151
|
Iacobucci I, Monaco V, Cozzolino F, Monti M. From classical to new generation approaches: An excursus of -omics methods for investigation of protein-protein interaction networks. J Proteomics 2020; 230:103990. [PMID: 32961344 DOI: 10.1016/j.jprot.2020.103990] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/11/2020] [Accepted: 08/31/2020] [Indexed: 01/24/2023]
Abstract
Functional Proteomics aims to the identification of in vivo protein-protein interaction (PPI) in order to piece together protein complexes, and therefore, cell pathways involved in biological processes of interest. Over the years, proteomic approaches used for protein-protein interaction investigation have relied on classical biochemical protocols adapted to a global overview of protein-protein interactions, within so-called "interactomics" investigation. In particular, their coupling with advanced mass spectrometry instruments and innovative analytical methods led to make great strides in the PPIs investigation in proteomics. In this review, an overview of protein complexes purification strategies, from affinity purification approaches, including proximity-dependent labeling techniques and cross-linking strategy for the identification of transient interactions, to Blue Native Gel Electrophoresis (BN-PAGE) and Size Exclusion Chromatography (SEC) employed in the "complexome profiling", has been reported, giving a look to their developments, strengths and weakness and providing to readers several recent applications of each strategy. Moreover, a section dedicated to bioinformatic databases and platforms employed for protein networks analyses was also included.
Collapse
Affiliation(s)
- Ilaria Iacobucci
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
| | - Vittoria Monaco
- CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
| | - Flora Cozzolino
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy.
| | - Maria Monti
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy.
| |
Collapse
|
152
|
Bosch JA, Chen CL, Perrimon N. Proximity-dependent labeling methods for proteomic profiling in living cells: An update. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2020; 10:e392. [PMID: 32909689 DOI: 10.1002/wdev.392] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/11/2020] [Accepted: 07/01/2020] [Indexed: 12/14/2022]
Abstract
Characterizing the proteome composition of organelles and subcellular regions of living cells can facilitate the understanding of cellular organization as well as protein interactome networks. Proximity labeling-based methods coupled with mass spectrometry (MS) offer a high-throughput approach for systematic analysis of spatially restricted proteomes. Proximity labeling utilizes enzymes that generate reactive radicals to covalently tag neighboring proteins. The tagged endogenous proteins can then be isolated for further analysis by MS. To analyze protein-protein interactions or identify components that localize to discrete subcellular compartments, spatial expression is achieved by fusing the enzyme to specific proteins or signal peptides that target to particular subcellular regions. Although these technologies have only been introduced recently, they have already provided deep insights into a wide range of biological processes. Here, we provide an updated description and comparison of proximity labeling methods, as well as their applications and improvements. As each method has its own unique features, the goal of this review is to describe how different proximity labeling methods can be used to answer different biological questions. This article is categorized under: Technologies > Analysis of Proteins.
Collapse
Affiliation(s)
- Justin A Bosch
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Chiao-Lin Chen
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Boston, Massachusetts, USA
| |
Collapse
|
153
|
Antonicka H, Lin ZY, Janer A, Aaltonen MJ, Weraarpachai W, Gingras AC, Shoubridge EA. A High-Density Human Mitochondrial Proximity Interaction Network. Cell Metab 2020; 32:479-497.e9. [PMID: 32877691 DOI: 10.1016/j.cmet.2020.07.017] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/24/2020] [Accepted: 07/28/2020] [Indexed: 12/17/2022]
Abstract
We used BioID, a proximity-dependent biotinylation assay with 100 mitochondrial baits from all mitochondrial sub-compartments, to create a high-resolution human mitochondrial proximity interaction network. We identified 1,465 proteins, producing 15,626 unique high-confidence proximity interactions. Of these, 528 proteins were previously annotated as mitochondrial, nearly half of the mitochondrial proteome defined by Mitocarta 2.0. Bait-bait analysis showed a clear separation of mitochondrial compartments, and correlation analysis among preys across all baits allowed us to identify functional clusters involved in diverse mitochondrial functions and to assign uncharacterized proteins to specific modules. We demonstrate that this analysis can assign isoforms of the same mitochondrial protein to different mitochondrial sub-compartments and show that some proteins may have multiple cellular locations. Outer membrane baits showed specific proximity interactions with cytosolic proteins and proteins in other organellar membranes, suggesting specialization of proteins responsible for contact site formation between mitochondria and individual organelles.
Collapse
Affiliation(s)
- Hana Antonicka
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada; Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada
| | - Alexandre Janer
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada; Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Mari J Aaltonen
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada; Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Woranontee Weraarpachai
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada; Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
| | - Eric A Shoubridge
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada; Department of Human Genetics, McGill University, Montreal, QC, Canada.
| |
Collapse
|
154
|
Chapman J, Ng YS, Nicholls TJ. The Maintenance of Mitochondrial DNA Integrity and Dynamics by Mitochondrial Membranes. Life (Basel) 2020; 10:life10090164. [PMID: 32858900 PMCID: PMC7555930 DOI: 10.3390/life10090164] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/20/2020] [Accepted: 08/23/2020] [Indexed: 12/18/2022] Open
Abstract
Mitochondria are complex organelles that harbour their own genome. Mitochondrial DNA (mtDNA) exists in the form of a circular double-stranded DNA molecule that must be replicated, segregated and distributed around the mitochondrial network. Human cells typically possess between a few hundred and several thousand copies of the mitochondrial genome, located within the mitochondrial matrix in close association with the cristae ultrastructure. The organisation of mtDNA around the mitochondrial network requires mitochondria to be dynamic and undergo both fission and fusion events in coordination with the modulation of cristae architecture. The dysregulation of these processes has profound effects upon mtDNA replication, manifesting as a loss of mtDNA integrity and copy number, and upon the subsequent distribution of mtDNA around the mitochondrial network. Mutations within genes involved in mitochondrial dynamics or cristae modulation cause a wide range of neurological disorders frequently associated with defects in mtDNA maintenance. This review aims to provide an understanding of the biological mechanisms that link mitochondrial dynamics and mtDNA integrity, as well as examine the interplay that occurs between mtDNA, mitochondrial dynamics and cristae structure.
Collapse
Affiliation(s)
- James Chapman
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK;
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Correspondence: (J.C.); (T.J.N.)
| | - Yi Shiau Ng
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK;
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Thomas J. Nicholls
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK;
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Correspondence: (J.C.); (T.J.N.)
| |
Collapse
|
155
|
Zhou Y, Zou P. The evolving capabilities of enzyme-mediated proximity labeling. Curr Opin Chem Biol 2020; 60:30-38. [PMID: 32801087 DOI: 10.1016/j.cbpa.2020.06.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 12/22/2022]
Abstract
The subcellular organization of proteins and RNA molecules is crucial for their proper functions. Over the past decade, both ligase-mediated and peroxidase-mediated proximity labeling (PL) techniques have been developed to map biomolecules at near-nanometer spatial resolution and subminute temporal resolution. These methods are shedding light on the spatial arrangement of proteome and transcriptome in their native context. Here, we review the recent evolution and applications of PL techniques, compare and contrast the two classes of methods, and highlight emerging trends and future opportunities.
Collapse
Affiliation(s)
- Ying Zhou
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Peng Zou
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China; Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, 100871, China.
| |
Collapse
|
156
|
Hannigan MM, Hoffman AM, Thompson JW, Zheng T, Nicchitta CV. Quantitative Proteomics Links the LRRC59 Interactome to mRNA Translation on the ER Membrane. Mol Cell Proteomics 2020; 19:1826-1849. [PMID: 32788342 DOI: 10.1074/mcp.ra120.002228] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/04/2020] [Indexed: 12/22/2022] Open
Abstract
Protein synthesis on the endoplasmic reticulum (ER) requires the dynamic coordination of numerous cellular components. Together, resident ER membrane proteins, cytoplasmic translation factors, and both integral membrane and cytosolic RNA-binding proteins operate in concert with membrane-associated ribosomes to facilitate ER-localized translation. Little is known, however, regarding the spatial organization of ER-localized translation. This question is of growing significance as it is now known that ER-bound ribosomes contribute to secretory, integral membrane, and cytosolic protein synthesis alike. To explore this question, we utilized quantitative proximity proteomics to identify neighboring protein networks for the candidate ribosome interactors SEC61β (subunit of the protein translocase), RPN1 (oligosaccharyltransferase subunit), SEC62 (translocation integral membrane protein), and LRRC59 (ribosome binding integral membrane protein). Biotin labeling time course studies of the four BioID reporters revealed distinct labeling patterns that intensified but only modestly diversified as a function of labeling time, suggesting that the ER membrane is organized into discrete protein interaction domains. Whereas SEC61β and RPN1 reporters identified translocon-associated networks, SEC62 and LRRC59 reporters revealed divergent protein interactomes. Notably, the SEC62 interactome is enriched in redox-linked proteins and ER luminal chaperones, with the latter likely representing proximity to an ER luminal chaperone reflux pathway. In contrast, the LRRC59 interactome is highly enriched in SRP pathway components, translation factors, and ER-localized RNA-binding proteins, uncovering a functional link between LRRC59 and mRNA translation regulation. Importantly, analysis of the LRRC59 interactome by native immunoprecipitation identified similar protein and functional enrichments. Moreover, [35S]-methionine incorporation assays revealed that siRNA silencing of LRRC59 expression reduced steady state translation levels on the ER by ca. 50%, and also impacted steady state translation levels in the cytosol compartment. Collectively, these data reveal a functional domain organization for the ER and identify a key role for LRRC59 in the organization and regulation of local translation.
Collapse
Affiliation(s)
- Molly M Hannigan
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Alyson M Hoffman
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA
| | - J Will Thompson
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina, USA; Department of Duke Proteomics and Metabolomics Shared Resource, Duke University School of Medicine, Durham, North Carolina, USA
| | - Tianli Zheng
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Christopher V Nicchitta
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA; Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA.
| |
Collapse
|
157
|
Lv SW, Shi ZG, Wang XH, Zheng PY, Li HB, Han QJ, Li ZJ. Ribosome Binding Protein 1 Correlates with Prognosis and Cell Proliferation in Bladder Cancer. Onco Targets Ther 2020; 13:6699-6707. [PMID: 32764960 PMCID: PMC7367924 DOI: 10.2147/ott.s252043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 05/13/2020] [Indexed: 12/14/2022] Open
Abstract
Introduction Ribosome binding protein 1 (RRBP1) is reported to be correlated with tumor formation and progression. However, the role of RRBP1 in bladder cancer is unclear. In this study, we aimed to investigate the expression of RRBP1 and its influence on cell proliferation in bladder cancer. Methods Quantification real-time polymerase chain reaction (qRT-PCR) and immunohistochemistry (IHC) were used to detect the expression levels of RRBP1 in 138 bladder cancer and matched adjacent normal bladder tissues. Then, the clinical significance of RRBP1 in bladder cancer was evaluated. The effect of RRBP1 on cell proliferation and its potential mechanism were further explored. Results Results show that the mRNA levels of RRBP1 in bladder cancer were significantly higher compared with those in normal tissues (P< 0.001). IHC results show the high-expression rate of RRBP1 in bladder cancer was 68.8%, which was significantly greater than those in normal tissues (40.6%, P< 0.001). RRBP1 high-expression was significantly associated with differentiation, T stage and lymph node metastasis in bladder cancer (P< 0.05). The overall survival time of patients with RRBP1 high-expression was significantly reduced compared to those with RRBP1 low-expression. Moreover, RRBP1 overexpression significantly promoted cell proliferation, which was correlated with Smad1/Smad3/TGF-β1 signal pathway. Conclusion RRBP1 high-expression correlates with prognosis and promotes cell proliferation in bladder cancer, which could be a potential biomarker.
