-mediated CFTR interactome remodeling reveals differential correction driven by mutation-specific translational dynamics. J Biol Chem 2023; 299:105242. [PMID: 37690692 PMCID: PMC10579539 DOI: 10.1016/j.jbc.2023.105242] [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: 02/06/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 09/12/2023] Open
Abstract
Cystic fibrosis (CF) is one of the most prevalent lethal genetic diseases with over 2000 identified mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Pharmacological chaperones such as lumacaftor (VX-809), tezacaftor (VX-661), and elexacaftor (VX-445) treat mutation-induced defects by stabilizing CFTR and are called correctors. These correctors improve proper folding and thus facilitate processing and trafficking to increase the amount of functional CFTR on the cell surface. Yet, CFTR variants display differential responses to each corrector. Here, we report that variants P67L and L206W respond similarly to VX-809 but divergently to VX-445 with P67L exhibiting little rescue when treated with VX-445. We investigate the underlying cellular mechanisms of how CFTR biogenesis is altered by correctors in these variants. Affinity purification-mass spectrometry multiplexed with isobaric tandem mass tags was used to quantify CFTR protein-protein interaction changes between variants P67L and L206W. VX-445 facilitates unique proteostasis factor interactions especially in translation, folding, and degradation pathways in a CFTR variant-dependent manner. A number of these interacting proteins knocked down by siRNA, such as ribosomal subunit proteins, moderately rescued fully glycosylated P67L. Importantly, these knockdowns sensitize P67L to VX-445 and further enhance the trafficking correction of this variant. Partial inhibition of protein translation also mildly sensitizes P67L CFTR to VX-445 correction, supporting a role for translational dynamics in the rescue mechanism of VX-445. Our results provide a better understanding of VX-445 biological mechanism of action and reveal cellular targets that may sensitize nonresponsive CFTR variants to known and available correctors.
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Affiliation(s)
- Minsoo Kim
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA; Program in Chemical and Physical Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Eli Fritz McDonald
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | | | - Bibek Timalsina
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Disha Joshi
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Jeong S Hong
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Andras Rab
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Eric J Sorscher
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Lars Plate
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA; Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA.
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5
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Höpfler M, Hegde RS. Control of mRNA fate by its encoded nascent polypeptide. Mol Cell 2023; 83:2840-2855. [PMID: 37595554 PMCID: PMC10501990 DOI: 10.1016/j.molcel.2023.07.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 08/20/2023]
Abstract
Cells tightly regulate mRNA processing, localization, and stability to ensure accurate gene expression in diverse cellular states and conditions. Most of these regulatory steps have traditionally been thought to occur before translation by the action of RNA-binding proteins. Several recent discoveries highlight multiple co-translational mechanisms that modulate mRNA translation, localization, processing, and stability. These mechanisms operate by recognition of the nascent protein, which is necessarily coupled to its encoding mRNA during translation. Hence, the distinctive sequence or structure of a particular nascent chain can recruit recognition factors with privileged access to the corresponding mRNA in an otherwise crowded cellular environment. Here, we draw on both well-established and recent examples to provide a conceptual framework for how cells exploit nascent protein recognition to direct mRNA fate. These mechanisms allow cells to dynamically and specifically regulate their transcriptomes in response to changes in cellular states to maintain protein homeostasis.
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6
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Pleiner T, Hazu M, Pinton Tomaleri G, Nguyen VN, Januszyk K, Voorhees RM. A selectivity filter in the ER membrane protein complex limits protein misinsertion at the ER. J Cell Biol 2023; 222:e202212007. [PMID: 37199759 PMCID: PMC10200711 DOI: 10.1083/jcb.202212007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 03/31/2023] [Accepted: 04/20/2023] [Indexed: 05/19/2023] Open
Abstract
Tail-anchored (TA) proteins play essential roles in mammalian cells, and their accurate localization is critical for proteostasis. Biophysical similarities lead to mistargeting of mitochondrial TA proteins to the ER, where they are delivered to the insertase, the ER membrane protein complex (EMC). Leveraging an improved structural model of the human EMC, we used mutagenesis and site-specific crosslinking to map the path of a TA protein from its cytosolic capture by methionine-rich loops to its membrane insertion through a hydrophilic vestibule. Positively charged residues at the entrance to the vestibule function as a selectivity filter that uses charge-repulsion to reject mitochondrial TA proteins. Similarly, this selectivity filter retains the positively charged soluble domains of multipass substrates in the cytosol, thereby ensuring they adopt the correct topology and enforcing the "positive-inside" rule. Substrate discrimination by the EMC provides a biochemical explanation for one role of charge in TA protein sorting and protects compartment integrity by limiting protein misinsertion.
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Affiliation(s)
- Tino Pleiner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Masami Hazu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Giovani Pinton Tomaleri
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Vy N. Nguyen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Kurt Januszyk
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Rebecca M. Voorhees
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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7
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Schieweck R, Ciccopiedi G, Klau K, Popper B. Monosomes buffer translational stress to allow for active ribosome elongation. Front Mol Biosci 2023; 10:1158043. [PMID: 37304066 PMCID: PMC10253174 DOI: 10.3389/fmolb.2023.1158043] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/10/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction: The synthesis of proteins is a fundamental process in the life-span of all cells. The activation of ribosomes on transcripts is the starting signal for elongation and, in turn, the translation of an mRNA. Thereby, most mRNAs circulate between single (monosomes) and multi ribosomal particles (polysomes), a process that defines their translational activity. The interplay between monosomes and polysomes is thought to crucially impact translation rate. How monosomes and polysomes are balanced during stress remains, however, elusive. Methods: Here, we set out to investigate the monosome and polysome levels as well as their kinetics under different translational stress conditions including mTOR inhibition, downregulation of the eukaryotic elongation factor 2 (eEF2) and amino acid depletion. Results: By using a timed ribosome runoff approach in combination with polysome profiling, we found that the used translational stressors show very distinct effects on translation. However, they all had in common that the activity of monosomes was preferentially affected. This adaptation seems to be needed for sufficient translation elongation. Even under harsh conditions such as amino acid starvation, we detected active polysomes while monosomes were mostly inactive. Hence, it is plausible that cells compensate the reduced availability of essential factors during stress by adapting the levels of active monosomes to favor sufficient elongation. Discussion: These results suggest that monosome and polysome levels are balanced under stress conditions. Together, our data argue for the existence of translational plasticity that ensure sufficient protein synthesis under stress conditions, a process that is necessary for cell survival and recovery.
