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Hasan MK, Jeannine Brady L. Nucleic acid-binding KH domain proteins influence a spectrum of biological pathways including as part of membrane-localized complexes. J Struct Biol X 2024; 10:100106. [PMID: 39040530 PMCID: PMC11261784 DOI: 10.1016/j.yjsbx.2024.100106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 06/18/2024] [Accepted: 06/24/2024] [Indexed: 07/24/2024] Open
Abstract
K-Homology domain (KH domain) proteins bind single-stranded nucleic acids, influence protein-protein interactions of proteins that harbor them, and are found in all kingdoms of life. In concert with other functional protein domains KH domains contribute to a variety of critical biological activities, often within higher order machineries including membrane-localized protein complexes. Eukaryotic KH domain proteins are linked to developmental processes, morphogenesis, and growth regulation, and their aberrant expression is often associated with cancer. Prokaryotic KH domain proteins are involved in integral cellular activities including cell division and protein translocation. Eukaryotic and prokaryotic KH domains share structural features, but are differentiated based on their structural organizations. In this review, we explore the structure/function relationships of known examples of KH domain proteins, and highlight cases in which they function within or at membrane surfaces. We also summarize examples of KH domain proteins that influence bacterial virulence and pathogenesis. We conclude the article by discussing prospective research avenues that could be pursued to better investigate this largely understudied protein category.
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Affiliation(s)
- Md Kamrul Hasan
- Department of Oral Biology, University of Florida, Gainesville, FL 32610, USA
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - L. Jeannine Brady
- Department of Oral Biology, University of Florida, Gainesville, FL 32610, USA
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2
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Chen S, Collart MA. Membrane-associated mRNAs: A Post-transcriptional Pathway for Fine-turning Gene Expression. J Mol Biol 2024; 436:168579. [PMID: 38648968 DOI: 10.1016/j.jmb.2024.168579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
Gene expression is a fundamental and highly regulated process involving a series of tightly coordinated steps, including transcription, post-transcriptional processing, translation, and post-translational modifications. A growing number of studies have revealed an additional layer of complexity in gene expression through the phenomenon of mRNA subcellular localization. mRNAs can be organized into membraneless subcellular structures within both the cytoplasm and the nucleus, but they can also targeted to membranes. In this review, we will summarize in particular our knowledge on localization of mRNAs to organelles, focusing on important regulators and available techniques for studying organellar localization, and significance of this localization in the broader context of gene expression regulation.
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Affiliation(s)
- Siyu Chen
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Institute of Genetics and Genomics of Geneva, Geneva, Switzerland.
| | - Martine A Collart
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Institute of Genetics and Genomics of Geneva, Geneva, Switzerland.
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3
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Li W, Maekiniemi A, Sato H, Osman C, Singer RH. An improved imaging system that corrects MS2-induced RNA destabilization. Nat Methods 2022; 19:1558-1562. [PMID: 36357695 PMCID: PMC7613886 DOI: 10.1038/s41592-022-01658-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 09/21/2022] [Indexed: 11/12/2022]
Abstract
The MS2 and MS2-coat protein (MS2-MCP) imaging system is widely used to study messenger RNA (mRNA) spatial distribution in living cells. Here, we report that the MS2-MCP system destabilizes some tagged mRNAs by activating the nonsense-mediated mRNA decay pathway. We introduce an improved version, which counteracts this effect by increasing the efficiency of translation termination of the tagged mRNAs. Improved versions were developed for both yeast and mammalian systems.
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Affiliation(s)
- Weihan Li
- Program in RNA Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA,Correspondence: Weihan Li (); Anna Maekiniemi (); Robert H. Singer ()
| | - Anna Maekiniemi
- Program in RNA Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA,Correspondence: Weihan Li (); Anna Maekiniemi (); Robert H. Singer ()
| | - Hanae Sato
- Program in RNA Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Christof Osman
- Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Robert H. Singer
- Program in RNA Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA,Correspondence: Weihan Li (); Anna Maekiniemi (); Robert H. Singer ()
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4
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Passaniti A, Kim MS, Polster BM, Shapiro P. Targeting mitochondrial metabolism for metastatic cancer therapy. Mol Carcinog 2022; 61:827-838. [PMID: 35723497 PMCID: PMC9378505 DOI: 10.1002/mc.23436] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 05/18/2022] [Accepted: 05/27/2022] [Indexed: 02/06/2023]
Abstract
Primary tumors evolve metabolic mechanisms favoring glycolysis for adenosine triphosphate (ATP) generation and antioxidant defenses. In contrast, metastatic cells frequently depend on mitochondrial respiration and oxidative phosphorylation (OxPhos). This reliance of metastatic cells on OxPhos can be exploited using drugs that target mitochondrial metabolism. Therefore, therapeutic agents that act via diverse mechanisms, including the activation of signaling pathways that promote the production of reactive oxygen species (ROS) and/or a reduction in antioxidant defenses may elevate oxidative stress and inhibit tumor cell survival. In this review, we will provide (1) a mechanistic analysis of function-selective extracellular signal-regulated kinase-1/2 (ERK1/2) inhibitors that inhibit cancer cells through enhanced ROS, (2) a review of the role of mitochondrial ATP synthase in redox regulation and drug resistance, (3) a rationale for inhibiting ERK signaling and mitochondrial OxPhos toward the therapeutic goal of reducing tumor metastasis and treatment resistance. Recent reports from our laboratories using metastatic melanoma and breast cancer models have shown the preclinical efficacy of novel and rationally designed therapeutic agents that target ERK1/2 signaling and mitochondrial ATP synthase, which modulate ROS events that may prevent or treat metastatic cancer. These findings and those of others suggest that targeting a tumor's metabolic requirements and vulnerabilities may inhibit metastatic pathways and tumor growth. Approaches that exploit the ability of therapeutic agents to alter oxidative balance in tumor cells may be selective for cancer cells and may ultimately have an impact on clinical efficacy and safety. Elucidating the translational potential of metabolic targeting could lead to the discovery of new approaches for treatment of metastatic cancer.