Collapse
Affiliation(s)
- Shuang-Wu Lv
- The First Affiliated Hospital and College of Clinical Medicineof Henan University of Science and Technology, Luoyang, Henan 471003, People's Republic of China
| | - Zhen-Guo Shi
- The First Affiliated Hospital and College of Clinical Medicineof Henan University of Science and Technology, Luoyang, Henan 471003, People's Republic of China
| | - Xiao-Hui Wang
- The First Affiliated Hospital and College of Clinical Medicineof Henan University of Science and Technology, Luoyang, Henan 471003, People's Republic of China
| | - Peng-Yi Zheng
- The First Affiliated Hospital and College of Clinical Medicineof Henan University of Science and Technology, Luoyang, Henan 471003, People's Republic of China
| | - Hui-Bing Li
- The First Affiliated Hospital and College of Clinical Medicineof Henan University of Science and Technology, Luoyang, Henan 471003, People's Republic of China
| | - Qing-Jiang Han
- The First Affiliated Hospital and College of Clinical Medicineof Henan University of Science and Technology, Luoyang, Henan 471003, People's Republic of China
| | - Zhi-Jun Li
- The First Affiliated Hospital and College of Clinical Medicineof Henan University of Science and Technology, Luoyang, Henan 471003, People's Republic of China
| |
Collapse
|
158
|
Yang M, Li C, Yang S, Xiao Y, Xiong X, Chen W, Zhao H, Zhang Q, Han Y, Sun L. Mitochondria-Associated ER Membranes - The Origin Site of Autophagy. Front Cell Dev Biol 2020; 8:595. [PMID: 32766245 PMCID: PMC7378804 DOI: 10.3389/fcell.2020.00595] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/18/2020] [Indexed: 12/21/2022] Open
Abstract
Autophagy is a process of intracellular self-recycling and degradation that plays an important role in maintaining cell homeostasis. However, the molecular mechanism of autophagy remains to be further studied. Mitochondria-associated endoplasmic reticulum membranes (MAMs) are the region of the ER that mediate communication between the ER and mitochondria. MAMs have been demonstrated to be involved in autophagy, Ca2+ transport and lipid metabolism. Here, we discuss the composition and function of MAMs, more specifically, to emphasize the role of MAMs in regulating autophagy. Finally, some key information that may be useful for future research is summarized.
Collapse
Affiliation(s)
- Ming Yang
- Hunan Key Laboratory of Kidney Disease and Blood Purification, Department of Nephrology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Chenrui Li
- Hunan Key Laboratory of Kidney Disease and Blood Purification, Department of Nephrology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Shikun Yang
- Department of Nephrology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Ying Xiao
- Hunan Key Laboratory of Kidney Disease and Blood Purification, Department of Nephrology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xiaofen Xiong
- Hunan Key Laboratory of Kidney Disease and Blood Purification, Department of Nephrology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Wei Chen
- Hunan Key Laboratory of Kidney Disease and Blood Purification, Department of Nephrology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Hao Zhao
- Hunan Key Laboratory of Kidney Disease and Blood Purification, Department of Nephrology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Qin Zhang
- Hunan Key Laboratory of Kidney Disease and Blood Purification, Department of Nephrology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Yachun Han
- Hunan Key Laboratory of Kidney Disease and Blood Purification, Department of Nephrology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Lin Sun
- Hunan Key Laboratory of Kidney Disease and Blood Purification, Department of Nephrology, The Second Xiangya Hospital of Central South University, Changsha, China
| |
Collapse
|
159
|
Frazier AE, Compton AG, Kishita Y, Hock DH, Welch AE, Amarasekera SSC, Rius R, Formosa LE, Imai-Okazaki A, Francis D, Wang M, Lake NJ, Tregoning S, Jabbari JS, Lucattini A, Nitta KR, Ohtake A, Murayama K, Amor DJ, McGillivray G, Wong FY, van der Knaap MS, Jeroen Vermeulen R, Wiltshire EJ, Fletcher JM, Lewis B, Baynam G, Ellaway C, Balasubramaniam S, Bhattacharya K, Freckmann ML, Arbuckle S, Rodriguez M, Taft RJ, Sadedin S, Cowley MJ, Minoche AE, Calvo SE, Mootha VK, Ryan MT, Okazaki Y, Stroud DA, Simons C, Christodoulou J, Thorburn DR. Fatal perinatal mitochondrial cardiac failure caused by recurrent de novo duplications in the ATAD3 locus. MED 2020; 2:49-73. [PMID: 33575671 DOI: 10.1016/j.medj.2020.06.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background In about half of all patients with a suspected monogenic disease, genomic investigations fail to identify the diagnosis. A contributing factor is the difficulty with repetitive regions of the genome, such as those generated by segmental duplications. The ATAD3 locus is one such region, in which recessive deletions and dominant duplications have recently been reported to cause lethal perinatal mitochondrial diseases characterized by pontocerebellar hypoplasia or cardiomyopathy, respectively. Methods Whole exome, whole genome and long-read DNA sequencing techniques combined with studies of RNA and quantitative proteomics were used to investigate 17 subjects from 16 unrelated families with suspected mitochondrial disease. Findings We report six different de novo duplications in the ATAD3 gene locus causing a distinctive presentation including lethal perinatal cardiomyopathy, persistent hyperlactacidemia, and frequently corneal clouding or cataracts and encephalopathy. The recurrent 68 Kb ATAD3 duplications are identifiable from genome and exome sequencing but usually missed by microarrays. The ATAD3 duplications result in the formation of identical chimeric ATAD3A/ATAD3C proteins, altered ATAD3 complexes and a striking reduction in mitochondrial oxidative phosphorylation complex I and its activity in heart tissue. Conclusions ATAD3 duplications appear to act in a dominant-negative manner and the de novo inheritance infers a low recurrence risk for families, unlike most pediatric mitochondrial diseases. More than 350 genes underlie mitochondrial diseases. In our experience the ATAD3 locus is now one of the five most common causes of nuclear-encoded pediatric mitochondrial disease but the repetitive nature of the locus means ATAD3 diagnoses may be frequently missed by current genomic strategies. Funding Australian NHMRC, US Department of Defense, Japanese AMED and JSPS agencies, Australian Genomics Health Alliance and Australian Mito Foundation.
Collapse
Affiliation(s)
- Ann E Frazier
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia.,These authors contributed equally: A.E. Frazier, A.G. Compton
| | - Alison G Compton
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia.,These authors contributed equally: A.E. Frazier, A.G. Compton
| | - Yoshihito Kishita
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - Daniella H Hock
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC 3052, Australia
| | - AnneMarie E Welch
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Sumudu S C Amarasekera
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Rocio Rius
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Luke E Formosa
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Atsuko Imai-Okazaki
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan.,Division of Genomic Medicine Research, Medical Genomics Center, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - David Francis
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Min Wang
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Nicole J Lake
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia.,Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Simone Tregoning
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Jafar S Jabbari
- Australian Genome Research Facility Ltd, Victorian Comprehensive Cancer Centre, Melbourne VIC 3052, Australia
| | - Alexis Lucattini
- Australian Genome Research Facility Ltd, Victorian Comprehensive Cancer Centre, Melbourne VIC 3052, Australia
| | - Kazuhiro R Nitta
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - Akira Ohtake
- Department of Pediatrics & Clinical Genomics, Saitama Medical University Hospital, Saitama, 350-0495, Japan
| | - Kei Murayama
- Department of Metabolism, Chiba Children's Hospital, Chiba, 266-0007, Japan
| | - David J Amor
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - George McGillivray
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Flora Y Wong
- Ritchie Centre, Hudson Institute of Medical Research; Department of Paediatrics, Monash University; and Monash Newborn, Monash Children's Hospital, Melbourne, VIC 3168, Australia
| | - Marjo S van der Knaap
- Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit and Amsterdam Neuroscience, 1081 HV Amsterdam, The Netherlands.,Functional Genomics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit and Amsterdam Neuroscience, 1081 HV Amsterdam, The Netherlands
| | - R Jeroen Vermeulen
- Department of Neurology, Maastricht University Medical Center, 6229 HX, Maastricht, The Netherlands
| | - Esko J Wiltshire
- Department of Paediatrics and Child Health, University of Otago Wellington and Capital and Coast District Health Board, Wellington 6021, New Zealand
| | - Janice M Fletcher
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Barry Lewis
- Department of Clinical Biochemistry, PathWest Laboratory Medicine Western Australia, Nedlands, WA 6009, Australia
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia and King Edward Memorial Hospital for Women Perth, Subiaco, WA 6008, Australia.,Telethon Kids Institute and School of Paediatrics and Child Health, The University of Western Australia, Perth, WA 6009, Australia
| | - Carolyn Ellaway
- Genetic Metabolic Disorders Service, Sydney Children's Hospital Network, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia.,Disciplines of Genomic Medicine and Child and Adolescent Health, Sydney Medical School, University of Sydney, NSW 2145, Australia
| | - Shanti Balasubramaniam
- Genetic Metabolic Disorders Service, Sydney Children's Hospital Network, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Kaustuv Bhattacharya
- Genetic Metabolic Disorders Service, Sydney Children's Hospital Network, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia.,Disciplines of Genomic Medicine and Child and Adolescent Health, Sydney Medical School, University of Sydney, NSW 2145, Australia
| | | | - Susan Arbuckle
- Department of Histopathology, The Children's Hospital at Westmead, Sydney Children's Hospital Network, Sydney, NSW 2145, Australia
| | - Michael Rodriguez
- Discipline of Pathology, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - Simon Sadedin
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Mark J Cowley
- Children's Cancer Institute, Kensington, NSW 2750, Australia; St Vincent's Clinical School, UNSW Sydney, Darlinghurst, NSW 2010, Australia.,Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - André E Minoche
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Sarah E Calvo
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02446, USA
| | - Vamsi K Mootha
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02446, USA
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Yasushi Okazaki
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - David A Stroud
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Cas Simons
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072 Australia
| | - John Christodoulou
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Disciplines of Genomic Medicine and Child and Adolescent Health, Sydney Medical School, University of Sydney, NSW 2145, Australia
| | - David R Thorburn
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia.,Lead contact
| |
Collapse
|
160
|
Ordureau A, Paulo JA, Zhang J, An H, Swatek KN, Cannon JR, Wan Q, Komander D, Harper JW. Global Landscape and Dynamics of Parkin and USP30-Dependent Ubiquitylomes in iNeurons during Mitophagic Signaling. Mol Cell 2020; 77:1124-1142.e10. [PMID: 32142685 PMCID: PMC7098486 DOI: 10.1016/j.molcel.2019.11.013] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 08/21/2019] [Accepted: 11/08/2019] [Indexed: 12/24/2022]
Abstract
The ubiquitin ligase Parkin, protein kinase PINK1, USP30 deubiquitylase, and p97 segregase function together to regulate turnover of damaged mitochondria via mitophagy, but our mechanistic understanding in neurons is limited. Here, we combine induced neurons (iNeurons) derived from embryonic stem cells with quantitative proteomics to reveal the dynamics and specificity of Parkin-dependent ubiquitylation under endogenous expression conditions. Targets showing elevated ubiquitylation in USP30−/− iNeurons are concentrated in components of the mitochondrial translocon, and the ubiquitylation kinetics of the vast majority of Parkin targets are unaffected, correlating with a modest kinetic acceleration in accumulation of pS65-Ub and mitophagic flux upon mitochondrial depolarization without USP30. Basally, ubiquitylated translocon import substrates accumulate, suggesting a quality control function for USP30. p97 was dispensable for Parkin ligase activity in iNeurons. This work provides an unprecedented quantitative landscape of the Parkin-modified ubiquitylome in iNeurons and reveals the underlying specificity of central regulatory elements in the pathway. Global phospho and ubiquitylome analysis of PINK1-Parkin pathway in iNeurons Dynamics and specificity of Parkin-mediated ubiquitylation revealed in iNeurons p97-mediated MFN turnover not required for Parkin substrate “gating” in iNeurons USP30 acts primarily on translocon and supports import quality control in iNeurons
Collapse
Affiliation(s)
- Alban Ordureau
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Jiuchun Zhang
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Heeseon An
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Kirby N Swatek
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Joe R Cannon
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Qiaoqiao Wan
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - David Komander
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Ubiquitin Signalling Division, The Walter and Eliza Hall Institute for Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
| |
Collapse
|
161
|
Tang Y, Huang A, Gu Y. Global profiling of plant nuclear membrane proteome in Arabidopsis. NATURE PLANTS 2020; 6:838-847. [PMID: 32601417 DOI: 10.1038/s41477-020-0700-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 05/18/2020] [Indexed: 05/26/2023]
Abstract
The nuclear envelope (NE) is structurally and functionally vital for eukaryotic cells, yet its protein constituents and their functions are poorly understood in plants. Here, we combined subtractive proteomics and proximity-labelling technology coupled with quantitative mass spectrometry to understand the landscape of NE membrane proteins in Arabidopsis. We identified ~200 potential candidates for plant NE transmembrane (PNET) proteins, which unravelled the compositional diversity and uniqueness of the plant NE. One of the candidates, named PNET1, is a homologue of human TMEM209, a critical driver for lung cancer. A functional investigation revealed that PNET1 is a bona fide nucleoporin in plants. It displays both physical and genetic interactions with the nuclear pore complex (NPC) and is essential for embryo development and reproduction in different NPC contexts. Our study substantially enlarges the plant NE proteome and sheds new light on the membrane composition and function of the NPC.