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Affiliation(s)
- Rico Schieweck
- Biomedical Center (BMC), Department for Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Munich, Germany
| | - Giuliana Ciccopiedi
- Biomedical Center (BMC), Department for Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Munich, Germany
| | - Kenneth Klau
- Biomedical Center (BMC), Department for Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Munich, Germany
| | - Bastian Popper
- Biomedical Center (BMC), Core Facility Animal Models, Ludwig-Maximilians-University, Munich, Germany
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8
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Kim M, McDonald EF, Sabusap CMP, Timalsina B, Joshi D, Hong JS, Rab A, Sorscher EJ, Plate L. Elexacaftor/VX-445-mediated CFTR interactome remodeling reveals differential correction driven by mutation-specific translational dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.04.527134. [PMID: 36778339 PMCID: PMC9915750 DOI: 10.1101/2023.02.04.527134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Cystic fibrosis (CF) is one of the most prevalent lethal genetic diseases with over 2000 identified mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Pharmacological chaperones such as Lumacaftor (VX-809), Tezacaftor (VX-661) and Elexacaftor (VX-445) treat mutation-induced defects by stabilizing CFTR and are called correctors. These correctors improve proper folding and thus facilitate processing and trafficking to increase the amount of functional CFTR on the cell surface. Yet, CFTR variants display differential responses to each corrector. Here, we report variants P67L and L206W respond similarly to VX-809 but divergently to VX-445 with P67L exhibiting little rescue when treated with VX-445. We investigate the underlying cellular mechanisms of how CFTR biogenesis is altered by correctors in these variants. Affinity purification-mass spectrometry (AP-MS) multiplexed with isobaric Tandem Mass Tags (TMT) was used to quantify CFTR protein-protein interaction changes between variants P67L and L206W. VX-445 facilitates unique proteostasis factor interactions especially in translation, folding, and degradation pathways in a CFTR variant-dependent manner. A number of these interacting proteins knocked down by siRNA, such as ribosomal subunit proteins, moderately rescued fully glycosylated P67L. Importantly, these knock-downs sensitize P67L to VX-445 and further enhance the correction of this variant. Our results provide a better understanding of VX-445 biological mechanism of action and reveal cellular targets that may sensitize unresponsive CFTR variants to known and available correctors.
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Affiliation(s)
- Minsoo Kim
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States of America
- Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN, United States of America
| | - Eli Fritz McDonald
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States of America
| | | | - Bibek Timalsina
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States of America
| | - Disha Joshi
- Department of Pediatrics, Emory University, Atlanta, GA, United States of America
| | - Jeong S. Hong
- Department of Pediatrics, Emory University, Atlanta, GA, United States of America
| | - Andras Rab
- Department of Pediatrics, Emory University, Atlanta, GA, United States of America
| | - Eric J. Sorscher
- Department of Pediatrics, Emory University, Atlanta, GA, United States of America
| | - Lars Plate
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States of America
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States of America
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States of America
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Li X, Gao X, Li A, Xu S, Zhou Q, Zhang L, Pan Y, Shi W, Song M, Shi P. Comparative cytotoxicity, endocrine-disrupting effects, oxidative stress of halophenolic disinfection byproducts and the underlying molecular mechanisms revealed by transcriptome analysis. WATER RESEARCH 2023; 229:119458. [PMID: 36516492 DOI: 10.1016/j.watres.2022.119458] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/30/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Halophenolic disinfection byproducts (DBPs) are a class of emerging pollutants whose adverse effects on human cells and the underlying molecular mechanisms still need further exploration. In this study, we found that when halophenolic DBPs were substituted with the same halogen, the more substitution sites, the more cytotoxic, while when they were substituted at the same sites, the most toxic chemical was iodophenols, followed by bromophenols and chlorophenols. In addition, several of them exerted significant endocrine-disrupting effects at sublethal concentrations. 2,4,6-triiodophenol (TIP) and 2,4-dichlorophenol (2,4-DCP) showed the highest estradiol equivalent factor (EEF) of 4.41 × 10-8 and flutamide equivalent factor (FEF) of 0.4, respectively. Furthermore, all of the halophenolic DBPs except for 2-chlorophenol (2-CP) and 2-bromophenol (2-BP) significantly increased the levels of reactive oxygen species (ROS) or 8-hydroxydeoxyguanosine (8-OHdG) in HepG2 cells. The lowest cytotoxicity and unchanged ROS and 8-OHdG levels after 2-CP exposure may result from the activation of the transporters of the adenosine triphosphate (ATP) binding cassette in cells. Transcriptome analysis revealed distinct grouping patterns of 2-CP, 2,6-dibromophenol (2,6-DBP), and TIP at the concentrations of EC20, and the top differentially expressed genes (DEGs) were involved in the antioxidant-, immune-, and endocrine-associated systems. The weighted gene correlation network analysis well connected the phenotypes (EC50, EEF, FEF, ROS, 8-OHdG, and ABC transporters) with the DEGs and revealed that the MAPK signaling pathway played a vital role in regulating the biological response after exposure to halophenolic DBPs. This study provides deep insights into the underlying mechanisms of the toxic effects induced by halophenolic DBPs.
