1
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Yang J, Kim SY, Hwang CS. Delineation of the substrate recognition domain of MARCHF6 E3 ubiquitin ligase in the Ac/N-degron pathway and its regulatory role in ferroptosis. J Biol Chem 2024:107731. [PMID: 39216628 DOI: 10.1016/j.jbc.2024.107731] [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: 06/29/2024] [Revised: 08/05/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024] Open
Abstract
Nα-terminal acetylation in eukaryotic proteins creates specific degradation signals (Ac/N-degrons) targeted for ubiquitin-mediated proteolysis via the Ac/N-degron pathway. Despite the identification of key components of the Ac/N-degron pathway over the past 15 years, the precise recognition domain (Ac/N domain) remains unclear. Here, we defined the Ac/N domain of the endoplasmic reticulum MARCHF6 E3 ubiquitin ligase through a systematic analysis of its cytosol-facing regions using alanine-stretch mutagenesis, chemical crosslinking-based co-immunoprecipitation-immunoblotting, and split-ubiquitin assays in human and yeast cells. The Ac/N domain of MARCHF6 exhibits preferential binding specificity to Nα-terminally acetylated proteins and peptides over their unacetylated counterparts, mediating the degradation of Ac/N-degron-bearing proteins, such as the G-protein regulator RGS2 and the lipid droplet protein PLIN2. Furthermore, abolishing the recognition of Ac/N-degrons by MARCHF6 stabilized RGS2 and PLIN2, thereby increasing the resistance to ferroptosis, an iron-dependent lipid peroxidation-mediated cell death. These findings provide mechanistic and functional insights into how MARCHF6 serves as a rheostatic modulator of ferroptosis by recognizing Ac/N-degron substrates via its Ac/N domain and non-Ac/N-degron substrates via distinct recognition sites.
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Affiliation(s)
- Jihye Yang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Sang-Yoon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Cheol-Sang Hwang
- Department of Life Sciences, Korea University, Seoul 02841, South Korea.
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2
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Shokeen K, Baroi MK, Chahar M, Das D, Saini H, Kumar S. Arginyltransferase 1 (ATE1)-mediated proteasomal degradation of viral haemagglutinin protein: a unique host defence mechanism. J Gen Virol 2024; 105. [PMID: 39207120 DOI: 10.1099/jgv.0.002020] [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] [Indexed: 09/04/2024] Open
Abstract
The extensive protein production in virus-infected cells can disrupt protein homeostasis and activate various proteolytic pathways. These pathways utilize post-translational modifications (PTMs) to drive the ubiquitin-mediated proteasomal degradation of surplus proteins. Protein arginylation is the least explored PTM facilitated by arginyltransferase 1 (ATE1) enzyme. Several studies have provided evidence supporting its importance in multiple physiological processes, including ageing, stress, nerve regeneration, actin formation and embryo development. However, its function in viral pathogenesis is still unexplored. The present work utilizes Newcastle disease virus (NDV) as a model to establish the role of the ATE1 enzyme and its activity in pathogenesis. Our data indicate a rise in levels of N-arginylated cellular proteins in the infected cells. Here, we also explore the haemagglutinin-neuraminidase (HN) protein of NDV as a presumable target for arginylation. The data indicate that the administration of Arg amplifies the arginylation process, resulting in reduced stability of the HN protein. ATE1 enzyme activity inhibition and gene expression knockdown studies were also conducted to analyse modulation in HN protein levels, which further substantiated the findings. Moreover, we also observed Arg addition and probable ubiquitin modification to the HN protein, indicating engagement of the proteasomal degradation machinery. Lastly, we concluded that the enhanced levels of the ATE1 enzyme could transfer the Arg residue to the N-terminus of the HN protein, ultimately driving its proteasomal degradation.
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Affiliation(s)
- Kamal Shokeen
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Malay Kumar Baroi
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, India
| | - Manjeet Chahar
- Centre for Medical Biotechnology, Maharshi Dayanand University, Rohtak, India
| | - Debapratim Das
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, India
| | - Harimohan Saini
- Centre for Medical Biotechnology, Maharshi Dayanand University, Rohtak, India
| | - Sachin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
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3
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Zhang L, Braynen J, Fahey A, Chopra K, Cifani P, Tadesse D, Regulski M, Hu F, van Dam HJJ, Xie M, Ware D, Blaby-Haas CE. Two related families of metal transferases, ZNG1 and ZNG2, are involved in acclimation to poor Zn nutrition in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2023; 14:1237722. [PMID: 37965006 PMCID: PMC10642216 DOI: 10.3389/fpls.2023.1237722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/02/2023] [Indexed: 11/16/2023]
Abstract
Metal homeostasis has evolved to tightly modulate the availability of metals within the cell, avoiding cytotoxic interactions due to excess and protein inactivity due to deficiency. Even in the presence of homeostatic processes, however, low bioavailability of these essential metal nutrients in soils can negatively impact crop health and yield. While research has largely focused on how plants assimilate metals, acclimation to metal-limited environments requires a suite of strategies that are not necessarily involved in metal transport across membranes. The identification of these mechanisms provides a new opportunity to improve metal-use efficiency and develop plant foodstuffs with increased concentrations of bioavailable metal nutrients. Here, we investigate the function of two distinct subfamilies of the nucleotide-dependent metallochaperones (NMCs), named ZNG1 and ZNG2, that are found in plants, using Arabidopsis thaliana as a reference organism. AtZNG1 (AT1G26520) is an ortholog of human and fungal ZNG1, and like its previously characterized eukaryotic relatives, localizes to the cytosol and physically interacts with methionine aminopeptidase type I (AtMAP1A). Analysis of AtZNG1, AtMAP1A, AtMAP2A, and AtMAP2B transgenic mutants are consistent with the role of Arabidopsis ZNG1 as a Zn transferase for AtMAP1A, as previously described in yeast and zebrafish. Structural modeling reveals a flexible cysteine-rich loop that we hypothesize enables direct transfer of Zn from AtZNG1 to AtMAP1A during GTP hydrolysis. Based on proteomics and transcriptomics, loss of this ancient and conserved mechanism has pleiotropic consequences impacting the expression of hundreds of genes, including those involved in photosynthesis and vesicle transport. Members of the plant-specific family of NMCs, ZNG2A1 (AT1G80480) and ZNG2A2 (AT1G15730), are also required during Zn deficiency, but their target protein(s) remain to be discovered. RNA-seq analyses reveal wide-ranging impacts across the cell when the genes encoding these plastid-localized NMCs are disrupted.
