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Hildebrandt ER, Sarkar A, Ravishankar R, Kim JH, Schmidt WK. Evaluating protein prenylation of human and viral CaaX sequences using a humanized yeast system. Dis Model Mech 2024; 17:dmm050516. [PMID: 38818856 PMCID: PMC11152559 DOI: 10.1242/dmm.050516] [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: 09/19/2023] [Accepted: 04/23/2024] [Indexed: 06/01/2024] Open
Abstract
Prenylated proteins are prevalent in eukaryotic biology (∼1-2% of proteins) and are associated with human disease, including cancer, premature aging and infections. Prenylated proteins with a C-terminal CaaX sequence are targeted by CaaX-type prenyltransferases and proteases. To aid investigations of these enzymes and their targets, we developed Saccharomyces cerevisiae strains that express these human enzymes instead of their yeast counterparts. These strains were developed in part to explore human prenyltransferase specificity because of findings that yeast FTase has expanded specificity for sequences deviating from the CaaX consensus (i.e. atypical sequence and length). The humanized yeast strains displayed robust prenyltransferase activity against CaaX sequences derived from human and pathogen proteins containing typical and atypical CaaX sequences. The system also recapitulated prenylation of heterologously expressed human proteins (i.e. HRas and DNAJA2). These results reveal that substrate specificity is conserved for yeast and human farnesyltransferases but is less conserved for type I geranylgeranyltransferases. These yeast systems can be easily adapted for investigating the prenylomes of other organisms and are valuable new tools for helping define the human prenylome, which includes physiologically important proteins for which the CaaX modification status is unknown.
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Affiliation(s)
- Emily R. Hildebrandt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Anushka Sarkar
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Rajani Ravishankar
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - June H. Kim
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Walter K. Schmidt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
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2
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Worman HJ, Michaelis S. Prelamin A and ZMPSTE24 in premature and physiological aging. Nucleus 2023; 14:2270345. [PMID: 37885131 PMCID: PMC10730219 DOI: 10.1080/19491034.2023.2270345] [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: 08/29/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023] Open
Abstract
As human longevity increases, understanding the molecular mechanisms that drive aging becomes ever more critical to promote health and prevent age-related disorders. Premature aging disorders or progeroid syndromes can provide critical insights into aspects of physiological aging. A major cause of progeroid syndromes which result from mutations in the genes LMNA and ZMPSTE24 is disruption of the final posttranslational processing step in the production of the nuclear scaffold protein lamin A. LMNA encodes the lamin A precursor, prelamin A and ZMPSTE24 encodes the prelamin A processing enzyme, the zinc metalloprotease ZMPSTE24. Progeroid syndromes resulting from mutations in these genes include the clinically related disorders Hutchinson-Gilford progeria syndrome (HGPS), mandibuloacral dysplasia-type B, and restrictive dermopathy. These diseases have features that overlap with one another and with some aspects of physiological aging, including bone defects resembling osteoporosis and atherosclerosis (the latter primarily in HGPS). The progeroid syndromes have ignited keen interest in the relationship between defective prelamin A processing and its accumulation in normal physiological aging. In this review, we examine the hypothesis that diminished processing of prelamin A by ZMPSTE24 is a driver of physiological aging. We review features a new mouse (LmnaL648R/L648R) that produces solely unprocessed prelamin A and provides an ideal model for examining the effects of its accumulation during aging. We also discuss existing data on the accumulation of prelamin A or its variants in human physiological aging, which call out for further validation and more rigorous experimental approaches to determine if prelamin A contributes to normal aging.