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Affiliation(s)
- Antonino Passaniti
- Research Health Scientist, The Veteran's Health Administration Research & Development Service (VAMHCS), VA Maryland Health Care System (VAMHCS), Baltimore VA Medical Center, Baltimore, Maryland, USA
- Department of Pathology and Department of Biochemistry & Molecular Biology, the Program in Molecular Medicine and the Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland USA
| | - Myoung Sook Kim
- Department of Pathology and Department of Biochemistry & Molecular Biology, the Program in Molecular Medicine and the Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland USA
| | - Brian M. Polster
- Department of Anesthesiology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Paul Shapiro
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore Maryland, USA
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5
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Harbauer AB, Hees JT, Wanderoy S, Segura I, Gibbs W, Cheng Y, Ordonez M, Cai Z, Cartoni R, Ashrafi G, Wang C, Perocchi F, He Z, Schwarz TL. Neuronal mitochondria transport Pink1 mRNA via synaptojanin 2 to support local mitophagy. Neuron 2022; 110:1516-1531.e9. [PMID: 35216662 PMCID: PMC9081165 DOI: 10.1016/j.neuron.2022.01.035] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 06/25/2021] [Accepted: 01/28/2022] [Indexed: 01/18/2023]
Abstract
PTEN-induced kinase 1 (PINK1) is a short-lived protein required for the removal of damaged mitochondria through Parkin translocation and mitophagy. Because the short half-life of PINK1 limits its ability to be trafficked into neurites, local translation is required for this mitophagy pathway to be active far from the soma. The Pink1 transcript is associated and cotransported with neuronal mitochondria. In concert with translation, the mitochondrial outer membrane proteins synaptojanin 2 binding protein (SYNJ2BP) and synaptojanin 2 (SYNJ2) are required for tethering Pink1 mRNA to mitochondria via an RNA-binding domain in SYNJ2. This neuron-specific adaptation for the local translation of PINK1 provides distal mitochondria with a continuous supply of PINK1 for the activation of mitophagy.
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Affiliation(s)
- Angelika B Harbauer
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA; Max Planck Institute of Neurobiology, Am Klopferspitz 18, 82152 Martinsried, Germany; Institute of Neuronal Cell Biology, Technical University of Munich, Biedersteiner Straße 29, 80802 Munich, Germany; Munich Cluster of Systems Neurology, Feodor-Lynen-Straße 17, 81377 Munich, Germany.
| | - J Tabitha Hees
- Max Planck Institute of Neurobiology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Simone Wanderoy
- Max Planck Institute of Neurobiology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Inmaculada Segura
- Max Planck Institute of Neurobiology, Am Klopferspitz 18, 82152 Martinsried, Germany; Ludwig-Maximilians-Universität München, Department of Cellular Physiology Biomedical Center Munich - BMC, Großhaderner Str. 9, 82152 Martinsried, Germany
| | - Whitney Gibbs
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Yiming Cheng
- Munich Cluster of Systems Neurology, Feodor-Lynen-Straße 17, 81377 Munich, Germany; Institute for Diabetes and Obesity, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Munich, Germany
| | - Martha Ordonez
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Zerong Cai
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Romain Cartoni
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Ghazaleh Ashrafi
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Chen Wang
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Fabiana Perocchi
- Institute of Neuronal Cell Biology, Technical University of Munich, Biedersteiner Straße 29, 80802 Munich, Germany; Munich Cluster of Systems Neurology, Feodor-Lynen-Straße 17, 81377 Munich, Germany; Institute for Diabetes and Obesity, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Munich, Germany
| | - Zhigang He
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas L Schwarz
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA.
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6
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Li Z, Liu R, Liu Y, Zhao M, Luan J, Wang Y, Shang W, Song X, Sun Y, Han F. H55 N variation in citrate synthase leads to decrement in the enzyme activity and transport rate to mitochondria in HEI-OC1 cells. Biochem Biophys Res Commun 2022; 612:134-140. [PMID: 35525197 DOI: 10.1016/j.bbrc.2022.04.104] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 04/22/2022] [Indexed: 11/16/2022]
Abstract
A/J mouse is a typical animal model of age-related deafness. Previous studies have shown that the mice suffer from progressive hearing loss and degeneration of cochlear cells, and a variation of H55 N in citrate synthase (CS) causes about 40% the hearing loss. CS is a key enzyme in the tricarboxylic acid cycle, which is transported from cytoplasm to mitochondria after synthesis, sorted by the mitochondrial targeting sequence (MTS). To explore the mechanism of CS (H55 N) variation in affecting its function, HEI-OC1 cells were infected with lentivirus particles to express CS-Flag or CS(H55 N)-Flag. The results showed that H55 N variation in CS, as purified by co-immunoprecipitation, decreased the enzyme activity by about 50%. Confocal microscope co-localization indicated that the CS (H55 N) variation led to a decrement in its mitochondrial content. Western blot also showed the amount of CS(H55 N)-Flag was more than that of CS(WT)-Flag in the cytosol. The results suggest H55 N variation in CS lead to decrement of its enzyme activity and targeting transport to mitochondria. We therefore conclude that decrement in CS activity and mitochondrial delivery contributes to the degeneration of cochlear cells and thus the hearing loss in A/J mice.
