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Otake M, Teranishi M, Komatsu C, Hara M, Yoshiyama KO, Hidema J. Poaceae plants transfer cyclobutane pyrimidine dimer photolyase to chloroplasts for ultraviolet-B resistance. PLANT PHYSIOLOGY 2024; 195:326-342. [PMID: 38345835 PMCID: PMC11060685 DOI: 10.1093/plphys/kiae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/07/2024] [Indexed: 05/02/2024]
Abstract
Photoreactivation enzyme that repairs cyclobutane pyrimidine dimer (CPD) induced by ultraviolet-B radiation, commonly called CPD photolyase (PHR) is essential for plants living under sunlight. Rice (Oryza sativa) PHR (OsPHR) is a unique triple-targeting protein. The signal sequences required for its translocation to the nucleus or mitochondria are located in the C-terminal region but have yet to be identified for chloroplasts. Here, we identified sequences located in the N-terminal region, including the serine-phosphorylation site at position 7 of OsPHR, and found that OsPHR is transported/localized to chloroplasts via a vesicle transport system under the control of serine-phosphorylation. However, the sequence identified in this study is only conserved in some Poaceae species, and in many other plants, PHR is not localized to the chloroplasts. Therefore, we reasoned that Poaceae species need the ability to repair CPD in the chloroplast genome to survive under sunlight and have uniquely acquired this mechanism for PHR chloroplast translocation.
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Affiliation(s)
- Momo Otake
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Mika Teranishi
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Chiharu Komatsu
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Mamoru Hara
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | | | - Jun Hidema
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
- Division for the Establishment of Frontier Sciences of the Organization for Advanced Studies, Tohoku University, Sendai, Miyagi 980-8577, Japan
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2
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Rashwan AM, El-Gendy SAA, Ez Elarab SM, Alsafy MAM. A comprehensive exploration of diverse skin cell types in the limb of the desert tortoise (Testudo graeca) through light, transmission, scanning electron microscopy, and immunofluorescence techniques. Tissue Cell 2024; 87:102335. [PMID: 38412578 DOI: 10.1016/j.tice.2024.102335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 02/18/2024] [Accepted: 02/20/2024] [Indexed: 02/29/2024]
Abstract
The Greek tortoise, inhabiting harsh desert environments, provides a compelling case for investigating skin adaptations to extreme conditions. We have utilized light microscopy, scanning electron microscopy (SEM), transmission electron microscopy (TEM), and immunofluorescence analysis to describe the structure of the arid-adapted limb skin in the Greek tortoise. Our aim was to identify the cell types that reflect the skin adaptation of this tortoise to arid conditions. Utilizing seven antibodies, we localized and elucidated the functions of various skin cells, shedding light on how the tortoise adapts to adverse environmental conditions. Our findings unveiled numerous scales on the limbs, varying in size and color, acting as protective armor against abrasions, bites, and other potential threats in their rocky habitats. The epidermis comprises four layers: stratum basalis, stratum spinosum, peri-corneous layer, and stratum corneum. Cytokeratin 14 (CK14) was explicitly detected in the basal layer of the epidermis, suggesting a role in maintaining epidermal integrity and cellular function. Langerhans cells were observed between epidermal cells filled with ribosomes and Birbeck granules. Numerous dendritic-shaped Langerhans cells revealed through E-Cadherin signify strong immunity in tortoises' skin. Melanophores were identified using the Melan-A antibody, labeling the cytoplasm, and the SOX10 antibody, labeling the nucleus, providing comprehensive insights into melanophores morphology and distribution. Two types of melanophores were found: dendritic below the stratum basalis of the epidermis and clustered oval melanophores in the deep dermal layer. Varied melanophores distribution resulted in a spotted skin pattern, potentially offering adaptive camouflage and protection against environmental challenges. Numerous myofibroblasts were discerned through alpha-smooth actin (α-SMA) expression, indicating that the Greek tortoise's skin possesses a robust tissue repair and remodeling capacity. B-cell lymphocytes detected via CD20 immunostaining exhibited sporadic distribution in the dermis, concentrating in lymphoid aggregates and around vessels, implying potential roles in local immune responses and inflammation modulation. Employing Tom20 to identify skin cells with abundant mitochondria revealed a notable presence in melanophores and the basal layer of the epidermis, suggesting high metabolic activity in these cell types and potentially influencing cellular functions. These findings contribute to our comprehension of tortoise skin anatomy and physiology, offering insights into the remarkable adaptations of this species finely tuned to their specific environmental habitats.
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Affiliation(s)
- Ahmed M Rashwan
- Department of Anatomy and Embryology, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511 Egypt; Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Samir A A El-Gendy
- Department of Anatomy and Embryology, Faculty of Veterinary Medicine, Alexandria University, Alexandria 21944, Egypt
| | - Samar M Ez Elarab
- Department of Histology and Cytology, Faculty of Veterinary Medicine, Alexandria University, Alexandria 21944, Egypt
| | - Mohamed A M Alsafy
- Department of Anatomy and Embryology, Faculty of Veterinary Medicine, Alexandria University, Alexandria 21944, Egypt.
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3
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Cui M, Lee S, Ban SH, Ryu JR, Shen M, Yang SH, Kim JY, Choi SK, Han J, Kim Y, Han K, Lee D, Sun W, Kwon HB, Lee D. A single-component, light-assisted uncaging switch for endoproteolytic release. Nat Chem Biol 2024; 20:353-364. [PMID: 37973890 DOI: 10.1038/s41589-023-01480-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/12/2023] [Indexed: 11/19/2023]
Abstract
Proteases function as pivotal molecular switches, initiating numerous biological events. Notably, potyviral protease, derived from plant viruses, has emerged as a trusted proteolytic switch in synthetic biological circuits. To harness their capabilities, we have developed a single-component photocleavable switch, termed LAUNCHER (Light-Assisted UNcaging switCH for Endoproteolytic Release), by employing a circularly permutated tobacco etch virus protease and a blue-light-gated substrate, which are connected by fine-tuned intermodular linkers. As a single-component system, LAUNCHER exhibits a superior signal-to-noise ratio compared with multi-component systems, enabling precise and user-controllable release of payloads. This characteristic renders LAUNCHER highly suitable for diverse cellular applications, including transgene expression, tailored subcellular translocation and optochemogenetics. Additionally, the plug-and-play integration of LAUNCHER into existing synthetic circuits facilitates the enhancement of circuit performance. The demonstrated efficacy of LAUNCHER in improving existing circuitry underscores its significant potential for expanding its utilization in various applications.
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Affiliation(s)
- Mingguang Cui
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seunghwan Lee
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Sung Hwan Ban
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jae Ryun Ryu
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Meiying Shen
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Soo Hyun Yang
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jin Young Kim
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seul Ki Choi
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jaemin Han
- Korea University College of Medicine, Seoul, Republic of Korea
| | - Yoonhee Kim
- Department of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kihoon Han
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea
| | - Donghun Lee
- Department of Physics, Korea University, Seoul, Republic of Korea
| | - Woong Sun
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hyung-Bae Kwon
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dongmin Lee
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea.
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea.
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4
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Lee A, Sung G, Shin S, Lee SY, Sim J, Nhung TTM, Nghi TD, Park SK, Sathieshkumar PP, Kang I, Mun JY, Kim JS, Rhee HW, Park KM, Kim K. OrthoID: profiling dynamic proteomes through time and space using mutually orthogonal chemical tools. Nat Commun 2024; 15:1851. [PMID: 38424052 PMCID: PMC10904832 DOI: 10.1038/s41467-024-46034-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024] Open
Abstract
Identifying proteins at organelle contact sites, such as mitochondria-associated endoplasmic reticulum membranes (MAM), is essential for understanding vital cellular processes, yet challenging due to their dynamic nature. Here we report "OrthoID", a proteomic method utilizing engineered enzymes, TurboID and APEX2, for the biotinylation (Bt) and adamantylation (Ad) of proteins close to the mitochondria and endoplasmic reticulum (ER), respectively, in conjunction with high-affinity binding pairs, streptavidin-biotin (SA-Bt) and cucurbit[7]uril-adamantane (CB[7]-Ad), for selective orthogonal enrichment of Bt- and Ad-labeled proteins. This approach effectively identifies protein candidates associated with the ER-mitochondria contact, including LRC59, whose roles at the contact site were-to the best of our knowledge-previously unknown, and tracks multiple protein sets undergoing structural and locational changes at MAM during mitophagy. These findings demonstrate that OrthoID could be a powerful proteomics tool for the identification and analysis of spatiotemporal proteins at organelle contact sites and revealing their dynamic behaviors in vital cellular processes.
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Affiliation(s)
- Ara Lee
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang, Republic of Korea
- Division of Advanced Materials Science (AMS), Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Gihyun Sung
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang, Republic of Korea
- Division of Advanced Materials Science (AMS), Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Sanghee Shin
- Center for RNA Research, Institute for Basic Science (IBS), Seoul, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Song-Yi Lee
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Jaehwan Sim
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Truong Thi My Nhung
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Tran Diem Nghi
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Sang Ki Park
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | | | - Imkyeung Kang
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu, Republic of Korea
- Department of Microbiology, University of Ulsan College of Medicine, Ulsan, Republic of Korea
| | - Ji Young Mun
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu, Republic of Korea
| | - Jong-Seo Kim
- Center for RNA Research, Institute for Basic Science (IBS), Seoul, Republic of Korea.
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea.
| | - Kyeng Min Park
- Department of Biochemistry, Daegu Catholic University School of Medicine, Daegu, Republic of Korea.
| | - Kimoon Kim
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang, Republic of Korea.
- Division of Advanced Materials Science (AMS), Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea.
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea.
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea.
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5
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Mei L, Chen X, Wei F, Huang X, Liu L, Yao J, Chen J, Luo X, Wang Z, Yang A. Tethering ATG16L1 or LC3 induces targeted autophagic degradation of protein aggregates and mitochondria. Autophagy 2023; 19:2997-3013. [PMID: 37424101 PMCID: PMC10549199 DOI: 10.1080/15548627.2023.2234797] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 06/23/2023] [Accepted: 07/05/2023] [Indexed: 07/11/2023] Open
Abstract
Proteolysis-targeting chimeras (PROTACs) based on the ubiquitin-proteasome system have made great progress in the field of drug discovery. There is mounting evidence that the accumulation of aggregation-prone proteins or malfunctioning organelles is associated with the occurrence of various age-related neurodegenerative disorders and cancers. However, PROTACs are inefficient for the degradation of such large targets due to the narrow entrance channel of the proteasome. Macroautophagy (hereafter referred to as autophagy) is known as a self-degradative process involved in the degradation of bulk cytoplasmic components or specific cargoes that are sequestered into autophagosomes. In the present study, we report the development of a generalizable strategy for the targeted degradation of large targets. Our results suggested that tethering large target models to phagophore-associated ATG16L1 or LC3 induced targeted autophagic degradation of the large target models. Furthermore, we successfully applied this autophagy-targeting degradation strategy to the targeted degradation of HTT65Q aggregates and mitochondria. Specifically, chimeras consisting of polyQ-binding peptide 1 (QBP) and ATG16L1-binding peptide (ABP) or LC3-interacting region (LIR) induced targeted autophagic degradation of pathogenic HTT65Q aggregates; and the chimeras consisting of mitochondria-targeting sequence (MTS) and ABP or LIR promoted targeted autophagic degradation of dysfunctional mitochondria, hence ameliorating mitochondrial dysfunction in a Parkinson disease cell model and protecting cells from apoptosis induced by the mitochondrial stress agent FCCP. Therefore, this study provides a new strategy for the selective proteolysis of large targets and enrich the toolkit for autophagy-targeting degradation.Abbreviations: ABP: ATG16L1-binding peptide; ATG16L1: autophagy related 16 like 1; ATTEC: autophagy-tethering compound; AUTAC: autophagy-targeting chimera; AUTOTAC: autophagy-targeting chimera; Baf A1: bafilomycin A1; BCL2: BCL2 apoptosis regulator; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; CASP3: caspase 3; CPP: cell-penetrating peptide; CQ: chloroquine phosphate; DAPI: 4',6-diamidino-2-phenylindole; DCM: dichloromethane; DMF: N,N-dimethylformamide; DMSO: dimethyl sulfoxide; EBSS: Earle's balanced salt solution; FCCP: carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone; FITC: fluorescein-5-isothiocyanate; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GFP: green fluorescent protein; HEK293: human embryonic kidney 293; HEK293T: human embryonic kidney 293T; HPLC: high-performance liquid chromatography; HRP: horseradish peroxidase; HTT: huntingtin; LIR: LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MFF: mitochondrial fission factor; MTS: mitochondria-targeting sequence; NBR1: NBR1 autophagy cargo receptor; NLRX1: NLR family member X1; OPTN: optineurin; P2A: self-cleaving 2A peptide; PB1: Phox and Bem1p; PBS: phosphate-buffered saline; PE: phosphatidylethanolamine; PINK1: PTEN induced kinase 1; PRKN: parkin RBR E3 ubiquitin protein ligase; PROTACs: proteolysis-targeting chimeras; QBP: polyQ-binding peptide 1; SBP: streptavidin-binding peptide; SDS-PAGE: sodium dodecyl sulfate-polyacrylamide gel electrophoresis; SPATA33: spermatogenesis associated 33; TIMM23: translocase of inner mitochondrial membrane 23; TMEM59: transmembrane protein 59; TOMM20: translocase of outer mitochondrial membrane 20; UBA: ubiquitin-associated; WT: wild type.