Collapse
Affiliation(s)
- Yu Tang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Aobo Huang
- Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yangnan Gu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
| |
Collapse
|
162
|
Li Y, Tian C, Liu K, Zhou Y, Yang J, Zou P. A Clickable APEX Probe for Proximity-Dependent Proteomic Profiling in Yeast. Cell Chem Biol 2020; 27:858-865.e8. [DOI: 10.1016/j.chembiol.2020.05.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/24/2019] [Accepted: 05/08/2020] [Indexed: 10/24/2022]
|
163
|
Gutiérrez T, Qi H, Yap MC, Tahbaz N, Milburn LA, Lucchinetti E, Lou PH, Zaugg M, LaPointe PG, Mercier P, Overduin M, Bischof H, Burgstaller S, Malli R, Ballanyi K, Shuai J, Simmen T. The ER chaperone calnexin controls mitochondrial positioning and respiration. Sci Signal 2020; 13:13/638/eaax6660. [DOI: 10.1126/scisignal.aax6660] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Chaperones in the endoplasmic reticulum (ER) control the flux of Ca2+ ions into mitochondria, thereby increasing or decreasing the energetic output of the oxidative phosphorylation pathway. An example is the abundant ER lectin calnexin, which interacts with sarco/endoplasmic reticulum Ca2+ ATPase (SERCA). We found that calnexin stimulated the ATPase activity of SERCA by maintaining its redox state. This function enabled calnexin to control how much ER Ca2+ was available for mitochondria, a key determinant for mitochondrial bioenergetics. Calnexin-deficient cells compensated for the loss of this function by partially shifting energy generation to the glycolytic pathway. These cells also showed closer apposition between the ER and mitochondria. Calnexin therefore controls the cellular energy balance between oxidative phosphorylation and glycolysis.
Collapse
Affiliation(s)
- Tomás Gutiérrez
- Faculty of Medicine and Dentistry, Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Hong Qi
- Complex Systems Research Center, Shanxi University, Taiyuan 030006, China
| | - Megan C. Yap
- Faculty of Medicine and Dentistry, Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Nasser Tahbaz
- Faculty of Medicine and Dentistry, Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Leanne A. Milburn
- Faculty of Medicine and Dentistry, Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Eliana Lucchinetti
- Department of Anesthesiology and Pain Medicine, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Phing-How Lou
- Department of Anesthesiology and Pain Medicine, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Michael Zaugg
- Department of Anesthesiology and Pain Medicine, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Paul G. LaPointe
- Faculty of Medicine and Dentistry, Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Pascal Mercier
- Department of Biochemistry and National Field Nuclear Magnetic Resonance Centre (Nanuc), University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Michael Overduin
- Department of Biochemistry and National Field Nuclear Magnetic Resonance Centre (Nanuc), University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Helmut Bischof
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, 8010 Graz, Austria
| | - Sandra Burgstaller
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, 8010 Graz, Austria
| | - Roland Malli
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, 8010 Graz, Austria
| | - Klaus Ballanyi
- Department of Physiology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Jianwei Shuai
- Department of Physics, and State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen 361005, China
| | - Thomas Simmen
- Faculty of Medicine and Dentistry, Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| |
Collapse
|
164
|
Crook OM, Smith T, Elzek M, Lilley KS. Moving Profiling Spatial Proteomics Beyond Discrete Classification. Proteomics 2020; 20:e1900392. [PMID: 32558233 DOI: 10.1002/pmic.201900392] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/18/2020] [Indexed: 12/12/2022]
Abstract
The spatial subcellular proteome is a dynamic environment; one that can be perturbed by molecular cues and regulated by post-translational modifications. Compartmentalization of this environment and management of these biomolecular dynamics allows for an array of ancillary protein functions. Profiling spatial proteomics has proved to be a powerful technique in identifying the primary subcellular localization of proteins. The approach has also been refashioned to study multi-localization and localization dynamics. Here, the analytical approaches that have been applied to spatial proteomics thus far are critiqued, and challenges particularly associated with multi-localization and dynamic relocalization is identified. To meet some of the current limitations in analytical processing, it is suggested that Bayesian modeling has clear benefits over the methods applied to date and should be favored whenever possible. Careful consideration of the limitations and challenges, and development of robust statistical frameworks, will ensure that profiling spatial proteomics remains a valuable technique as its utility is expanded.
Collapse
Affiliation(s)
- Oliver M Crook
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tom Smith
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Mohamed Elzek
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
| |
Collapse
|
165
|
Cho KF, Branon TC, Rajeev S, Svinkina T, Udeshi ND, Thoudam T, Kwak C, Rhee HW, Lee IK, Carr SA, Ting AY. Split-TurboID enables contact-dependent proximity labeling in cells. Proc Natl Acad Sci U S A 2020; 117:12143-12154. [PMID: 32424107 PMCID: PMC7275672 DOI: 10.1073/pnas.1919528117] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proximity labeling catalyzed by promiscuous enzymes, such as TurboID, have enabled the proteomic analysis of subcellular regions difficult or impossible to access by conventional fractionation-based approaches. Yet some cellular regions, such as organelle contact sites, remain out of reach for current PL methods. To address this limitation, we split the enzyme TurboID into two inactive fragments that recombine when driven together by a protein-protein interaction or membrane-membrane apposition. At endoplasmic reticulum-mitochondria contact sites, reconstituted TurboID catalyzed spatially restricted biotinylation, enabling the enrichment and identification of >100 endogenous proteins, including many not previously linked to endoplasmic reticulum-mitochondria contacts. We validated eight candidates by biochemical fractionation and overexpression imaging. Overall, split-TurboID is a versatile tool for conditional and spatially specific proximity labeling in cells.
Collapse
Affiliation(s)
- Kelvin F Cho
- Cancer Biology Program, Stanford University, Stanford, CA 94305
| | - Tess C Branon
- Department of Genetics, Stanford University, Stanford, CA 94305
- Department of Biology, Stanford University, Stanford, CA 94305
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Sanjana Rajeev
- Department of Genetics, Stanford University, Stanford, CA 94305
| | | | | | - Themis Thoudam
- Research Institute of Aging and Metabolism, Kyungpook National University, 37224 Daegu, South Korea
| | - Chulhwan Kwak
- Department of Chemistry, Seoul National University, 08826 Seoul, South Korea
- Department of Chemistry, Ulsan National Institute of Science and Technology, 44919 Ulsan, South Korea
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, 08826 Seoul, South Korea
- School of Biological Sciences, Seoul National University, 08826 Seoul, South Korea
| | - In-Kyu Lee
- Research Institute of Aging and Metabolism, Kyungpook National University, 37224 Daegu, South Korea
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, 41944 Daegu, South Korea
- Leading-edge Research Center for Drug Discovery and Development for Diabetes and Metabolic Disease, Kyungpook National University, 41944 Daegu, South Korea
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Alice Y Ting
- Department of Genetics, Stanford University, Stanford, CA 94305;
- Department of Biology, Stanford University, Stanford, CA 94305
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Chan Zuckerberg Biohub, San Francisco, CA 94158
| |
Collapse
|
166
|
Eberhardt EL, Ludlam AV, Tan Z, Cianfrocco MA. Miro: A molecular switch at the center of mitochondrial regulation. Protein Sci 2020; 29:1269-1284. [PMID: 32056317 PMCID: PMC7255519 DOI: 10.1002/pro.3839] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/03/2020] [Accepted: 02/06/2020] [Indexed: 12/24/2022]
Abstract
The orchestration of mitochondria within the cell represents a critical aspect of cell biology. At the center of this process is the outer mitochondrial membrane protein, Miro. Miro coordinates diverse cellular processes by regulating connections between organelles and the cytoskeleton that range from mediating contacts between the endoplasmic reticulum and mitochondria to the regulation of both actin and microtubule motor proteins. Recently, a number of cell biological, biochemical, and protein structure studies have helped to characterize the myriad roles played by Miro. In addition to answering questions regarding Miro's function, these studies have opened the door to new avenues in the study of Miro in the cell. This review will focus on summarizing recent findings for Miro's structure, function, and activity while highlighting key questions that remain unanswered.
Collapse
Affiliation(s)
- Emily L. Eberhardt
- Life Sciences Institute, Department of Biological ChemistryUniversity of MichiganAnn ArborMichigan
- Cellular and Molecular Biology ProgramUniversity of MichiganAnn ArborMichigan
| | - Anthony V. Ludlam
- Life Sciences Institute, Department of Biological ChemistryUniversity of MichiganAnn ArborMichigan
| | - Zhenyu Tan
- Life Sciences Institute, Department of Biological ChemistryUniversity of MichiganAnn ArborMichigan
- Biophysics ProgramUniversity of MichiganAnn ArborMichigan
| | - Michael A. Cianfrocco
- Life Sciences Institute, Department of Biological ChemistryUniversity of MichiganAnn ArborMichigan
| |
Collapse
|
167
|
Long MJC, Zhao Y, Aye Y. Neighborhood watch: tools for defining locale-dependent subproteomes and their contextual signaling activities. RSC Chem Biol 2020; 1:42-55. [PMID: 34458747 PMCID: PMC8341840 DOI: 10.1039/d0cb00041h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 05/16/2020] [Indexed: 12/21/2022] Open
Abstract
Transient associations between numerous organelles-e.g., the endoplasmic reticulum and the mitochondria-forge highly-coordinated, particular environments essential for cross-compartment information flow. Our perspective summarizes chemical-biology tools that have enabled identifying proteins present within these itinerant communities against the bulk proteome, even when a particular protein's presence is fleeting/substoichiometric. However, proteins resident at these ephemeral junctions also experience transitory changes to their interactomes, small-molecule signalomes, and, importantly, functions. Thus, a thorough census of sub-organellar communities necessitates functionally probing context-dependent signaling properties of individual protein-players. Our perspective accordingly further discusses how repurposing of existing tools could allow us to glean a functional understanding of protein-specific signaling activities altered as a result of organelles pulling together. Collectively, our perspective strives to usher new chemical-biology techniques that could, in turn, open doors to modulate functions of specific subproteomes/organellar junctions underlying the nuanced regulatory subsystem broadly termed as contactology.
Collapse
Affiliation(s)
| | - Yi Zhao
- Swiss Federal Institute of Technology Lausanne (EPFL), Institute of Chemical Sciences and Engineering 1015 Lausanne Switzerland
| | - Yimon Aye
- Swiss Federal Institute of Technology Lausanne (EPFL), Institute of Chemical Sciences and Engineering 1015 Lausanne Switzerland
| |
Collapse
|
168
|
Jadiya P, Tomar D. Mitochondrial Protein Quality Control Mechanisms. Genes (Basel) 2020; 11:genes11050563. [PMID: 32443488 PMCID: PMC7290828 DOI: 10.3390/genes11050563] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 02/08/2023] Open
Abstract
Mitochondria serve as a hub for many cellular processes, including bioenergetics, metabolism, cellular signaling, redox balance, calcium homeostasis, and cell death. The mitochondrial proteome includes over a thousand proteins, encoded by both the mitochondrial and nuclear genomes. The majority (~99%) of proteins are nuclear encoded that are synthesized in the cytosol and subsequently imported into the mitochondria. Within the mitochondria, polypeptides fold and assemble into their native functional form. Mitochondria health and integrity depend on correct protein import, folding, and regulated turnover termed as mitochondrial protein quality control (MPQC). Failure to maintain these processes can cause mitochondrial dysfunction that leads to various pathophysiological outcomes and the commencement of diseases. Here, we summarize the current knowledge about the role of different MPQC regulatory systems such as mitochondrial chaperones, proteases, the ubiquitin-proteasome system, mitochondrial unfolded protein response, mitophagy, and mitochondria-derived vesicles in the maintenance of mitochondrial proteome and health. The proper understanding of mitochondrial protein quality control mechanisms will provide relevant insights to treat multiple human diseases.
Collapse
Affiliation(s)
- Pooja Jadiya
- Correspondence: (P.J.); (D.T.); Tel.: +1-215-707-9144 (D.T.)
| | - Dhanendra Tomar
- Correspondence: (P.J.); (D.T.); Tel.: +1-215-707-9144 (D.T.)
| |
Collapse
|
169
|
Balla T, Kim YJ, Alvarez-Prats A, Pemberton J. Lipid Dynamics at Contact Sites Between the Endoplasmic Reticulum and Other Organelles. Annu Rev Cell Dev Biol 2020; 35:85-109. [PMID: 31590585 DOI: 10.1146/annurev-cellbio-100818-125251] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Phospholipids are synthesized primarily within the endoplasmic reticulum and are subsequently distributed to various subcellular membranes to maintain the unique lipid composition of specific organelles. As a result, in most cases, the steady-state localization of membrane phospholipids does not match their site of synthesis. This raises the question of how diverse lipid species reach their final membrane destinations and what molecular processes provide the energy to maintain the lipid gradients that exist between various membrane compartments. Recent studies have highlighted the role of inositol phospholipids in the nonvesicular transport of lipids at membrane contact sites. This review attempts to summarize our current understanding of these complex lipid dynamics and highlights their implications for defining future research directions.