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Affiliation(s)
- Howard J. Worman
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Susan Michaelis
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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3
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Runnebohm AM, Indovina CJ, Turk SM, Bailey CG, Orchard CJ, Wade L, Overton DL, Snow BJ, Rubenstein EM. Methionine Restriction Impairs Degradation of a Protein that Aberrantly Engages the Endoplasmic Reticulum Translocon. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.001021. [PMID: 38021175 PMCID: PMC10667923 DOI: 10.17912/micropub.biology.001021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 12/01/2023]
Abstract
Proteins that persistently engage endoplasmic reticulum (ER) translocons are degraded by multiple translocon quality control (TQC) mechanisms. In Saccharomyces cerevisiae , the model translocon-associated protein Deg1 -Sec62 is subject to ER-associated degradation (ERAD) by the Hrd1 ubiquitin ligase and, to a lesser extent, proteolysis mediated by the Ste24 protease. In a recent screen, we identified nine methionine-biosynthetic genes as candidate TQC regulators. Here, we found methionine restriction impairs Hrd1-independent Deg1 -Sec62 degradation. Beyond revealing methionine as a novel regulator of TQC, our results urge caution when working with laboratory yeast strains with auxotrophic mutations, often presumed not to influence cellular processes under investigation.
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Affiliation(s)
- Avery M. Runnebohm
- Department of Biology, Ball State University, Muncie, Indiana, United States
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States
| | | | - Samantha M. Turk
- Department of Biology, Ball State University, Muncie, Indiana, United States
- St. Jude Graduate School of Biomedical Science, Memphis, Tennessee, United States
| | - Connor G. Bailey
- Department of Biology, Ball State University, Muncie, Indiana, United States
- AllSource PPS, United States
| | - Cade J. Orchard
- Department of Biology, Ball State University, Muncie, Indiana, United States
- Department of Geology, University of Georgia, Athens, Georgia, United States
| | - Lauren Wade
- Department of Biology, Ball State University, Muncie, Indiana, United States
- Flow Cytometry Department, LabCorp, United States
| | - Danielle L. Overton
- Department of Biology, Ball State University, Muncie, Indiana, United States
- Department of Biology, Indiana University – Purdue University Indianapolis, Indianapolis, Indiana, United States
| | - Brian J. Snow
- Department of Biology, Ball State University, Muncie, Indiana, United States
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, Wisconsin, United States
| | - Eric M. Rubenstein
- Department of Biology, Ball State University, Muncie, Indiana, United States
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Hildebrandt ER, Sarkar A, Ravishankar R, Kim JH, Schmidt WK. A Humanized Yeast System for Evaluating the Protein Prenylation of a Wide Range of Human and Viral CaaX Sequences. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.19.558494. [PMID: 37786692 PMCID: PMC10541624 DOI: 10.1101/2023.09.19.558494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
The C-terminal CaaX sequence (cysteine-aliphatic-aliphatic-any of several amino acids) is subject to isoprenylation on the conserved cysteine and is estimated to occur in 1-2% of proteins within yeast and human proteomes. Recently, non-canonical CaaX sequences in addition to shorter and longer length CaX and CaaaX sequences have been identified that can be prenylated. Much of the characterization of prenyltransferases has relied on the yeast system because of its genetic tractability and availability of reporter proteins, such as the a-factor mating pheromone, Ras GTPase, and Ydj1 Hsp40 chaperone. To compare the properties of yeast and human prenyltransferases, including the recently expanded target specificity of yeast farnesyltransferase, we have developed yeast strains that express human farnesyltransferase or geranylgeranyltransferase-I in lieu of their yeast counterparts. The humanized yeast strains display robust prenyltransferase activity that functionally replaces yeast prenyltransferase activity in a wide array of tests, including the prenylation of a wide variety of canonical and non-canonical human CaaX sequences, virus encoded CaaX sequences, non-canonical length sequences, and heterologously expressed human proteins HRas and DNAJA2. These results reveal highly overlapping substrate specificity for yeast and human farnesyltransferase, and mostly overlapping substrate specificity for GGTase-I. This yeast system is a valuable tool for further defining the prenylome of humans and other organisms, identifying proteins for which prenylation status has not yet been determined.