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Affiliation(s)
- Ligang Mei
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Xiaorong Chen
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Fujing Wei
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Xue Huang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Lu Liu
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Jia Yao
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Jing Chen
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Xunguang Luo
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Zhuolin Wang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Aimin Yang
- School of Life Sciences, Chongqing University, Chongqing, China
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6
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Wong HTC, Lukasz D, Drerup CM, Kindt KS. In vivo investigation of mitochondria in lateral line afferent neurons and hair cells. Hear Res 2023; 431:108740. [PMID: 36948126 PMCID: PMC10079644 DOI: 10.1016/j.heares.2023.108740] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 02/17/2023] [Accepted: 03/12/2023] [Indexed: 03/16/2023]
Abstract
To process sensory stimuli, intense energy demands are placed on hair cells and primary afferents. Hair cells must both mechanotransduce and maintain pools of synaptic vesicles for neurotransmission. Furthermore, both hair cells and afferent neurons must continually maintain a polarized membrane to propagate sensory information. These processes are energy demanding and therefore both cell types are critically reliant on mitochondrial health and function for their activity and maintenance. Based on these demands, it is not surprising that deficits in mitochondrial health can negatively impact the auditory and vestibular systems. In this review, we reflect on how mitochondrial function and dysfunction are implicated in hair cell-mediated sensory system biology. Specifically, we focus on live imaging approaches that have been applied to study mitochondria using the zebrafish lateral-line system. We highlight the fluorescent dyes and genetically encoded biosensors that have been used to study mitochondria in lateral-line hair cells and afferent neurons. We then describe the impact this in vivo work has had on the field of mitochondrial biology as well as the relationship between mitochondria and sensory system development, function, and survival. Finally, we delineate the areas in need of further exploration. This includes in vivo analyses of mitochondrial dynamics and biogenesis, which will round out our understanding of mitochondrial biology in this sensitive sensory system.
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Affiliation(s)
- Hiu-Tung C Wong
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Daria Lukasz
- Section on Sensory Cell Development and Function, National Institute of Deafness and other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Catherine M Drerup
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Katie S Kindt
- Section on Sensory Cell Development and Function, National Institute of Deafness and other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA.
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7
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Busch JD, Fielden LF, Pfanner N, Wiedemann N. Mitochondrial protein transport: Versatility of translocases and mechanisms. Mol Cell 2023; 83:890-910. [PMID: 36931257 DOI: 10.1016/j.molcel.2023.02.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 03/17/2023]
Abstract
Biogenesis of mitochondria requires the import of approximately 1,000 different precursor proteins into and across the mitochondrial membranes. Mitochondria exhibit a wide variety of mechanisms and machineries for the translocation and sorting of precursor proteins. Five major import pathways that transport proteins to their functional intramitochondrial destination have been elucidated; these pathways range from the classical amino-terminal presequence-directed pathway to pathways using internal or even carboxy-terminal targeting signals in the precursors. Recent studies have provided important insights into the structural organization of membrane-embedded preprotein translocases of mitochondria. A comparison of the different translocases reveals the existence of at least three fundamentally different mechanisms: two-pore-translocase, β-barrel switching, and transport cavities open to the lipid bilayer. In addition, translocases are physically engaged in dynamic interactions with respiratory chain complexes, metabolite transporters, quality control factors, and machineries controlling membrane morphology. Thus, mitochondrial preprotein translocases are integrated into multi-functional networks of mitochondrial and cellular machineries.
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Affiliation(s)
- Jakob D Busch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Laura F Fielden
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
| | - Nils Wiedemann
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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8
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Mahajan D, Madugula V, Lu L. Rab8 and TNPO1 are ciliary transport adaptors for GTPase Arl13b by interacting with its RVEP motif-containing ciliary targeting sequence. J Biol Chem 2023; 299:104604. [PMID: 36907439 PMCID: PMC10124946 DOI: 10.1016/j.jbc.2023.104604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 03/04/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
Arl13b, an ARF/Arl-family GTPase, is highly enriched in the cilium. Recent studies have established Arl13b as one of the most crucial regulators for ciliary organization, trafficking, and signaling. The ciliary localization of Arl13b is known to require the RVEP motif. However, its cognitive ciliary transport adaptor has been elusive. Here, by imaging the ciliary localization of truncation and point mutations, we defined the ciliary targeting sequence (CTS) of Arl13b as a C-terminal stretch of 17 amino acids containing the RVEP motif. We found Rab8-GDP, but not Rab8-GTP, and TNPO1 simultaneously and directly bind to the CTS of Arl13b in pull-down assays using cell lysates or purified recombinant proteins. Furthermore, Rab8-GDP substantially enhances the interaction between TNPO1 and CTS. Additionally, we determined that the RVEP motif is an essential element as its mutation abolishes the interaction of the CTS with Rab8-GDP and TNPO1 in pull-down and TurboID-based proximity ligation assays. Finally, knockdown of endogenous Rab8 or TNPO1 decreases the ciliary localization of endogenous Arl13b. Therefore, our results suggest Rab8 and TNPO1 might function together as a ciliary transport adaptor for Arl13b by interacting with its RVEP-containing CTS.
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Affiliation(s)
- Divyanshu Mahajan
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Viswanadh Madugula
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Lei Lu
- School of Biological Sciences, Nanyang Technological University, Singapore.
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9
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Lee J, Moon B, Lee DW, Hwang I. Translation rate underpins specific targeting of N-terminal transmembrane proteins to mitochondria. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36897023 DOI: 10.1111/jipb.13475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Protein biogenesis is a complex process, and complexity is greatly increased in eukaryotic cells through specific targeting of proteins to different organelles. To direct targeting, organellar proteins carry an organelle-specific targeting signal for recognition by organelle-specific import machinery. However, the situation is confusing for transmembrane domain (TMD)-containing signal-anchored (SA) proteins of various organelles because TMDs function as an endoplasmic reticulum (ER) targeting signal. Although ER targeting of SA proteins is well understood, how they are targeted to mitochondria and chloroplasts remains elusive. Here, we investigated how the targeting specificity of SA proteins is determined for specific targeting to mitochondria and chloroplasts. Mitochondrial targeting requires multiple motifs around and within TMDs: a basic residue and an arginine-rich region flanking the N- and C-termini of TMDs, respectively, and an aromatic residue in the C-terminal side of the TMD that specify mitochondrial targeting in an additive manner. These motifs play a role in slowing down the elongation speed during translation, thereby ensuring mitochondrial targeting in a co-translational manner. By contrast, the absence of any of these motifs individually or together causes at varying degrees chloroplast targeting that occurs in a post-translational manner.
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Affiliation(s)
- Junho Lee
- Department of Life Science, Pohang University of Science and Technology, Pohang, 790-784, South Korea
| | - Byeongho Moon
- Department of Life Science, Pohang University of Science and Technology, Pohang, 790-784, South Korea
| | - Dong Wook Lee
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, 61186, South Korea
- Department Bioenergy Science and Technology, Chonnam National University, Gwangju, 61186, South Korea
| | - Inhwan Hwang
- Department of Life Science, Pohang University of Science and Technology, Pohang, 790-784, South Korea
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10
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Kempmann A, Gensch T, Offenhäusser A, Tihaa I, Maybeck V, Balfanz S, Baumann A. The Functional Characterization of GCaMP3.0 Variants Specifically Targeted to Subcellular Domains. Int J Mol Sci 2022; 23:ijms23126593. [PMID: 35743038 PMCID: PMC9223625 DOI: 10.3390/ijms23126593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 05/31/2022] [Accepted: 06/06/2022] [Indexed: 11/16/2022] Open
Abstract
Calcium (Ca2+) ions play a pivotal role in physiology and cellular signaling. The intracellular Ca2+ concentration ([Ca2+]i) is about three orders of magnitude lower than the extracellular concentration, resulting in a steep transmembrane concentration gradient. Thus, the spatial and the temporal dynamics of [Ca2+]i are ideally suited to modulate Ca2+-mediated cellular responses to external signals. A variety of highly sophisticated methods have been developed to gain insight into cellular Ca2+ dynamics. In addition to electrophysiological measurements and the application of synthetic dyes that change their fluorescent properties upon interaction with Ca2+, the introduction and the ongoing development of genetically encoded Ca2+ indicators (GECI) opened a new era to study Ca2+-driven processes in living cells and organisms. Here, we have focused on one well-established GECI, i.e., GCaMP3.0. We have systematically modified the protein with sequence motifs, allowing localization of the sensor in the nucleus, in the mitochondrial matrix, at the mitochondrial outer membrane, and at the plasma membrane. The individual variants and a cytosolic version of GCaMP3.0 were overexpressed and purified from E. coli cells to study their biophysical properties in solution. All versions were examined to monitor Ca2+ signaling in stably transfected cell lines and in primary cortical neurons transduced with recombinant Adeno-associated viruses (rAAV). In this comparative study, we provide evidence for a robust approach to reliably trace Ca2+ signals at the (sub)-cellular level with pronounced temporal resolution.
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Affiliation(s)
- Annika Kempmann
- Institute of Biological Information Processing, IBI-1, Research Center Jülich, 52428 Jülich, Germany; (A.K.); (T.G.); (S.B.)
| | - Thomas Gensch
- Institute of Biological Information Processing, IBI-1, Research Center Jülich, 52428 Jülich, Germany; (A.K.); (T.G.); (S.B.)
| | - Andreas Offenhäusser
- Institute of Biological Information Processing, IBI-3, Research Center Jülich, 52428 Jülich, Germany; (A.O.); (I.T.); (V.M.)
| | - Irina Tihaa
- Institute of Biological Information Processing, IBI-3, Research Center Jülich, 52428 Jülich, Germany; (A.O.); (I.T.); (V.M.)
| | - Vanessa Maybeck
- Institute of Biological Information Processing, IBI-3, Research Center Jülich, 52428 Jülich, Germany; (A.O.); (I.T.); (V.M.)
| | - Sabine Balfanz
- Institute of Biological Information Processing, IBI-1, Research Center Jülich, 52428 Jülich, Germany; (A.K.); (T.G.); (S.B.)
| | - Arnd Baumann
- Institute of Biological Information Processing, IBI-1, Research Center Jülich, 52428 Jülich, Germany; (A.K.); (T.G.); (S.B.)