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Affiliation(s)
- Lifang Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Janeen Braynen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Audrey Fahey
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Kriti Chopra
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY, United States
| | - Paolo Cifani
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Dimiru Tadesse
- Biology Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Michael Regulski
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Fangle Hu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Hubertus J. J. van Dam
- Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Meng Xie
- Biology Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
- USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY, United States
| | - Crysten E. Blaby-Haas
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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4
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Haarer BK, Pimm ML, de Jong EP, Amberg DC, Henty-Ridilla JL. Purification of human β- and γ-actin from budding yeast. J Cell Sci 2023; 136:jcs260540. [PMID: 37070275 PMCID: PMC10184827 DOI: 10.1242/jcs.260540] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 04/04/2023] [Indexed: 04/19/2023] Open
Abstract
Biochemical studies of human actin and its binding partners rely heavily on abundant and easily purified α-actin from skeletal muscle. Therefore, muscle actin has been used to evaluate and determine the activities of most actin regulatory proteins but there is an underlying concern that these proteins perform differently from actin present in non-muscle cells. To provide easily accessible and relatively abundant sources of human β- or γ-actin (i.e. cytoplasmic actins), we developed Saccharomyces cerevisiae strains that express each as their sole source of actin. Both β- or γ-actin purified in this system polymerize and interact with various binding partners, including profilin, mDia1 (formin), fascin and thymosin-β4 (Tβ4). Notably, Tβ4 and profilin bind to β- or γ-actin with higher affinity than to α-actin, emphasizing the value of testing actin ligands with specific actin isoforms. These reagents will make specific isoforms of actin more accessible for future studies on actin regulation.
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Affiliation(s)
- Brian K. Haarer
- Department of Biochemistry and Molecular Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, NY 13210, USA
| | - Morgan L. Pimm
- Department of Biochemistry and Molecular Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, NY 13210, USA
| | | | - David C. Amberg
- Department of Biochemistry and Molecular Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, NY 13210, USA
| | - Jessica L. Henty-Ridilla
- Department of Biochemistry and Molecular Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, NY 13210, USA
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
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5
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Seo DY, Kim D, Nguyen KT, Oh J, Lee JS, Hwang CS. N-Terminally arginylated ubiquitin is attached to histone H2A by RING1B E3 ligase in human cells. Biochem Biophys Res Commun 2023; 666:186-194. [PMID: 36932026 DOI: 10.1016/j.bbrc.2023.02.022] [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: 01/30/2023] [Accepted: 02/09/2023] [Indexed: 02/11/2023]
Abstract
Ubiquitin (Ub) is highly conserved in all eukaryotic organisms and begins at the N-terminus with Met and Gln. Our recent research demonstrates that N-terminally (Nt-) arginylated Ub can be produced in the yeast Saccharomyces cerevisiae. However, the existence of Nt-arginylated Ub in multicellular organisms remains unknown. Here we explore the mechanism for creating Nt-arginylated Ub using human embryonic kidney HEK293 cells that express various Nt-modified Ubs. We found that Gln-starting Q-Ub was converted into Glu-starting E-Ub by NTAQ1 Nt-deamidase and subsequently Nt-arginylated by ATE1 arginyltransferase in HEK293 cells. We also found that the resulting Arg-Glu-starting RE-Ub was mainly deposited on the Lys119 residue of histone H2A. Furthermore, RING1B E3 Ub ligase mediated the attachment of RE-Ub to H2A. These findings reveal a previously unknown type of histone ubiquitylation which greatly increases the combinatorial complexity of histone and ubiquitin codes.
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Affiliation(s)
- Dong-Young Seo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Dasom Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Kha The Nguyen
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Junsoo Oh
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, Kangwon, 24341, Republic of Korea
| | - Jung-Shin Lee
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, Kangwon, 24341, Republic of Korea
| | - Cheol-Sang Hwang
- Department of Life Sciences, Korea University, Seoul, 02841, Republic of Korea.