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Affiliation(s)
| | - Anushka Sarkar
- Department of Biochemistry and Molecular Biology, University of Georgia
| | | | - June H. Kim
- Department of Biochemistry and Molecular Biology, University of Georgia
| | - Walter K. Schmidt
- Department of Biochemistry and Molecular Biology, University of Georgia
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5
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Doss EM, Moore JM, Harman BH, Doud EH, Rubenstein EM, Bernstein DA. Characterization of endoplasmic reticulum-associated degradation in the human fungal pathogen Candida albicans. PeerJ 2023; 11:e15897. [PMID: 37645016 PMCID: PMC10461541 DOI: 10.7717/peerj.15897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/24/2023] [Indexed: 08/31/2023] Open
Abstract
Background Candida albicans is the most prevalent human fungal pathogen. In immunocompromised individuals, C. albicans can cause serious systemic disease, and patients infected with drug-resistant isolates have few treatment options. The ubiquitin-proteasome system has not been thoroughly characterized in C. albicans. Research from other organisms has shown ubiquitination is important for protein quality control and regulated protein degradation at the endoplasmic reticulum (ER) via ER-associated protein degradation (ERAD). Methods Here we perform the first characterization, to our knowledge, of ERAD in a human fungal pathogen. We generated functional knockouts of C. albicans genes encoding three proteins predicted to play roles in ERAD, the ubiquitin ligases Hrd1 and Doa10 and the ubiquitin-conjugating enzyme Ubc7. We assessed the fitness of each mutant in the presence of proteotoxic stress, and we used quantitative tandem mass tag mass spectrometry to characterize proteomic alterations in yeast lacking each gene. Results Consistent with a role in protein quality control, yeast lacking proteins thought to contribute to ERAD displayed hypersensitivity to proteotoxic stress. Furthermore, each mutant displayed distinct proteomic profiles, revealing potential physiological ERAD substrates, co-factors, and compensatory stress response factors. Among candidate ERAD substrates are enzymes contributing to ergosterol synthesis, a known therapeutic vulnerability of C. albicans. Together, our results provide the first description of ERAD function in C. albicans, and, to our knowledge, any pathogenic fungus.
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Affiliation(s)
- Ellen M. Doss
- Department of Biology, Ball State University, Muncie, Indiana, United States
- Mode of Action and Resistance Management Center of Expertise, Corteva Agriscience, Indianapolis, Indiana, United States
| | - Joshua M. Moore
- Department of Biology, Ball State University, Muncie, Indiana, United States
| | - Bryce H. Harman
- Department of Biology, Ball State University, Muncie, Indiana, United States
| | - Emma H. Doud
- Center for Proteome Analysis, Indiana University School of Medicine, Indianapolis, Indiana, United States
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States
| | - Eric M. Rubenstein
- Department of Biology, Ball State University, Muncie, Indiana, United States
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Tipper DJ, Harley CA. Spf1 and Ste24: quality controllers of transmembrane protein topology in the eukaryotic cell. Front Cell Dev Biol 2023; 11:1220441. [PMID: 37635876 PMCID: PMC10456885 DOI: 10.3389/fcell.2023.1220441] [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: 05/10/2023] [Accepted: 07/14/2023] [Indexed: 08/29/2023] Open
Abstract
DNA replication, transcription, and translation in eukaryotic cells occur with decreasing but still high fidelity. In contrast, for the estimated 33% of the human proteome that is inserted as transmembrane (TM) proteins, insertion with a non-functional inverted topology is frequent. Correct topology is essential for function and trafficking to appropriate cellular compartments and is controlled principally by responses to charged residues within 15 residues of the inserted TM domain (TMD); the flank with the higher positive charge remains in the cytosol (inside), following the positive inside rule (PIR). Yeast (Saccharomyces cerevisiae) mutants that increase insertion contrary to the PIR were selected. Mutants with strong phenotypes were found only in SPF1 and STE24 (human cell orthologs are ATP13A1 and ZMPSte24) with, at the time, no known relevant functions. Spf1/Atp13A1 is now known to dislocate to the cytosol TM proteins inserted contrary to the PIR, allowing energy-conserving reinsertion. We hypothesize that Spf1 and Ste24 both recognize the short, positively charged ER luminal peptides of TM proteins inserted contrary to the PIR, accepting these peptides into their large membrane-spanning, water-filled cavities through interaction with their many interior surface negative charges. While entry was demonstrated for Spf1, no published evidence directly demonstrates substrate entry to the Ste24 cavity, internal access to its zinc metalloprotease (ZMP) site, or active withdrawal of fragments, which may be essential for function. Spf1 and Ste24 comprise a PIR quality control system that is conserved in all eukaryotes and presumably evolved in prokaryotic progenitors as they gained differentiated membrane functions. About 75% of the PIR is imposed by this quality control system, which joins the UPR, ERAD, and autophagy (ER-phagy) in coordinated, overlapping quality control of ER protein function.