- Correspondence: ; Tel.: +49-2461-614014
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11
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Tan C, Wang SSH, de Nola G, Kaeser PS. Rebuilding essential active zone functions within a synapse. Neuron 2022; 110:1498-1515.e8. [PMID: 35176221 PMCID: PMC9081183 DOI: 10.1016/j.neuron.2022.01.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 12/21/2021] [Accepted: 01/24/2022] [Indexed: 01/15/2023]
Abstract
Presynaptic active zones are molecular machines that control neurotransmitter secretion. They form sites for vesicle docking and priming and couple vesicles to Ca2+ entry for release triggering. The complexity of active zone machinery has made it challenging to determine its mechanisms in release. Simultaneous knockout of the active zone proteins RIM and ELKS disrupts active zone assembly, abolishes vesicle docking, and impairs release. We here rebuild docking, priming, and Ca2+ secretion coupling in these mutants without reinstating active zone networks. Re-expression of RIM zinc fingers recruited Munc13 to undocked vesicles and rendered the vesicles release competent. Action potential triggering of release was reconstituted by docking these primed vesicles to Ca2+ channels through attaching RIM zinc fingers to CaVβ4-subunits. Our work identifies an 80-kDa β4-Zn protein that bypasses the need for megadalton-sized secretory machines, establishes that fusion competence and docking are mechanistically separable, and defines RIM zinc finger-Munc13 complexes as hubs for active zone function.
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Affiliation(s)
- Chao Tan
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Shan Shan H Wang
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Giovanni de Nola
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Pascal S Kaeser
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA.
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12
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Keren-Kaplan T, Sarić A, Ghosh S, Williamson CD, Jia R, Li Y, Bonifacino JS. RUFY3 and RUFY4 are ARL8 effectors that promote coupling of endolysosomes to dynein-dynactin. Nat Commun 2022; 13:1506. [PMID: 35314674 PMCID: PMC8938451 DOI: 10.1038/s41467-022-28952-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 02/18/2022] [Indexed: 11/10/2022] Open
Abstract
The small GTPase ARL8 associates with endolysosomes, leading to the recruitment of several effectors that couple endolysosomes to kinesins for anterograde transport along microtubules, and to tethering factors for eventual fusion with other organelles. Herein we report the identification of the RUN- and FYVE-domain-containing proteins RUFY3 and RUFY4 as ARL8 effectors that promote coupling of endolysosomes to dynein-dynactin for retrograde transport along microtubules. Using various methodologies, we find that RUFY3 and RUFY4 interact with both GTP-bound ARL8 and dynein-dynactin. In addition, we show that RUFY3 and RUFY4 promote concentration of endolysosomes in the juxtanuclear area of non-neuronal cells, and drive redistribution of endolysosomes from the axon to the soma in hippocampal neurons. The function of RUFY3 in retrograde transport contributes to the juxtanuclear redistribution of endolysosomes upon cytosol alkalinization. These studies thus identify RUFY3 and RUFY4 as ARL8-dependent, dynein-dynactin adaptors or regulators, and highlight the role of ARL8 in the control of both anterograde and retrograde endolysosome transport. Organellar transport is carefully regulated, and endolysosome localized ARL8 is important for kinesin recruitment and anterograde movement. Here, the authors show that RUFY3 and RUFY4 promote retrograde transport of endolysosomes by mediating interaction of ARL8 with dynein-dynactin.
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13
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Serrat R, Oliveira-Pinto A, Marsicano G, Pouvreau S. Imaging mitochondrial calcium dynamics in the central nervous system. J Neurosci Methods 2022; 373:109560. [PMID: 35320763 DOI: 10.1016/j.jneumeth.2022.109560] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 03/04/2022] [Accepted: 03/06/2022] [Indexed: 12/28/2022]
Abstract
Mitochondrial calcium handling is a particularly active research area in the neuroscience field, as it plays key roles in the regulation of several functions of the central nervous system, such as synaptic transmission and plasticity, astrocyte calcium signaling, neuronal activity… In the last few decades, a panel of techniques have been developed to measure mitochondrial calcium dynamics, relying mostly on photonic microscopy, and including synthetic sensors, hybrid sensors and genetically encoded calcium sensors. The goal of this review is to endow the reader with a deep knowledge of the historical and latest tools to monitor mitochondrial calcium events in the brain, as well as a comprehensive overview of the current state of the art in brain mitochondrial calcium signaling. We will discuss the main calcium probes used in the field, their mitochondrial targeting strategies, their key properties and major drawbacks. In addition, we will detail the main roles of mitochondrial calcium handling in neuronal tissues through an extended report of the recent studies using mitochondrial targeted calcium sensors in neuronal and astroglial cells, in vitro and in vivo.
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Affiliation(s)
- Roman Serrat
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1215 NeuroCentre Magendie, France; University of Bordeaux, Bordeaux 33077, France
| | - Alexandre Oliveira-Pinto
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1215 NeuroCentre Magendie, France; University of Bordeaux, Bordeaux 33077, France
| | - Giovanni Marsicano
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1215 NeuroCentre Magendie, France; University of Bordeaux, Bordeaux 33077, France
| | - Sandrine Pouvreau
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1215 NeuroCentre Magendie, France; University of Bordeaux, Bordeaux 33077, France.
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14
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Oxygen-sensitive methylation of ULK1 is required for hypoxia-induced autophagy. Nat Commun 2022; 13:1172. [PMID: 35246531 PMCID: PMC8897422 DOI: 10.1038/s41467-022-28831-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 02/10/2022] [Indexed: 02/05/2023] Open
Abstract
Hypoxia is a physiological stress that frequently occurs in solid tissues. Autophagy, a ubiquitous degradation/recycling system in eukaryotic cells, renders cells tolerant to multiple stressors. However, the mechanisms underlying autophagy initiation upon hypoxia remains unclear. Here we show that protein arginine methyltransferase 5 (PRMT5) catalyzes symmetrical dimethylation of the autophagy initiation protein ULK1 at arginine 170 (R170me2s), a modification removed by lysine demethylase 5C (KDM5C). Despite unchanged PRMT5-mediated methylation, low oxygen levels decrease KDM5C activity and cause accumulation of ULK1 R170me2s. Dimethylation of ULK1 promotes autophosphorylation at T180, a prerequisite for ULK1 activation, subsequently causing phosphorylation of Atg13 and Beclin 1, autophagosome formation, mitochondrial clearance and reduced oxygen consumption. Further, expression of a ULK1 R170K mutant impaired cell proliferation under hypoxia. This study identifies an oxygen-sensitive methylation of ULK1 with an important role in hypoxic stress adaptation by promoting autophagy induction.
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15
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Hao K, Chen Y, Yan X, Zhu X. Cilia locally synthesize proteins to sustain their ultrastructure and functions. Nat Commun 2021; 12:6971. [PMID: 34848703 PMCID: PMC8632896 DOI: 10.1038/s41467-021-27298-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 11/09/2021] [Indexed: 12/26/2022] Open
Abstract
Cilia are microtubule-based hair-like organelles propelling locomotion and extracellular liquid flow or sensing environmental stimuli. As cilia are diffusion barrier-gated subcellular compartments, their protein components are thought to come from the cell body through intraflagellar transport or diffusion. Here we show that cilia locally synthesize proteins to maintain their structure and functions. Multicilia of mouse ependymal cells are abundant in ribosomal proteins, translation initiation factors, and RNA, including 18 S rRNA and tubulin mRNA. The cilia actively generate nascent peptides, including those of tubulin. mRNA-binding protein Fmrp localizes in ciliary central lumen and appears to function in mRNA delivery into the cilia. Its depletion by RNAi impairs ciliary local translation and induces multicilia degeneration. Expression of exogenous Fmrp, but not an isoform tethered to mitochondria, rescues the degeneration defects. Therefore, local translation defects in cilia might contribute to the pathology of ciliopathies and other diseases such as Fragile X syndrome.
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Affiliation(s)
- Kai Hao
- grid.507739.f0000 0001 0061 254XState Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 320 Yueyang Road, 200031 Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Yawen Chen
- grid.507739.f0000 0001 0061 254XState Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 320 Yueyang Road, 200031 Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Xiumin Yan
- Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Institute of Early Life Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, 200092, Shanghai, China.
| | - Xueliang Zhu
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China. .,University of Chinese Academy of Sciences, 100049, Beijing, China. .,School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 310024, Hangzhou, China.
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16
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Li H, Doric Z, Berthet A, Jorgens DM, Nguyen MK, Hsieh I, Margulis J, Fang R, Debnath J, Sesaki H, Finkbeiner S, Huang E, Nakamura K. Longitudinal tracking of neuronal mitochondria delineates PINK1/Parkin-dependent mechanisms of mitochondrial recycling and degradation. SCIENCE ADVANCES 2021; 7:7/32/eabf6580. [PMID: 34362731 PMCID: PMC8346224 DOI: 10.1126/sciadv.abf6580] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 06/17/2021] [Indexed: 06/13/2023]
Abstract
Altered mitochondrial quality control and dynamics may contribute to neurodegenerative diseases, including Parkinson's disease, but we understand little about these processes in neurons. We combined time-lapse microscopy and correlative light and electron microscopy to track individual mitochondria in neurons lacking the fission-promoting protein dynamin-related protein 1 (Drp1) and delineate the kinetics of PINK1-dependent pathways of mitochondrial quality control. Depolarized mitochondria recruit Parkin to the outer mitochondrial membrane, triggering autophagosome formation, rapid lysosomal fusion, and Parkin redistribution. Unexpectedly, these mitolysosomes are dynamic and persist for hours. Some are engulfed by healthy mitochondria, and others are deacidified before bursting. In other cases, Parkin is directly recruited to the matrix of polarized mitochondria. Loss of PINK1 blocks Parkin recruitment, causes LC3 accumulation within mitochondria, and exacerbates Drp1KO toxicity to dopamine neurons. These results define a distinct neuronal mitochondrial life cycle, revealing potential mechanisms of mitochondrial recycling and signaling relevant to neurodegeneration.
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Affiliation(s)
- Huihui Li
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Zak Doric
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA 94158, USA
- Graduate Program in Neuroscience, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Amandine Berthet
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Danielle M Jorgens
- Electron Microscope Laboratory, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Mai K Nguyen
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ivy Hsieh
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Julia Margulis
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Rebecca Fang
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA 94158, USA
- Graduate Program in Neuroscience, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jayanta Debnath
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
- Graduate Program in Biomedical Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Hiromi Sesaki
- Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Steve Finkbeiner
- Graduate Program in Neuroscience, University of California, San Francisco, San Francisco, CA 94158, USA
- Graduate Program in Biomedical Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Center for Systems and Therapeutics, Gladstone Institutes, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Eric Huang
- Graduate Program in Neuroscience, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
- Graduate Program in Biomedical Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ken Nakamura
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA 94158, USA.
- Graduate Program in Neuroscience, University of California, San Francisco, San Francisco, CA 94158, USA
- Graduate Program in Biomedical Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
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17
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Drwesh L, Rapaport D. Biogenesis pathways of α-helical mitochondrial outer membrane proteins. Biol Chem 2021; 401:677-686. [PMID: 32017702 DOI: 10.1515/hsz-2019-0440] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 01/21/2020] [Indexed: 01/23/2023]
Abstract
Mitochondria harbor in their outer membrane (OM) proteins of different topologies. These proteins are encoded by the nuclear DNA, translated on cytosolic ribosomes and inserted into their target organelle by sophisticated protein import machineries. Recently, considerable insights have been accumulated on the insertion pathways of proteins into the mitochondrial OM. In contrast, little is known regarding the early cytosolic stages of their biogenesis. It is generally presumed that chaperones associate with these proteins following their synthesis in the cytosol, thereby keeping them in an import-competent conformation and preventing their aggregation and/or mis-folding and degradation. In this review, we outline the current knowledge about the biogenesis of different mitochondrial OM proteins with various topologies, and highlight the recent findings regarding their import pathways starting from early cytosolic events until their recognition on the mitochondrial surface that lead to their final insertion into the mitochondrial OM.