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6
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In vitro production of N-degron fused proteins and its application. Methods Enzymol 2023. [PMID: 37532410 DOI: 10.1016/bs.mie.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
The N-degron pathway, first discovered several decades ago by Varshavsky's laboratory, controls the half-life of target proteins depending on their N-terminal residues. In vivo cell biology studies have established the physiological role of the N-degron pathway. However, in vitro studies such as biochemical assays and structural biology studies are relatively limited. The N-degron substrates cannot be obtained via simple protein expression. The N-degron residues are exposed via the proteolytic process from the translated nascent polypeptide chains. Thus, methods for the fusion expression with several cleavable tags and subsequent treatment with specific proteases to design the exposed N-degron signals have been introduced. Recently, we developed a unique fusion technique using microtubule-associated protein 1A/1B light chain 3B (LC3B), a key marker protein of autophagy, to obtain a high yield of the purified target proteins with variable N-terminal residues for various biochemical studies including enzymatic and binding assays, and crystallization of N-degron complex. This chapter describes the protocols that include the vector map designed for producing LC3B fused target proteins, methods for expression and purification of an example protein, p62/SQSMT1, using different N-terminal residues, and methods to obtain the purified ATG4B protease, which is used for processing LC3B tag and exposing the required N-terminal residues of the target protein.
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7
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Bolgi O, Silva-Garcia M, Ross B, Pilla E, Kari V, Killisch M, Spitzner M, Stark N, Lenz C, Weiss K, Donzelli L, Gorrell MD, Grade M, Riemer J, Urlaub H, Dobbelstein M, Huber R, Geiss-Friedlander R. Dipeptidyl peptidase 9 triggers BRCA2 degradation and promotes DNA damage repair. EMBO Rep 2022; 23:e54136. [PMID: 35912982 PMCID: PMC9535758 DOI: 10.15252/embr.202154136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 07/01/2022] [Accepted: 07/07/2022] [Indexed: 12/30/2022] Open
Abstract
N-terminal sequences are important sites for post-translational modifications that alter protein localization, activity, and stability. Dipeptidyl peptidase 9 (DPP9) is a serine aminopeptidase with the rare ability to cleave off N-terminal dipeptides with imino acid proline in the second position. Here, we identify the tumor-suppressor BRCA2 as a DPP9 substrate and show this interaction to be induced by DNA damage. We present crystallographic structures documenting intracrystalline enzymatic activity of DPP9, with the N-terminal Met1-Pro2 of a BRCA21-40 peptide captured in its active site. Intriguingly, DPP9-depleted cells are hypersensitive to genotoxic agents and are impaired in the repair of DNA double-strand breaks by homologous recombination. Mechanistically, DPP9 targets BRCA2 for degradation and promotes the formation of RAD51 foci, the downstream function of BRCA2. N-terminal truncation mutants of BRCA2 that mimic a DPP9 product phenocopy reduced BRCA2 stability and rescue RAD51 foci formation in DPP9-deficient cells. Taken together, we present DPP9 as a regulator of BRCA2 stability and propose that by fine-tuning the cellular concentrations of BRCA2, DPP9 alters the BRCA2 interactome, providing a possible explanation for DPP9's role in cancer.
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Affiliation(s)
- Oguz Bolgi
- Institute of Molecular Medicine and Cell Research, Medical Faculty, University of Freiburg, Freiburg, Germany.,Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Maria Silva-Garcia
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Breyan Ross
- Max Planck Institut für Biochemie, Martinsried, Germany.,Proteros Biostructures GmbH, Martinsried, Germany
| | - Esther Pilla
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Vijayalakshmi Kari
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Markus Killisch
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Melanie Spitzner
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Nadine Stark
- Institute of Molecular Oncology, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, Göttingen, Germany
| | - Christof Lenz
- Bioanalytics, Institute of Clinical Chemistry, University Medical Center, Göttingen, Germany.,Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Konstantin Weiss
- Institute of Biochemistry, Redox Biochemistry, and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Laura Donzelli
- Institute of Molecular Medicine and Cell Research, Medical Faculty, University of Freiburg, Freiburg, Germany
| | - Mark D Gorrell
- Centenary Institute, The University of Sydney Faculty of Medicine and Health, Sydney, NSW, Australia
| | - Marian Grade
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Jan Riemer
- Institute of Biochemistry, Redox Biochemistry, and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Henning Urlaub
- Bioanalytics, Institute of Clinical Chemistry, University Medical Center, Göttingen, Germany.,Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Matthias Dobbelstein
- Institute of Molecular Oncology, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, Göttingen, Germany
| | - Robert Huber
- Max Planck Institut für Biochemie, Martinsried, Germany.,Zentrum für Medizinische Biotechnologie, Universität Duisburg-Essen, Essen, Germany.,Fakultät für Chemie, Technische Universität München, Garching, Germany
| | - Ruth Geiss-Friedlander
- Institute of Molecular Medicine and Cell Research, Medical Faculty, University of Freiburg, Freiburg, Germany.,Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
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8
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Rincón-Betancurt O, Aceituno-Medina M, Verónica García-Fajardo L, Hernández E. Effect of larval nutrition on the hemolymph protein composition during metamorphosis of Anastrepha obliqua. BULLETIN OF ENTOMOLOGICAL RESEARCH 2022; 112:593-603. [PMID: 35199634 DOI: 10.1017/s0007485321001188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Few studies have focused on how nutrition affects the bioavailability and investment of protein during the metamorphosis of tephritids. Our study allowed us to observe how the type and particle size of the bulking agent affected the protein composition in the hemolymph of the larva and adult of Anastrepha obliqua. Results indicated that, true protein bioavailability and protein profile was greatly modified by the bulking agent and its particle size. The physical structure of the food matrix affected the content of crude fiber (F), crude protein (P), F/P ratio, non-protein nitrogen, ammoniacal nitrogen, and α-amylase and trypsin inhibitors. Results from SDS-PAGE revealed 45 fractions with well-defined bands ranging from ~28 to ~401 kDa in larvae and adults, we found the main differences between the samples from different food matrices within the 75-100 kDa range. Hemolymph of adults from the coarse coconut fiber food matrix treatment showed a single band with a molecular weight close to 250 kDa, probably associated with a storage protein such as lipophorins. The food matrix with a coarse bulking agent had a high concentration of ammoniacal nitrogen, suggesting high microbial activity. In conclusion, the particle size of the bulking agent of the food matrix changes the bioavailability of protein in hemolymph in the adult regardless of the total concentration of protein. Also, when the particle size of the bulking agent favored the F/P ratio, higher larval density resulted in higher individual larval weight, larval yield, and adult emergence.