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Affiliation(s)
- Xiuwen Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Road, Nanjing 210023, China
| | - Xinran Gao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Road, Nanjing 210023, China
| | - Aimin Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Road, Nanjing 210023, China
| | - Shuhui Xu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Road, Nanjing 210023, China
| | - Qing Zhou
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Road, Nanjing 210023, China.
| | - Lulu Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Road, Nanjing 210023, China
| | - Yang Pan
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Road, Nanjing 210023, China
| | - Wei Shi
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Road, Nanjing 210023, China
| | - Maoyong Song
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Peng Shi
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Road, Nanjing 210023, China.
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10
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Eisenack TJ, Trentini DB. Ending a bad start: Triggers and mechanisms of co-translational protein degradation. Front Mol Biosci 2023; 9:1089825. [PMID: 36660423 PMCID: PMC9846516 DOI: 10.3389/fmolb.2022.1089825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/15/2022] [Indexed: 01/05/2023] Open
Abstract
Proteins are versatile molecular machines that control and execute virtually all cellular processes. They are synthesized in a multilayered process requiring transfer of information from DNA to RNA and finally into polypeptide, with many opportunities for error. In addition, nascent proteins must successfully navigate a complex folding-energy landscape, in which their functional native state represents one of many possible outcomes. Consequently, newly synthesized proteins are at increased risk of misfolding and toxic aggregation. To maintain proteostasis-the state of proteome balance-cells employ a plethora of molecular chaperones that guide proteins along a productive folding pathway and quality control factors that direct misfolded species for degradation. Achieving the correct balance between folding and degradation therefore represents a fundamental task for the proteostasis network. While many chaperones act co-translationally, protein quality control is generally considered to be a post-translational process, as the majority of proteins will only achieve their final native state once translation is completed. Nevertheless, it has been observed that proteins can be ubiquitinated during synthesis. The extent and the relevance of co-translational protein degradation, as well as the underlying molecular mechanisms, remain areas of open investigation. Recent studies made seminal advances in elucidating ribosome-associated quality control processes, and how their loss of function can lead to proteostasis failure and disease. Here, we discuss current understanding of the situations leading to the marking of nascent proteins for degradation before synthesis is completed, and the emerging quality controls pathways engaged in this task in eukaryotic cells. We also highlight the methods used to study co-translational quality control.
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Affiliation(s)
- Tom Joshua Eisenack
- University of Cologne, Faculty of Medicine, University Hospital of Cologne, Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Débora Broch Trentini
- University of Cologne, Faculty of Medicine, University Hospital of Cologne, Center for Molecular Medicine Cologne (CMMC), Cologne, Germany,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany,*Correspondence: Débora Broch Trentini,
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11
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O'Keefe S, Pool MR, High S. Membrane protein biogenesis at the ER: the highways and byways. FEBS J 2022; 289:6835-6862. [PMID: 33960686 DOI: 10.1111/febs.15905] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/19/2021] [Accepted: 04/28/2021] [Indexed: 01/13/2023]
Abstract
The Sec61 complex is the major protein translocation channel of the endoplasmic reticulum (ER), where it plays a central role in the biogenesis of membrane and secretory proteins. Whilst Sec61-mediated protein translocation is typically coupled to polypeptide synthesis, suggestive of significant complexity, an obvious characteristic of this core translocation machinery is its surprising simplicity. Over thirty years after its initial discovery, we now understand that the Sec61 complex is in fact the central piece of an elaborate jigsaw puzzle, which can be partly solved using new research findings. We propose that the Sec61 complex acts as a dynamic hub for co-translational protein translocation at the ER, proactively recruiting a range of accessory complexes that enhance and regulate its function in response to different protein clients. It is now clear that the Sec61 complex does not have a monopoly on co-translational insertion, with some transmembrane proteins preferentially utilising the ER membrane complex instead. We also have a better understanding of post-insertion events, where at least one membrane-embedded chaperone complex can capture the newly inserted transmembrane domains of multi-span proteins and co-ordinate their assembly into a native structure. Having discovered this array of Sec61-associated components and competitors, our next challenge is to understand how they act together in order to expand the range and complexity of the membrane proteins that can be synthesised at the ER. Furthermore, this diversity of components and pathways may open up new opportunities for targeted therapeutic interventions designed to selectively modulate protein biogenesis at the ER.
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Affiliation(s)
- Sarah O'Keefe
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Martin R Pool
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Stephen High
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
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12
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Lyu Z, Sycks MM, Espinoza MF, Nguyen KK, Montoya MR, Galapate CM, Mei L, Genereux JC. Monitoring Protein Import into the Endoplasmic Reticulum in Living Cells with Proximity Labeling. ACS Chem Biol 2022; 17:1963-1977. [PMID: 35675579 DOI: 10.1021/acschembio.2c00405] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The proper trafficking of eukaryotic proteins is essential to cellular function. Genetic, environmental, and other stresses can induce protein mistargeting and, in turn, threaten cellular protein homeostasis. Current methods for measuring protein mistargeting are difficult to translate to living cells, and thus the role of cellular signaling networks in stress-dependent protein mistargeting processes, such as ER pre-emptive quality control (ER pQC), is difficult to parse. Herein, we use genetically encoded peroxidases to characterize protein import into the endoplasmic reticulum (ER). We show that the ERHRP/cytAPEX pair provides good selectivity and sensitivity for both multiplexed protein labeling and for identifying protein mistargeting, using the known ER pQC substrate transthyretin (TTR). Although ERHRP labeling induces formation of detergent-resistant TTR aggregates, this is minimized by using low ERHRP expression, without loss of labeling efficiency. cytAPEX labeling recovers TTR that is mistargeted as a consequence of Sec61 inhibition or ER stress-induced ER pQC. Furthermore, we discover that stress-free activation of the ER stress-associated transcription factor ATF6 recapitulates the TTR import deficiency of ER pQC. Hence, proximity labeling is an effective strategy for characterizing factors that influence ER protein import in living cells.