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Affiliation(s)
- Layla Drwesh
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
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18
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Nyitrai H, Wang SSH, Kaeser PS. ELKS1 Captures Rab6-Marked Vesicular Cargo in Presynaptic Nerve Terminals. Cell Rep 2021; 31:107712. [PMID: 32521280 PMCID: PMC7360120 DOI: 10.1016/j.celrep.2020.107712] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/07/2020] [Accepted: 05/06/2020] [Indexed: 11/28/2022] Open
Abstract
Neurons face unique transport challenges. They need to deliver cargo over long axonal distances and to many presynaptic nerve terminals. Rab GTPases are master regulators of vesicular traffic, but essential presynaptic Rabs have not been identified. Here, we find that Rab6, a Golgi-derived GTPase for constitutive secretion, associates with mobile axonal cargo and localizes to nerve terminals. ELKS1 is a stationary presynaptic protein with Golgin homology that binds to Rab6. Knockout and rescue experiments for ELKS1 and Rab6 establish that ELKS1 captures Rab6 cargo. The ELKS1-Rab6-capturing mechanism can be transferred to mitochondria by mistargeting ELKS1 or Rab6 to them. We conclude that nerve terminals have repurposed mechanisms from constitutive exocytosis for their highly regulated secretion. By employing Golgin-like mechanisms with anchored ELKS extending its coiled-coils to capture Rab6 cargo, they have spatially separated cargo capture from fusion. ELKS complexes connect to active zones and may mediate vesicle progression toward release sites.
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Affiliation(s)
- Hajnalka Nyitrai
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Shan Shan H Wang
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Pascal S Kaeser
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA.
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19
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Kowada T, Arai K, Yoshimura A, Matsui T, Kikuchi K, Mizukami S. Optical Manipulation of Subcellular Protein Translocation Using a Photoactivatable Covalent Labeling System. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Toshiyuki Kowada
- Institute of Multidisciplinary Research for Advanced Materials Tohoku University Sendai Miyagi 980-8577 Japan
- Graduate School of Life Sciences Tohoku University Sendai Miyagi 980-8577 Japan
| | - Keisuke Arai
- Graduate School of Life Sciences Tohoku University Sendai Miyagi 980-8577 Japan
| | - Akimasa Yoshimura
- Graduate School of Engineering Osaka University 2-1 Yamadaoka, Suita Osaka 565-0871 Japan
| | - Toshitaka Matsui
- Institute of Multidisciplinary Research for Advanced Materials Tohoku University Sendai Miyagi 980-8577 Japan
- Graduate School of Life Sciences Tohoku University Sendai Miyagi 980-8577 Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering Osaka University 2-1 Yamadaoka, Suita Osaka 565-0871 Japan
- Immunology Frontier Research Center Osaka University 2-1 Yamadaoka, Suita Osaka 565-0871 Japan
- Center for Quantum Information and Quantum Biology Osaka University 2-1 Yamadaoka, Suita Osaka 565-0871 Japan
| | - Shin Mizukami
- Institute of Multidisciplinary Research for Advanced Materials Tohoku University Sendai Miyagi 980-8577 Japan
- Graduate School of Life Sciences Tohoku University Sendai Miyagi 980-8577 Japan
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20
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Kowada T, Arai K, Yoshimura A, Matsui T, Kikuchi K, Mizukami S. Optical Manipulation of Subcellular Protein Translocation Using a Photoactivatable Covalent Labeling System. Angew Chem Int Ed Engl 2021; 60:11378-11383. [PMID: 33644979 DOI: 10.1002/anie.202016684] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/15/2021] [Indexed: 12/21/2022]
Abstract
The photoactivatable chemically induced dimerization (photo-CID) technique for tag-fused proteins is one of the most promising methods for regulating subcellular protein translocations and protein-protein interactions. However, light-induced covalent protein dimerization in living cells has yet to be established, despite its various advantages. Herein, we developed a photoactivatable covalent protein-labeling technology by applying a caged ligand to the BL-tag system, a covalent protein labeling system that uses mutant β-lactamase. We further developed CBHD, a caged protein dimerizer, using caged BL-tag and HaloTag ligands, and achieved light-induced protein translocation from the cytoplasm to subcellular regions. In addition, this covalent photo-CID system enabled quick protein translocation to a laser-illuminated microregion. These results indicate that the covalent photo-CID system will expand the scope of CID applications in the optical manipulation of cellular functions.
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Affiliation(s)
- Toshiyuki Kowada
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, 980-8577, Japan.,Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Keisuke Arai
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Akimasa Yoshimura
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Toshitaka Matsui
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, 980-8577, Japan.,Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Immunology Frontier Research Center, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Center for Quantum Information and Quantum Biology, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shin Mizukami
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, 980-8577, Japan.,Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan
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21
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Tan P, He L, Zhou Y. Engineering Supramolecular Organizing Centers for Optogenetic Control of Innate Immune Responses. Adv Biol (Weinh) 2021; 5:e2000147. [PMID: 34028210 PMCID: PMC8144545 DOI: 10.1002/adbi.202000147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/18/2020] [Indexed: 12/20/2022]
Abstract
The spatiotemporal organization of oligomeric protein complexes, such as the supramolecular organizing centers (SMOCs) made of MyDDosome and MAVSome, is essential for transcriptional activation of host inflammatory responses and immunometabolism. Light-inducible assembly of MyDDosome and MAVSome is presented herein to induce activation of nuclear factor-kB and type-I interferons. Engineering of SMOCs and the downstream transcription factor permits programmable and customized innate immune operations in a light-dependent manner. These synthetic molecular tools will likely enable optical and user-defined modulation of innate immunity at a high spatiotemporal resolution to facilitate mechanistic studies of distinct modes of innate immune activations and potential intervention of immune disorders and cancer.
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Affiliation(s)
- Peng Tan
- Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX, 77030, USA
| | - Lian He
- Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX, 77030, USA
| | - Yubin Zhou
- Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX, 77030, USA
- Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, 77030, USA
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22
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Lee CQE, Kerouanton B, Chothani S, Zhang S, Chen Y, Mantri CK, Hock DH, Lim R, Nadkarni R, Huynh VT, Lim D, Chew WL, Zhong FL, Stroud DA, Schafer S, Tergaonkar V, St John AL, Rackham OJL, Ho L. Coding and non-coding roles of MOCCI (C15ORF48) coordinate to regulate host inflammation and immunity. Nat Commun 2021; 12:2130. [PMID: 33837217 PMCID: PMC8035321 DOI: 10.1038/s41467-021-22397-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/10/2021] [Indexed: 02/01/2023] Open
Abstract
Mito-SEPs are small open reading frame-encoded peptides that localize to the mitochondria to regulate metabolism. Motivated by an intriguing negative association between mito-SEPs and inflammation, here we screen for mito-SEPs that modify inflammatory outcomes and report a mito-SEP named "Modulator of cytochrome C oxidase during Inflammation" (MOCCI) that is upregulated during inflammation and infection to promote host-protective resolution. MOCCI, a paralog of the NDUFA4 subunit of cytochrome C oxidase (Complex IV), replaces NDUFA4 in Complex IV during inflammation to lower mitochondrial membrane potential and reduce ROS production, leading to cyto-protection and dampened immune response. The MOCCI transcript also generates miR-147b, which targets the NDUFA4 mRNA with similar immune dampening effects as MOCCI, but simultaneously enhances RIG-I/MDA-5-mediated viral immunity. Our work uncovers a dual-component pleiotropic regulation of host inflammation and immunity by MOCCI (C15ORF48) for safeguarding the host during infection and inflammation.
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Affiliation(s)
- Cheryl Q. E. Lee
- grid.414735.00000 0004 0367 4692Institute of Medical Biology, A*STAR, Singapore, Singapore
| | - Baptiste Kerouanton
- grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Program in Cardiovascular and Metabolic Disorders, Singapore, Singapore
| | - Sonia Chothani
- grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Program in Cardiovascular and Metabolic Disorders, Singapore, Singapore
| | - Shan Zhang
- grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Program in Cardiovascular and Metabolic Disorders, Singapore, Singapore
| | - Ying Chen
- grid.418812.60000 0004 0620 9243Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Chinmay Kumar Mantri
- grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Program in Emerging Infectious Diseases, Singapore, Singapore
| | - Daniella Helena Hock
- grid.1008.90000 0001 2179 088XDepartment of Biochemistry and Molecular Biology, The Bio21 Molecular Science & Biotechnology Institute, University of Melbourne, Melbourne, VIC Australia
| | - Radiance Lim
- grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Program in Cardiovascular and Metabolic Disorders, Singapore, Singapore
| | - Rhea Nadkarni
- grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Program in Cardiovascular and Metabolic Disorders, Singapore, Singapore
| | - Vinh Thang Huynh
- grid.418812.60000 0004 0620 9243Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore ,grid.59025.3b0000 0001 2224 0361Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
| | - Daryl Lim
- grid.418377.e0000 0004 0620 715XGenome Institute Singapore, A*STAR, Singapore, Singapore
| | - Wei Leong Chew
- grid.418377.e0000 0004 0620 715XGenome Institute Singapore, A*STAR, Singapore, Singapore
| | - Franklin L. Zhong
- grid.59025.3b0000 0001 2224 0361Nanyang Technological University, Skin Diseases and Wound Repair Program, Singapore, Singapore ,grid.185448.40000 0004 0637 0221Skin Research Institute of Singapore, A*STAR, Singapore, Singapore
| | - David Arthur Stroud
- grid.1008.90000 0001 2179 088XDepartment of Biochemistry and Molecular Biology, The Bio21 Molecular Science & Biotechnology Institute, University of Melbourne, Melbourne, VIC Australia
| | - Sebastian Schafer
- grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Program in Cardiovascular and Metabolic Disorders, Singapore, Singapore ,grid.419385.20000 0004 0620 9905National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore
| | - Vinay Tergaonkar
- grid.418812.60000 0004 0620 9243Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ashley L. St John
- grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Program in Emerging Infectious Diseases, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore ,grid.189509.c0000000100241216Department of Pathology, Duke University Medical Center, Durham, NC USA
| | - Owen J. L. Rackham
- grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Program in Cardiovascular and Metabolic Disorders, Singapore, Singapore
| | - Lena Ho
- grid.414735.00000 0004 0367 4692Institute of Medical Biology, A*STAR, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Program in Cardiovascular and Metabolic Disorders, Singapore, Singapore ,grid.418812.60000 0004 0620 9243Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
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Avellaneda J, Rodier C, Daian F, Brouilly N, Rival T, Luis NM, Schnorrer F. Myofibril and mitochondria morphogenesis are coordinated by a mechanical feedback mechanism in muscle. Nat Commun 2021; 12:2091. [PMID: 33828099 PMCID: PMC8027795 DOI: 10.1038/s41467-021-22058-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 02/23/2021] [Indexed: 02/01/2023] Open
Abstract
Complex animals build specialised muscles to match specific biomechanical and energetic needs. Hence, composition and architecture of sarcomeres and mitochondria are muscle type specific. However, mechanisms coordinating mitochondria with sarcomere morphogenesis are elusive. Here we use Drosophila muscles to demonstrate that myofibril and mitochondria morphogenesis are intimately linked. In flight muscles, the muscle selector spalt instructs mitochondria to intercalate between myofibrils, which in turn mechanically constrain mitochondria into elongated shapes. Conversely in cross-striated leg muscles, mitochondria networks surround myofibril bundles, contacting myofibrils only with thin extensions. To investigate the mechanism causing these differences, we manipulated mitochondrial dynamics and found that increased mitochondrial fusion during myofibril assembly prevents mitochondrial intercalation in flight muscles. Strikingly, this causes the expression of cross-striated muscle specific sarcomeric proteins. Consequently, flight muscle myofibrils convert towards a partially cross-striated architecture. Together, these data suggest a biomechanical feedback mechanism downstream of spalt synchronizing mitochondria with myofibril morphogenesis.