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Affiliation(s)
- Zhen Li
- Key Laboratory for Genetic Hearing Disorders in Shandong, Department of Biochemistry and Molecular Biology, Binzhou Medical University, 346 Guanhai Road, Yantai, 264003, Shandong, PR China; Department of Otorhinolaryngology Head and Neck Surgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20 East, Yuhuangding Road, Yantai, 264000, Shandong, PR China; Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, No. 20 East, Yuhuangding Road, Yantai, 264000, Shandong, PR China
| | - Rongrong Liu
- Key Laboratory for Genetic Hearing Disorders in Shandong, Department of Biochemistry and Molecular Biology, Binzhou Medical University, 346 Guanhai Road, Yantai, 264003, Shandong, PR China; Department of Otorhinolaryngology Head and Neck Surgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20 East, Yuhuangding Road, Yantai, 264000, Shandong, PR China
| | - Yingying Liu
- Key Laboratory for Genetic Hearing Disorders in Shandong, Department of Biochemistry and Molecular Biology, Binzhou Medical University, 346 Guanhai Road, Yantai, 264003, Shandong, PR China
| | - Mengmeng Zhao
- Key Laboratory for Genetic Hearing Disorders in Shandong, Department of Biochemistry and Molecular Biology, Binzhou Medical University, 346 Guanhai Road, Yantai, 264003, Shandong, PR China; Department of Otorhinolaryngology Head and Neck Surgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20 East, Yuhuangding Road, Yantai, 264000, Shandong, PR China
| | - Jun Luan
- Key Laboratory for Genetic Hearing Disorders in Shandong, Department of Biochemistry and Molecular Biology, Binzhou Medical University, 346 Guanhai Road, Yantai, 264003, Shandong, PR China
| | - Yan Wang
- Key Laboratory for Genetic Hearing Disorders in Shandong, Department of Biochemistry and Molecular Biology, Binzhou Medical University, 346 Guanhai Road, Yantai, 264003, Shandong, PR China
| | - Wenjing Shang
- Key Laboratory for Genetic Hearing Disorders in Shandong, Department of Biochemistry and Molecular Biology, Binzhou Medical University, 346 Guanhai Road, Yantai, 264003, Shandong, PR China
| | - Xicheng Song
- Department of Otorhinolaryngology Head and Neck Surgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20 East, Yuhuangding Road, Yantai, 264000, Shandong, PR China; Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, No. 20 East, Yuhuangding Road, Yantai, 264000, Shandong, PR China
| | - Yan Sun
- Department of Otorhinolaryngology Head and Neck Surgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20 East, Yuhuangding Road, Yantai, 264000, Shandong, PR China; Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, No. 20 East, Yuhuangding Road, Yantai, 264000, Shandong, PR China.
| | - Fengchan Han
- Key Laboratory for Genetic Hearing Disorders in Shandong, Department of Biochemistry and Molecular Biology, Binzhou Medical University, 346 Guanhai Road, Yantai, 264003, Shandong, PR China.
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7
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The Mitochondrial Genome in Aging and Disease and the Future of Mitochondrial Therapeutics. Biomedicines 2022; 10:biomedicines10020490. [PMID: 35203698 PMCID: PMC8962324 DOI: 10.3390/biomedicines10020490] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/10/2022] [Accepted: 02/16/2022] [Indexed: 11/29/2022] Open
Abstract
Mitochondria are intracellular organelles that utilize nutrients to generate energy in the form of ATP by oxidative phosphorylation. Mitochondrial DNA (mtDNA) in humans is a 16,569 base pair double-stranded circular DNA that encodes for 13 vital proteins of the electron transport chain. Our understanding of the mitochondrial genome’s transcription, translation, and maintenance is still emerging, and human pathologies caused by mtDNA dysfunction are widely observed. Additionally, a correlation between declining mitochondrial DNA quality and copy number with organelle dysfunction in aging is well-documented in the literature. Despite tremendous advancements in nuclear gene-editing technologies and their value in translational avenues, our ability to edit mitochondrial DNA is still limited. In this review, we discuss the current therapeutic landscape in addressing the various pathologies that result from mtDNA mutations. We further evaluate existing gene therapy efforts, particularly allotopic expression and its potential to become an indispensable tool for restoring mitochondrial health in disease and aging.
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8
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Claus S, Jezierska S, Elbourne LDH, Van Bogaert I. Exploring the transportome of the biosurfactant producing yeast Starmerella bombicola. BMC Genomics 2022; 23:22. [PMID: 34998388 PMCID: PMC8742932 DOI: 10.1186/s12864-021-08177-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/16/2021] [Indexed: 12/13/2022] Open
Abstract
Starmerella bombicola is a non-conventional yeast mainly known for its capacity to produce high amounts of the glycolipids 'sophorolipids'. Although its product has been used as biological detergent for a couple of decades, the genetics of S. bombicola are still largely unknown. Computational analysis of the yeast's genome enabled us to identify 254 putative transporter genes that make up the entire transportome. For each of them, a potential substrate was predicted using homology analysis, subcellular localization prediction and RNA sequencing in different stages of growth. One transporter family is of exceptional importance to this yeast: the ATP Binding Cassette (ABC) transporter Superfamily, because it harbors the main driver behind the highly efficient sophorolipid export. Furthermore, members of this superfamily translocate a variety of compounds ranging from antibiotics to hydrophobic molecules. We conducted an analysis of this family by creating deletion mutants to understand their role in the export of hydrophobic compounds, antibiotics and sophorolipids. Doing this, we could experimentally confirm the transporters participating in the efflux of medium chain fatty alcohols, particularly decanol and undecanol, and identify a second sophorolipid transporter that is located outside the sophorolipid biosynthetic gene cluster.
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Affiliation(s)
- Silke Claus
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Sylwia Jezierska
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Liam D H Elbourne
- Department of Molecular Sciences, Macquarie University, Macquarie Park, NSW, 2109, Australia
| | - Inge Van Bogaert
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
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9
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Seeking a Role for Translational Control by Alternative Polyadenylation in Saccharomyces cerevisiae. Microorganisms 2021; 9:microorganisms9091885. [PMID: 34576779 PMCID: PMC8464734 DOI: 10.3390/microorganisms9091885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/29/2021] [Accepted: 08/30/2021] [Indexed: 11/17/2022] Open
Abstract
Alternative polyadenylation (APA) represents an important mechanism for regulating isoform-specific translation efficiency, stability, and localisation. Though some progress has been made in understanding its consequences in metazoans, the role of APA in the model organism Saccharomyces cerevisiae remains a relative mystery because, despite abundant studies on the translational state of mRNA, none differentiate mRNA isoforms’ alternative 3′-end. This review discusses the implications of alternative polyadenylation in S. cerevisiae using other organisms to draw inferences. Given the foundational role that research in this yeast has played in the discovery of the mechanisms of cleavage and polyadenylation and in the drivers of APA, it is surprising that such an inference is required. However, because advances in ribosome profiling are insensitive to APA, how it impacts translation is still unclear. To bridge the gap between widespread observed APA and the discovery of any functional consequence, we also provide a review of the experimental techniques used to uncover the functional importance of 3′ UTR isoforms on translation.