Collapse
Affiliation(s)
- Tamas Balla
- Section on Molecular Signal Transduction, Program for Developmental Neuroscience, Eunice Kennedy Shriver NICHD, National Institutes of Health, Bethesda, Maryland 20892, USA;
| | - Yeun Ju Kim
- Section on Molecular Signal Transduction, Program for Developmental Neuroscience, Eunice Kennedy Shriver NICHD, National Institutes of Health, Bethesda, Maryland 20892, USA;
| | - Alejandro Alvarez-Prats
- Section on Molecular Signal Transduction, Program for Developmental Neuroscience, Eunice Kennedy Shriver NICHD, National Institutes of Health, Bethesda, Maryland 20892, USA;
| | - Joshua Pemberton
- Section on Molecular Signal Transduction, Program for Developmental Neuroscience, Eunice Kennedy Shriver NICHD, National Institutes of Health, Bethesda, Maryland 20892, USA;
| |
Collapse
|
170
|
The mystery of mitochondria-ER contact sites in physiology and pathology: A cancer perspective. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165834. [PMID: 32437958 DOI: 10.1016/j.bbadis.2020.165834] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 04/29/2020] [Accepted: 05/01/2020] [Indexed: 12/13/2022]
Abstract
Mitochondria-associated membranes (MAM), physical platforms that enable communication between mitochondria and the endoplasmic reticulum (ER), are enriched with many proteins and enzymes involved in several crucial cellular processes, such as calcium (Ca2+) homeostasis, lipid synthesis and trafficking, autophagy and reactive oxygen species (ROS) production. Accumulating studies indicate that tumor suppressors and oncogenes are present at these intimate contacts between mitochondria and the ER, where they influence Ca2+ flux between mitochondria and the ER or affect lipid homeostasis at MAM, consequently impacting cell metabolism and cell fate. Understanding these fundamental roles of mitochondria-ER contact sites as important domains for tumor suppressors and oncogenes can support the search for new and more precise anticancer therapies. In the present review, we summarize the current understanding of basic MAM biology, composition and function and discuss the possible role of MAM-resident oncogenes and tumor suppressors.
Collapse
|
171
|
Patel PA, Liang C, Arora A, Vijayan S, Ahuja S, Wagley PK, Settlage R, LaConte LEW, Goodkin HP, Lazar I, Srivastava S, Mukherjee K. Haploinsufficiency of X-linked intellectual disability gene CASK induces post-transcriptional changes in synaptic and cellular metabolic pathways. Exp Neurol 2020; 329:113319. [PMID: 32305418 DOI: 10.1016/j.expneurol.2020.113319] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 04/04/2020] [Accepted: 04/15/2020] [Indexed: 12/17/2022]
Abstract
Heterozygous mutations in the X-linked gene CASK are associated with intellectual disability, microcephaly, pontocerebellar hypoplasia, optic nerve hypoplasia and partially penetrant seizures in girls. The Cask+/- heterozygous knockout female mouse phenocopies the human disorder and exhibits postnatal microencephaly, cerebellar hypoplasia and optic nerve hypoplasia. It is not known if Cask+/- mice also display seizures, nor is known the molecular mechanism by which CASK haploinsufficiency produces the numerous documented phenotypes. 24-h video electroencephalography demonstrates that despite sporadic seizure activity, the overall electrographic patterns remain unaltered in Cask+/- mice. Additionally, seizure threshold to the commonly used kindling agent, pentylenetetrazol, remains unaltered in Cask+/- mice, indicating that even in mice the seizure phenotype is only partially penetrant and may have an indirect mechanism. RNA sequencing experiments on Cask+/- mouse brain uncovers a very limited number of changes, with most differences arising in the transcripts of extracellular matrix proteins and the transcripts of a group of nuclear proteins. In contrast to limited changes at the transcript level, quantitative whole-brain proteomics using iTRAQ quantitative mass-spectrometry reveals major changes in synaptic, metabolic/mitochondrial, cytoskeletal, and protein metabolic pathways. Unbiased protein-protein interaction mapping using affinity chromatography demonstrates that CASK may form complexes with proteins belonging to the same functional groups in which altered protein levels are observed. We discuss the mechanism of the observed changes in the context of known molecular function/s of CASK. Overall, our data indicate that the phenotypic spectrum of female Cask+/- mice includes sporadic seizures and thus closely parallels that of CASK haploinsufficient girls; the Cask+/- mouse is thus a face-validated model for CASK-related pathologies. We therefore surmise that CASK haploinsufficiency is likely to affect brain structure and function due to dysregulation of several cellular pathways including synaptic signaling and cellular metabolism.
Collapse
Affiliation(s)
- P A Patel
- Center for Neurobiology Research, Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, VA, United States; Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, VA, United States
| | - C Liang
- Center for Neurobiology Research, Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, VA, United States
| | - A Arora
- Center for Neurobiology Research, Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, VA, United States
| | - S Vijayan
- School of Neuroscience, Virginia Tech, Blacksburg, VA, United States
| | - S Ahuja
- Biological Sciences, Virginia Tech, Blacksburg, VA, United States
| | - P K Wagley
- Neurology, University of Virginia, Charlottesville, VA, USA
| | - R Settlage
- Advanced Research Computing, Virginia Tech, Blacksburg, VA, United States
| | - L E W LaConte
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, VA, United States
| | - H P Goodkin
- Neurology, University of Virginia, Charlottesville, VA, USA
| | - I Lazar
- Biological Sciences, Virginia Tech, Blacksburg, VA, United States
| | - S Srivastava
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, VA, United States
| | - K Mukherjee
- Center for Neurobiology Research, Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, VA, United States; Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, VA, United States; Department of Psychiatry and Behavioral Medicine, Virginia Tech Carilion School of Medicine, Roanoke, VA, United States.
| |
Collapse
|
172
|
Hartmann C, Schwietzer YA, Kummer D, Kirschnick N, Hoppe E, Thüring EM, Glaesner-Ebnet M, Brinkmann F, Gerke V, Reuter S, Nakayama M, Ebnet K. The mitochondrial outer membrane protein SYNJ2BP interacts with the cell adhesion molecule TMIGD1 and can recruit it to mitochondria. BMC Mol Cell Biol 2020; 21:30. [PMID: 32303178 PMCID: PMC7164261 DOI: 10.1186/s12860-020-00274-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 04/06/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Transmembrane and immunoglobulin domain-containing protein 1 (TMIGD1) is a recently identified cell adhesion molecule which is predominantly expressed by epithelial cells of the intestine and the kidney. Its expression is downregulated in both colon and renal cancer suggesting a tumor suppressive activity. The function of TMIGD1 at the cellular level is largely unclear. Published work suggests a protective role of TMIGD1 during oxidative stress in kidney epithelial cells, but the underlying molecular mechanisms are unknown. RESULTS In this study, we address the subcellular localization of TMIGD1 in renal epithelial cells and identify a cytoplasmic scaffold protein as interaction partner of TMIGD1. We find that TMIGD1 localizes to different compartments in renal epithelial cells and that this localization is regulated by cell confluency. Whereas it localizes to mitochondria in subconfluent cells it is localized at cell-cell contacts in confluent cells. We find that cell-cell contact localization is regulated by N-glycosylation and that both the extracellular and the cytoplasmic domain contribute to this localization. We identify Synaptojanin 2-binding protein (SYNJ2BP), a PDZ domain-containing cytoplasmic protein, which localizes to both mitochondria and the plasma membrane, as interaction partner of TMIGD1. The interaction of TMIGD1 and SYNJ2BP is mediated by the PDZ domain of SYNJ2BP and the C-terminal PDZ domain-binding motif of TMIGD1. We also find that SYNJ2BP can actively recruit TMIGD1 to mitochondria providing a potential mechanism for the localization of TMIGD1 at mitochondria. CONCLUSIONS This study describes TMIGD1 as an adhesion receptor that can localize to both mitochondria and cell-cell junctions in renal epithelial cells. It identifies SYNJ2BP as an interaction partner of TMIGD1 providing a potential mechanism underlying the localization of TMIGD1 at mitochondria. The study thus lays the basis for a better understanding of the molecular function of TMIGD1 during oxidative stress regulation.
Collapse
Affiliation(s)
- Christian Hartmann
- Institute-Associated Research Group "Cell adhesion and cell polarity", University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany.,Institute of Medical Biochemistry, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany
| | - Ysabel Alessa Schwietzer
- Institute-Associated Research Group "Cell adhesion and cell polarity", University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany.,Institute of Medical Biochemistry, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany
| | - Daniel Kummer
- Institute-Associated Research Group "Cell adhesion and cell polarity", University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany.,Institute of Medical Biochemistry, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany.,Interdisciplinary Clinical Research Center (IZKF), University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany
| | - Nils Kirschnick
- Institute-Associated Research Group "Cell adhesion and cell polarity", University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany.,Institute of Medical Biochemistry, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany
| | - Esther Hoppe
- Institute-Associated Research Group "Cell adhesion and cell polarity", University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany.,Institute of Medical Biochemistry, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany
| | - Eva-Maria Thüring
- Institute-Associated Research Group "Cell adhesion and cell polarity", University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany.,Institute of Medical Biochemistry, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany
| | - Mark Glaesner-Ebnet
- Institute-Associated Research Group "Cell adhesion and cell polarity", University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany.,Institute of Medical Biochemistry, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany
| | - Frauke Brinkmann
- Institute-Associated Research Group "Cell adhesion and cell polarity", University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany.,Institute of Medical Biochemistry, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany
| | - Volker Gerke
- Institute of Medical Biochemistry, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany
| | - Stefan Reuter
- Department of Medicine D, Division of General Internal Medicine, Nephrology and Rheumatology, University Hospital of Münster, 48149, Münster, Germany
| | - Masanori Nakayama
- Laboratory for Cell Polarity and Organogenesis, Max-Planck-Institute for Heart and Lung Research, 61231, Bad Nauheim, Germany
| | - Klaus Ebnet
- Institute-Associated Research Group "Cell adhesion and cell polarity", University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany. .,Institute of Medical Biochemistry, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany. .,Interdisciplinary Clinical Research Center (IZKF), University of Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany. .,Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, 48419, Münster, Germany.
| |
Collapse
|
173
|
Sung AY, Floyd BJ, Pagliarini DJ. Systems Biochemistry Approaches to Defining Mitochondrial Protein Function. Cell Metab 2020; 31:669-678. [PMID: 32268114 PMCID: PMC7176052 DOI: 10.1016/j.cmet.2020.03.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/06/2020] [Accepted: 03/13/2020] [Indexed: 02/07/2023]
Abstract
Defining functions for the full complement of proteins is a grand challenge in the post-genomic era and is essential for our understanding of basic biology and disease pathogenesis. In recent times, this endeavor has benefitted from a combination of modern large-scale and classical reductionist approaches-a process we refer to as "systems biochemistry"-that helps surmount traditional barriers to the characterization of poorly understood proteins. This strategy is proving to be particularly effective for mitochondria, whose well-defined proteome has enabled comprehensive analyses of the full mitochondrial system that can position understudied proteins for fruitful mechanistic investigations. Recent systems biochemistry approaches have accelerated the identification of new disease-related mitochondrial proteins and of long-sought "missing" proteins that fulfill key functions. Collectively, these studies are moving us toward a more complete understanding of mitochondrial activities and providing a molecular framework for the investigation of mitochondrial pathogenesis.