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Affiliation(s)
- Jerome Avellaneda
- Aix Marseille University, CNRS, IBDM, Turing Center for Living Systems, Marseille, France
| | - Clement Rodier
- Aix Marseille University, CNRS, IBDM, Turing Center for Living Systems, Marseille, France
| | - Fabrice Daian
- Aix Marseille University, CNRS, IBDM, Turing Center for Living Systems, Marseille, France
| | - Nicolas Brouilly
- Aix Marseille University, CNRS, IBDM, Turing Center for Living Systems, Marseille, France
| | - Thomas Rival
- Aix Marseille University, CNRS, IBDM, Turing Center for Living Systems, Marseille, France
| | - Nuno Miguel Luis
- Aix Marseille University, CNRS, IBDM, Turing Center for Living Systems, Marseille, France.
| | - Frank Schnorrer
- Aix Marseille University, CNRS, IBDM, Turing Center for Living Systems, Marseille, France.
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24
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Wojcik S, Kriechbaumer V. Go your own way: membrane-targeting sequences. PLANT PHYSIOLOGY 2021; 185:608-618. [PMID: 33822216 PMCID: PMC8133554 DOI: 10.1093/plphys/kiaa058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/19/2020] [Indexed: 05/05/2023]
Abstract
Membrane-targeting sequences, connected targeting mechanisms, and co-factors orchestrate primary targeting of proteins to membranes.
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Affiliation(s)
- Stefan Wojcik
- Plant Cell Biology, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Verena Kriechbaumer
- Plant Cell Biology, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
- Author for communication: (V.K.)
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25
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Chen YC, Huang HR, Hsu CH, Ou CY. CRMP/UNC-33 organizes microtubule bundles for KIF5-mediated mitochondrial distribution to axon. PLoS Genet 2021; 17:e1009360. [PMID: 33571181 PMCID: PMC7904166 DOI: 10.1371/journal.pgen.1009360] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 02/24/2021] [Accepted: 11/11/2020] [Indexed: 12/13/2022] Open
Abstract
Neurons are highly specialized cells with polarized cellular processes and subcellular domains. As vital organelles for neuronal functions, mitochondria are distributed by microtubule-based transport systems. Although the essential components of mitochondrial transport including motors and cargo adaptors are identified, it is less clear how mitochondrial distribution among somato-dendritic and axonal compartment is regulated. Here, we systematically study mitochondrial motors, including four kinesins, KIF5, KIF17, KIF1, KLP-6, and dynein, and transport regulators in C. elegans PVD neurons. Among all these motors, we found that mitochondrial export from soma to neurites is mainly mediated by KIF5/UNC-116. Interestingly, UNC-116 is especially important for axonal mitochondria, while dynein removes mitochondria from all plus-end dendrites and the axon. We surprisingly found one mitochondrial transport regulator for minus-end dendritic compartment, TRAK-1, and two mitochondrial transport regulators for axonal compartment, CRMP/UNC-33 and JIP3/UNC-16. While JIP3/UNC-16 suppresses axonal mitochondria, CRMP/UNC-33 is critical for axonal mitochondria; nearly no axonal mitochondria present in unc-33 mutants. We showed that UNC-33 is essential for organizing the population of UNC-116-associated microtubule bundles, which are tracks for mitochondrial trafficking. Disarrangement of these tracks impedes mitochondrial transport to the axon. In summary, we identified a compartment-specific transport regulation of mitochondria by UNC-33 through organizing microtubule tracks for different kinesin motors other than microtubule polarity.
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Affiliation(s)
- Ying-Chun Chen
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hao-Ru Huang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chia-Hao Hsu
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chan-Yen Ou
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
- * E-mail:
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26
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Gupta A, Becker T. Mechanisms and pathways of mitochondrial outer membrane protein biogenesis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148323. [PMID: 33035511 DOI: 10.1016/j.bbabio.2020.148323] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/26/2020] [Accepted: 09/29/2020] [Indexed: 11/29/2022]
Abstract
Outer membrane proteins integrate mitochondria into the cellular environment. They warrant exchange of small molecules like metabolites and ions, transport proteins into mitochondria, form contact sites to other cellular organelles for lipid exchange, constitute a signaling platform for apoptosis and inflammation and mediate organelle fusion and fission. The outer membrane contains two types of integral membrane proteins. Proteins with a transmembrane β-barrel structure and proteins with a single or multiple α-helical membrane spans. All outer membrane proteins are produced on cytosolic ribosomes and imported into the target organelle. Precursors of β-barrel and α-helical proteins are transported into the outer membrane via distinct import routes. The translocase of the outer membrane (TOM complex) transports β-barrel precursors across the outer membrane and the sorting and assembly machinery (SAM complex) inserts them into the target membrane. The mitochondrial import (MIM) complex constitutes the major integration site for α-helical embedded proteins. The import of some MIM-substrates involves TOM receptors, while others are imported in a TOM-independent manner. Remarkably, TOM, SAM and MIM complexes dynamically interact to import a large set of different proteins and to coordinate their assembly into protein complexes. Thus, protein import into the mitochondrial outer membrane involves a dynamic platform of protein translocases.
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Affiliation(s)
- Arushi Gupta
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
| | - Thomas Becker
- Institut für Biochemie und Molekularbiologie, Medizinische Fakultät, Universität Bonn, Nussallee 11, 53115 Bonn, Germany.
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27
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Mitochondrial peptide BRAWNIN is essential for vertebrate respiratory complex III assembly. Nat Commun 2020; 11:1312. [PMID: 32161263 PMCID: PMC7066179 DOI: 10.1038/s41467-020-14999-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 02/14/2020] [Indexed: 11/08/2022] Open
Abstract
The emergence of small open reading frame (sORF)-encoded peptides (SEPs) is rapidly expanding the known proteome at the lower end of the size distribution. Here, we show that the mitochondrial proteome, particularly the respiratory chain, is enriched for small proteins. Using a prediction and validation pipeline for SEPs, we report the discovery of 16 endogenous nuclear encoded, mitochondrial-localized SEPs (mito-SEPs). Through functional prediction, proteomics, metabolomics and metabolic flux modeling, we demonstrate that BRAWNIN, a 71 a.a. peptide encoded by C12orf73, is essential for respiratory chain complex III (CIII) assembly. In human cells, BRAWNIN is induced by the energy-sensing AMPK pathway, and its depletion impairs mitochondrial ATP production. In zebrafish, Brawnin deletion causes complete CIII loss, resulting in severe growth retardation, lactic acidosis and early death. Our findings demonstrate that BRAWNIN is essential for vertebrate oxidative phosphorylation. We propose that mito-SEPs are an untapped resource for essential regulators of oxidative metabolism.
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28
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Farrants H, Tarnawski M, Müller TG, Otsuka S, Hiblot J, Koch B, Kueblbeck M, Kräusslich HG, Ellenberg J, Johnsson K. Chemogenetic Control of Nanobodies. Nat Methods 2020; 17:279-282. [PMID: 32066961 DOI: 10.1038/s41592-020-0746-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 12/01/2019] [Accepted: 01/15/2020] [Indexed: 12/30/2022]
Abstract
We introduce an engineered nanobody whose affinity to green fluorescent protein (GFP) can be switched on and off with small molecules. By controlling the cellular localization of GFP fusion proteins, the engineered nanobody allows interrogation of their roles in basic biological processes, an approach that should be applicable to numerous previously described GFP fusions. We also outline how the binding affinities of other nanobodies can be controlled by small molecules.
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Affiliation(s)
- Helen Farrants
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany.,Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Miroslaw Tarnawski
- Protein Expression and Characterization Facility, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Thorsten G Müller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Shotaro Otsuka
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Max Perutz Labs, a joint venture of the University of Vienna and the Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Julien Hiblot
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Birgit Koch
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Moritz Kueblbeck
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany. .,Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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29
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The C Protein Is Recruited to Measles Virus Ribonucleocapsids by the Phosphoprotein. J Virol 2020; 94:JVI.01733-19. [PMID: 31748390 DOI: 10.1128/jvi.01733-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/08/2019] [Indexed: 11/20/2022] Open
Abstract
Measles virus (MeV), like all viruses of the order Mononegavirales, utilizes a complex consisting of genomic RNA, nucleoprotein, the RNA-dependent RNA polymerase, and a polymerase cofactor, the phosphoprotein (P), for transcription and replication. We previously showed that a recombinant MeV that does not express another viral protein, C, has severe transcription and replication deficiencies, including a steeper transcription gradient than the parental virus and generation of defective interfering RNA. This virus is attenuated in vitro and in vivo However, how the C protein operates and whether it is a component of the replication complex remained unclear. Here, we show that C associates with the ribonucleocapsid and forms a complex that can be purified by immunoprecipitation or ultracentrifugation. In the presence of detergent, the C protein is retained on purified ribonucleocapsids less efficiently than the P protein and the polymerase. The C protein is recruited to the ribonucleocapsid through its interaction with the P protein, as shown by immunofluorescence microscopy of cells expressing different combinations of viral proteins and by split luciferase complementation assays. Forty amino-terminal C protein residues are dispensable for the interaction with P, and the carboxyl-terminal half of P is sufficient for the interaction with C. Thus, the C protein, rather than being an "accessory" protein as qualified in textbooks so far, is a ribonucleocapsid-associated protein that interacts with P, thereby increasing replication accuracy and processivity of the polymerase complex.IMPORTANCE Replication of negative-strand RNA viruses relies on two components: a helical ribonucleocapsid and an RNA-dependent RNA polymerase composed of a catalytic subunit, the L protein, and a cofactor, the P protein. We show that the measles virus (MeV) C protein is an additional component of the replication complex. We provide evidence that the C protein is recruited to the ribonucleocapsid by the P protein and map the interacting segments of both C and P proteins. We conclude that the primary function of MeV C is to improve polymerase processivity and accuracy, rather than uniquely to antagonize the type I interferon response. Since most viruses of the Paramyxoviridae family express C proteins, their primary function may be conserved.
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30
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Ashrafi G, de Juan-Sanz J, Farrell RJ, Ryan TA. Molecular Tuning of the Axonal Mitochondrial Ca 2+ Uniporter Ensures Metabolic Flexibility of Neurotransmission. Neuron 2019; 105:678-687.e5. [PMID: 31862210 DOI: 10.1016/j.neuron.2019.11.020] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/16/2019] [Accepted: 11/12/2019] [Indexed: 01/08/2023]
Abstract
The brain is a vulnerable metabolic organ and must adapt to different fuel conditions to sustain function. Nerve terminals are a locus of this vulnerability, but how they regulate ATP synthesis as fuel conditions vary is unknown. We show that synapses can switch from glycolytic to oxidative metabolism, but to do so, they rely on activity-driven presynaptic mitochondrial Ca2+ uptake to accelerate ATP production. We demonstrate that, whereas mitochondrial Ca2+ uptake requires elevated extramitochondrial Ca2+ in non-neuronal cells, axonal mitochondria readily take up Ca2+ in response to small changes in external Ca2+. We identified the brain-specific protein MICU3 as a critical driver of this tuning of Ca2+ sensitivity. Ablation of MICU3 renders axonal mitochondria similar to non-neuronal mitochondria, prevents acceleration of local ATP synthesis, and impairs presynaptic function under oxidative conditions. Thus, presynaptic mitochondria rely on MICU3 to facilitate mitochondrial Ca2+ uptake during activity and achieve metabolic flexibility.
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Affiliation(s)
- Ghazaleh Ashrafi
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jaime de Juan-Sanz
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ryan J Farrell
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA; David Rockefeller Graduate Program, Rockefeller University, New York, NY 10065, USA
| | - Timothy A Ryan
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA.