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10
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Mitschka S, Fansler MM, Mayr C. Generation of 3'UTR knockout cell lines by CRISPR/Cas9-mediated genome editing. Methods Enzymol 2021; 655:427-457. [PMID: 34183132 DOI: 10.1016/bs.mie.2021.03.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In addition to the protein code, messenger RNAs (mRNAs) also contain untranslated regions (UTRs). 3'UTRs span the region between the translational stop codon and the poly(A) tail. Sequence elements located in 3'UTRs are essential for pre-mRNA processing. 3'UTRs also contain elements that can regulate protein abundance, localization, and function. At least half of all human genes use alternative cleavage and polyadenylation (APA) to further diversify the regulatory potential of protein functions. Traditional gene editing approaches are designed to disrupt the production of functional proteins. Here, we describe a method that allows investigators to manipulate 3'UTR sequences of endogenous genes for both single- 3'UTR and multi-3'UTR genes. As 3'UTRs can regulate individual functions of proteins, techniques to manipulate 3'UTRs at endogenous gene loci will help to disentangle multi-functionality of proteins. Furthermore, the ability to directly examine the impact of gene regulatory elements in 3'UTRs will provide further insights into their functional significance.
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Affiliation(s)
- Sibylle Mitschka
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Mervin M Fansler
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States; Tri-Institutional Training Program in Computational Biology and Medicine, Weill-Cornell Graduate College, New York, NY, United States
| | - Christine Mayr
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States; Tri-Institutional Training Program in Computational Biology and Medicine, Weill-Cornell Graduate College, New York, NY, United States.
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11
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Needs HI, Protasoni M, Henley JM, Prudent J, Collinson I, Pereira GC. Interplay between Mitochondrial Protein Import and Respiratory Complexes Assembly in Neuronal Health and Degeneration. Life (Basel) 2021; 11:432. [PMID: 34064758 PMCID: PMC8151517 DOI: 10.3390/life11050432] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/27/2021] [Accepted: 05/02/2021] [Indexed: 12/14/2022] Open
Abstract
The fact that >99% of mitochondrial proteins are encoded by the nuclear genome and synthesised in the cytosol renders the process of mitochondrial protein import fundamental for normal organelle physiology. In addition to this, the nuclear genome comprises most of the proteins required for respiratory complex assembly and function. This means that without fully functional protein import, mitochondrial respiration will be defective, and the major cellular ATP source depleted. When mitochondrial protein import is impaired, a number of stress response pathways are activated in order to overcome the dysfunction and restore mitochondrial and cellular proteostasis. However, prolonged impaired mitochondrial protein import and subsequent defective respiratory chain function contributes to a number of diseases including primary mitochondrial diseases and neurodegeneration. This review focuses on how the processes of mitochondrial protein translocation and respiratory complex assembly and function are interlinked, how they are regulated, and their importance in health and disease.
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Affiliation(s)
- Hope I. Needs
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK; (H.I.N.); (J.M.H.)
| | - Margherita Protasoni
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; (M.P.); (J.P.)
| | - Jeremy M. Henley
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK; (H.I.N.); (J.M.H.)
- Centre for Neuroscience and Regenerative Medicine, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Julien Prudent
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; (M.P.); (J.P.)
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK; (H.I.N.); (J.M.H.)
| | - Gonçalo C. Pereira
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; (M.P.); (J.P.)
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12
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Kim MS, Gernapudi R, Cedeño YC, Polster BM, Martinez R, Shapiro P, Kesari S, Nurmemmedov E, Passaniti A. Targeting breast cancer metabolism with a novel inhibitor of mitochondrial ATP synthesis. Oncotarget 2020; 11:3863-3885. [PMID: 33196708 PMCID: PMC7597410 DOI: 10.18632/oncotarget.27743] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 08/24/2020] [Indexed: 01/17/2023] Open
Abstract
Inhibitors of mitochondrial respiration and ATP synthesis may promote the selective killing of respiration-competent cancer cells that are critical for tumor progression. We previously reported that CADD522, a small molecule inhibitor of the RUNX2 transcription factor, has potential for breast cancer treatment. In the current study, we show that CADD522 inhibits mitochondrial oxidative phosphorylation by decreasing the mitochondrial oxygen consumption rate (OCR) and ATP production in human breast cancer cells in a RUNX2-independent manner. The enzyme activity of mitochondrial ATP synthase was inhibited by CADD522 treatment. Importantly, results from cellular thermal shift assays that detect drug-induced protein stabilization revealed that CADD522 interacts with both α and β subunits of the F1-ATP synthase complex. Differential scanning fluorimetry also demonstrated interaction of α subunits of the F1-ATP synthase to CADD522. These results suggest that CADD522 might target the enzymatic F1 subunits in the ATP synthase complex. CADD522 increased the levels of intracellular reactive oxygen species (ROS), which was prevented by MitoQ, a mitochondria-targeted antioxidant, suggesting that cancer cells exposed to CADD522 may elevate ROS from mitochondria. CADD522-increased mitochondrial ROS levels were enhanced by exogenously added pro-oxidants such as hydrogen peroxide or tert-butyl hydroperoxide. Conversely, CADD522-mediated cell growth inhibition was blocked by N-acetyl-l-cysteine, a general ROS scavenger. Therefore, CADD522 may exert its antitumor activity by increasing mitochondrial driven cellular ROS levels. Collectively, our data suggest in vitro proof-of-concept that supports inhibition of mitochondrial ATP synthase and ROS generation as contributors to the effectiveness of CADD522 in suppression of tumor growth.