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Affiliation(s)
- Donald J. Tipper
- University of Massachusetts Medical School, Worcester, MA, United States
| | - Carol A. Harley
- i3S-Instituto de Investigação e Inovação em Saude, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
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7
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Turk SM, Indovina CJ, Miller JM, Overton DL, Runnebohm AM, Orchard CJ, Tragesser-Tiña ME, Gosser SK, Doss EM, Richards KA, Irelan CB, Daraghmi MM, Bailey CG, Niekamp JM, Claypool KP, Engle SM, Buchanan BW, Woodruff KA, Olesen JB, Smaldino PJ, Rubenstein EM. Lipid biosynthesis perturbation impairs endoplasmic reticulum-associated degradation. J Biol Chem 2023; 299:104939. [PMID: 37331602 PMCID: PMC10372827 DOI: 10.1016/j.jbc.2023.104939] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/02/2023] [Accepted: 06/09/2023] [Indexed: 06/20/2023] Open
Abstract
The relationship between lipid homeostasis and protein homeostasis (proteostasis) is complex and remains incompletely understood. We conducted a screen for genes required for efficient degradation of Deg1-Sec62, a model aberrant translocon-associated substrate of the endoplasmic reticulum (ER) ubiquitin ligase Hrd1, in Saccharomyces cerevisiae. This screen revealed that INO4 is required for efficient Deg1-Sec62 degradation. INO4 encodes one subunit of the Ino2/Ino4 heterodimeric transcription factor, which regulates expression of genes required for lipid biosynthesis. Deg1-Sec62 degradation was also impaired by mutation of genes encoding several enzymes mediating phospholipid and sterol biosynthesis. The degradation defect in ino4Δ yeast was rescued by supplementation with metabolites whose synthesis and uptake are mediated by Ino2/Ino4 targets. Stabilization of a panel of substrates of the Hrd1 and Doa10 ER ubiquitin ligases by INO4 deletion indicates ER protein quality control is generally sensitive to perturbed lipid homeostasis. Loss of INO4 sensitized yeast to proteotoxic stress, suggesting a broad requirement for lipid homeostasis in maintaining proteostasis. A better understanding of the dynamic relationship between lipid homeostasis and proteostasis may lead to improved understanding and treatment of several human diseases associated with altered lipid biosynthesis.
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Affiliation(s)
- Samantha M Turk
- Department of Biology, Ball State University, Muncie, Indiana, USA
| | | | - Jacob M Miller
- Department of Biology, Ball State University, Muncie, Indiana, USA
| | | | | | - Cade J Orchard
- Department of Biology, Ball State University, Muncie, Indiana, USA
| | | | | | - Ellen M Doss
- Department of Biology, Ball State University, Muncie, Indiana, USA
| | - Kyle A Richards
- Department of Biology, Ball State University, Muncie, Indiana, USA
| | | | | | - Connor G Bailey
- Department of Biology, Ball State University, Muncie, Indiana, USA
| | - Julia M Niekamp
- Department of Biology, Ball State University, Muncie, Indiana, USA
| | | | - Sarah M Engle
- Department of Biology, Ball State University, Muncie, Indiana, USA
| | - Bryce W Buchanan
- Department of Biology, Ball State University, Muncie, Indiana, USA
| | | | - James B Olesen
- Department of Biology, Ball State University, Muncie, Indiana, USA
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8
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Hosomi A, Okachi C, Fujiwara Y. Human SOD1 is secreted via a conventional secretion pathway in Saccharomyces cerevisiae. Biochem Biophys Res Commun 2023; 666:101-106. [PMID: 37182284 DOI: 10.1016/j.bbrc.2023.05.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 04/27/2023] [Accepted: 05/04/2023] [Indexed: 05/16/2023]
Abstract
Soluble proteins sorted through the secretory pathway contain an N-terminal signal peptide that induces their translocation into the endoplasmic reticulum (ER) from the cytosol. However, a few proteins that lack a signal peptide are still translocated into the ER, such as SOD1. SOD1 is a causative gene of amyotrophic lateral sclerosis (ALS). A relationship has been suggested between the secretion of SOD1 and the pathogenesis of ALS; however, the transport mechanism of SOD1 remains unclear. We herein report that SOD1 was translocated into the ER lumen through the translocon Sec61 and was then secreted extracellularly. The present results indicate the potential of suppressing the secretion of SOD1 as a therapeutic target for ALS.