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Affiliation(s)
- Ziqi Lyu
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Melody M Sycks
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Mateo F Espinoza
- Graduate Program of Microbiology, University of California, Riverside, California 92521, United States
| | - Khanh K Nguyen
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Maureen R Montoya
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Cheska M Galapate
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Liangyong Mei
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Joseph C Genereux
- Department of Chemistry, University of California, Riverside, California 92521, United States.,Graduate Program of Microbiology, University of California, Riverside, California 92521, United States
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13
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Zinnall U, Milek M, Minia I, Vieira-Vieira CH, Müller S, Mastrobuoni G, Hazapis OG, Del Giudice S, Schwefel D, Bley N, Voigt F, Chao JA, Kempa S, Hüttelmaier S, Selbach M, Landthaler M. HDLBP binds ER-targeted mRNAs by multivalent interactions to promote protein synthesis of transmembrane and secreted proteins. Nat Commun 2022; 13:2727. [PMID: 35585045 PMCID: PMC9117268 DOI: 10.1038/s41467-022-30322-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 04/13/2022] [Indexed: 01/09/2023] Open
Abstract
The biological role of RNA-binding proteins in the secretory pathway is not well established. Here, we describe that human HDLBP/Vigilin directly interacts with more than 80% of ER-localized mRNAs. PAR-CLIP analysis reveals that these transcripts represent high affinity HDLBP substrates and are specifically bound in their coding sequences (CDS), in contrast to CDS/3’UTR-bound cytosolic mRNAs. HDLBP crosslinks strongly to long CU-rich motifs, which frequently reside in CDS of ER-localized mRNAs and result in high affinity multivalent interactions. In addition to HDLBP-ncRNA interactome, quantification of HDLBP-proximal proteome confirms association with components of the translational apparatus and the signal recognition particle. Absence of HDLBP results in decreased translation efficiency of HDLBP target mRNAs, impaired protein synthesis and secretion in model cell lines, as well as decreased tumor growth in a lung cancer mouse model. These results highlight a general function for HDLBP in the translation of ER-localized mRNAs and its relevance for tumor progression. RNA binding protein HDLBP (or Vigilin) localizes in the endoplasmic reticulum (ER) membrane. Here the authors show that HDLBP contributes to translation of ER-targeted mRNAs.
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Affiliation(s)
- Ulrike Zinnall
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Miha Milek
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany. .,National Institute of Chemistry, Ljubljana, Slovenia. .,Core Unit Bioinformatics, Berlin Institute of Health at Charité, Berlin, Germany.
| | - Igor Minia
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Carlos H Vieira-Vieira
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Simon Müller
- Institute of Molecular Medicine, Medical Faculty, Martin Luther University, Halle, Germany
| | - Guido Mastrobuoni
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Orsalia-Georgia Hazapis
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Simone Del Giudice
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - David Schwefel
- Charite-Universitätsmedizin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Nadine Bley
- Institute of Molecular Medicine, Medical Faculty, Martin Luther University, Halle, Germany
| | - Franka Voigt
- Friedrich Miescher Institute for Biomedical Research, 4058, Basel, Switzerland
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, 4058, Basel, Switzerland
| | - Stefan Kempa
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Medical Faculty, Martin Luther University, Halle, Germany
| | - Matthias Selbach
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany.,Charite-Universitätsmedizin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Markus Landthaler
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany. .,IRI Life Sciences, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
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14
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Characterisation of Bacteriophage vB_SmaM_Ps15 Infective to Stenotrophomonas maltophilia Clinical Ocular Isolates. Viruses 2022; 14:v14040709. [PMID: 35458438 PMCID: PMC9025141 DOI: 10.3390/v14040709] [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: 02/10/2022] [Revised: 03/18/2022] [Accepted: 03/24/2022] [Indexed: 11/16/2022] Open
Abstract
Recent acknowledgment that multidrug resistant Stenotrophomonas maltophilia strains can cause severe infections has led to increasing global interest in addressing its pathogenicity. While being primarily associated with hospital-acquired respiratory tract infections, this bacterial species is also relevant to ophthalmology, particularly to contact lens-related diseases. In the current study, the capacity of Stenotrophomonas phage vB_SmaM_Ps15 to infect ocular S. maltophilia strains was investigated to explore its future potential as a phage therapeutic. The phage proved to be lytic to a range of clinical isolates collected in Australia from eye swabs, contact lenses and contact lens cases that had previously shown to be resistant to several antibiotics and multipurpose contact lenses disinfectant solutions. Morphological analysis by transmission electron microscopy placed the phage into the Myoviridae family. Its genome size was 161,350 bp with a G + C content of 54.2%, containing 276 putative protein-encoding genes and 24 tRNAs. A detailed comparative genomic analysis positioned vB_SmaM_Ps15 as a new species of the Menderavirus genus, which currently contains six very similar globally distributed members. It was confirmed as a virulent phage, free of known lysogenic and pathogenicity determinants, which supports its potential use for the treatment of S. maltophilia eye infections.