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Affiliation(s)
- Myoung Sook Kim
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA
- The Marlene & Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | - Ramkishore Gernapudi
- Department of Biochemistry & Molecular Biology and Program in Molecular Medicine, Baltimore, MD, USA
- The Marlene & Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | | | - Brian M. Polster
- Department of Anesthesiology, University of Maryland School of Medicine, Baltimore, MD, USA
- Research Health Scientist, The Veteran's Health Administration Research & Development Service (VAMHCS), Baltimore, MD, USA
| | - Ramon Martinez
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, USA
| | - Paul Shapiro
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, USA
| | - Santosh Kesari
- John Wayne Cancer Institute and Pacific Neuroscience Institute at Providence Saint John’s Health Center, Santa Monica, CA, USA
| | - Elmar Nurmemmedov
- John Wayne Cancer Institute and Pacific Neuroscience Institute at Providence Saint John’s Health Center, Santa Monica, CA, USA
| | - Antonino Passaniti
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Biochemistry & Molecular Biology and Program in Molecular Medicine, Baltimore, MD, USA
- The Marlene & Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
- Research Health Scientist, The Veteran's Health Administration Research & Development Service (VAMHCS), Baltimore, MD, USA
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13
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Cytosolic Events in the Biogenesis of Mitochondrial Proteins. Trends Biochem Sci 2020; 45:650-667. [DOI: 10.1016/j.tibs.2020.04.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 03/18/2020] [Accepted: 04/02/2020] [Indexed: 01/08/2023]
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14
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Avendaño-Monsalve MC, Ponce-Rojas JC, Funes S. From cytosol to mitochondria: the beginning of a protein journey. Biol Chem 2020; 401:645-661. [DOI: 10.1515/hsz-2020-0110] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 02/24/2020] [Indexed: 01/18/2023]
Abstract
AbstractMitochondrial protein import is one of the key processes during mitochondrial biogenesis that involves a series of events necessary for recognition and delivery of nucleus-encoded/cytosol-synthesized mitochondrial proteins into the organelle. The past research efforts have mainly unraveled how membrane translocases ensure the correct protein sorting within the different mitochondrial subcompartments. However, early steps of recognition and delivery remain relatively uncharacterized. In this review, we discuss our current understanding about the signals on mitochondrial proteins, as well as in the mRNAs encoding them, which with the help of cytosolic chaperones and membrane receptors support protein targeting to the organelle in order to avoid improper localization. In addition, we discuss recent findings that illustrate how mistargeting of mitochondrial proteins triggers stress responses, aiming to restore cellular homeostasis.
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Affiliation(s)
- Maria Clara Avendaño-Monsalve
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n Ciudad Universitaria Coyoacán, México, Cd.Mx. 04510, Mexico
| | - José Carlos Ponce-Rojas
- Department of Molecular, Cellular, and Developmental Biology, University of California at Santa Barbara, Santa Barbara, CA 93106-9625, USA
| | - Soledad Funes
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n Ciudad Universitaria Coyoacán, México, Cd.Mx. 04510, Mexico
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15
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Chaudhuri A, Das S, Das B. Localization elements and zip codes in the intracellular transport and localization of messenger RNAs in Saccharomyces cerevisiae. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1591. [PMID: 32101377 DOI: 10.1002/wrna.1591] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 12/13/2022]
Abstract
Intracellular trafficking and localization of mRNAs provide a mechanism of regulation of expression of genes with excellent spatial control. mRNA localization followed by localized translation appears to be a mechanism of targeted protein sorting to a specific cell-compartment, which is linked to the establishment of cell polarity, cell asymmetry, embryonic axis determination, and neuronal plasticity in metazoans. However, the complexity of the mechanism and the components of mRNA localization in higher organisms prompted the use of the unicellular organism Saccharomyces cerevisiae as a simplified model organism to study this vital process. Current knowledge indicates that a variety of mRNAs are asymmetrically and selectively localized to the tip of the bud of the daughter cells, to the vicinity of endoplasmic reticulum, mitochondria, and nucleus in this organism, which are connected to diverse cellular processes. Interestingly, specific cis-acting RNA localization elements (LEs) or RNA zip codes play a crucial role in the localization and trafficking of these localized mRNAs by providing critical binding sites for the specific RNA-binding proteins (RBPs). In this review, we present a comprehensive account of mRNA localization in S. cerevisiae, various types of localization elements influencing the mRNA localization, and the RBPs, which bind to these LEs to implement a number of vital physiological processes. Finally, we emphasize the significance of this process by highlighting their connection to several neuropathological disorders and cancers. This article is categorized under: RNA Export and Localization > RNA Localization.
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Affiliation(s)
- Anusha Chaudhuri
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| | - Subhadeep Das
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| | - Biswadip Das
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
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16
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Schatton D, Rugarli EI. A concert of RNA-binding proteins coordinates mitochondrial function. Crit Rev Biochem Mol Biol 2019; 53:652-666. [DOI: 10.1080/10409238.2018.1553927] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Désirée Schatton
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Elena I. Rugarli
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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17
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Olgeiser L, Haag C, Boerner S, Ule J, Busch A, Koepke J, König J, Feldbrügge M, Zarnack K. The key protein of endosomal mRNP transport Rrm4 binds translational landmark sites of cargo mRNAs. EMBO Rep 2018; 20:embr.201846588. [PMID: 30552148 DOI: 10.15252/embr.201846588] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 11/09/2018] [Accepted: 11/09/2018] [Indexed: 01/09/2023] Open
Abstract
RNA-binding proteins (RBPs) determine spatiotemporal gene expression by mediating active transport and local translation of cargo mRNAs. Here, we cast a transcriptome-wide view on the transported mRNAs and cognate RBP binding sites during endosomal messenger ribonucleoprotein (mRNP) transport in Ustilago maydis Using individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP), we compare the key transport RBP Rrm4 and the newly identified endosomal mRNP component Grp1 that is crucial to coordinate hyphal growth. Both RBPs bind predominantly in the 3' untranslated region of thousands of shared cargo mRNAs, often in close proximity. Intriguingly, Rrm4 precisely binds at stop codons, which constitute landmark sites of translation, suggesting an intimate connection of mRNA transport and translation. Towards uncovering the code of recognition, we identify UAUG as specific binding motif of Rrm4 that is bound by its third RRM domain. Altogether, we provide first insights into the positional organisation of co-localising RBPs on individual cargo mRNAs.