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31
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An YA, Crewe C, Asterholm IW, Sun K, Chen S, Zhang F, Shao M, Funcke JB, Zhang Z, Straub L, Yoshino J, Klein S, Kusminski CM, Scherer PE. Dysregulation of Amyloid Precursor Protein Impairs Adipose Tissue Mitochondrial Function and Promotes Obesity. Nat Metab 2019; 1:1243-1257. [PMID: 31984308 PMCID: PMC6980705 DOI: 10.1038/s42255-019-0149-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/07/2019] [Indexed: 12/22/2022]
Abstract
Mitochondrial function in white adipose tissue (WAT) is an important yet understudied aspect in adipocyte biology. Here, we report a role for amyloid precursor protein (APP) in compromising WAT mitochondrial function through a high-fat diet (HFD)-induced, unconventional mis-localization to mitochondria that further promotes obesity. In humans and mice, obese conditions significantly induce APP production in WAT and its enrichment in mitochondria. Mechanistically, a HFD-induced dysregulation of signal recognition particle subunit 54c is responsible for the mis-targeting of APP to adipocyte mitochondria. Mis-localized APP blocks the protein import machinery, leading to mitochondrial dysfunction in WAT. Adipocyte-specific and mitochondria-targeted APP overexpressing mice display increased body mass and reduced insulin sensitivity, along with dysfunctional WAT due to a dramatic hypertrophic program in adipocytes. Elimination of adipocyte APP rescues HFD-impaired mitochondrial function with significant protection from weight gain and systemic metabolic deficiency. Our data highlights an important role of APP in modulating WAT mitochondrial function and obesity-associated metabolic dysfunction.
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Affiliation(s)
- Yu A An
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Clair Crewe
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ingrid Wernstedt Asterholm
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Institute of Neuroscience and Physiology (Metabolic Physiology), Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Kai Sun
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Metabolic and Degenerative Diseases, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Shiuhwei Chen
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Fang Zhang
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Fundus Disease, Shanghai, China
| | - Mengle Shao
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jan-Bernd Funcke
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Zhuzhen Zhang
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Leon Straub
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jun Yoshino
- Center for Human Nutrition, Washington University School of Medicine, St. Louis, MO, USA
| | - Samuel Klein
- Center for Human Nutrition, Washington University School of Medicine, St. Louis, MO, USA
| | - Christine M Kusminski
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Philipp E Scherer
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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32
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Niu K, Fang H, Chen Z, Zhu Y, Tan Q, Wei D, Li Y, Balajee AS, Zhao Y. USP33 deubiquitinates PRKN/parkin and antagonizes its role in mitophagy. Autophagy 2019; 16:724-734. [PMID: 31432739 DOI: 10.1080/15548627.2019.1656957] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
PRKN/parkin activation through phosphorylation of its ubiquitin and ubiquitin-like domain by PINK1 is critical in mitophagy induction for eliminating the damaged mitochondria. Deubiquitinating enzymes (DUBs) functionally reversing PRKN ubiquitination are critical in controlling the magnitude of PRKN-mediated mitophagy process. However, potential DUBs that directly target PRKN and antagonize its pro-mitophagy effect remains to be identified and characterized. Here, we demonstrated that USP33/VDU1 is localized at the outer membrane of mitochondria and serves as a PRKN DUB through their interaction. Cellular and in vitro assays illustrated that USP33 deubiquitinates PRKN in a DUB activity-dependent manner. USP33 prefers to remove K6, K11, K48 and K63-linked ubiquitin conjugates from PRKN, and deubiquitinates PRKN mainly at Lys435. Mutation of this site leads to a significantly decreased level of K63-, but not K48-linked PRKN ubiquitination. USP33 deficiency enhanced both K48- and K63-linked PRKN ubiquitination, but only K63-linked PRKN ubiquitination was significantly increased under mitochondrial depolarization. Further, USP33 knockdown increased both PRKN protein stabilization and its translocation to depolarized mitochondria leading to the enhancement of mitophagy. Moreover, USP33 silencing protects SH-SY5Y human neuroblastoma cells from the neurotoxin MPTP-induced apoptotic cell death. Our findings convincingly demonstrate that USP33 is a novel PRKN deubiquitinase antagonizing its regulatory roles in mitophagy and SH-SY5Y neuron-like cell survival. Thus, USP33 inhibition may represents an attractive new therapeutic strategy for PD patients.Abbreviations: CCCP: carbonyl cyanide 3-chlorophenylhydrazone; DUB: deubiquitinating enzymes; MPTP: 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine; OMM: outer mitochondrial membrane; PD: Parkinson disease; PINK1: PTEN induced kinase 1; PRKN/PARK2: parkin RBR E3 ubiquitin protein ligase; ROS: reactive oxygen species; TM: transmembrane; Ub: ubiquitin; UBA1: ubiquitin like modifier activating enzyme 1; UBE2L3/UbcH7: ubiquitin conjugating enzyme E2 L3; USP33: ubiquitin specific peptidase 33; WT: wild type.
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Affiliation(s)
- Kaifeng Niu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hongbo Fang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Zixiang Chen
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuqi Zhu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qunsong Tan
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Di Wei
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yueyang Li
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Adayabalam S Balajee
- REAC/TS, Oak Ridge Associated Universities, Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Yongliang Zhao
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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33
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MacDonald JA, Bothun AM, Annis SN, Sheehan H, Ray S, Gao Y, Ivanov AR, Khrapko K, Tilly JL, Woods DC. A nanoscale, multi-parametric flow cytometry-based platform to study mitochondrial heterogeneity and mitochondrial DNA dynamics. Commun Biol 2019; 2:258. [PMID: 31312727 PMCID: PMC6624292 DOI: 10.1038/s42003-019-0513-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 06/18/2019] [Indexed: 12/27/2022] Open
Abstract
Mitochondria are well-characterized regarding their function in both energy production and regulation of cell death; however, the heterogeneity that exists within mitochondrial populations is poorly understood. Typically analyzed as pooled samples comprised of millions of individual mitochondria, there is little information regarding potentially different functionality across subpopulations of mitochondria. Herein we present a new methodology to analyze mitochondria as individual components of a complex and heterogeneous network, using a nanoscale and multi-parametric flow cytometry-based platform. We validate the platform using multiple downstream assays, including electron microscopy, ATP generation, quantitative mass-spectrometry proteomic profiling, and mtDNA analysis at the level of single organelles. These strategies allow robust analysis and isolation of mitochondrial subpopulations to more broadly elucidate the underlying complexities of mitochondria as these organelles function collectively within a cell.
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Affiliation(s)
- Julie A. MacDonald
- Department of Biology, Laboratory of Aging and Infertility Research, Northeastern University, Boston, MA 02115 USA
| | - Alisha M. Bothun
- Department of Biology, Laboratory of Aging and Infertility Research, Northeastern University, Boston, MA 02115 USA
| | - Sofia N. Annis
- Department of Biology, Laboratory of Aging and Infertility Research, Northeastern University, Boston, MA 02115 USA
| | - Hannah Sheehan
- Department of Biology, Laboratory of Aging and Infertility Research, Northeastern University, Boston, MA 02115 USA
| | - Somak Ray
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115 USA
- Barnett Institute for Chemical and Biological Analysis, Northeastern University, Boston, MA 02115 USA
| | - Yuanwei Gao
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115 USA
- Barnett Institute for Chemical and Biological Analysis, Northeastern University, Boston, MA 02115 USA
| | - Alexander R. Ivanov
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115 USA
- Barnett Institute for Chemical and Biological Analysis, Northeastern University, Boston, MA 02115 USA
| | - Konstantin Khrapko
- Department of Biology, Laboratory of Aging and Infertility Research, Northeastern University, Boston, MA 02115 USA
| | - Jonathan L. Tilly
- Department of Biology, Laboratory of Aging and Infertility Research, Northeastern University, Boston, MA 02115 USA
| | - Dori C. Woods
- Department of Biology, Laboratory of Aging and Infertility Research, Northeastern University, Boston, MA 02115 USA
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Kitamata M, Hanawa-Suetsugu K, Maruyama K, Suetsugu S. Membrane-Deformation Ability of ANKHD1 Is Involved in the Early Endosome Enlargement. iScience 2019; 17:101-118. [PMID: 31255983 PMCID: PMC6606961 DOI: 10.1016/j.isci.2019.06.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 03/22/2019] [Accepted: 06/12/2019] [Indexed: 02/06/2023] Open
Abstract
Ankyrin-repeat domains (ARDs) are conserved in large numbers of proteins. ARDs are composed of various numbers of ankyrin repeats (ANKs). ARDs often adopt curved structures reminiscent of the Bin-Amphiphysin-Rvs (BAR) domain, which is the dimeric scaffold for membrane tubulation. BAR domains sometimes have amphipathic helices for membrane tubulation and vesiculation. However, it is unclear whether ARD-containing proteins exhibit similar membrane deformation properties. We found that the ARD of ANK and KH domain-containing protein 1 (ANKHD1) dimerize and deform membranes into tubules and vesicles. Among 25 ANKs of ANKHD1, the first 15 ANKs can form a dimer and the latter 10 ANKs enable membrane tubulation and vesiculation through an adjacent amphipathic helix and a predicted curved structure with a positively charged surface, analogous to BAR domains. Knockdown and localization of ANKHD1 suggested its involvement in the negative regulation of early endosome enlargement owing to its membrane vesiculation. ANKHD1 is a large protein of 270 kDa, containing 25 ankyrin repeats ANKHD1 generates membrane tubules and vesicles by its ankyrin-repeat domain (ARD). The ARD has an amphipathic helix and a predicted curved structure, like BAR domains ANKHD1 negatively regulates early endosome enlargement by its vesiculation ability
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Affiliation(s)
- Manabu Kitamata
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Kyoko Hanawa-Suetsugu
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Kohei Maruyama
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Shiro Suetsugu
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan.
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35
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Reversible association with motor proteins (RAMP): A streptavidin-based method to manipulate organelle positioning. PLoS Biol 2019; 17:e3000279. [PMID: 31100061 PMCID: PMC6542540 DOI: 10.1371/journal.pbio.3000279] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 05/30/2019] [Accepted: 05/03/2019] [Indexed: 01/18/2023] Open
Abstract
We report the development and characterization of a method, named reversible association with motor proteins (RAMP), for manipulation of organelle positioning within the cytoplasm. RAMP consists of coexpressing in cultured cells (i) an organellar protein fused to the streptavidin-binding peptide (SBP) and (ii) motor, neck, and coiled-coil domains from a plus-end-directed or minus-end-directed kinesin fused to streptavidin. The SBP-streptavidin interaction drives accumulation of organelles at the plus or minus end of microtubules, respectively. Importantly, competition of the streptavidin-SBP interaction by the addition of biotin to the culture medium rapidly dissociates the motor construct from the organelle, allowing restoration of normal patterns of organelle transport and distribution. A distinctive feature of this method is that organelles initially accumulate at either end of the microtubule network in the initial state and are subsequently released from this accumulation, allowing analyses of the movement of a synchronized population of organelles by endogenous motors.
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36
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Ackerman CM, Weber PK, Xiao T, Thai B, Kuo TJ, Zhang E, Pett-Ridge J, Chang CJ. Multimodal LA-ICP-MS and nanoSIMS imaging enables copper mapping within photoreceptor megamitochondria in a zebrafish model of Menkes disease. Metallomics 2018; 10:474-485. [PMID: 29507920 DOI: 10.1039/c7mt00349h] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Copper is essential for eukaryotic life, and animals must acquire this nutrient through the diet and distribute it to cells and organelles for proper function of biological targets. Indeed, mutations in the central copper exporter ATP7A contribute to a spectrum of diseases, including Menkes disease, with symptoms ranging from neurodegeneration to lax connective tissue. As such, a better understanding of the fundamental impacts of ATP7A mutations on in vivo copper distributions is of relevance to those affected by these diseases. Here we combine metal imaging and optical imaging techniques at a variety of spatial resolutions to identify tissues and structures with altered copper levels in the Calamitygw71 zebrafish model of Menkes disease. Rapid profiling of tissue slices with LA-ICP-MS identified reduced copper levels in the brain, neuroretina, and liver of Menkes fish compared to control specimens. High resolution nanoSIMS imaging of the neuroretina, combined with electron and confocal microscopies, identified the megamitochondria of photoreceptors as loci of copper accumulation in wildtype fish, with lower levels of megamitochondrial copper observed in Calamitygw71 zebrafish. Interestingly, this localized copper decrease does not result in impaired photoreceptor development or altered megamitochondrial morphology, suggesting the prioritization of copper at sufficient levels for maintaining essential mitochondrial functions. Together, these data establish the Calamitygw71 zebrafish as an optically transparent in vivo model for the study of neural copper misregulation, illuminate a role for the ATP7A copper exporter in trafficking copper to the neuroretina, and highlight the utility of combining multiple imaging techniques for studying metals in whole organism settings with spatial resolution.