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15
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Abstract
The endoplasmic reticulum (ER) is the site of membrane protein insertion, folding, and assembly in eukaryotes. Over the past few years, a combination of genetic and biochemical studies have implicated an abundant factor termed the ER membrane protein complex (EMC) in several aspects of membrane protein biogenesis. This large nine-protein complex is built around a deeply conserved core formed by the EMC3-EMC6 subcomplex. EMC3 belongs to the universally conserved Oxa1 superfamily of membrane protein transporters, whereas EMC6 is an ancient, widely conserved obligate partner. EMC has an established role in the insertion of transmembrane domains (TMDs) and less understood roles during the later steps of membrane protein folding and assembly. Several recent structures suggest hypotheses about the mechanism(s) of TMD insertion by EMC, with various biochemical and proteomics studies beginning to reveal the range of EMC's membrane protein substrates. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Ramanujan S Hegde
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom;
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16
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Gaspar CJ, Vieira LC, Santos CC, Christianson JC, Jakubec D, Strisovsky K, Adrain C, Domingos PM. EMC is required for biogenesis of Xport-A, an essential chaperone of Rhodopsin-1 and the TRP channel. EMBO Rep 2022; 23:e53210. [PMID: 34918864 PMCID: PMC8728618 DOI: 10.15252/embr.202153210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 10/26/2021] [Accepted: 11/10/2021] [Indexed: 01/07/2023] Open
Abstract
The ER membrane protein complex (EMC) is required for the biogenesis of a subset of tail anchored (TA) and polytopic membrane proteins, including Rhodopsin-1 (Rh1) and the TRP channel. To understand the physiological implications of EMC-dependent membrane protein biogenesis, we perform a bioinformatic identification of Drosophila TA proteins. From 254 predicted TA proteins, screening in larval eye discs identified two proteins that require EMC for their biogenesis: fan and Xport-A. Fan is required for male fertility in Drosophila and we show that EMC is also required for this process. Xport-A is essential for the biogenesis of both Rh1 and TRP, raising the possibility that disruption of Rh1 and TRP biogenesis in EMC mutants is secondary to the Xport-A defect. We show that EMC is required for Xport-A TMD membrane insertion and that EMC-independent Xport-A mutants rescue Rh1 and TRP biogenesis in EMC mutants. Finally, our work also reveals a role for Xport-A in a glycosylation-dependent triage mechanism during Rh1 biogenesis in the endoplasmic reticulum.
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Affiliation(s)
- Catarina J Gaspar
- Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa (ITQB‐NOVA)OeirasPortugal
- Membrane Traffic LabInstituto Gulbenkian de Ciência (IGC)OeirasPortugal
| | - Lígia C Vieira
- Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa (ITQB‐NOVA)OeirasPortugal
- Present address:
Center for Genomics and Systems BiologyNew York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - Cristiana C Santos
- Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa (ITQB‐NOVA)OeirasPortugal
| | - John C Christianson
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal SciencesBotnar Research CentreUniversity of OxfordOxfordUK
| | - David Jakubec
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesPragueCzech Republic
| | - Kvido Strisovsky
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesPragueCzech Republic
| | - Colin Adrain
- Membrane Traffic LabInstituto Gulbenkian de Ciência (IGC)OeirasPortugal
- Patrick G Johnston Centre for Cancer ResearchQueen’s UniversityBelfastUK
| | - Pedro M Domingos
- Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa (ITQB‐NOVA)OeirasPortugal
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17
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Park J, Park J, Lee J, Lim C. The trinity of ribosome-associated quality control and stress signaling for proteostasis and neuronal physiology. BMB Rep 2021. [PMID: 34488933 PMCID: PMC8505234 DOI: 10.5483/bmbrep.2021.54.9.097] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Translating ribosomes accompany co-translational regulation of nascent polypeptide chains, including subcellular targeting, protein folding, and covalent modifications. Ribosome-associated quality control (RQC) is a co-translational surveillance mechanism triggered by ribosomal collisions, an indication of atypical translation. The ribosome-associated E3 ligase ZNF598 ubiquitinates small subunit proteins at the stalled ribosomes. A series of RQC factors are then recruited to dissociate and triage aberrant translation intermediates. Regulatory ribosomal stalling may occur on endogenous transcripts for quality gene expression, whereas ribosomal collisions are more globally induced by ribotoxic stressors such as translation inhibitors, ribotoxins, and UV radiation. The latter are sensed by ribosome-associated kinases GCN2 and ZAKα, activating integrated stress response (ISR) and ribotoxic stress response (RSR), respectively. Hierarchical crosstalks among RQC, ISR, and RSR pathways are readily detectable since the collided ribosome is their common substrate for activation. Given the strong implications of RQC factors in neuronal physiology and neurological disorders, the interplay between RQC and ribosome-associated stress signaling may sustain proteostasis, adaptively determine cell fate, and contribute to neural pathogenesis. The elucidation of underlying molecular principles in relevant human diseases should thus provide unexplored therapeutic opportunities.
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Affiliation(s)
- Jumin Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Jongmin Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Jongbin Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Chunghun Lim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
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18
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Weber R, Chung MY, Keskeny C, Zinnall U, Landthaler M, Valkov E, Izaurralde E, Igreja C. 4EHP and GIGYF1/2 Mediate Translation-Coupled Messenger RNA Decay. Cell Rep 2021; 33:108262. [PMID: 33053355 DOI: 10.1016/j.celrep.2020.108262] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 08/26/2020] [Accepted: 09/22/2020] [Indexed: 12/13/2022] Open
Abstract
Current models of mRNA turnover indicate that cytoplasmic degradation is coupled with translation. However, our understanding of the molecular events that coordinate ribosome transit with the mRNA decay machinery is still limited. Here, we show that 4EHP-GIGYF1/2 complexes trigger co-translational mRNA decay. Human cells lacking these proteins accumulate mRNAs with prominent ribosome pausing. They include, among others, transcripts encoding secretory and membrane-bound proteins or tubulin subunits. In addition, 4EHP-GIGYF1/2 complexes fail to reduce mRNA levels in the absence of ribosome stalling or upon disruption of their interaction with the cap structure, DDX6, and ZNF598. We further find that co-translational binding of GIGYF1/2 to the mRNA marks transcripts with perturbed elongation to decay. Our studies reveal how a repressor complex linked to neurological disorders minimizes the protein output of a subset of mRNAs.