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Affiliation(s)
- Lilli Olgeiser
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Carl Haag
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Susan Boerner
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jernej Ule
- The Francis Crick Institute, London, UK.,Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Anke Busch
- Institute of Molecular Biology gGmbH, Mainz, Germany
| | - Janine Koepke
- Medical Clinic II (Molecular Pneumology), Excellence Cluster Cardio-Pulmonary System, Justus Liebig University of Gießen, Gießen, Germany
| | - Julian König
- Institute of Molecular Biology gGmbH, Mainz, Germany
| | - Michael Feldbrügge
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany
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18
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Béthune J, Jansen RP, Feldbrügge M, Zarnack K. Membrane-Associated RNA-Binding Proteins Orchestrate Organelle-Coupled Translation. Trends Cell Biol 2018; 29:178-188. [PMID: 30455121 DOI: 10.1016/j.tcb.2018.10.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/28/2018] [Accepted: 10/29/2018] [Indexed: 02/02/2023]
Abstract
Proteins are positioned and act at defined subcellular locations. This is particularly important in eukaryotic cells that deliver proteins to membrane-bound organelles such as the endoplasmic reticulum (ER), mitochondria, or endosomes. It is axiomatic that organelle targeting depends mainly on polypeptide signals. However, recent results demonstrate that targeting elements within the encoding transcripts are essential for efficient protein localisation. Key readers of these elements are membrane-associated RNA-binding proteins (memRBPs) that orchestrate organelle-coupled translation. The translation products then either cross the membrane for organelle entry or hitchhike on organelle surfaces for complex assembly and co-transport. Understanding the interaction of protein- and RNA-based targeting signals is essential to decipher the molecular basis for mutant phenotypes in disease.
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Affiliation(s)
- Julien Béthune
- Heidelberg University, Biochemistry Center, Cluster of Excellence CellNetworks, 69120 Heidelberg, Germany
| | - Ralf-Peter Jansen
- Eberhard-Karls-University Tübingen, Interfaculty Institute of Biochemistry, Hoppe-Seyler-Straße 4, 72076 Tübingen, Germany
| | - Michael Feldbrügge
- Heinrich-Heine University Düsseldorf, Institute for Microbiology, Cluster of Excellence on Plant Sciences, 40204 Düsseldorf, Germany.
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.
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19
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Schatton D, Rugarli EI. Post-transcriptional regulation of mitochondrial function. CURRENT OPINION IN PHYSIOLOGY 2018. [DOI: 10.1016/j.cophys.2017.12.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Schatton D, Pla-Martin D, Marx MC, Hansen H, Mourier A, Nemazanyy I, Pessia A, Zentis P, Corona T, Kondylis V, Barth E, Schauss AC, Velagapudi V, Rugarli EI. CLUH regulates mitochondrial metabolism by controlling translation and decay of target mRNAs. J Cell Biol 2017; 216:675-693. [PMID: 28188211 PMCID: PMC5350512 DOI: 10.1083/jcb.201607019] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 12/06/2016] [Accepted: 01/06/2017] [Indexed: 12/21/2022] Open
Abstract
Mitochondria are essential organelles that host crucial metabolic pathways and produce adenosine triphosphate. The mitochondrial proteome is heterogeneous among tissues and can dynamically change in response to different metabolic conditions. Although the transcriptional programs that govern mitochondrial biogenesis and respiratory function are well known, posttranscriptional regulatory mechanisms remain unclear. In this study, we show that the cytosolic RNA-binding protein clustered mitochondria homologue (CLUH) regulates the expression of a mitochondrial protein network supporting key metabolic programs required under nutrient deprivation. CLUH exerts its function by controlling the stability and translation of target messenger RNAs. In the absence of Cluh, mitochondria are severely depleted of crucial enzymes involved in catabolic energy-converting pathways. CLUH preserves oxidative mitochondrial function and glucose homeostasis, thus preventing death at the fetal-neonatal transition. In the adult liver, CLUH ensures maximal respiration capacity and the metabolic response to starvation. Our results shed new light on the posttranscriptional mechanisms controlling the expression of mitochondrial proteins and suggest novel strategies to tailor mitochondrial function to physiological and pathological conditions.
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Affiliation(s)
- Désirée Schatton
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50931 Cologne, Germany
| | - David Pla-Martin
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50931 Cologne, Germany
| | - Marie-Charlotte Marx
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50931 Cologne, Germany
| | - Henriette Hansen
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50931 Cologne, Germany
| | - Arnaud Mourier
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Ivan Nemazanyy
- Paris Descartes University, Sorbonne Paris Cité, 75006 Paris, France
| | - Alberto Pessia
- Metabolomics Unit, Institute for Molecular Medicine Finland, University of Helsinki, 00290 Helsinki, Finland
| | - Peter Zentis
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50931 Cologne, Germany
| | - Teresa Corona
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50931 Cologne, Germany
| | - Vangelis Kondylis
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50931 Cologne, Germany
| | - Esther Barth
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50931 Cologne, Germany
| | - Astrid C Schauss
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50931 Cologne, Germany
| | - Vidya Velagapudi
- Metabolomics Unit, Institute for Molecular Medicine Finland, University of Helsinki, 00290 Helsinki, Finland
| | - Elena I Rugarli
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50931 Cologne, Germany
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21
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Ponce-Rojas JC, Avendaño-Monsalve MC, Yañez-Falcón AR, Jaimes-Miranda F, Garay E, Torres-Quiroz F, DeLuna A, Funes S. αβ'-NAC cooperates with Sam37 to mediate early stages of mitochondrial protein import. FEBS J 2017; 284:814-830. [PMID: 28109174 DOI: 10.1111/febs.14024] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 12/20/2016] [Accepted: 01/18/2017] [Indexed: 11/30/2022]
Abstract
The mitochondrial proteome is mostly composed of nuclear-encoded proteins. Such polypeptides are synthesized with signals that guide their intracellular transport to the surface of the organelle and later within the different mitochondrial subcompartments until they reach their functional destination. It has been suggested that the nascent-polypeptide associated complex (NAC) - a cytosolic chaperone that recognizes nascent chains on translationally active ribosomes - has a role in the import of nuclear-encoded mitochondrial proteins. However, the molecular mechanisms that regulate the NAC-mediated cotranslational import are still not clear. Here, we show that a particular NAC heterodimer formed by subunits α and β' in Saccharomyces cerevisiae is specifically involved in the process of mitochondrial import and functionally cooperates with Sam37, an outer membrane protein subunit of the sorting and assembly machinery complex. Mutants in both components display growth defects, incorrectly accumulate precursor forms of mitochondrial proteins in the cytosol, and have an altered mitochondrial protein content. We propose that αβ'-NAC and Sam37 are members of the system that recognizes mitochondrial proteins at early stages of their synthesis, escorting them to the import machinery of mitochondria.