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Affiliation(s)
- Akira Hosomi
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minamiminowa, Kamiina, Nagano, 399-4598, Japan; Faculty of Agriculture, Shinshu University, 8304 Minamiminowa, Kamiina, Nagano, 399-4598, Japan.
| | - Chinatsu Okachi
- Faculty of Agriculture, Shinshu University, 8304 Minamiminowa, Kamiina, Nagano, 399-4598, Japan
| | - Yudai Fujiwara
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minamiminowa, Kamiina, Nagano, 399-4598, Japan
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Ji C. Molecular Factors and Pathways of Hepatotoxicity Associated with HIV/SARS-CoV-2 Protease Inhibitors. Int J Mol Sci 2023; 24:ijms24097938. [PMID: 37175645 PMCID: PMC10178330 DOI: 10.3390/ijms24097938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Antiviral protease inhibitors are peptidomimetic molecules that block the active catalytic center of viral proteases and, thereby, prevent the cleavage of viral polyprotein precursors into maturation. They continue to be a key class of antiviral drugs that can be used either as boosters for other classes of antivirals or as major components of current regimens in therapies for the treatment of infections with human immunodeficiency virus (HIV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, sustained/lifelong treatment with the drugs or drugs combined with other substance(s) often leads to severe hepatic side effects such as lipid abnormalities, insulin resistance, and hepatotoxicity. The underlying pathogenic mechanisms are not fully known and are under continuous investigation. This review focuses on the general as well as specific molecular mechanisms of the protease inhibitor-induced hepatotoxicity involving transporter proteins, apolipoprotein B, cytochrome P450 isozymes, insulin-receptor substrate 1, Akt/PKB signaling, lipogenic factors, UDP-glucuronosyltransferase, pregnane X receptor, hepatocyte nuclear factor 4α, reactive oxygen species, inflammatory cytokines, off-target proteases, and small GTPase Rab proteins related to ER-Golgi trafficking, organelle stress, and liver injury. Potential pharmaceutical/therapeutic solutions to antiviral drug-induced hepatic side effects are also discussed.
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Affiliation(s)
- Cheng Ji
- Research Center for Liver Disease, GI/Liver Division, Department of Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA 90089, USA
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10
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Daraghmi MM, Miller JM, Bailey CG, Doss EM, Kalinski AL, Smaldino PJ, Rubenstein EM. Macro-ER-phagy receptors Atg39p and Atg40p confer resistance to aminoglycoside hygromycin B in S. cerevisiae. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000738. [PMID: 36818312 PMCID: PMC9932795 DOI: 10.17912/micropub.biology.000738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 02/24/2023]
Abstract
Receptor-mediated autophagic turnover of portions of the endoplasmic reticulum (ER) is mediated by macro-ER-phagy. We hypothesized macro-ER-phagy promotes proteotoxic stress resistance. We predicted Saccharomyces cerevisiae lacking macro-ER-phagy receptors would exhibit enhanced sensitivity to hygromycin B, which reduces translational fidelity and is expected to globally disrupt protein homeostasis, including at the ER. We observed that loss of either of two yeast macro-ER-phagy receptors (Atg39p or Atg40p) compromised cellular resistance to hygromycin B to a similar extent as loss of ER-associated degradation (ERAD) ubiquitin ligases Hrd1p and Doa10p. Our data are consistent with a model whereby macro-ER-phagy and ERAD collaborate to mediate ER protein quality control. Disruptions of macro-ER-phagy have been linked to neuropathy, dementia, and cancer. A dampened capacity to mediate protein quality control may contribute to these conditions.