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Affiliation(s)
- Olivia Rincón-Betancurt
- Universidad Autónoma de Chiapas, Blvd. Príncipe Akishino S/N, Solidaridad 2000. Tapachula, Chiapas, 30798, México
- Programa Moscamed SADER-SENASICA, Camino a los Cacahotales S/N, Metapa de Domínguez, Chiapas, 30860, México
| | - Marysol Aceituno-Medina
- Universidad Autónoma de Chiapas, Blvd. Príncipe Akishino S/N, Solidaridad 2000. Tapachula, Chiapas, 30798, México
- Programa Moscamed SADER-SENASICA, Camino a los Cacahotales S/N, Metapa de Domínguez, Chiapas, 30860, México
| | | | - Emilio Hernández
- Universidad Autónoma de Chiapas, Blvd. Príncipe Akishino S/N, Solidaridad 2000. Tapachula, Chiapas, 30798, México
- Programa Moscamed SADER-SENASICA, Camino a los Cacahotales S/N, Metapa de Domínguez, Chiapas, 30860, México
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9
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Nguyen KT, Ju S, Kim SY, Lee CS, Lee C, Hwang CS. N-Terminal Modifications of Ubiquitin via Methionine Excision, Deamination, and Arginylation Expand the Ubiquitin Code. Mol Cells 2022; 45:158-167. [PMID: 35253655 PMCID: PMC8926867 DOI: 10.14348/molcells.2022.2027] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/16/2021] [Accepted: 01/12/2022] [Indexed: 11/27/2022] Open
Abstract
Ubiquitin (Ub) is post-translationally modified by Ub itself or Ub-like proteins, phosphorylation, and acetylation, among others, which elicits a variety of Ub topologies and cellular functions. However, N-terminal (Nt) modifications of Ub remain unknown, except the linear head-to-tail ubiquitylation via Nt-Met. Here, using the yeast Saccharomyces cerevisiae and an Nt-arginylated Ub-specific antibody, we found that the detectable level of Ub undergoes Nt-Met excision, Nt-deamination, and Nt-arginylation. The resulting Nt-arginylated Ub and its conjugated proteins are upregulated in the stationary-growth phase or by oxidative stress. We further proved the existence of Nt-arginylated Ub in vivo and identified Nt-arginylated Ub-protein conjugates using stable isotope labeling by amino acids in cell culture (SILAC)-based tandem mass spectrometry. In silico structural modeling of Nt-arginylated Ub predicted that Nt-Arg flexibly protrudes from the surface of the Ub, thereby most likely providing a docking site for the factors that recognize it. Collectively, these results reveal unprecedented Nt-arginylated Ub and the pathway by which it is produced, which greatly expands the known complexity of the Ub code.
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Affiliation(s)
- Kha The Nguyen
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Shinyeong Ju
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Korea
| | - Sang-Yoon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Chang-Seok Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Korea
| | - Cheol-Sang Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
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10
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Wang Z, Zhang L, Yuan W, Zhang Y, Lu H. SAPT, a Fast and Efficient Approach for Simultaneous Profiling of Protein N- and C-Terminome. Anal Chem 2021; 93:10553-10560. [PMID: 34297549 DOI: 10.1021/acs.analchem.1c01598] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Protein termini play pivotal roles in various biological processes. Although several terminomic strategies have been proposed for the analysis of protein N-termini or protein C-termini separately, few can analyze both ends of proteins at the same time. Herein, we developed a workflow, termed Simultaneous Analysis of Protein N- and C-Terminome (SAPT) based on strong cation exchange chromatography (SCX) fractionation. Taking advantage of terminal peptides' reduced charge states in low pH SCX for their selective separation, we identified 3724 canonical human protein N-termini and 3129 canonical human protein C-termini, as well as 1463 neo-N-termini from the HeLa cell line, representing the largest human protein C-termini data set and the second largest human protein N-termini data set so far. The whole fractionation procedure was simple and rapid with considerable selectivity by utilizing a commercially available SCX-SPE column. In addition, we report for the first time the comprehensive screening of protein N-terminal and C-terminal modifications, leading to an identification of 8 kinds of protein N-terminal PTMs other than acetylation and 1 kind of protein C-terminal PTM other than amidation. Our results demonstrate the excellent performance and great potential of SAPT in terminomic studies. Data are available via ProteomeXchange with identifier PXD024573.