Collapse
Affiliation(s)
- Andrew Y Sung
- Morgridge Institute for Research, Madison, WI, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA; School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Brendan J Floyd
- Morgridge Institute for Research, Madison, WI, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA; Department of Pediatrics, Stanford School of Medicine, Stanford, CA, USA
| | - David J Pagliarini
- Morgridge Institute for Research, Madison, WI, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
| |
Collapse
|
174
|
Huang X, Jiang C, Yu L, Yang A. Current and Emerging Approaches for Studying Inter-Organelle Membrane Contact Sites. Front Cell Dev Biol 2020; 8:195. [PMID: 32292782 PMCID: PMC7118198 DOI: 10.3389/fcell.2020.00195] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/09/2020] [Indexed: 12/24/2022] Open
Abstract
Inter-organelle membrane contact sites (MCSs) are classically defined as areas of close proximity between heterologous membranes and established by specific proteins (termed tethers). The interest on MCSs has rapidly increased in the last years, since MCSs play a crucial role in the transfer of cellular components between different organelles and have been involved in important cellular functions such as apoptosis, organelle division and biogenesis, and cell growth. Recently, an unprecedented depth and breadth in insights into the details of MCSs have been uncovered. On one hand, extensive MCSs (organelles interactome) are revealed by comprehensive analysis of organelle network with high temporal-spatial resolution at the system level. On the other hand, more and more tethers involving in MCSs are identified and further works are focusing on addressing the role of these tethers in regulating the function of MCSs at the molecular level. These enormous progresses largely depend on the powerful approaches, including several different types of microscopies and various biochemical techniques. These approaches have greatly accelerated recent advances in MCSs at the system and molecular level. In this review, we summarize the current and emerging approaches for studying MCSs, such as various microscopies, proximity-driven fluorescent signal generation and proximity-dependent biotinylation. In addition, we highlight the advantages and disadvantages of the techniques to provide a general guidance for the study of MCSs.
Collapse
Affiliation(s)
- Xue Huang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Chen Jiang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Lihua Yu
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Aimin Yang
- School of Life Sciences, Chongqing University, Chongqing, China
| |
Collapse
|
175
|
Bechtel TJ, Li C, Kisty EA, Maurais AJ, Weerapana E. Profiling Cysteine Reactivity and Oxidation in the Endoplasmic Reticulum. ACS Chem Biol 2020; 15:543-553. [PMID: 31899610 DOI: 10.1021/acschembio.9b01014] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The endoplasmic reticulum (ER) is the initial site of biogenesis of secretory pathway proteins, including proteins localized to the ER, Golgi, lysosomes, intracellular vesicles, plasma membrane, and extracellular compartments. Proteins within the secretory pathway contain a high abundance of disulfide bonds to protect against the oxidative extracellular environment. These disulfide bonds are typically formed within the ER by a variety of oxidoreductases, including members of the protein disulfide isomerase (PDI) family. Here, we establish chemoproteomic platforms to identify oxidized and reduced cysteine residues within the ER. Subcellular fractionation methods were utilized to enrich for the ER and significantly enhance the coverage of ER-localized cysteine residues. Reactive-cysteine profiling ranked ∼900 secretory pathway cysteines by reactivity with an iodoacetamide-alkyne probe, revealing functional cysteines annotated to participate in disulfide bonds, or S-palmitoylation sites within proteins. Through application of a variation of the OxICAT protocol for quantifying cysteine oxidation, the percentages of oxidation for each of ∼700 ER-localized cysteines were calculated. Lastly, perturbation of ER function, through chemical induction of ER stress, was used to investigate the effect of initiation of the unfolded protein response (UPR) on ER-localized cysteine oxidation. Together, these studies establish a platform for identifying reactive and functional cysteine residues on proteins within the secretory pathway as well as for interrogating the effects of diverse cellular stresses on ER-localized cysteine oxidation.
Collapse
Affiliation(s)
- Tyler J. Bechtel
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Chun Li
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Eleni A. Kisty
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Aaron J. Maurais
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| |
Collapse
|
176
|
Stefely JA, Zhang Y, Freiberger EC, Kwiecien NW, Thomas HE, Davis AM, Lowry ND, Vincent CE, Shishkova E, Clark NA, Medvedovic M, Coon JJ, Pagliarini DJ, Mercer CA. Mass spectrometry proteomics reveals a function for mammalian CALCOCO1 in MTOR-regulated selective autophagy. Autophagy 2020; 16:2219-2237. [PMID: 31971854 DOI: 10.1080/15548627.2020.1719746] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Macroautophagy/autophagy is suppressed by MTOR (mechanistic target of rapamycin kinase) and is an anticancer target under active investigation. Yet, MTOR-regulated autophagy remains incompletely mapped. We used proteomic profiling to identify proteins in the MTOR-autophagy axis. Wild-type (WT) mouse cell lines and cell lines lacking individual autophagy genes (Atg5 or Ulk1/Ulk2) were treated with an MTOR inhibitor to induce autophagy and cultured in media with either glucose or galactose. Mass spectrometry proteome profiling revealed an elevation of known autophagy proteins and candidates for new autophagy components, including CALCOCO1 (calcium binding and coiled-coil domain protein 1). We show that CALCOCO1 physically interacts with MAP1LC3C, a key protein in the machinery of autophagy. Genetic deletion of CALCOCO1 disrupted autophagy of the endoplasmic reticulum (reticulophagy). Together, these results reveal a role for CALCOCO1 in MTOR-regulated selective autophagy. More generally, the resource generated by this work provides a foundation for establishing links between the MTOR-autophagy axis and proteins not previously linked to this pathway. Abbreviations: ATG: autophagy-related; CALCOCO1: calcium binding and coiled-coil domain protein 1; CALCOCO2/NDP52: calcium binding and coiled-coil domain protein 2; CLIR: MAP1LC3C-interacting region; CQ: chloroquine; KO: knockout; LIR: MAP1LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MEF: mouse embryonic fibroblast; MLN: MLN0128 ATP-competitive MTOR kinase inhibitor; MTOR: mechanistic target of rapamycin kinase; reticulophagy: selective autophagy of the endoplasmic reticulum; TAX1BP1/CALCOCO3: TAX1 binding protein 1; ULK: unc 51-like autophagy activating kinase; WT: wild-type.
Collapse
Affiliation(s)
- Jonathan A Stefely
- Morgridge Institute for Research , Madison, WI, USA.,Medical Scientist Training Program, School of Medicine and Public Health, University of Wisconsin-Madison , Madison, WI, USA.,Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
| | - Yu Zhang
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
| | - Elyse C Freiberger
- Department of Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Department of Biomolecular Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Genome Center of Wisconsin , Madison, WI, USA.,Department of Biochemistry, University ofWisconsin-Madison , Madison, Madison, WI, USA
| | - Nicholas W Kwiecien
- Department of Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Department of Biomolecular Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Genome Center of Wisconsin , Madison, WI, USA.,Department of Biochemistry, University ofWisconsin-Madison , Madison, Madison, WI, USA
| | - Hala Elnakat Thomas
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
| | - Alexander M Davis
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
| | - Nathaniel D Lowry
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
| | - Catherine E Vincent
- Genome Center of Wisconsin , Madison, WI, USA.,Department of Chemistry, Hartwick College , Oneonta, NY, USA
| | | | - Nicholas A Clark
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati , Cincinnati, OH, USA
| | - Mario Medvedovic
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati , Cincinnati, OH, USA
| | - Joshua J Coon
- Morgridge Institute for Research , Madison, WI, USA.,Department of Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Department of Biomolecular Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Genome Center of Wisconsin , Madison, WI, USA
| | - David J Pagliarini
- Morgridge Institute for Research , Madison, WI, USA.,Department of Biochemistry, University ofWisconsin-Madison , Madison, Madison, WI, USA
| | - Carol A Mercer
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
| |
Collapse
|
177
|
Abstract
Mitochondria are essential organelles of eukaryotic cells. They consist of hundreds of different proteins that exhibit crucial activities in respiration, catabolic metabolism and the synthesis of amino acids, lipids, heme and iron-sulfur clusters. With the exception of a handful of hydrophobic mitochondrially encoded membrane proteins, all these proteins are synthesized on cytosolic ribosomes, targeted to receptors on the mitochondrial surface, and transported across or inserted into the outer and inner mitochondrial membrane before they are folded and assembled into their final native structure. This review article provides a comprehensive overview of the mechanisms and components of the mitochondrial protein import systems with a particular focus on recent developments in the field.
Collapse
Affiliation(s)
- Katja G Hansen
- Cell Biology, University of Kaiserslautern, Erwin-Schrödinger-Strasse 13, 67663, Kaiserslautern, Germany
| | - Johannes M Herrmann
- Cell Biology, University of Kaiserslautern, Erwin-Schrödinger-Strasse 13, 67663, Kaiserslautern, Germany.
| |
Collapse
|
178
|
Abstract
The premise of this book is the importance of the tumor microenvironment (TME). Until recently, most research on and clinical attention to cancer biology, diagnosis, and prognosis were focused on the malignant (or premalignant) cellular compartment that could be readily appreciated using standard morphology-based imaging.
Collapse
|
179
|
Nguyen TMT, Kim J, Doan TT, Lee MW, Lee M. APEX Proximity Labeling as a Versatile Tool for Biological Research. Biochemistry 2019; 59:260-269. [PMID: 31718172 DOI: 10.1021/acs.biochem.9b00791] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Most proteins are specifically localized in membrane-encapsulated organelles or non-membrane-bound compartments. The subcellular localization of proteins facilitates their functions and integration into functional networks; therefore, protein localization is tightly regulated in diverse biological contexts. However, protein localization has been mainly analyzed through immunohistochemistry or the fractionation of subcellular compartments, each of which has major drawbacks. Immunohistochemistry can examine only a handful of proteins at a time, and fractionation inevitably relies on the lysis of cells, which disrupts native cellular conditions. Recently, an engineered ascorbate peroxidase (APEX)-based proximity labeling technique combined with mass spectrometry was developed, which allows for temporally and spatially resolved proteomic mapping. In the presence of H2O2, engineered APEX oxidizes biotin-phenols into biotin-phenoxyl radicals, and these short-lived radicals biotinylate electron-rich amino acids within a radius of several nanometers. Biotinylated proteins are subsequently enriched by streptavidin and identified by mass spectrometry. This permits the sensitive and efficient labeling of proximal proteins around locally expressed APEX. Through the targeted expression of APEX in the subcellular region of interest, proteomic profiling of submitochondrial spaces, the outer mitochondrial membrane, the endoplasmic reticulum (ER)-mitochondrial contact, and the ER membrane has been performed. Furthermore, this method has been modified to define interaction networks in the vicinity of target proteins and has also been applied to analyze the spatial transcriptome. In this Perspective, we provide an outline of this newly developed technique and discuss its potential applications to address diverse biological questions.
Collapse
Affiliation(s)
- Thanh My Thi Nguyen
- Soonchunhyang Institute of Medi-bio Science , Soonchunhyang University , Cheonan-si , Chungcheongnam-do 31151 , Republic of Korea
| | - Junhyung Kim
- Soonchunhyang Institute of Medi-bio Science , Soonchunhyang University , Cheonan-si , Chungcheongnam-do 31151 , Republic of Korea
| | - Thi Tram Doan
- Soonchunhyang Institute of Medi-bio Science , Soonchunhyang University , Cheonan-si , Chungcheongnam-do 31151 , Republic of Korea
| | - Min-Woo Lee
- Soonchunhyang Institute of Medi-bio Science , Soonchunhyang University , Cheonan-si , Chungcheongnam-do 31151 , Republic of Korea
| | - Mihye Lee
- Soonchunhyang Institute of Medi-bio Science , Soonchunhyang University , Cheonan-si , Chungcheongnam-do 31151 , Republic of Korea
| |
Collapse
|
180
|
Galmozzi A, Kok BP, Kim AS, Montenegro-Burke JR, Lee JY, Spreafico R, Mosure S, Albert V, Cintron-Colon R, Godio C, Webb WR, Conti B, Solt LA, Kojetin D, Parker CG, Peluso JJ, Pru JK, Siuzdak G, Cravatt BF, Saez E. PGRMC2 is an intracellular haem chaperone critical for adipocyte function. Nature 2019; 576:138-142. [PMID: 31748741 PMCID: PMC6895438 DOI: 10.1038/s41586-019-1774-2] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 10/01/2019] [Indexed: 12/16/2022]
Abstract
Heme is an essential prosthetic group of numerous proteins and a central signaling molecule in many physiologic processes1,2. The chemical reactivity of heme requires that a network of intracellular chaperone proteins exist to avert the cytotoxic effects of free heme, but the constituents of such trafficking pathways are unknown3,4. Heme synthesis is completed in mitochondria, with ferrochelatase (FECH) adding iron to protoporphyrin IX. How this vital but highly reactive metabolite is delivered from mitochondria to hemoproteins throughout the cell remains poorly defined3,4. Here, we show that PGRMC2 is required for delivery of labile, or signaling heme, to the nucleus. Deletion of PGMRC2 in brown fat, which has a high demand for heme, reduced labile heme in the nucleus and increased stability of the heme-responsive transcriptional repressors Rev-Erbα and BACH1. Ensuing alterations in gene expression spawn severe mitochondrial defects that rendered adipose-specific PGRMC2-null mice unable to activate adaptive thermogenesis and prone to greater metabolic deterioration when fed a high-fat diet. In contrast, obese-diabetic mice treated with a small-molecule PGRMC2 activator showed substantial improvement of diabetic features. These studies uncover a role for PGRMC2 in intracellular heme transport, reveal the impact of adipose tissue heme dynamics on physiology, and suggest that modulation of PGRMC2 may revert obesity-linked defects in adipocytes.