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Affiliation(s)
- José Carlos Ponce-Rojas
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico
| | - Maria Clara Avendaño-Monsalve
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico
| | - Armando Roberto Yañez-Falcón
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico
| | - Fabiola Jaimes-Miranda
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico
| | - Erika Garay
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Mexico
| | - Francisco Torres-Quiroz
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico
| | - Alexander DeLuna
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Mexico
| | - Soledad Funes
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico
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22
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Delaveau T, Davoine D, Jolly A, Vallot A, Rouvière JO, Gerber A, Brochet S, Plessis M, Roquigny R, Merhej J, Leger T, Garcia C, Lelandais G, Laine E, Palancade B, Devaux F, Garcia M. Tma108, a putative M1 aminopeptidase, is a specific nascent chain-associated protein in Saccharomyces cerevisiae. Nucleic Acids Res 2016; 44:8826-8841. [PMID: 27580715 PMCID: PMC5062994 DOI: 10.1093/nar/gkw732] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 08/11/2016] [Indexed: 01/21/2023] Open
Abstract
The discovery of novel specific ribosome-associated factors challenges the assumption that translation relies on standardized molecular machinery. In this work, we demonstrate that Tma108, an uncharacterized translation machinery-associated factor in yeast, defines a subpopulation of cellular ribosomes specifically involved in the translation of less than 200 mRNAs encoding proteins with ATP or Zinc binding domains. Using ribonucleoparticle dissociation experiments we established that Tma108 directly interacts with the nascent protein chain. Additionally, we have shown that translation of the first 35 amino acids of Asn1, one of the Tma108 targets, is necessary and sufficient to recruit Tma108, suggesting that it is loaded early during translation. Comparative genomic analyses, molecular modeling and directed mutagenesis point to Tma108 as an original M1 metallopeptidase, which uses its putative catalytic peptide-binding pocket to bind the N-terminus of its targets. The involvement of Tma108 in co-translational regulation is attested by a drastic change in the subcellular localization of ATP2 mRNA upon Tma108 inactivation. Tma108 is a unique example of a nascent chain-associated factor with high selectivity and its study illustrates the existence of other specific translation-associated factors besides RNA binding proteins.
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Affiliation(s)
- Thierry Delaveau
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie computationnelle et quantitative - Institut de Biologie Paris Seine (LCQB - IBPS), 75005 Paris, France
| | - Dimitri Davoine
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie computationnelle et quantitative - Institut de Biologie Paris Seine (LCQB - IBPS), 75005 Paris, France
| | - Ariane Jolly
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie computationnelle et quantitative - Institut de Biologie Paris Seine (LCQB - IBPS), 75005 Paris, France
| | - Antoine Vallot
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie computationnelle et quantitative - Institut de Biologie Paris Seine (LCQB - IBPS), 75005 Paris, France
| | - Jérôme O Rouvière
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Athenaïs Gerber
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie computationnelle et quantitative - Institut de Biologie Paris Seine (LCQB - IBPS), 75005 Paris, France
| | - Sandra Brochet
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie computationnelle et quantitative - Institut de Biologie Paris Seine (LCQB - IBPS), 75005 Paris, France
| | - Marion Plessis
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie computationnelle et quantitative - Institut de Biologie Paris Seine (LCQB - IBPS), 75005 Paris, France
| | - Roxane Roquigny
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie computationnelle et quantitative - Institut de Biologie Paris Seine (LCQB - IBPS), 75005 Paris, France
| | - Jawad Merhej
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie computationnelle et quantitative - Institut de Biologie Paris Seine (LCQB - IBPS), 75005 Paris, France
| | - Thibaut Leger
- Proteomics facility, Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Camille Garcia
- Proteomics facility, Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Gaëlle Lelandais
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Elodie Laine
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie computationnelle et quantitative - Institut de Biologie Paris Seine (LCQB - IBPS), 75005 Paris, France
| | - Benoit Palancade
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Frédéric Devaux
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie computationnelle et quantitative - Institut de Biologie Paris Seine (LCQB - IBPS), 75005 Paris, France
| | - Mathilde Garcia
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie computationnelle et quantitative - Institut de Biologie Paris Seine (LCQB - IBPS), 75005 Paris, France
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23
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Aschrafi A, Kar AN, Gale JR, Elkahloun AG, Vargas JNS, Sales N, Wilson G, Tompkins M, Gioio AE, Kaplan BB. A heterogeneous population of nuclear-encoded mitochondrial mRNAs is present in the axons of primary sympathetic neurons. Mitochondrion 2016; 30:18-23. [PMID: 27318271 DOI: 10.1016/j.mito.2016.06.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 05/18/2016] [Accepted: 06/14/2016] [Indexed: 10/21/2022]
Abstract
Mitochondria are enriched in subcellular regions of high energy consumption, such as axons and pre-synaptic nerve endings. Accumulating evidence suggests that mitochondrial maintenance in these distal structural/functional domains of the neuron depends on the "in-situ" translation of nuclear-encoded mitochondrial mRNAs. In support of this notion, we recently provided evidence for the axonal targeting of several nuclear-encoded mRNAs, such as cytochrome c oxidase, subunit 4 (COXIV) and ATP synthase, H+ transporting and mitochondrial Fo complex, subunit C1 (ATP5G1). Furthermore, we showed that axonal trafficking and local translation of these mRNAs plays a critical role in the generation of axonal ATP. Using a global gene expression analysis, this study identified a highly diverse population of nuclear-encoded mRNAs that were enriched in the axon and presynaptic nerve terminals. Among this population of mRNAs, fifty seven were found to be at least two-fold more abundant in distal axons, as compared with the parental cell bodies. Gene ontology analysis of the nuclear-encoded mitochondrial mRNAs suggested functions for these gene products in molecular and biological processes, including but not limited to oxidoreductase and electron carrier activity and proton transport. Based on these results, we postulate that local translation of nuclear-encoded mitochondrial mRNAs present in the axons may play an essential role in local energy production and maintenance of mitochondrial function.