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Affiliation(s)
- Zhongjie Wang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
| | - Lei Zhang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
| | - Wenjuan Yuan
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
| | - Ying Zhang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China.,Department of Chemistry and Key Laboratory of Glycoconjugates Research Ministry of Public Health, Fudan University, Shanghai 200433, P. R. China
| | - Haojie Lu
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China.,Department of Chemistry and Key Laboratory of Glycoconjugates Research Ministry of Public Health, Fudan University, Shanghai 200433, P. R. China
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11
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Collier MP, Moreira KB, Li KH, Chen YC, Itzhak D, Samant R, Leitner A, Burlingame A, Frydman J. Native mass spectrometry analyses of chaperonin complex TRiC/CCT reveal subunit N-terminal processing and re-association patterns. Sci Rep 2021; 11:13084. [PMID: 34158536 PMCID: PMC8219831 DOI: 10.1038/s41598-021-91086-6] [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] [Received: 11/03/2020] [Accepted: 05/05/2021] [Indexed: 11/14/2022] Open
Abstract
The eukaryotic chaperonin TRiC/CCT is a large ATP-dependent complex essential for cellular protein folding. Its subunit arrangement into two stacked eight-membered hetero-oligomeric rings is conserved from yeast to man. A recent breakthrough enables production of functional human TRiC (hTRiC) from insect cells. Here, we apply a suite of mass spectrometry techniques to characterize recombinant hTRiC. We find all subunits CCT1-8 are N-terminally processed by combinations of methionine excision and acetylation observed in native human TRiC. Dissociation by organic solvents yields primarily monomeric subunits with a small population of CCT dimers. Notably, some dimers feature non-canonical inter-subunit contacts absent in the initial hTRiC. This indicates individual CCT monomers can promiscuously re-assemble into dimers, and lack the information to assume the specific interface pairings in the holocomplex. CCT5 is consistently the most stable subunit and engages in the greatest number of non-canonical dimer pairings. These findings confirm physiologically relevant post-translational processing and function of recombinant hTRiC and offer quantitative insight into the relative stabilities of TRiC subunits and interfaces, a key step toward reconstructing its assembly mechanism. Our results also highlight the importance of assigning contacts identified by native mass spectrometry after solution dissociation as canonical or non-canonical when investigating multimeric assemblies.
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Affiliation(s)
| | | | - Kathy H Li
- Department of Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Yu-Chan Chen
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Rahul Samant
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, Zurich, Switzerland
| | - Alma Burlingame
- Department of Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA, USA.
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12
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Winter N, Novatchkova M, Bachmair A. Cellular Control of Protein Turnover via the Modification of the Amino Terminus. Int J Mol Sci 2021; 22:ijms22073545. [PMID: 33805528 PMCID: PMC8037982 DOI: 10.3390/ijms22073545] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 12/13/2022] Open
Abstract
The first amino acid of a protein has an important influence on its metabolic stability. A number of ubiquitin ligases contain binding domains for different amino-terminal residues of their substrates, also known as N-degrons, thereby mediating turnover. This review summarizes, in an exemplary way, both older and more recent findings that unveil how destabilizing amino termini are generated. In most cases, a step of proteolytic cleavage is involved. Among the over 500 proteases encoded in the genome of higher eukaryotes, only a few are known to contribute to the generation of N-degrons. It can, therefore, be expected that many processing paths remain to be discovered.
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Affiliation(s)
- Nikola Winter
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, A-1030 Vienna, Austria;
| | - Maria Novatchkova
- Vienna BioCenter, Research Institute of Molecular Pathology, A-1030 Vienna, Austria;
- Vienna BioCenter, Institute of Molecular Biotechnology, A-1030 Vienna, Austria
| | - Andreas Bachmair
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, A-1030 Vienna, Austria;
- Correspondence:
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13
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Structural basis of Naa20 activity towards a canonical NatB substrate. Commun Biol 2021; 4:2. [PMID: 33398031 PMCID: PMC7782713 DOI: 10.1038/s42003-020-01546-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/30/2020] [Indexed: 01/29/2023] Open
Abstract
N-terminal acetylation is one of the most common protein modifications in eukaryotes and is carried out by N-terminal acetyltransferases (NATs). It plays important roles in protein homeostasis, localization, and interactions and is linked to various human diseases. NatB, one of the major co-translationally active NATs, is composed of the catalytic subunit Naa20 and the auxiliary subunit Naa25, and acetylates about 20% of the proteome. Here we show that NatB substrate specificity and catalytic mechanism are conserved among eukaryotes, and that Naa20 alone is able to acetylate NatB substrates in vitro. We show that Naa25 increases the Naa20 substrate affinity, and identify residues important for peptide binding and acetylation activity. We present the first Naa20 crystal structure in complex with the competitive inhibitor CoA-Ac-MDEL. Our findings demonstrate how Naa20 binds its substrates in the absence of Naa25 and support prospective endeavors to derive specific NAT inhibitors for drug development.