Collapse
Affiliation(s)
- Andrea Galmozzi
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Bernard P Kok
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Arthur S Kim
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Jae Y Lee
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Roberto Spreafico
- Institute for Quantitative and Computational Biology, University of California, Los Angeles, CA, USA
| | - Sarah Mosure
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, USA
| | - Verena Albert
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Rigo Cintron-Colon
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Cristina Godio
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - William R Webb
- Scripps Center for Metabolomics, The Scripps Research Institute, La Jolla, CA, USA
| | - Bruno Conti
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Laura A Solt
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Douglas Kojetin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, USA
| | - Christopher G Parker
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA.,Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - John J Peluso
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - James K Pru
- Center for Reproductive Biology, Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Gary Siuzdak
- Scripps Center for Metabolomics, The Scripps Research Institute, La Jolla, CA, USA.,Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Enrique Saez
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
| |
Collapse
|
181
|
Heo JM, Harper NJ, Paulo JA, Li M, Xu Q, Coughlin M, Elledge SJ, Harper JW. Integrated proteogenetic analysis reveals the landscape of a mitochondrial-autophagosome synapse during PARK2-dependent mitophagy. SCIENCE ADVANCES 2019; 5:eaay4624. [PMID: 31723608 PMCID: PMC6834391 DOI: 10.1126/sciadv.aay4624] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/16/2019] [Indexed: 05/08/2023]
Abstract
The PINK1 protein kinase activates the PARK2 ubiquitin ligase to promote mitochondrial ubiquitylation and recruitment of ubiquitin-binding mitophagy receptors typified by OPTN and TAX1BP1. Here, we combine proximity biotinylation of OPTN and TAX1BP1 with CRISPR-Cas9-based screens for mitophagic flux to develop a spatial proteogenetic map of PARK2-dependent mitophagy. Proximity labeling of OPTN allowed visualization of a "mitochondrial-autophagosome synapse" upon mitochondrial depolarization. Proximity proteomics of OPTN and TAX1BP1 revealed numerous proteins at the synapse, including both PARK2 substrates and autophagy components. Parallel mitophagic flux screens identified proteins with roles in autophagy, vesicle formation and fusion, as well as PARK2 targets, many of which were also identified via proximity proteomics. One protein identified in both approaches, HK2, promotes assembly of a high-molecular weight complex of PINK1 and phosphorylation of ubiquitin in response to mitochondrial damage. This work provides a resource for understanding the spatial and molecular landscape of PARK2-dependent mitophagy.
Collapse
Affiliation(s)
- Jin-Mi Heo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Nathan J. Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Mamie Li
- Department of Genetics, Harvard Medical School, Howard Hughes Medical Institute; Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Qikai Xu
- Department of Genetics, Harvard Medical School, Howard Hughes Medical Institute; Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Margaret Coughlin
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Stephen J. Elledge
- Department of Genetics, Harvard Medical School, Howard Hughes Medical Institute; Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - J. Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Corresponding author.
| |
Collapse
|
182
|
Chu Q, Martinez TF, Novak SW, Donaldson CJ, Tan D, Vaughan JM, Chang T, Diedrich JK, Andrade L, Kim A, Zhang T, Manor U, Saghatelian A. Regulation of the ER stress response by a mitochondrial microprotein. Nat Commun 2019; 10:4883. [PMID: 31653868 PMCID: PMC6814811 DOI: 10.1038/s41467-019-12816-z] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/13/2019] [Indexed: 12/14/2022] Open
Abstract
Cellular homeostasis relies on having dedicated and coordinated responses to a variety of stresses. The accumulation of unfolded proteins in the endoplasmic reticulum (ER) is a common stress that triggers a conserved pathway called the unfolded protein response (UPR) that mitigates damage, and dysregulation of UPR underlies several debilitating diseases. Here, we discover that a previously uncharacterized 54-amino acid microprotein PIGBOS regulates UPR. PIGBOS localizes to the mitochondrial outer membrane where it interacts with the ER protein CLCC1 at ER–mitochondria contact sites. Functional studies reveal that the loss of PIGBOS leads to heightened UPR and increased cell death. The characterization of PIGBOS reveals an undiscovered role for a mitochondrial protein, in this case a microprotein, in the regulation of UPR originating in the ER. This study demonstrates microproteins to be an unappreciated class of genes that are critical for inter-organelle communication, homeostasis, and cell survival. Cells trigger an unfolded protein response (UPR) in the endoplasmic reticulum, but its regulation by mitochondria is unclear. Here, the authors report a 54-residue microprotein PIGBOS that participates in inter-organelle contact between the endoplasmic reticulum and the mitochondria and may regulate UPR.
Collapse
Affiliation(s)
- Qian Chu
- The Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, 10010N. Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Thomas F Martinez
- The Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, 10010N. Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Sammy Weiser Novak
- The Salk Institute for Biological Studies, Waitt Advanced Biophotonics Center, 10010N. Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Cynthia J Donaldson
- The Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, 10010N. Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Dan Tan
- The Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, 10010N. Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Joan M Vaughan
- The Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, 10010N. Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Tina Chang
- The Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, 10010N. Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Jolene K Diedrich
- The Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, 10010N. Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Leo Andrade
- The Salk Institute for Biological Studies, Waitt Advanced Biophotonics Center, 10010N. Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Andrew Kim
- The Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, 10010N. Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Tong Zhang
- The Salk Institute for Biological Studies, Waitt Advanced Biophotonics Center, 10010N. Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Uri Manor
- The Salk Institute for Biological Studies, Waitt Advanced Biophotonics Center, 10010N. Torrey Pines Rd, La Jolla, CA, 92037, USA.
| | - Alan Saghatelian
- The Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, 10010N. Torrey Pines Rd, La Jolla, CA, 92037, USA.
| |
Collapse
|
183
|
Mair A, Xu SL, Branon TC, Ting AY, Bergmann DC. Proximity labeling of protein complexes and cell-type-specific organellar proteomes in Arabidopsis enabled by TurboID. eLife 2019; 8:e47864. [PMID: 31535972 PMCID: PMC6791687 DOI: 10.7554/elife.47864] [Citation(s) in RCA: 138] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 09/15/2019] [Indexed: 12/15/2022] Open
Abstract
Defining specific protein interactions and spatially or temporally restricted local proteomes improves our understanding of all cellular processes, but obtaining such data is challenging, especially for rare proteins, cell types, or events. Proximity labeling enables discovery of protein neighborhoods defining functional complexes and/or organellar protein compositions. Recent technological improvements, namely two highly active biotin ligase variants (TurboID and miniTurbo), allowed us to address two challenging questions in plants: (1) what are in vivo partners of a low abundant key developmental transcription factor and (2) what is the nuclear proteome of a rare cell type? Proteins identified with FAMA-TurboID include known interactors of this stomatal transcription factor and novel proteins that could facilitate its activator and repressor functions. Directing TurboID to stomatal nuclei enabled purification of cell type- and subcellular compartment-specific proteins. Broad tests of TurboID and miniTurbo in Arabidopsis and Nicotiana benthamiana and versatile vectors enable customization by plant researchers.
Collapse
Affiliation(s)
- Andrea Mair
- Department of BiologyStanford UniversityStanfordUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| | - Shou-Ling Xu
- Department of Plant BiologyCarnegie Institution for ScienceStanfordUnited States
| | - Tess C Branon
- Department of BiologyStanford UniversityStanfordUnited States
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeUnited States
- Department of GeneticsStanford UniversityStanfordUnited States
- Department of ChemistryStanford UniversityStanfordUnited States
| | - Alice Y Ting
- Department of BiologyStanford UniversityStanfordUnited States
- Department of GeneticsStanford UniversityStanfordUnited States
- Department of ChemistryStanford UniversityStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Dominique C Bergmann
- Department of BiologyStanford UniversityStanfordUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| |
Collapse
|
184
|
James C, Müller M, Goldberg MW, Lenz C, Urlaub H, Kehlenbach RH. Proteomic mapping by rapamycin-dependent targeting of APEX2 identifies binding partners of VAPB at the inner nuclear membrane. J Biol Chem 2019; 294:16241-16254. [PMID: 31519755 DOI: 10.1074/jbc.ra118.007283] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 08/05/2019] [Indexed: 11/06/2022] Open
Abstract
Vesicle-associated membrane protein-associated protein B (VAPB) is a tail-anchored protein that is present at several contact sites of the endoplasmic reticulum (ER). We now show by immunoelectron microscopy that VAPB also localizes to the inner nuclear membrane (INM). Using a modified enhanced ascorbate peroxidase 2 (APEX2) approach with rapamycin-dependent targeting of the peroxidase to a protein of interest, we searched for proteins that are in close proximity to VAPB, particularly at the INM. In combination with stable isotope labeling with amino acids in cell culture (SILAC), we confirmed many well-known interaction partners at the level of the ER with a clear distinction between specific and nonspecific hits. Furthermore, we identified emerin, TMEM43, and ELYS as potential interaction partners of VAPB at the INM and the nuclear pore complex, respectively.
Collapse
Affiliation(s)
- Christina James
- Department of Molecular Biology, Faculty of Medicine, Göttingen Center for Molecular Biosciences (GZMB), Georg August University Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Marret Müller
- Department of Molecular Biology, Faculty of Medicine, Göttingen Center for Molecular Biosciences (GZMB), Georg August University Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Martin W Goldberg
- School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Christof Lenz
- Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany.,Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany.,Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Ralph H Kehlenbach
- Department of Molecular Biology, Faculty of Medicine, Göttingen Center for Molecular Biosciences (GZMB), Georg August University Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| |
Collapse
|
185
|
Mechanistic Connections between Endoplasmic Reticulum (ER) Redox Control and Mitochondrial Metabolism. Cells 2019; 8:cells8091071. [PMID: 31547228 PMCID: PMC6769559 DOI: 10.3390/cells8091071] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/06/2019] [Accepted: 09/07/2019] [Indexed: 12/21/2022] Open
Abstract
The past decade has seen the emergence of endoplasmic reticulum (ER) chaperones as key determinants of contact formation between mitochondria and the ER on the mitochondria-associated membrane (MAM). Despite the known roles of ER–mitochondria tethering factors like PACS-2 and mitofusin-2, it is not yet entirely clear how they mechanistically interact with the ER environment to determine mitochondrial metabolism. In this article, we review the mechanisms used to communicate ER redox and folding conditions to the mitochondria, presumably with the goal of controlling mitochondrial metabolism at the Krebs cycle and at the electron transport chain, leading to oxidative phosphorylation (OXPHOS). To achieve this goal, redox nanodomains in the ER and the interorganellar cleft influence the activities of ER chaperones and Ca2+-handling proteins to signal to mitochondria. This mechanism, based on ER chaperones like calnexin and ER oxidoreductases like Ero1α, controls reactive oxygen production within the ER, which can chemically modify the proteins controlling ER–mitochondria tethering, or mitochondrial membrane dynamics. It can also lead to the expression of apoptotic or metabolic transcription factors. The link between mitochondrial metabolism and ER homeostasis is evident from the specific functions of mitochondria–ER contact site (MERC)-localized Ire1 and PERK. These functions allow these two transmembrane proteins to act as mitochondria-preserving guardians, a function that is apparently unrelated to their functions in the unfolded protein response (UPR). In scenarios where ER stress cannot be resolved via the activation of mitochondrial OXPHOS, MAM-localized autophagosome formation acts to remove defective portions of the ER. ER chaperones such as calnexin are again critical regulators of this MERC readout.
Collapse
|
186
|
Hashimoto Y, Greco TM, Cristea IM. Contribution of Mass Spectrometry-Based Proteomics to Discoveries in Developmental Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:143-154. [PMID: 31347046 DOI: 10.1007/978-3-030-15950-4_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Understanding multicellular organism development from a molecular perspective is no small feat, yet this level of comprehension affords clinician-scientists the ability to identify root causes and mechanisms of congenital diseases. Inarguably, the maturation of molecular biology tools has significantly contributed to the identification of genetic loci that underlie normal and aberrant developmental programs. In combination with cell biology approaches, these tools have begun to elucidate the spatiotemporal expression and function of developmentally-regulated proteins. The emergence of quantitative mass spectrometry (MS) for biological applications has accelerated the pace at which these proteins can be functionally characterized, driving the construction of an increasingly detailed systems biology picture of developmental processes. Here, we review the quantitative MS-based proteomic technologies that have contributed significantly to understanding the role of proteome regulation in developmental processes. We provide a brief overview of these methodologies, focusing on their ability to provide precise and accurate proteome measurements. We then highlight the use of discovery-based and targeted mass spectrometry approaches in model systems to study cellular differentiation states, tissue phenotypes, and spatiotemporal subcellular organization. We also discuss the current application and future perspectives of MS proteomics to study PTM coordination and the role of protein complexes during development.