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Affiliation(s)
- Ramona Weber
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
| | - Min-Yi Chung
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
| | - Csilla Keskeny
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
| | - Ulrike Zinnall
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115 Berlin, Germany; IRI Life Sciences, Institute für Biologie, Humboldt Universität zu Berlin, 10115 Berlin, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115 Berlin, Germany; IRI Life Sciences, Institute für Biologie, Humboldt Universität zu Berlin, 10115 Berlin, Germany
| | - Eugene Valkov
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
| | - Elisa Izaurralde
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
| | - Cátia Igreja
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany.
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19
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Phillips BP, Miller EA. Membrane protein folding and quality control. Curr Opin Struct Biol 2021; 69:50-54. [PMID: 33857720 PMCID: PMC8422161 DOI: 10.1016/j.sbi.2021.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/01/2021] [Accepted: 03/09/2021] [Indexed: 12/21/2022]
Abstract
Membrane proteins account for a quarter of cellular proteins, and most are synthesised at the endoplasmic reticulum (ER). Insertion and folding of polypeptides in the membrane environment is prone to error, necessitating diverse quality control systems. Recent discoveries have demonstrated how forces act on the nascent chain during insertion, and revealed new translocon components and accessories that facilitate the correct biogenesis of substrates. Our understanding of one of the best studied quality control systems-ER-associated degradation-has been advanced through new structural and functional studies of the core Hrd1 complex, and through the discovery of a new branch of this degradative pathway. New data also reveal how cells resolve clogged translocons, which would otherwise be unable to function. Finally, new work elucidates how mitochondrial tail-anchored proteins that have been mistargeted to the ER are identified and destroyed. Overall, we describe an emerging picture of an increasingly complex quality control network.
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Affiliation(s)
- Ben P Phillips
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Elizabeth A Miller
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.
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20
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Han P, Shichino Y, Schneider-Poetsch T, Mito M, Hashimoto S, Udagawa T, Kohno K, Yoshida M, Mishima Y, Inada T, Iwasaki S. Genome-wide Survey of Ribosome Collision. Cell Rep 2021; 31:107610. [PMID: 32375038 DOI: 10.1016/j.celrep.2020.107610] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 03/18/2020] [Accepted: 04/13/2020] [Indexed: 12/31/2022] Open
Abstract
Ribosome movement is not always smooth and is rather often impeded. For ribosome pauses, fundamental issues remain to be addressed, including where ribosomes pause on mRNAs, what kind of RNA/amino acid sequence causes this pause, and the physiological significance of this attenuation of protein synthesis. Here, we survey the positions of ribosome collisions caused by ribosome pauses in humans and zebrafish using modified ribosome profiling. Collided ribosomes, i.e., disomes, emerge at various sites: Pro-Pro/Gly/Asp motifs; Arg-X-Lys motifs; stop codons; and 3' untranslated regions. The electrostatic interaction between the charged nascent chain and the ribosome exit tunnel determines the eIF5A-mediated disome rescue at the Pro-Pro sites. In particular, XBP1u, a precursor of endoplasmic reticulum (ER)-stress-responsive transcription factor, shows striking queues of collided ribosomes and thus acts as a degradation substrate by ribosome-associated quality control. Our results provide insight into the causes and consequences of ribosome pause by dissecting collided ribosomes.
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Affiliation(s)
- Peixun Han
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan; RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Tilman Schneider-Poetsch
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Satoshi Hashimoto
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Tsuyoshi Udagawa
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Kenji Kohno
- Institute for Research Initiatives, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yuichiro Mishima
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Toshifumi Inada
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Shintaro Iwasaki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan; RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan.
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21
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Weichenrieder O. Cellular Traffic Jam and Disease Due to Mutations in SRP54. Structure 2021; 29:3-5. [PMID: 33417891 DOI: 10.1016/j.str.2020.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In this issue of Structure, Juaire et al. use X-ray crystallography, biophysical tools, and cell-based assays to investigate disease-associated variants of the SRP54 GTPase and to demonstrate that defects in SRP-mediated protein secretion can explain phenotypes of severe neutropenia with Shwachman-Diamond-syndrome-like symptoms.
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Affiliation(s)
- Oliver Weichenrieder
- Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany.
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22
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Yip MCJ, Shao S. Detecting and Rescuing Stalled Ribosomes. Trends Biochem Sci 2021; 46:731-743. [PMID: 33966939 DOI: 10.1016/j.tibs.2021.03.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/18/2021] [Accepted: 03/30/2021] [Indexed: 11/24/2022]
Abstract
Ribosomes that stall inappropriately during protein synthesis harbor proteotoxic components linked to cellular stress and neurodegenerative diseases. Molecular mechanisms that rescue stalled ribosomes must selectively detect rare aberrant translational complexes and process the heterogeneous components. Ribosome-associated quality control pathways eliminate problematic messenger RNAs and nascent proteins on stalled translational complexes. In addition, recent studies have uncovered general principles of stall recognition upstream of quality control pathways and fail-safe mechanisms that ensure nascent proteome integrity. Here, we discuss developments in our mechanistic understanding of the detection and rescue of stalled ribosomal complexes in eukaryotes.