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14
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Exploring the Complexity of Protein-Level Dosage Compensation that Fine-Tunes Stoichiometry of Multiprotein Complexes. PLoS Genet 2020; 16:e1009091. [PMID: 33112847 PMCID: PMC7652333 DOI: 10.1371/journal.pgen.1009091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 11/09/2020] [Accepted: 08/31/2020] [Indexed: 11/19/2022] Open
Abstract
Proper control of gene expression levels upon various perturbations is a fundamental aspect of cellular robustness. Protein-level dosage compensation is one mechanism buffering perturbations to stoichiometry of multiprotein complexes through accelerated proteolysis of unassembled subunits. Although N-terminal acetylation- and ubiquitin-mediated proteasomal degradation by the Ac/N-end rule pathway enables selective compensation of excess subunits, it is unclear how widespread this pathway contributes to stoichiometry control. Here we report that dosage compensation depends only partially on the Ac/N-end rule pathway. Our analysis of genetic interactions between 18 subunits and 12 quality control factors in budding yeast demonstrated that multiple E3 ubiquitin ligases and N-acetyltransferases are involved in dosage compensation. We find that N-acetyltransferases-mediated compensation is not simply predictable from N-terminal sequence despite their sequence specificity for N-acetylation. We also find that the compensation of Pop3 and Bet4 is due in large part to a minor N-acetyltransferase NatD. Furthermore, canonical NatD substrates histone H2A/H4 were compensated even in its absence, suggesting N-acetylation-independent stoichiometry control. Our study reveals the complexity and robustness of the stoichiometry control system. Quality control of multiprotein complexes is important for maintaining homeostasis in cellular systems that are based on functional complexes. Proper stoichiometry of multiprotein complexes is achieved by the balance between protein synthesis and degradation. Recent studies showed that translation efficiency tends to scale with stoichiometry of their subunits. On the other hand, although protein N-terminal acetylation- and ubiquitin-mediated proteolysis pathway is involved in selective degradation of excess subunits, it is unclear how widespread this pathway contributes to stoichiometry control due to the lack of a systematic investigation using endogenous proteins. To better understand the landscape of the stoichiometry control system, we examined genetic interactions between 18 subunits and 12 quality control factors (E3 ubiquitin ligases and N-acetyltransferases), in total 114 combinations. Our data suggest that N-acetyltransferases are partially responsible for stoichiometry control and that N-acetylation-independent pathway is also involved in selective degradation of excess subunits. Therefore, this study reveals the complexity and robustness of the stoichiometry control system. Further dissection of this complexity will help to understand the mechanisms buffering gene expression perturbations and shaping proteome stoichiometry.
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15
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Recognition of nonproline N-terminal residues by the Pro/N-degron pathway. Proc Natl Acad Sci U S A 2020; 117:14158-14167. [PMID: 32513738 DOI: 10.1073/pnas.2007085117] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Eukaryotic N-degron pathways are proteolytic systems whose unifying feature is their ability to recognize proteins containing N-terminal (Nt) degradation signals called N-degrons, and to target these proteins for degradation by the 26S proteasome or autophagy. GID4, a subunit of the GID ubiquitin ligase, is the main recognition component of the proline (Pro)/N-degron pathway. GID4 targets proteins through their Nt-Pro residue or a Pro at position 2, in the presence of specific downstream sequence motifs. Here we show that human GID4 can also recognize hydrophobic Nt-residues other than Pro. One example is the sequence Nt-IGLW, bearing Nt-Ile. Nt-IGLW binds to wild-type human GID4 with a K d of 16 μM, whereas the otherwise identical Nt-Pro-bearing sequence PGLW binds to GID4 more tightly, with a K d of 1.9 μM. Despite this difference in affinities of GID4 for Nt-IGLW vs. Nt-PGLW, we found that the GID4-mediated Pro/N-degron pathway of the yeast Saccharomyces cerevisiae can target an Nt-IGLW-bearing protein for rapid degradation. We solved crystal structures of human GID4 bound to a peptide bearing Nt-Ile or Nt-Val. We also altered specific residues of human GID4 and measured the affinities of resulting mutant GID4s for Nt-IGLW and Nt-PGLW, thereby determining relative contributions of specific GID4 residues to the GID4-mediated recognition of Nt-Pro vs. Nt-residues other than Pro. These and related results advance the understanding of targeting by the Pro/N-degron pathway and greatly expand the substrate recognition range of the GID ubiquitin ligase in both human and yeast cells.
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16
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Abstract
The nucleus is enclosed by a double-membrane structure, the nuclear envelope, which separates the nucleoplasm from the cytoplasm. The outer nuclear membrane is continuous with the endoplasmic reticulum (ER), whereas the inner nuclear membrane (INM) is a specialized compartment with a unique proteome. In order to ensure compartmental homeostasis, INM-associated degradation (INMAD) is required for both protein quality control and regulated proteolysis of INM proteins. INMAD shares similarities with ER-associated degradation (ERAD). The mechanism of ERAD is well characterized, whereas the INMAD pathway requires further definition. Here we review the three different branches of INMAD, mediated by their respective E3 ubiquitin ligases: Doa10, Asi1-3, and APC/C. We clarify the distinction between ERAD and INMAD, their substrate recognition signals, and the subsequent processing by their respective degradation machineries. We also discuss the significance of cell-cycle and developmental regulation of protein clearance at the INM, and its relationship to human disease.