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Affiliation(s)
- Cheri M Ackerman
- Department of Chemistry, University of California, Berkeley, California, USA.
| | - Peter K Weber
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California, USA.
| | - Tong Xiao
- Department of Chemistry, University of California, Berkeley, California, USA. and Howard Hughes Medical Institute, University of California, Berkeley, California, USA
| | - Bao Thai
- Department of Chemistry, University of California, Berkeley, California, USA.
| | - Tiffani J Kuo
- Department of Chemistry, University of California, Berkeley, California, USA.
| | - Emily Zhang
- Department of Chemistry, University of California, Berkeley, California, USA.
| | - Jennifer Pett-Ridge
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California, USA.
| | - Christopher J Chang
- Department of Chemistry, University of California, Berkeley, California, USA. and Howard Hughes Medical Institute, University of California, Berkeley, California, USA and Department of Molecular and Cellular Biology, University of California, Berkeley, California, USA and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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37
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O'Banion CP, Priestman MA, Hughes RM, Herring LE, Capuzzi SJ, Lawrence DS. Design and Profiling of a Subcellular Targeted Optogenetic cAMP-Dependent Protein Kinase. Cell Chem Biol 2018; 25:100-109.e8. [PMID: 29104065 PMCID: PMC5777159 DOI: 10.1016/j.chembiol.2017.09.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/21/2017] [Accepted: 09/27/2017] [Indexed: 11/30/2022]
Abstract
Although the cAMP-dependent protein kinase (PKA) is ubiquitously expressed, it is sequestered at specific subcellular locations throughout the cell, thereby resulting in compartmentalized cellular signaling that triggers site-specific behavioral phenotypes. We developed a three-step engineering strategy to construct an optogenetic PKA (optoPKA) and demonstrated that, upon illumination, optoPKA migrates to specified intracellular sites. Furthermore, we designed intracellular spatially segregated reporters of PKA activity and confirmed that optoPKA phosphorylates these reporters in a light-dependent fashion. Finally, proteomics experiments reveal that light activation of optoPKA results in the phosphorylation of known endogenous PKA substrates as well as potential novel substrates.
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Affiliation(s)
- Colin P O'Banion
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Melanie A Priestman
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Robert M Hughes
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Chemistry; East Carolina University, Greenville, NC 27858, USA
| | - Laura E Herring
- UNC Proteomics Core, Department of Pharmacology, UNC School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Stephen J Capuzzi
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA
| | - David S Lawrence
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA.
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38
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Harmon M, Larkman P, Hardingham G, Jackson M, Skehel P. A Bi-fluorescence complementation system to detect associations between the Endoplasmic reticulum and mitochondria. Sci Rep 2017; 7:17467. [PMID: 29234100 PMCID: PMC5727038 DOI: 10.1038/s41598-017-17278-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 11/22/2017] [Indexed: 12/15/2022] Open
Abstract
Close contacts between the endoplasmic reticulum membrane and the mitochondrial outer membrane facilitate efficient transfer of lipids between the organelles and coordinate Ca2+ signalling and stress responses. Changes to this coupling is associated with a number of metabolic disorders and neurodegenerative diseases including Alzheimer’s, Parkinson’s and motor neuron disease. The distance between the two membranes at regions of close apposition is below the resolution of conventional light microscopy, which makes analysis of these interactions challenging. Here we describe a new bifluorescence complementation (BiFC) method that labels a subset of ER-mitochondrial associations in fixed and living cells. The total number of ER-mitochondria associations detected by this approach increases in response to tunicamycin-induced ER stress, serum deprivation or reduced levels of mitofusin 2 (MFN2). This method will facilitate the analysis of dynamic interactions between the ER and mitochondrial membranes.
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Affiliation(s)
- Mark Harmon
- Centre for Integrative Physiology, Euan MacDonald Centre for Motor Neurone Disease Research, The University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Philip Larkman
- Centre for Integrative Physiology, Euan MacDonald Centre for Motor Neurone Disease Research, The University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Giles Hardingham
- UK Dementia Research Institute at the University of Edinburgh, Edinburgh Medical School, Edinburgh EH8 9XD, UK
| | - Mandy Jackson
- Centre for Integrative Physiology, Euan MacDonald Centre for Motor Neurone Disease Research, The University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Paul Skehel
- Centre for Integrative Physiology, Euan MacDonald Centre for Motor Neurone Disease Research, The University of Edinburgh, Edinburgh EH8 9XD, UK.
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39
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Shimoji M, Figueroa RA, Neve E, Maksel D, Imreh G, Morgenstern R, Hallberg E. Molecular basis for the dual subcellular distribution of microsomal glutathione transferase 1. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:238-244. [DOI: 10.1016/j.bbamem.2016.11.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 11/11/2016] [Accepted: 11/28/2016] [Indexed: 02/07/2023]
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40
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Bruggisser J, Käser S, Mani J, Schneider A. Biogenesis of a Mitochondrial Outer Membrane Protein in Trypanosoma brucei: TARGETING SIGNAL AND DEPENDENCE ON A UNIQUE BIOGENESIS FACTOR. J Biol Chem 2017; 292:3400-3410. [PMID: 28100781 DOI: 10.1074/jbc.m116.755983] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 01/16/2017] [Indexed: 11/06/2022] Open
Abstract
The mitochondrial outer membrane (OM) contains single and multiple membrane-spanning proteins that need to contain signals that ensure correct targeting and insertion into the OM. The biogenesis of such proteins has so far essentially only been studied in yeast and related organisms. Here we show that POMP10, an OM protein of the early diverging protozoan Trypanosoma brucei, is signal-anchored. Transgenic cells expressing variants of POMP10 fused to GFP demonstrate that the N-terminal membrane-spanning domain flanked by a few positively charged or neutral residues is both necessary and sufficient for mitochondrial targeting. Carbonate extraction experiments indicate that although the presence of neutral instead of positively charged residues did not interfere with POMP10 localization, it weakened its interaction with the OM. Expression of GFP-tagged POMP10 in inducible RNAi cell lines shows that its mitochondrial localization depends on pATOM36 but does not require Sam50 or ATOM40, the trypanosomal analogue of the Tom40 import pore. pATOM36 is a kinetoplastid-specific OM protein that has previously been implicated in the assembly of OM proteins and in mitochondrial DNA inheritance. In summary, our results show that although the features of the targeting signal in signal-anchored proteins are widely conserved, the protein machinery that mediates their biogenesis is not.
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Affiliation(s)
- Julia Bruggisser
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Sandro Käser
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Jan Mani
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - André Schneider
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
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41
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Wang H, Hahn KM. LOVTRAP: A Versatile Method to Control Protein Function with Light. ACTA ACUST UNITED AC 2016; 73:21.10.1-21.10.14. [PMID: 27906450 DOI: 10.1002/cpcb.12] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We describe a detailed procedure for the use of LOVTRAP, an approach to reversibly sequester and release proteins from cellular membranes using light. In the application described here, proteins that act at the plasma membrane are held at mitochondria in the dark, and reversibly released by irradiation. The technique relies on binding of an engineered Zdk domain to a LOV2 domain, with affinity <30 nM in the dark and >500 nM upon irradiation between 400 and 500 nm. LOVTRAP can be applied to diverse proteins, as it requires attaching only one member of the Zdk/LOV2 pair to the target protein, and the other to the membrane where the target protein is to be sequestered. Light-induced protein release occurs in less than a second, and the half-life of return can be adjusted using LOV point mutations (∼2 to 500 sec). © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Hui Wang
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Klaus M Hahn
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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42
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Cook EM, Lindorfer MA, van der Horst H, Oostindie S, Beurskens FJ, Schuurman J, Zent CS, Burack R, Parren PWHI, Taylor RP. Antibodies That Efficiently Form Hexamers upon Antigen Binding Can Induce Complement-Dependent Cytotoxicity under Complement-Limiting Conditions. THE JOURNAL OF IMMUNOLOGY 2016; 197:1762-75. [PMID: 27474078 DOI: 10.4049/jimmunol.1600648] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/28/2016] [Indexed: 11/19/2022]
Abstract
Recently, we demonstrated that IgG Abs can organize into ordered hexamers after binding their cognate Ags expressed on cell surfaces. This process is dependent on Fc:Fc interactions, which promote C1q binding, the first step in classical pathway complement activation. We went on to engineer point mutations that stimulated IgG hexamer formation and complement-dependent cytotoxicity (CDC). The hexamer formation-enhanced (HexaBody) CD20 and CD38 mAbs support faster, more robust CDC than their wild-type counterparts. To further investigate the CDC potential of these mAbs, we used flow cytometry, high-resolution digital imaging, and four-color confocal microscopy to examine their activity against B cell lines and primary chronic lymphocytic leukemia cells in sera depleted of single complement components. We also examined the CDC activity of alemtuzumab (anti-CD52) and mAb W6/32 (anti-HLA), which bind at high density to cells and promote substantial complement activation. Although we observed little CDC for mAb-opsonized cells reacted with sera depleted of early complement components, we were surprised to discover that the Hexabody mAbs, as well as ALM and W6/32, were all quite effective at promoting CDC in sera depleted of individual complement components C6 to C9. However, neutralization studies conducted with an anti-C9 mAb verified that C9 is required for CDC activity against cell lines. These highly effective complement-activating mAbs efficiently focus activated complement components on the cell, including C3b and C9, and promote CDC with a very low threshold of MAC binding, thus providing additional insight into their enhanced efficacy in promoting CDC.
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Affiliation(s)
- Erika M Cook
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908
| | - Margaret A Lindorfer
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908
| | | | | | | | | | - Clive S Zent
- Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642
| | - Richard Burack
- Department of Pathology, University of Rochester Medical Center, Rochester, NY 14642; and
| | - Paul W H I Parren
- Genmab, 3584 CM Utrecht, the Netherlands; Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Ronald P Taylor
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908;
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43
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Wang H, Vilela M, Winkler A, Tarnawski M, Schlichting I, Yumerefendi H, Kuhlman B, Liu R, Danuser G, Hahn KM. LOVTRAP: an optogenetic system for photoinduced protein dissociation. Nat Methods 2016; 13:755-8. [PMID: 27427858 PMCID: PMC5137947 DOI: 10.1038/nmeth.3926] [Citation(s) in RCA: 209] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 06/16/2016] [Indexed: 01/03/2023]
Abstract
Here we introduce LOVTRAP, an optogenetic approach for reversible, light-induced protein dissociation. LOVTRAP is based on protein A fragments that bind to the LOV domain only in the dark, with tunable kinetics and a >150-fold change in Kd. By reversibly sequestering proteins at mitochondria, we precisely modulated the proteins’ access to the cell edge, demonstrating a naturally occurring 3 mHz cell edge oscillation driven by interactions of Vav2, Rac1 and PI3K.