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Affiliation(s)
- Matthew C J Yip
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Sichen Shao
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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23
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Matsuo Y, Inada T. The ribosome collision sensor Hel2 functions as preventive quality control in the secretory pathway. Cell Rep 2021; 34:108877. [PMID: 33761353 DOI: 10.1016/j.celrep.2021.108877] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 12/18/2020] [Accepted: 02/25/2021] [Indexed: 12/14/2022] Open
Abstract
Ribosome collision because of translational stalling is recognized as a problematic event in translation by the E3 ubiquitin ligase Hel2, leading to non-canonical subunit dissociation followed by targeting of the faulty nascent peptides for degradation. Although Hel2-mediated quality control greatly contributes to maintenance of cellular protein homeostasis, its physiological role in dealing with endogenous substrates remains unclear. This study utilizes genome-wide analysis, based on selective ribosome profiling, to survey the endogenous substrates for Hel2. This survey reveals that Hel2 binds preferentially to the pre-engaged secretory ribosome-nascent chain complexes (RNCs), which translate upstream of targeting signals. Notably, Hel2 recruitment into secretory RNCs is elevated under signal recognition particle (SRP)-deficient conditions. Moreover, the mitochondrial defects caused by insufficient SRP are enhanced by hel2 deletion, along with mistargeting of secretory proteins into mitochondria. These findings provide insights into risk management in the secretory pathway that maintains cellular protein homeostasis.
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Affiliation(s)
- Yoshitaka Matsuo
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan.
| | - Toshifumi Inada
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan; Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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24
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Nicolaus F, Metola A, Mermans D, Liljenström A, Krč A, Abdullahi SM, Zimmer M, Miller Iii TF, von Heijne G. Residue-by-residue analysis of cotranslational membrane protein integration in vivo. eLife 2021; 10:64302. [PMID: 33554862 PMCID: PMC7886326 DOI: 10.7554/elife.64302] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/05/2021] [Indexed: 12/16/2022] Open
Abstract
We follow the cotranslational biosynthesis of three multispanning Escherichia coli inner membrane proteins in vivo using high-resolution force profile analysis. The force profiles show that the nascent chain is subjected to rapidly varying pulling forces during translation and reveal unexpected complexities in the membrane integration process. We find that an N-terminal cytoplasmic domain can fold in the ribosome exit tunnel before membrane integration starts, that charged residues and membrane-interacting segments such as re-entrant loops and surface helices flanking a transmembrane helix (TMH) can advance or delay membrane integration, and that point mutations in an upstream TMH can affect the pulling forces generated by downstream TMHs in a highly position-dependent manner, suggestive of residue-specific interactions between TMHs during the integration process. Our results support the 'sliding' model of translocon-mediated membrane protein integration, in which hydrophobic segments are continually exposed to the lipid bilayer during their passage through the SecYEG translocon.
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Affiliation(s)
- Felix Nicolaus
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Ane Metola
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Daphne Mermans
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Amanda Liljenström
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Ajda Krč
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | | | - Matthew Zimmer
- California Institute of Technology, Division of Chemistry and Chemical Engineering, Pasadena, United States
| | - Thomas F Miller Iii
- California Institute of Technology, Division of Chemistry and Chemical Engineering, Pasadena, United States
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory Stockholm University, Solna, Sweden
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25
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Wang L, Ye Y. Clearing Traffic Jams During Protein Translocation Across Membranes. Front Cell Dev Biol 2021; 8:610689. [PMID: 33490075 PMCID: PMC7820333 DOI: 10.3389/fcell.2020.610689] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/27/2020] [Indexed: 11/13/2022] Open
Abstract
Protein translocation across membranes is a critical facet of protein biogenesis in compartmentalized cells as proteins synthesized in the cytoplasm often need to traverse across lipid bilayers via proteinaceous channels to reach their final destinations. It is well established that protein biogenesis is tightly linked to various protein quality control processes, which monitor errors in protein folding, modification, and localization. However, little is known about how cells cope with translocation defective polypeptides that clog translocation channels (translocons) during protein translocation. This review summarizes recent studies, which collectively reveal a set of translocon-associated quality control strategies for eliminating polypeptides stuck in protein-conducting channels in the endoplasmic reticulum and mitochondria.
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Affiliation(s)
| | - Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
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26
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Phillips BP, Miller EA. Ribosome-associated quality control of membrane proteins at the endoplasmic reticulum. J Cell Sci 2020; 133:133/22/jcs251983. [PMID: 33247003 PMCID: PMC7116877 DOI: 10.1242/jcs.251983] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Protein synthesis is an energetically costly, complex and risky process. Aberrant protein biogenesis can result in cellular toxicity and disease, with membrane-embedded proteins being particularly challenging for the cell. In order to protect the cell from consequences of defects in membrane proteins, quality control systems act to maintain protein homeostasis. The majority of these pathways act post-translationally; however, recent evidence reveals that membrane proteins are also subject to co-translational quality control during their synthesis in the endoplasmic reticulum (ER). This newly identified quality control pathway employs components of the cytosolic ribosome-associated quality control (RQC) machinery but differs from canonical RQC in that it responds to biogenesis state of the substrate rather than mRNA aberrations. This ER-associated RQC (ER-RQC) is sensitive to membrane protein misfolding and malfunctions in the ER insertion machinery. In this Review, we discuss the advantages of co-translational quality control of membrane proteins, as well as potential mechanisms of substrate recognition and degradation. Finally, we discuss some outstanding questions concerning future studies of ER-RQC of membrane proteins.