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Affiliation(s)
| | | | | | | | | | | | - Eric M. Rubenstein
- Department of Biology, Ball State University
,
Correspondence to: Eric M. Rubenstein (
)
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11
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Mehrtash AB, Hochstrasser M. Ectopic RING activity at the ER membrane differentially impacts ERAD protein quality control pathways. J Biol Chem 2023; 299:102927. [PMID: 36682496 PMCID: PMC9950527 DOI: 10.1016/j.jbc.2023.102927] [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: 10/29/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/20/2023] Open
Abstract
Endoplasmic reticulum-associated degradation (ERAD) is a protein quality control pathway that ensures misfolded proteins are removed from the ER and destroyed. In ERAD, membrane and luminal substrates are ubiquitylated by ER-resident RING-type E3 ubiquitin ligases, retrotranslocated into the cytosol, and degraded by the proteasome. Overexpression of ERAD factors is frequently used in yeast and mammalian cells to study this process. Here, we analyze the impact of ERAD E3 overexpression on substrate turnover in yeast, where there are three ERAD E3 complexes (Doa10, Hrd1, and Asi1-3). Elevated Doa10 or Hrd1 (but not Asi1) RING activity at the ER membrane resulting from protein overexpression inhibits the degradation of specific Doa10 substrates. The ERAD E2 ubiquitin-conjugating enzyme Ubc6 becomes limiting under these conditions, and UBC6 overexpression restores Ubc6-mediated ERAD. Using a subset of the dominant-negative mutants, which contain the Doa10 RING domain but lack the E2-binding region, we show that they induce degradation of membrane tail-anchored Ubc6 independently of endogenous Doa10 and the other ERAD E3 complexes. This remains true even if the cells lack the Dfm1 rhomboid pseudoprotease, which is also a proposed retrotranslocon. Hence, rogue RING activity at the ER membrane elicits a highly specific off-pathway defect in the Doa10 pathway, and the data point to an additional ERAD E3-independent retrotranslocation mechanism.
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Affiliation(s)
- Adrian B Mehrtash
- Department of Molecular, Cellular, & Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Mark Hochstrasser
- Department of Molecular, Cellular, & Developmental Biology, Yale University, New Haven, Connecticut, USA; Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, USA.
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12
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Shilagardi K, Spear ED, Abraham R, Griffin DE, Michaelis S. The Integral Membrane Protein ZMPSTE24 Protects Cells from SARS-CoV-2 Spike-Mediated Pseudovirus Infection and Syncytia Formation. mBio 2022; 13:e0254322. [PMID: 36197088 PMCID: PMC9601121 DOI: 10.1128/mbio.02543-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 11/26/2022] Open
Abstract
COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had a devastating impact on global public health, emphasizing the importance of understanding innate immune mechanisms and cellular restriction factors that cells can harness to fight viral infections. The multimembrane-spanning zinc metalloprotease ZMPSTE24 is one such restriction factor. ZMPSTE24 has a well-characterized proteolytic role in the maturation of prelamin A, precursor of the nuclear scaffold protein lamin A. An apparently unrelated role for ZMPSTE24 in viral defense involves its interaction with the interferon-inducible membrane proteins (IFITMs), which block virus-host cell fusion by rigidifying cellular membranes and thereby prevent viral infection. ZMPSTE24, like the IFITMs, defends cells against a broad spectrum of enveloped viruses. However, its ability to protect against coronaviruses has never been examined. Here, we show that overexpression of ZMPSTE24 reduces the efficiency of cellular infection by SARS-CoV-2 Spike-pseudotyped lentivirus and that genetic knockout or small interfering RNA-mediated knockdown of endogenous ZMPSTE24 enhances infectivity. We further demonstrate a protective role for ZMPSTE24 in a Spike-ACE2-dependent cell-cell fusion assay. In both assays, a catalytic dead version of ZMPSTE24 is equally as protective as the wild-type protein, indicating that ZMPSTE24's proteolytic activity is not required for defense against SARS-CoV-2. Finally, we demonstrate by plaque assays that Zmpste24-/- mouse cells show enhanced infection by a genuine coronavirus, mouse hepatitis virus (MHV). This study extends the range of viral protection afforded by ZMPSTE24 to include coronaviruses and suggests that targeting ZMPSTE24's mechanism of viral defense could have therapeutic benefit. IMPORTANCE The COVID-19 pandemic caused by the coronavirus SARS-CoV-2 has underscored the importance of understanding intrinsic cellular components that can be harnessed as the cell's first line of defense to fight against viral infection. Our paper focuses on one such protein, the integral membrane protease ZMPSTE24, which interacts with interferon-inducible transmembrane proteins (IFITMs). IFITMs interfere with virus entry by inhibiting fusion between viral and host cell membranes, and ZMPSTE24 appears to contribute to this inhibitory activity. ZMPSTE24 has been shown to defend cells against several, but not all, enveloped viruses. In this study, we extend ZMPSTE24's reach to include coronaviruses, by showing that ZMPSTE24 protects cells from SARS-CoV-2 pseudovirus infection, Spike protein-mediated cell-cell fusion, and infection by the mouse coronavirus MHV. This work lays the groundwork for further studies to decipher the mechanistic role of ZMPSTE24 in blocking the entry of SARS-CoV-2 and other viruses into cells.