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Affiliation(s)
- Bailey Koch
- a Department of Biological Science, The Florida State University , Tallahassee , FL , USA
| | - Hong-Guo Yu
- a Department of Biological Science, The Florida State University , Tallahassee , FL , USA
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17
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Huber M, Bienvenut WV, Linster E, Stephan I, Armbruster L, Sticht C, Layer D, Lapouge K, Meinnel T, Sinning I, Giglione C, Hell R, Wirtz M. NatB-Mediated N-Terminal Acetylation Affects Growth and Biotic Stress Responses. PLANT PHYSIOLOGY 2020; 182:792-806. [PMID: 31744933 PMCID: PMC6997699 DOI: 10.1104/pp.19.00792] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 11/07/2019] [Indexed: 05/22/2023]
Abstract
N∝-terminal acetylation (NTA) is one of the most abundant protein modifications in eukaryotes. In humans, NTA is catalyzed by seven Nα-acetyltransferases (NatA-F and NatH). Remarkably, the plant Nat machinery and its biological relevance remain poorly understood, although NTA has gained recognition as a key regulator of crucial processes such as protein turnover, protein-protein interaction, and protein targeting. In this study, we combined in vitro assays, reverse genetics, quantitative N-terminomics, transcriptomics, and physiological assays to characterize the Arabidopsis (Arabidopsis thaliana) NatB complex. We show that the plant NatB catalytic (NAA20) and auxiliary subunit (NAA25) form a stable heterodimeric complex that accepts canonical NatB-type substrates in vitro. In planta, NatB complex formation was essential for enzymatic activity. Depletion of NatB subunits to 30% of the wild-type level in three Arabidopsis T-DNA insertion mutants (naa20-1, naa20-2, and naa25-1) caused a 50% decrease in plant growth. A complementation approach revealed functional conservation between plant and human catalytic NatB subunits, whereas yeast NAA20 failed to complement naa20-1 Quantitative N-terminomics of approximately 1000 peptides identified 32 bona fide substrates of the plant NatB complex. In vivo, NatB was seen to preferentially acetylate N termini starting with the initiator Met followed by acidic amino acids and contributed 20% of the acetylation marks in the detected plant proteome. Global transcriptome and proteome analyses of NatB-depleted mutants suggested a function of NatB in multiple stress responses. Indeed, loss of NatB function, but not NatA, increased plant sensitivity toward osmotic and high-salt stress, indicating that NatB is required for tolerance of these abiotic stressors.
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Affiliation(s)
- Monika Huber
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Willy V Bienvenut
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Eric Linster
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Iwona Stephan
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Laura Armbruster
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | | | - Dominik Layer
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Ruediger Hell
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Markus Wirtz
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
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18
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Holdsworth MJ, Vicente J, Sharma G, Abbas M, Zubrycka A. The plant N-degron pathways of ubiquitin-mediated proteolysis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:70-89. [PMID: 31638740 DOI: 10.1111/jipb.12882] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 10/20/2019] [Indexed: 05/29/2023]
Abstract
The amino-terminal residue of a protein (or amino-terminus of a peptide following protease cleavage) can be an important determinant of its stability, through the Ubiquitin Proteasome System associated N-degron pathways. Plants contain a unique combination of N-degron pathways (previously called the N-end rule pathways) E3 ligases, PROTEOLYSIS (PRT)6 and PRT1, recognizing non-overlapping sets of amino-terminal residues, and others remain to be identified. Although only very few substrates of PRT1 or PRT6 have been identified, substrates of the oxygen and nitric oxide sensing branch of the PRT6 N-degron pathway include key nuclear-located transcription factors (ETHYLENE RESPONSE FACTOR VIIs and LITTLE ZIPPER 2) and the histone-modifying Polycomb Repressive Complex 2 component VERNALIZATION 2. In response to reduced oxygen or nitric oxide levels (and other mechanisms that reduce pathway activity) these stabilized substrates regulate diverse aspects of growth and development, including response to flooding, salinity, vernalization (cold-induced flowering) and shoot apical meristem function. The N-degron pathways show great promise for use in the improvement of crop performance and for biotechnological applications. Upstream proteases, components of the different pathways and associated substrates still remain to be identified and characterized to fully appreciate how regulation of protein stability through the amino-terminal residue impacts plant biology.
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Affiliation(s)
| | - Jorge Vicente
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Gunjan Sharma
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Mohamad Abbas
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Agata Zubrycka
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
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19
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Yang CI, Hsieh HH, Shan SO. Timing and specificity of cotranslational nascent protein modification in bacteria. Proc Natl Acad Sci U S A 2019; 116:23050-23060. [PMID: 31666319 PMCID: PMC6859321 DOI: 10.1073/pnas.1912264116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The nascent polypeptide exit site of the ribosome is a crowded environment where multiple ribosome-associated protein biogenesis factors (RPBs) compete for the nascent polypeptide to influence their localization, folding, or quality control. Here we address how N-terminal methionine excision (NME), a ubiquitous process crucial for the maturation of over 50% of the bacterial proteome, occurs in a timely and selective manner in this crowded environment. In bacteria, NME is mediated by 2 essential enzymes, peptide deformylase (PDF) and methionine aminopeptidase (MAP). We show that the reaction of MAP on ribosome-bound nascent chains approaches diffusion-limited rates, allowing immediate methionine excision of optimal substrates after deformylation. Specificity is achieved by kinetic competition of NME with translation elongation and by regulation from other RPBs, which selectively narrow the processing time window for suboptimal substrates. A mathematical model derived from the data accurately predicts cotranslational NME efficiency in the cytosol. Our results demonstrate how a fundamental enzymatic activity is reshaped by its associated macromolecular environment to optimize both efficiency and selectivity, and provides a platform to study other cotranslational protein biogenesis pathways.