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Affiliation(s)
- Ben P Phillips
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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27
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Vind AC, Genzor AV, Bekker-Jensen S. Ribosomal stress-surveillance: three pathways is a magic number. Nucleic Acids Res 2020; 48:10648-10661. [PMID: 32941609 PMCID: PMC7641731 DOI: 10.1093/nar/gkaa757] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/28/2020] [Accepted: 09/06/2020] [Indexed: 12/15/2022] Open
Abstract
Cells rely on stress response pathways to uphold cellular homeostasis and limit the negative effects of harmful environmental stimuli. The stress- and mitogen-activated protein (MAP) kinases, p38 and JNK, are at the nexus of numerous stress responses, among these the ribotoxic stress response (RSR). Ribosomal impairment is detrimental to cell function as it disrupts protein synthesis, increase inflammatory signaling and, if unresolved, lead to cell death. In this review, we offer a general overview of the three main translation surveillance pathways; the RSR, Ribosome-associated Quality Control (RQC) and the Integrated Stress Response (ISR). We highlight recent advances made in defining activation mechanisms for these pathways and discuss their commonalities and differences. Finally, we reflect on the physiological role of the RSR and consider the therapeutic potential of targeting the sensing kinase ZAKα for treatment of ribotoxin exposure.
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Affiliation(s)
- Anna Constance Vind
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Aitana Victoria Genzor
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Simon Bekker-Jensen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
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28
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Abstract
Stalled protein synthesis produces defective nascent chains that can harm cells. In response, cells degrade these nascent chains via a process called ribosome-associated quality control (RQC). Here, we review the irregularities in the translation process that cause ribosomes to stall as well as how cells use RQC to detect stalled ribosomes, ubiquitylate their tethered nascent chains, and deliver the ubiquitylated nascent chains to the proteasome. We additionally summarize how cells respond to RQC failure.
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Affiliation(s)
- Cole S Sitron
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany;
| | - Onn Brandman
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA;
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29
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O'Donnell JP, Phillips BP, Yagita Y, Juszkiewicz S, Wagner A, Malinverni D, Keenan RJ, Miller EA, Hegde RS. The architecture of EMC reveals a path for membrane protein insertion. eLife 2020; 9:e57887. [PMID: 32459176 PMCID: PMC7292650 DOI: 10.7554/elife.57887] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/26/2020] [Indexed: 12/29/2022] Open
Abstract
Approximately 25% of eukaryotic genes code for integral membrane proteins that are assembled at the endoplasmic reticulum. An abundant and widely conserved multi-protein complex termed EMC has been implicated in membrane protein biogenesis, but its mechanism of action is poorly understood. Here, we define the composition and architecture of human EMC using biochemical assays, crystallography of individual subunits, site-specific photocrosslinking, and cryo-EM reconstruction. Our results suggest that EMC's cytosolic domain contains a large, moderately hydrophobic vestibule that can bind a substrate's transmembrane domain (TMD). The cytosolic vestibule leads into a lumenally-sealed, lipid-exposed intramembrane groove large enough to accommodate a single substrate TMD. A gap between the cytosolic vestibule and intramembrane groove provides a potential path for substrate egress from EMC. These findings suggest how EMC facilitates energy-independent membrane insertion of TMDs, explain why only short lumenal domains are translocated by EMC, and constrain models of EMC's proposed chaperone function.
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Affiliation(s)
| | - Ben P Phillips
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Yuichi Yagita
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | | | | | | | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
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30
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Phillips BP, Gomez-Navarro N, Miller EA. Protein quality control in the endoplasmic reticulum. Curr Opin Cell Biol 2020; 65:96-102. [PMID: 32408120 PMCID: PMC7588826 DOI: 10.1016/j.ceb.2020.04.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/02/2020] [Accepted: 04/02/2020] [Indexed: 11/30/2022]
Abstract
Misfolded and mistargeted proteins in the early secretory pathway present significant risks to the cell. A diverse and integrated network of quality control pathways protects the cell from these threats. We focus on the discovery of new mechanisms that contribute to this protective network. Biochemical and structural advances in endoplasmic reticulum targeting fidelity, and in the redistribution of mistargeted substrates are discussed. We further review new discoveries in quality control at the inner nuclear membrane in the context of orphaned subunits. We consider developments in our understanding of cargo selection for endoplasmic reticulum export. Conflicting data on quality control by cargo receptor proteins are discussed and we look to important future questions for the field.
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31
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Volkmar N, Christianson JC. Squaring the EMC - how promoting membrane protein biogenesis impacts cellular functions and organismal homeostasis. J Cell Sci 2020; 133:133/8/jcs243519. [PMID: 32332093 PMCID: PMC7188443 DOI: 10.1242/jcs.243519] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Integral membrane proteins play key functional roles at organelles and the plasma membrane, necessitating their efficient and accurate biogenesis to ensure appropriate targeting and activity. The endoplasmic reticulum membrane protein complex (EMC) has recently emerged as an important eukaryotic complex for biogenesis of integral membrane proteins by promoting insertion and stability of atypical and sub-optimal transmembrane domains (TMDs). Although confirmed as a bona fide complex almost a decade ago, light is just now being shed on the mechanism and selectivity underlying the cellular responsibilities of the EMC. In this Review, we revisit the myriad of functions attributed the EMC through the lens of these new mechanistic insights, to address questions of the cellular and organismal roles the EMC has evolved to undertake. Summary: The EMC is an important factor facilitating membrane protein biogenesis. Here we discuss the broad cellular and organismal responsibilities overseen by client proteins requiring the EMC for maturation.
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Affiliation(s)
- Norbert Volkmar
- Jeffrey Cheah Biomedical Centre, Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - John C Christianson
- Oxford Centre for Translational Myeloma Research, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Botnar Research Centre, Headington, Oxford OX3 7LD, UK
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