Collapse
Affiliation(s)
- Yutaka Hashimoto
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Todd M Greco
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA.
| |
Collapse
|
187
|
Yagensky O, Kohansal-Nodehi M, Gunaseelan S, Rabe T, Zafar S, Zerr I, Härtig W, Urlaub H, Chua JJ. Increased expression of heme-binding protein 1 early in Alzheimer's disease is linked to neurotoxicity. eLife 2019; 8:47498. [PMID: 31453805 PMCID: PMC6739868 DOI: 10.7554/elife.47498] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/25/2019] [Indexed: 12/15/2022] Open
Abstract
Alzheimer’s disease is the most prevalent neurodegenerative disorder leading to progressive cognitive decline. Despite decades of research, understanding AD progression at the molecular level, especially at its early stages, remains elusive. Here, we identified several presymptomatic AD markers by investigating brain proteome changes over the course of neurodegeneration in a transgenic mouse model of AD (3×Tg-AD). We show that one of these markers, heme-binding protein 1 (Hebp1), is elevated in the brains of both 3×Tg-AD mice and patients affected by rapidly-progressing forms of AD. Hebp1, predominantly expressed in neurons, interacts with the mitochondrial contact site complex (MICOS) and exhibits a perimitochondrial localization. Strikingly, wildtype, but not Hebp1-deficient, neurons showed elevated cytotoxicity in response to heme-induced apoptosis. Increased survivability in Hebp1-deficient neurons is conferred by blocking the activation of the mitochondrial-associated caspase signaling pathway. Taken together, our data highlight a role of Hebp1 in progressive neuronal loss during AD progression.
Collapse
Affiliation(s)
- Oleksandr Yagensky
- Research Group Protein Trafficking in Synaptic Development and Function, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | | | - Saravanan Gunaseelan
- Interactomics and Intracellular Trafficking Laboratory, Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Tamara Rabe
- Department of Genes and Behavior, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Saima Zafar
- Biomedical Engineering and Sciences Department, School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Islamabad, Pakistan.,Clinical Dementia Center, Department of Neurology, German Center for Neurodegenerative Diseases, University Medical Center Göttingen, Göttingen, Germany
| | - Inga Zerr
- Clinical Dementia Center, Department of Neurology, German Center for Neurodegenerative Diseases, University Medical Center Göttingen, Göttingen, Germany
| | - Wolfgang Härtig
- Paul Flechsig Institute for Brain Research, University of Leipzig, Leipzig, Germany
| | - Henning Urlaub
- Research Group Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - John Je Chua
- Research Group Protein Trafficking in Synaptic Development and Function, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Interactomics and Intracellular Trafficking Laboratory, Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,LSI Neurobiology Programme, National University of Singapore, Singapore, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
| |
Collapse
|
188
|
Moltedo O, Remondelli P, Amodio G. The Mitochondria-Endoplasmic Reticulum Contacts and Their Critical Role in Aging and Age-Associated Diseases. Front Cell Dev Biol 2019; 7:172. [PMID: 31497601 PMCID: PMC6712070 DOI: 10.3389/fcell.2019.00172] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/07/2019] [Indexed: 02/03/2023] Open
Abstract
The recent discovery of interconnections between the endoplasmic reticulum (ER) membrane and those of almost all the cell compartments is providing novel perspectives for the understanding of the molecular events underlying cellular mechanisms in both physiological and pathological conditions. In particular, growing evidence strongly supports the idea that the molecular interactions occurring between ER and mitochondrial membranes, referred as the mitochondria (MT)-ER contacts (MERCs), may play a crucial role in aging and in the development of age-associated diseases. As emerged in the last decade, MERCs behave as signaling hubs composed by structural components that act as critical players in different age-associated disorders, such as neurodegenerative diseases and motor disorders, cancer, metabolic syndrome, as well as cardiovascular diseases. Age-associated disorders often derive from mitochondrial or ER dysfunction as consequences of oxidative stress, mitochondrial DNA mutations, accumulation of misfolded proteins, and defective organelle turnover. In this review, we discuss the recent advances associating MERCs to aging in the context of ER-MT crosstalk regulating redox signaling, ER-to MT lipid transfer, mitochondrial dynamics, and autophagy.
Collapse
Affiliation(s)
- Ornella Moltedo
- Department of Pharmacy, University of Salerno, Fisciano, Italy
| | - Paolo Remondelli
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana," University of Salerno, Baronissi, Italy
| | - Giuseppina Amodio
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana," University of Salerno, Baronissi, Italy
| |
Collapse
|
189
|
Zhou Y, Wang G, Wang P, Li Z, Yue T, Wang J, Zou P. Expanding APEX2 Substrates for Proximity‐Dependent Labeling of Nucleic Acids and Proteins in Living Cells. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905949] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ying Zhou
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Gang Wang
- Academy for Advanced Interdisciplinary Studies Peking University Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
| | - Pengchong Wang
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
- School of Life Sciences Tsinghua University Beijing 100084 China
| | - Zeyao Li
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
- Peking-Tsinghua-NIBS Joint Graduate Program Tsinghua University Beijing 100084 China
| | - Tieqiang Yue
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Jianbin Wang
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
- School of Life Sciences Tsinghua University Beijing 100084 China
| | - Peng Zou
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
- PKU-IDG/McGovern Institute for Brain Research Beijing 100871 China
| |
Collapse
|
190
|
Zhou Y, Wang G, Wang P, Li Z, Yue T, Wang J, Zou P. Expanding APEX2 Substrates for Proximity‐Dependent Labeling of Nucleic Acids and Proteins in Living Cells. Angew Chem Int Ed Engl 2019; 58:11763-11767. [DOI: 10.1002/anie.201905949] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/24/2019] [Indexed: 01/19/2023]
Affiliation(s)
- Ying Zhou
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Gang Wang
- Academy for Advanced Interdisciplinary Studies Peking University Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
| | - Pengchong Wang
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
- School of Life Sciences Tsinghua University Beijing 100084 China
| | - Zeyao Li
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
- Peking-Tsinghua-NIBS Joint Graduate Program Tsinghua University Beijing 100084 China
| | - Tieqiang Yue
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Jianbin Wang
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
- School of Life Sciences Tsinghua University Beijing 100084 China
| | - Peng Zou
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
- PKU-IDG/McGovern Institute for Brain Research Beijing 100871 China
| |
Collapse
|
191
|
Nightingale DJH, Lilley KS, Oliver SG. A Protocol to Map the Spatial Proteome Using HyperLOPIT in Saccharomyces cerevisiae. Bio Protoc 2019; 9:e3303. [PMID: 33654815 PMCID: PMC7854154 DOI: 10.21769/bioprotoc.3303] [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: 03/26/2019] [Revised: 05/12/2019] [Accepted: 06/25/2019] [Indexed: 11/02/2022] Open
Abstract
The correct subcellular localization of proteins is vital for cellular function and the study of this process at the systems level will therefore enrich our understanding of the roles of proteins within the cell. Multiple methods are available for the study of protein subcellular localization, including fluorescence microscopy, organelle cataloging, proximity labeling methods, and whole-cell protein correlation profiling methods. We provide here a protocol for the systems-level study of the subcellular localization of the yeast proteome, using a version of hyperplexed Localization of Organelle Proteins by Isotope Tagging (hyperLOPIT) that has been optimized for use with Saccharomyces cerevisiae. The entire protocol encompasses cell culture, cell lysis by nitrogen cavitation, subcellular fractionation, monitoring of the fractionation using Western blotting, labeling of samples with TMT isobaric tags and mass spectrometric analysis. Also included is a brief explanation of downstream processing of the mass spectrometry data to produce a map of the spatial proteome. If required, the nitrogen cavitation lysis and Western blotting portions of the protocol may be performed independently of the mass spectrometry analysis. The protocol in its entirety, however, enables the unbiased, systems-level and high-resolution analysis of the localizations of thousands of proteins in parallel within a single experiment.
Collapse
Affiliation(s)
- Daniel J. H. Nightingale
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, United Kingdom
- Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, United Kingdom
| | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, United Kingdom
- Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, United Kingdom
| | - Stephen G. Oliver
- Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, United Kingdom
| |
Collapse
|
192
|
Huang MS, Lin WC, Chang JH, Cheng CH, Wang HY, Mou KY. The cysteine-free single mutant C32S of APEX2 is a highly expressed and active fusion tag for proximity labeling applications. Protein Sci 2019; 28:1703-1712. [PMID: 31306516 DOI: 10.1002/pro.3685] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/09/2019] [Accepted: 07/09/2019] [Indexed: 12/21/2022]
Abstract
APEX2, an engineered ascorbate peroxidase for high activity, is a powerful tool for proximity labeling applications. Owing to its lack of disulfides and the calcium-independent activity, APEX2 can be applied intracellularly for targeted electron microscopy imaging or interactome mapping when fusing to a protein of interest. However, APEX2 fusion is often deleterious to the protein expression, which seriously hampers its wide utility. This problem is especially compelling when APEX2 is fused to structurally delicate proteins, such as multi-pass membrane proteins. In this study, we found that a cysteine-free single mutant C32S of APEX2 dramatically improved the expression of fusion proteins in mammalian cells without compromising the enzyme activity. We fused APEX2 and APEX2C32S to four multi-transmembrane solute carriers (SLCs), SLC1A5, SLC6A5, SLC6A14, and SLC7A1, and compared their expressions in stable HEK293T cell lines. Except the SLC6A5 fusions expressing at decent levels for both APEX2 (70%) and APEX2C32S (73%), other three SLC proteins showed significantly better expression when fusing to APEX2C32S (69 ± 13%) than APEX2 (29 ± 15%). Immunofluorescence and western blot experiments showed correct plasma membrane localization and strong proximity labeling efficiency in all four SLC-APEX2C32S cells. Enzyme kinetic experiments revealed that APEX2 and APEX2C32S have comparable activities in terms of oxidizing guaiacol. Overall, we believe APEX2C32S is a superior fusion tag to APEX2 for proximity labeling applications, especially when mismatched disulfide bonding or poor expression is a concern.
Collapse
Affiliation(s)
- Meng-Sen Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Wen-Ching Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Jen-Hsuan Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Cheng-Hung Cheng
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Han Ying Wang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Kurt Yun Mou
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| |
Collapse
|
193
|
Fazal FM, Han S, Parker KR, Kaewsapsak P, Xu J, Boettiger AN, Chang HY, Ting AY. Atlas of Subcellular RNA Localization Revealed by APEX-Seq. Cell 2019; 178:473-490.e26. [PMID: 31230715 PMCID: PMC6786773 DOI: 10.1016/j.cell.2019.05.027] [Citation(s) in RCA: 339] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 12/31/2018] [Accepted: 05/14/2019] [Indexed: 01/25/2023]
Abstract
We introduce APEX-seq, a method for RNA sequencing based on direct proximity labeling of RNA using the peroxidase enzyme APEX2. APEX-seq in nine distinct subcellular locales produced a nanometer-resolution spatial map of the human transcriptome as a resource, revealing extensive patterns of localization for diverse RNA classes and transcript isoforms. We uncover a radial organization of the nuclear transcriptome, which is gated at the inner surface of the nuclear pore for cytoplasmic export of processed transcripts. We identify two distinct pathways of messenger RNA localization to mitochondria, each associated with specific sets of transcripts for building complementary macromolecular machines within the organelle. APEX-seq should be widely applicable to many systems, enabling comprehensive investigations of the spatial transcriptome.