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Affiliation(s)
- Chien-I Yang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Hao-Hsuan Hsieh
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Shu-Ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
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20
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Eldeeb MA, Fahlman RP, Ragheb MA, Esmaili M. Does N‐Terminal Protein Acetylation Lead to Protein Degradation? Bioessays 2019; 41:e1800167. [DOI: 10.1002/bies.201800167] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 08/12/2019] [Indexed: 12/29/2022]
Affiliation(s)
- Mohamed A. Eldeeb
- Department of Chemistry (Biochemistry Division)Faculty of ScienceCairo University Giza 12613 Egypt
- Department of Neurology and NeurosurgeryMontreal Neurological InstituteMcGill University Montreal Quebec H3A 2B4 Canada
| | - Richard P. Fahlman
- Department of BiochemistryUniversity of Alberta Edmonton Alberta T6G 2R3 Canada
| | - Mohamed A. Ragheb
- Department of Chemistry (Biochemistry Division)Faculty of ScienceCairo University Giza 12613 Egypt
| | - Mansoore Esmaili
- Department of BiochemistryUniversity of Alberta Edmonton Alberta T6G 2R3 Canada
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21
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Melnykov A, Chen SJ, Varshavsky A. Gid10 as an alternative N-recognin of the Pro/N-degron pathway. Proc Natl Acad Sci U S A 2019; 116:15914-15923. [PMID: 31337681 PMCID: PMC6689949 DOI: 10.1073/pnas.1908304116] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In eukaryotes, N-degron pathways (formerly "N-end rule pathways") comprise a set of proteolytic systems whose unifying feature is their ability to recognize proteins containing N-terminal degradation signals called N-degrons, thereby causing degradation of these proteins by the 26S proteasome or autophagy. Gid4, a subunit of the GID ubiquitin ligase in the yeast Saccharomyces cerevisiae, is the recognition component (N-recognin) of the GID-mediated Pro/N-degron pathway. Gid4 targets proteins by recognizing their N-terminal Pro residues or a Pro at position 2, in the presence of distinct adjoining sequence motifs. Under conditions of low or absent glucose, cells make it through gluconeogenesis. When S. cerevisiae grows on a nonfermentable carbon source, its gluconeogenic enzymes Fbp1, Icl1, Mdh2, and Pck1 are expressed and long-lived. Transition to a medium containing glucose inhibits the synthesis of these enzymes and induces their degradation by the Gid4-dependent Pro/N-degron pathway. While studying yeast Gid4, we identified a similar but uncharacterized yeast protein (YGR066C), which we named Gid10. A screen for N-terminal peptide sequences that can bind to Gid10 showed that substrate specificities of Gid10 and Gid4 overlap but are not identical. Gid10 is not expressed under usual (unstressful) growth conditions, but is induced upon starvation or osmotic stresses. Using protein binding analyses and degradation assays with substrates of GID, we show that Gid10 can function as a specific N-recognin of the Pro/N-degron pathway.
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Affiliation(s)
- Artem Melnykov
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Shun-Jia Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Alexander Varshavsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
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22
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Tran A. The N-end rule pathway and Ubr1 enforce protein compartmentalization via P2-encoded cellular location signals. J Cell Sci 2019; 132:jcs.231662. [PMID: 30940687 DOI: 10.1242/jcs.231662] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 03/22/2019] [Indexed: 12/24/2022] Open
Abstract
The Arg/N-end rule pathway and Ubr1, a ubiquitin E3 ligase conserved from yeast to humans, is involved in the degradation of misfolded proteins in the cytosol. However, the root physiological purpose of this activity is not completely understood. Through a systematic examination of single-residue P2-position mutants of misfolded proteins, and global and targeted bioinformatic analyses of the Saccharomyces cerevisiae proteome, it was determined that Ubr1 preferentially targets mistranslocated secretory and mitochondrial proteins in the cytosol. Degradation by Ubr1 is dependent on the recognition of cellular location signals that are naturally embedded into the second amino acid residue of most proteins. This P2-encoded location signaling mechanism may shed light on how Ubr1 and the N-end rule pathway are involved in neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. A corollary to this discovery is that the N-end rule pathway enforces the compartmentalization of secretory and mitochondrial proteins by degrading those that fail to reach their intended subcellular locations. The N-end rule pathway is therefore likely to have been critical to the evolution of endosymbiotic relationships that paved the way for advanced eukaryotic cellular life. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Anthony Tran
- National University of Singapore, Department of Biological Sciences, Singapore 117604
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23
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Dissmeyer N. Conditional Protein Function via N-Degron Pathway-Mediated Proteostasis in Stress Physiology. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:83-117. [PMID: 30892918 DOI: 10.1146/annurev-arplant-050718-095937] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The N-degron pathway, formerly the N-end rule pathway, regulates functions of regulatory proteins. It impacts protein half-life and therefore directs the actual presence of target proteins in the cell. The current concept holds that the N-degron pathway depends on the identity of the amino (N)-terminal amino acid and many other factors, such as the follow-up sequence at the N terminus, conformation, flexibility, and protein localization. It is evolutionarily conserved throughout the kingdoms. One possible entry point for substrates of the N-degron pathway is oxidation of N-terminal Cys residues. Oxidation of N-terminal Cys is decisive for further enzymatic modification of various neo-N termini by arginylation that generates potentially neofunctionalized or instable proteoforms. Here, I focus on the posttranslational modifications that are encompassed by protein degradation via the Cys/Arg branch of the N-degron pathway-part of the PROTEOLYSIS 6 (PRT6)/N-degron pathway-as well as the underlying physiological principles of this branch and its biological significance in stress response.
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Affiliation(s)
- Nico Dissmeyer
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry (IPB) and ScienceCampus Halle-Plant-Based Bioeconomy, D-06120 Halle (Saale), Germany; ; Twitter: @NDissmeyer
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