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Affiliation(s)
- Hui Wang
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Marco Vilela
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Andreas Winkler
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Miroslaw Tarnawski
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Hayretin Yumerefendi
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Rihe Liu
- Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Klaus M Hahn
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Lineberger Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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44
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Revisiting trends on mitochondrial mega-channels for the import of proteins and nucleic acids. J Bioenerg Biomembr 2016; 49:75-99. [DOI: 10.1007/s10863-016-9662-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/25/2016] [Indexed: 12/14/2022]
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45
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Krol A, Henle SJ, Goodrich LV. Fat3 and Ena/VASP proteins influence the emergence of asymmetric cell morphology in the developing retina. Development 2016; 143:2172-82. [PMID: 27122175 DOI: 10.1242/dev.133678] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 04/14/2016] [Indexed: 12/27/2022]
Abstract
Neurons exhibit asymmetric morphologies throughout development - from migration to the elaboration of axons and dendrites - that are correctly oriented for the flow of information. For instance, retinal amacrine cells migrate towards the inner plexiform layer (IPL) and then retract their trailing processes, thereby acquiring a unipolar morphology with a single dendritic arbor restricted to the IPL. Here, we provide evidence that the Fat-like cadherin Fat3 acts during multiple stages of amacrine cell development in mice to orient overall changes in cell shape towards the IPL. Using a time-lapse imaging assay, we found that developing amacrine cells are less directed towards the IPL in the absence of Fat3, during both migration and retraction. Consistent with its predicted role as a cell-surface receptor, Fat3 functions cell-autonomously and is able to influence the cytoskeleton directly through its intracellular domain, which can bind and localize Ena/VASP family actin regulators. Indeed, a change in Ena/VASP protein distribution is sufficient to recapitulate the Fat3 mutant amacrine cell phenotype. Thus, Fat-like proteins might control the polarized development of tissues by sculpting the cytoskeleton of individual cells.
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Affiliation(s)
- Alexandra Krol
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Steven J Henle
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Lisa V Goodrich
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
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46
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Jun YW, Park H, Lee YK, Kaang BK, Lee JA, Jang DJ. D-AKAP1a is a signal-anchored protein in the mitochondrial outer membrane. FEBS Lett 2016; 590:954-61. [PMID: 26950402 DOI: 10.1002/1873-3468.12123] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 03/03/2016] [Indexed: 11/08/2022]
Abstract
Dual A-kinase anchoring protein 1a (D-AKAP1a, AKAP1) regulates cAMP signaling in mitochondria. However, it is not clear how D-AKAP1a is associated with mitochondria. In this study, we show that D-AKAP1a is a transmembrane protein in the mitochondrial outer membrane (MOM). We revealed that the N-terminus of D-AKAP1a is exposed to the intermembrane space of mitochondria and that its C-terminus is located on the cytoplasmic side of the MOM. Moderate hydrophobicity and the positively charged flanking residues of the transmembrane domain of D-AKAP1a were important for targeting. Taken together, D-AKAP1a can be classified as a signal-anchored protein in the MOM. Our topological study provides valuable information about the molecular and cellular mechanisms of mitochondrial targeting of AKAP1.
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Affiliation(s)
- Yong-Woo Jun
- Department of Ecological Science, College of Ecology and Environment, Kyungpook National University, Sangju-si, Gyeongsangbuk-do, Korea
| | - Heeju Park
- Department of Applied Biology, College of Ecology and Environment, Kyungpook National University, Sangju-si, Gyeongsangbuk-do, Korea
| | - You-Kyung Lee
- Department of Biological Science and Biotechnology, College of Life Science and Nano Technology, Hannam University, Yuseong-gu, Daejeon, Korea
| | - Bong-Kiun Kaang
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Gwanak-gu, Seoul, Korea
| | - Jin-A Lee
- Department of Biological Science and Biotechnology, College of Life Science and Nano Technology, Hannam University, Yuseong-gu, Daejeon, Korea
| | - Deok-Jin Jang
- Department of Ecological Science, College of Ecology and Environment, Kyungpook National University, Sangju-si, Gyeongsangbuk-do, Korea.,Department of Applied Biology, College of Ecology and Environment, Kyungpook National University, Sangju-si, Gyeongsangbuk-do, Korea
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47
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Sudhaharan T, Sem KP, Liew HF, Yu YH, Goh WI, Chou AM, Ahmed S. Rho GTPase Rif signals through IRTKS, Eps8 and WAVE2 to generate dorsal membrane ruffles and filopodia. J Cell Sci 2016; 129:2829-40. [DOI: 10.1242/jcs.179655] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 05/27/2016] [Indexed: 11/20/2022] Open
Abstract
Rif induces dorsal filopodia but the signalling pathway responsible for this has not been identified. We show here that Rif interacts with the I-BAR family protein IRTKS via its I-BAR domain. Rif also interacts with Pinkbar in N1E-115 mouse neuroblastoma cells. IRTKS and Rif induce dorsal membrane ruffles and filopodia. Dominant negative Rif inhibits the formation of IRTKS-induced morphological structures and Rif activity is blocked in IRTKS KO cells. To further define the Rif-IRTKS signalling pathway, we identify Eps8 and WAVE2 as IRTKS interactors. We find that Eps8 regulates the size and number of dorsal filopodia and membrane ruffles downstream of Rif-IRTKS, while WAVE2 modulates dorsal membrane ruffling. Furthermore, our data suggests that Tir, a protein essential for enterohemorrhagic E.coli infection, may compete for Rif for interaction with the I-BAR domain of IRKS. Based on these evidences we propose a model in which Rho family GTPases use the I-BAR proteins, IRSp53, IRTKS and Pinkbar, as a central mechanism to modulate cell morphology.
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Affiliation(s)
- Thankiah Sudhaharan
- Neural Stem Cell Laboratory, Institute of Medical Biology, 8A Biomedical Grove, Immunos, Singapore 138648
| | - Kai Ping Sem
- Neural Stem Cell Laboratory, Institute of Medical Biology, 8A Biomedical Grove, Immunos, Singapore 138648
| | - Hwi Fen Liew
- Neural Stem Cell Laboratory, Institute of Medical Biology, 8A Biomedical Grove, Immunos, Singapore 138648
| | - Yuan Hong Yu
- Neural Stem Cell Laboratory, Institute of Medical Biology, 8A Biomedical Grove, Immunos, Singapore 138648
| | - Wah Ing Goh
- Neural Stem Cell Laboratory, Institute of Medical Biology, 8A Biomedical Grove, Immunos, Singapore 138648
- Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, Singapore 117411
| | - Ai Mei Chou
- Neural Stem Cell Laboratory, Institute of Medical Biology, 8A Biomedical Grove, Immunos, Singapore 138648
| | - Sohail Ahmed
- Neural Stem Cell Laboratory, Institute of Medical Biology, 8A Biomedical Grove, Immunos, Singapore 138648
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Sakaue H, Iwashita S, Yamashita Y, Kida Y, Sakaguchi M. The N-terminal motif of PMP70 suppresses cotranslational targeting to the endoplasmic reticulum. J Biochem 2015; 159:539-51. [PMID: 26711236 DOI: 10.1093/jb/mvv132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/06/2015] [Indexed: 11/13/2022] Open
Abstract
Many membrane proteins possessing hydrophobic transmembrane (TM) segments are cotranslationally integrated into the endoplasmic reticulum (ER) membrane. Various peroxisomal and mitochondrial membrane proteins escape the ER-targeting mechanism and are targeted to their destinations. Here, we discovered a short segment in the 70-kDa peroxisomal membrane protein (PMP70) that suppresses ER targeting. The first TM segment has an intrinsic signal function that targets the nascent chain to the ER. The ER targeting was suppressed by a short N-terminal sequence of nine residues that is 80 residues upstream of the TM segment. Among the nine residues, Ser(5) is indispensable. The short segment also suppressed the signal peptide function of an authentic secretory protein. This function of the short segment was suppressed by the recombinant motif-GST fusion protein. The 50-kDa and 20-kDa proteins were crosslinked with the motif. The PMP70 molecule with the Ser5Ala point mutation predominantly localized to the ER. We propose the concept of an ER-targeting suppressor that suppresses the ER-targeting mechanism via a binding factor.
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Affiliation(s)
- Haruka Sakaue
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan
| | - Shohei Iwashita
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan
| | - Yukari Yamashita
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan
| | - Yuichiro Kida
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan
| | - Masao Sakaguchi
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan
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Lindorfer MA, Cook EM, Tupitza JC, Zent CS, Burack R, de Jong RN, Beurskens FJ, Schuurman J, Parren PWHI, Taylor RP. Real-time analysis of the detailed sequence of cellular events in mAb-mediated complement-dependent cytotoxicity of B-cell lines and of chronic lymphocytic leukemia B-cells. Mol Immunol 2015; 70:13-23. [PMID: 26690706 DOI: 10.1016/j.molimm.2015.12.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 12/03/2015] [Accepted: 12/04/2015] [Indexed: 12/16/2022]
Abstract
Complement-dependent cytotoxicity is an important mechanism of action of certain mAbs used in cancer immunotherapy, including ofatumumab and rituximab. However, the detailed sequence of cellular changes that occur in nucleated cells attacked by mAb and complement has not been delineated. Recently developed CD20 mAbs, engineered to form hexamers on binding to cells, react with B-cells in serum, chelate C1q, and then activate complement and promote cell killing considerably more effectively than their wild-type precursors. We used these engineered mAbs as a model to investigate the sequence of events that occur when mAbs bind to B-cell lines and to primary cells from patients with chronic lymphocytic leukemia and then activate complement. Based on four-color confocal microscopy real-time movies and high resolution digital imaging, we find that after CD20 mAb binding and C1q uptake, C3b deposits on cells, followed by Ca(2+) influx, revealed by bright green signals generated on cells labeled with FLUO-4, a Ca(2+) indicator. The bright FLUO-4/Ca(2+) signal fades, replaced by punctate green signals in mitochondria, indicating Ca(2+) localization. This step leads to mitochondrial poisoning followed by cell death. The entire sequence is completed in <2 min for hexamerization-enhanced CD20 mAb-mediated killing. To our knowledge this is the first time the entire process has been characterized in detail in real time. By identifying multiple discrete steps in the cytotoxic pathway for nucleated cells our findings may inform future development and more effective application of complement-fixing mAbs to cancer treatment.
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Affiliation(s)
- Margaret A Lindorfer
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Erika M Cook
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Jillian C Tupitza
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Clive S Zent
- Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA
| | - Richard Burack
- Department of Pathology, University of Rochester Medical Center, Rochester, NY, USA
| | | | | | | | | | - Ronald P Taylor
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
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Shneyer BI, Ušaj M, Henn A. Myo19 is an outer mitochondrial membrane motor and effector of starvation-induced filopodia. J Cell Sci 2015; 129:543-56. [PMID: 26659663 DOI: 10.1242/jcs.175349] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 12/05/2015] [Indexed: 12/13/2022] Open
Abstract
Mitochondria respond to environmental cues and stress conditions. Additionally, the disruption of the mitochondrial network dynamics and its distribution is implicated in a variety of neurodegenerative diseases. Here, we reveal a new function for Myo19 in mitochondrial dynamics and localization during the cellular response to glucose starvation. Ectopically expressed Myo19 localized with mitochondria to the tips of starvation-induced filopodia. Corollary to this, RNA interference (RNAi)-mediated knockdown of Myo19 diminished filopodia formation without evident effects on the mitochondrial network. We analyzed the Myo19-mitochondria interaction, and demonstrated that Myo19 is uniquely anchored to the outer mitochondrial membrane (OMM) through a 30-45-residue motif, indicating that Myo19 is a stably attached OMM molecular motor. Our work reveals a new function for Myo19 in mitochondrial positioning under stress.
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Affiliation(s)
- Boris I Shneyer
- Department of Biology, Technion Israel Institute of Technology, Haifa 3200003, Israel
| | - Marko Ušaj
- Department of Biology, Technion Israel Institute of Technology, Haifa 3200003, Israel
| | - Arnon Henn
- Department of Biology, Technion Israel Institute of Technology, Haifa 3200003, Israel
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