Collapse
Affiliation(s)
- Furqan M Fazal
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shuo Han
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Kevin R Parker
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Pornchai Kaewsapsak
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Jin Xu
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alistair N Boettiger
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Alice Y Ting
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| |
Collapse
|
194
|
A new class of protein biomarkers based on subcellular distribution: application to a mouse liver cancer model. Sci Rep 2019; 9:6913. [PMID: 31061415 PMCID: PMC6502816 DOI: 10.1038/s41598-019-43091-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 04/15/2019] [Indexed: 12/18/2022] Open
Abstract
To-date, most proteomic studies aimed at discovering tissue-based cancer biomarkers have compared the quantity of selected proteins between case and control groups. However, proteins generally function in association with other proteins to form modules localized in particular subcellular compartments in specialized cell types and tissues. Sub-cellular mislocalization of proteins has in fact been detected as a key feature in a variety of cancer cells. Here, we describe a strategy for tissue-biomarker detection based on a mitochondrial fold enrichment (mtFE) score, which is sensitive to protein abundance changes as well as changes in subcellular distribution between mitochondria and cytosol. The mtFE score integrates protein abundance data from total cellular lysates and mitochondria-enriched fractions, and provides novel information for the classification of cancer samples that is not necessarily apparent from conventional abundance measurements alone. We apply this new strategy to a panel of wild-type and mutant mice with a liver-specific gene deletion of Liver receptor homolog 1 (Lrh-1hep−/−), with both lines containing control individuals as well as individuals with liver cancer induced by diethylnitrosamine (DEN). Lrh-1 gene deletion attenuates cancer cell metabolism in hepatocytes through mitochondrial glutamine processing. We show that proteome changes based on mtFE scores outperform protein abundance measurements in discriminating DEN-induced liver cancer from healthy liver tissue, and are uniquely robust against genetic perturbation. We validate the capacity of selected proteins with informative mtFE scores to indicate hepatic malignant changes in two independent mouse models of hepatocellular carcinoma (HCC), thus demonstrating the robustness of this new approach to biomarker research. Overall, the method provides a novel, sensitive approach to cancer biomarker discovery that considers contextual information of tested proteins.
Collapse
|
195
|
Hoffman AM, Chen Q, Zheng T, Nicchitta CV. Heterogeneous translational landscape of the endoplasmic reticulum revealed by ribosome proximity labeling and transcriptome analysis. J Biol Chem 2019; 294:8942-8958. [PMID: 31004035 DOI: 10.1074/jbc.ra119.007996] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/27/2019] [Indexed: 12/21/2022] Open
Abstract
The endoplasmic reticulum (ER) is a nexus for mRNA localization and translation, and recent studies have demonstrated that ER-bound ribosomes also play a transcriptome-wide role in regulating proteome composition. The Sec61 translocon (SEC61) serves as the receptor for ribosomes that translate secretory/integral membrane protein-encoding mRNAs, but whether SEC61 also serves as a translation site for cytosolic protein-encoding mRNAs remains unknown. Here, using a BioID proximity-labeling approach in HEK293T Flp-In cell lines, we examined interactions between ER-resident proteins and ribosomes in vivo Using in vitro analyses, we further focused on bona fide ribosome interactors (i.e. SEC61) and ER proteins (ribophorin I, leucine-rich repeat-containing 59 (LRRC59), and SEC62) previously implicated in associating with ribosomes. We observed labeling of ER-bound ribosomes with the SEC61β and LRRC59 BioID reporters, comparatively modest labeling with the ribophorin I reporter, and no labeling with the SEC62 reporter. A biotin pulse-chase/subcellular fractionation approach to examine ribosome exchange at the SEC61β and LRRC59 sites revealed that, at steady state, ribosomes at these sites comprise both rapid- and slow-exchanging pools. Global translational initiation arrest elicited by the inhibitor harringtonine accelerated SEC61β reporter-labeled ribosome exchange. RNA-Seq analyses of the mRNAs associated with SEC61β- and LRRC59-labeled ribosomes revealed both site-enriched and shared mRNAs and further established that the ER has a transcriptome-wide role in regulating proteome composition. These results provide evidence that ribosomes interact with the ER membrane via multiple modes and suggest regulatory mechanisms that control global proteome composition via ER membrane-bound ribosomes.
Collapse
Affiliation(s)
| | - Qiang Chen
- Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Tianli Zheng
- Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Christopher V Nicchitta
- From the Departments of Biochemistry and .,Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710
| |
Collapse
|
196
|
Han Y, Branon TC, Martell JD, Boassa D, Shechner D, Ellisman MH, Ting A. Directed Evolution of Split APEX2 Peroxidase. ACS Chem Biol 2019; 14:619-635. [PMID: 30848125 PMCID: PMC6548188 DOI: 10.1021/acschembio.8b00919] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
APEX is an engineered peroxidase that catalyzes the oxidation of a wide range of substrates, facilitating its use in a variety of applications from subcellular staining for electron microscopy to proximity biotinylation for spatial proteomics and transcriptomics. To further advance the capabilities of APEX, we used directed evolution to engineer a split APEX tool (sAPEX). A total of 20 rounds of fluorescence activated cell sorting (FACS)-based selections from yeast-displayed fragment libraries, using 3 different surface display configurations, produced a 200-amino-acid N-terminal fragment (with 9 mutations relative to APEX2) called "AP" and a 50-amino-acid C-terminal fragment called "EX". AP and EX fragments were each inactive on their own but were reconstituted to give peroxidase activity when driven together by a molecular interaction. We demonstrate sAPEX reconstitution in the mammalian cytosol, on engineered RNA motifs within a non-coding RNA scaffold, and at mitochondria-endoplasmic reticulum contact sites.
Collapse
Affiliation(s)
- Yisu Han
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Biology, Stanford University, Stanford, California, USA
- Department of Chemistry, Stanford University, Stanford, California, USA
| | - Tess Caroline Branon
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Biology, Stanford University, Stanford, California, USA
- Department of Chemistry, Stanford University, Stanford, California, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Jeffrey D. Martell
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA
| | - Daniela Boassa
- Department of Neuroscience, University of California San Diego, La Jolla, California, USA
| | - David Shechner
- Department of Pharmacology, University of Washington, Seattle, Washington, USA
| | - Mark H. Ellisman
- Department of Neuroscience, University of California San Diego, La Jolla, California, USA
| | - Alice Ting
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Biology, Stanford University, Stanford, California, USA
- Department of Chemistry, Stanford University, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| |
Collapse
|
197
|
TEX264 Is an Endoplasmic Reticulum-Resident ATG8-Interacting Protein Critical for ER Remodeling during Nutrient Stress. Mol Cell 2019; 74:891-908.e10. [PMID: 31006537 DOI: 10.1016/j.molcel.2019.03.034] [Citation(s) in RCA: 177] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/15/2019] [Accepted: 03/27/2019] [Indexed: 01/16/2023]
Abstract
Cells respond to nutrient stress by trafficking cytosolic contents to lysosomes for degradation via macroautophagy. The endoplasmic reticulum (ER) serves as an initiation site for autophagosomes and is also remodeled in response to nutrient stress through ER-phagy, a form of selective autophagy. Quantitative proteome analysis during nutrient stress identified an unstudied single-pass transmembrane ER protein, TEX264, as an ER-phagy receptor. TEX264 uses an LC3-interacting region (LIR) to traffic into ATG8-positive puncta that often initiate from three-way ER tubule junctions and subsequently fuse with lysosomes. Interaction and proximity biotinylation proteomics identified a cohort of autophagy regulatory proteins and cargo adaptors located near TEX264 in an LIR-dependent manner. Global proteomics and ER-phagy flux analysis revealed the stabilization of a cohort of ER proteins in TEX264-/- cells during nutrient stress. This work reveals TEX264 as an unrecognized ER-phagy receptor that acts independently of other candidate ER-phagy receptors to remodel the ER during nutrient stress.
Collapse
|
198
|
Folding Status Is Determinant over Traffic-Competence in Defining CFTR Interactors in the Endoplasmic Reticulum. Cells 2019; 8:cells8040353. [PMID: 31014000 PMCID: PMC6523853 DOI: 10.3390/cells8040353] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/09/2019] [Accepted: 04/12/2019] [Indexed: 12/15/2022] Open
Abstract
The most common cystic fibrosis-causing mutation (F508del, present in ~85% of CF patients) leads to CFTR misfolding, which is recognized by the endoplasmic reticulum (ER) quality control (ERQC), resulting in ER retention and early degradation. It is known that CFTR exit from the ER is mediated by specific retention/sorting signals that include four arginine-framed tripeptide (AFT) retention motifs and a diacidic (DAD) exit code that controls the interaction with the COPII machinery. Here, we aim at obtaining a global view of the protein interactors that regulate CFTR exit from the ER. We used mass spectrometry-based interaction proteomics and bioinformatics analyses to identify and characterize proteins interacting with selected CFTR peptide motifs or full-length CFTR variants retained or bypassing these ERQC checkpoints. We conclude that these ERQC trafficking checkpoints rely on fundamental players in the secretory pathway, detecting key components of the protein folding machinery associated with the AFT recognition and of the trafficking machinery recognizing the diacidic code. Furthermore, a greater similarity in terms of interacting proteins is observed for variants sharing the same folding defect over those reaching the same cellular location, evidencing that folding status is dominant over ER escape in shaping the CFTR interactome.
Collapse
|
199
|
Proteomic navigation using proximity-labeling. Methods 2019; 164-165:67-72. [PMID: 30953756 DOI: 10.1016/j.ymeth.2019.03.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 10/27/2022] Open
Abstract
The identification of bona fide protein-protein interactions and the mapping of proteomes was greatly enhanced by protein tagging for generic affinity purification methods and analysis by mass spectrometry (AP-MS). The high quality of AP-MS data permitted the development of proteomic navigation by sequential tagging of identified interactions. However AP-MS is laborious and limited to relatively high affinity protein-protein interactions. Proximity labeling, first with the biotin ligase BirA, termed BioID, and then with ascorbate peroxidase, termed APEX, permits a greater reach into the proteome than AP-MS enabling both the identification of a wider field and weaker protein-protein interactions. This additional reach comes with the need for stringent controls. Proximity labeling also permits experiments in living cells allowing spatiotemporal investigations of the proteome. Here we discuss proximity labeling with accompanying methodological descriptions for E. coli and mammalian cells.
Collapse
|
200
|
Dickinson MS, Anderson LN, Webb-Robertson BJM, Hansen JR, Smith RD, Wright AT, Hybiske K. Proximity-dependent proteomics of the Chlamydia trachomatis inclusion membrane reveals functional interactions with endoplasmic reticulum exit sites. PLoS Pathog 2019; 15:e1007698. [PMID: 30943267 PMCID: PMC6464245 DOI: 10.1371/journal.ppat.1007698] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 04/15/2019] [Accepted: 03/12/2019] [Indexed: 11/18/2022] Open
Abstract
Chlamydia trachomatis is the most common cause of bacterial sexually transmitted infection, responsible for millions of infections each year. Despite this high prevalence, the elucidation of the molecular mechanisms of Chlamydia pathogenesis has been difficult due to limitations in genetic tools and its intracellular developmental cycle. Within a host epithelial cell, chlamydiae replicate within a vacuole called the inclusion. Many Chlamydia-host interactions are thought to be mediated by the Inc family of type III secreted proteins that are anchored in the inclusion membrane, but their array of host targets are largely unknown. To investigate how the inclusion membrane proteome changes over the course of an infected cell, we have adapted the APEX2 system of proximity-dependent biotinylation. APEX2 is capable of specifically labeling proteins within a 20 nm radius in living cells. We transformed C. trachomatis to express the enzyme APEX2 fused to known inclusion membrane proteins, allowing biotinylation and purification of inclusion-associated proteins. Using quantitative mass spectrometry against APEX2 labeled samples, we identified over 400 proteins associated with the inclusion membrane at early, middle, and late stages of epithelial cell infection. This system was sensitive enough to detect inclusion interacting proteins early in the developmental cycle, at 8 hours post infection, a previously intractable time point. Mass spectrometry analysis revealed a novel, early association between C. trachomatis inclusions and endoplasmic reticulum exit sites (ERES), functional regions of the ER where COPII-coated vesicles originate. Pharmacological and genetic disruption of ERES function severely restricted early chlamydial growth and the development of infectious progeny. APEX2 is therefore a powerful in situ approach for identifying critical protein interactions on the membranes of pathogen-containing vacuoles. Furthermore, the data derived from proteomic mapping of Chlamydia inclusions has illuminated an important functional role for ERES in promoting chlamydial developmental growth.
Collapse
Affiliation(s)
- Mary S. Dickinson
- Department of Global Health, Graduate Program in Pathobiology, University of Washington, Seattle, WA, United States of America
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Reemerging Infectious Disease (CERID), University of Washington, Seattle, WA, United States of America
| | - Lindsey N. Anderson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | | | - Joshua R. Hansen
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Aaron T. Wright
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States of America
- The Gene and Linda Voiland College of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, United States of America
| | - Kevin Hybiske
- Department of Global Health, Graduate Program in Pathobiology, University of Washington, Seattle, WA, United States of America
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Reemerging Infectious Disease (CERID), University of Washington, Seattle, WA, United States of America
| |
Collapse
|