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Affiliation(s)
- Khurts Shilagardi
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Eric D. Spear
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Rachy Abraham
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Diane E. Griffin
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Susan Michaelis
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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Abolishing the prelamin A ZMPSTE24 cleavage site leads to progeroid phenotypes with near-normal longevity in mice. Proc Natl Acad Sci U S A 2022; 119:2118695119. [PMID: 35197292 PMCID: PMC8892526 DOI: 10.1073/pnas.2118695119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2022] [Indexed: 01/13/2023] Open
Abstract
The zinc metalloprotease ZMPSTE24 removes the last 15 amino acids of prelamin A, including a farnesylated cysteine, to produce mature lamin A. The premature aging disorder Hutchinson–Gilford progeria syndrome is caused by a permanently farnesylated prelamin A variant lacking the ZMPSTE24 cleavage site. ZMPSTE24 loss of function leads to the accumulation of farnesylated prelamin A and causes progeroid disorders. Some studies have implicated prelamin A in physiological aging. We describe mice with an amino acid substitution in prelamin A that blocks the ZMPSTE24-catalyzed cleavage. These mice develop progeroid phenotypes but, in contrast to those modeling Hutchinson–Gilford progeria syndrome or ZMPSTE24 deficiency, have near-normal lifespans, thus providing a model to study the effects of farnesylated prelamin A during aging. Prelamin A is a farnesylated precursor of lamin A, a nuclear lamina protein. Accumulation of the farnesylated prelamin A variant progerin, with an internal deletion including its processing site, causes Hutchinson–Gilford progeria syndrome. Loss-of-function mutations in ZMPSTE24, which encodes the prelamin A processing enzyme, lead to accumulation of full-length farnesylated prelamin A and cause related progeroid disorders. Some data suggest that prelamin A also accumulates with physiological aging. Zmpste24−/− mice die young, at ∼20 wk. Because ZMPSTE24 has functions in addition to prelamin A processing, we generated a mouse model to examine effects solely due to the presence of permanently farnesylated prelamin A. These mice have an L648R amino acid substitution in prelamin A that blocks ZMPSTE24-catalyzed processing to lamin A. The LmnaL648R/L648R mice express only prelamin and no mature protein. Notably, nearly all survive to 65 to 70 wk, with ∼40% of male and 75% of female LmnaL648R/L648R mice having near-normal lifespans of 90 wk (almost 2 y). Starting at ∼10 wk of age, LmnaL648R/L648R mice of both sexes have lower body masses than controls. By ∼20 to 30 wk of age, they exhibit detectable cranial, mandibular, and dental defects similar to those observed in Zmpste24−/− mice and have decreased vertebral bone density compared to age- and sex-matched controls. Cultured embryonic fibroblasts from LmnaL648R/L648R mice have aberrant nuclear morphology that is reversible by treatment with a protein farnesyltransferase inhibitor. These novel mice provide a model to study the effects of farnesylated prelamin A during physiological aging.
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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: 14] [Impact Index Per Article: 4.7] [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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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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