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Affiliation(s)
- Armaz Aschrafi
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amar N Kar
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jenna R Gale
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Abdel G Elkahloun
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jose Noberto S Vargas
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Naomi Sales
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gabriel Wilson
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Miranda Tompkins
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anthony E Gioio
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Barry B Kaplan
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA.
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24
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Abstract
Local synthesis of proteins near their activity site has been demonstrated in many biological systems, and has diverse contributions to cellular functions. Studies in recent years have revealed that hundreds of mitochondria-destined proteins are synthesized by cytosolic ribosomes near the mitochondrial outer membrane, indicating that localized translation also occurs at this cellular locus. Furthermore, in the last year central factors that are involved in this process were identified in yeast, Drosophila, and human cells. Herein we review the experimental evidence for localized translation on the cytosolic side of the mitochondrial outer membrane; in addition, we describe the factors that are involved in this process and discuss the conservation of this mechanism among various species. We also describe the relationship between localized translation and import into the mitochondria and suggest avenues of study that look beyond cotranslational import. Finally we discuss future challenges in characterizing the mechanisms for localized translation and its physiological significance.
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Affiliation(s)
- Chen Lesnik
- a Department of Biology ; Technion - Israel Institute of Technology ; Haifa , Israel
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25
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Lehmann G, Udasin RG, Ciechanover A. On the linkage between the ubiquitin-proteasome system and the mitochondria. Biochem Biophys Res Commun 2016; 473:80-86. [DOI: 10.1016/j.bbrc.2016.03.055] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 03/14/2016] [Indexed: 12/20/2022]
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26
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Yeast mRNA localization: protein asymmetry, organelle localization and response to stress. Biochem Soc Trans 2015; 42:1256-60. [PMID: 25110034 DOI: 10.1042/bst20140086] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The localization of mRNA forms a key facet of the post-transcriptional control of gene expression and recent evidence suggests that it may be considerably more widespread than previously anticipated. For example, defined mRNA-containing granules can be associated with translational repression or activation. Furthermore, mRNA P-bodies (processing bodies) harbour much of the mRNA decay machinery and stress granules are thought to play a role in mRNA storage. In the present review, we explore the process of mRNA localization in the yeast Saccharomyces cerevisiae, examining connections between organellar mRNA localization and the response to stress. We also review recent data suggesting that even where there is a global relocalization of mRNA, the specificity and kinetics of this process can be regulated.
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Zhang X, Gao X, Coots RA, Conn CS, Liu B, Qian SB. Translational control of the cytosolic stress response by mitochondrial ribosomal protein L18. Nat Struct Mol Biol 2015; 22:404-10. [PMID: 25866880 PMCID: PMC4424103 DOI: 10.1038/nsmb.3010] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 03/13/2015] [Indexed: 12/27/2022]
Abstract
In response to stress, cells attenuate global protein synthesis but permit efficient translation of mRNAs encoding heat-shock proteins (HSPs). Although decades have passed since the first description of the heat-shock response, how cells achieve translational control of HSP synthesis remains enigmatic. Here we report an unexpected role for mitochondrial ribosomal protein L18 (MRPL18) in the mammalian cytosolic stress response. MRPL18 bears a downstream CUG start codon and generates a cytosolic isoform in a stress-dependent manner. Cytosolic MRPL18 incorporates into the 80S ribosome and facilitates ribosome engagement on mRNAs selected for translation during stress. MRPL18 knockdown has minimal effects on mitochondrial function but substantially dampens cytosolic HSP expression at the level of translation. Our results uncover a hitherto-uncharacterized stress-adaptation mechanism in mammalian cells, which involves formation of a 'hybrid' ribosome responsible for translational regulation during the cytosolic stress response.
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Affiliation(s)
- Xingqian Zhang
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Xiangwei Gao
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Ryan Alex Coots
- 1] Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA. [2] Graduate Field of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Crystal S Conn
- Graduate Field of Genetics, Genomics and Development, Cornell University, Ithaca, New York, USA
| | - Botao Liu
- Graduate Field of Genetics, Genomics and Development, Cornell University, Ithaca, New York, USA
| | - Shu-Bing Qian
- 1] Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA. [2] Graduate Field of Nutritional Sciences, Cornell University, Ithaca, New York, USA. [3] Graduate Field of Genetics, Genomics and Development, Cornell University, Ithaca, New York, USA
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A Perspective on Transport of Proteins into Mitochondria: A Myriad of Open Questions. J Mol Biol 2015; 427:1135-58. [DOI: 10.1016/j.jmb.2015.02.001] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 01/30/2015] [Accepted: 02/02/2015] [Indexed: 11/22/2022]
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Gao J, Schatton D, Martinelli P, Hansen H, Pla-Martin D, Barth E, Becker C, Altmueller J, Frommolt P, Sardiello M, Rugarli EI. CLUH regulates mitochondrial biogenesis by binding mRNAs of nuclear-encoded mitochondrial proteins. ACTA ACUST UNITED AC 2015; 207:213-23. [PMID: 25349259 PMCID: PMC4210445 DOI: 10.1083/jcb.201403129] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
CLUH is a cytosolic mRNA-binding protein that specifically binds a subset of mRNAs encoding mitochondrial proteins and may regulate their localized translation. Mitochondrial function requires coordination of two genomes for protein biogenesis, efficient quality control mechanisms, and appropriate distribution of the organelles within the cell. How these mechanisms are integrated is currently not understood. Loss of the Clu1/CluA homologue (CLUH) gene led to clustering of the mitochondrial network by an unknown mechanism. We find that CLUH is coregulated both with genes encoding mitochondrial proteins and with genes involved in ribosomal biogenesis and translation. Our functional analysis identifies CLUH as a cytosolic messenger ribonucleic acid (RNA; mRNA)–binding protein. RNA immunoprecipitation experiments followed by next-generation sequencing demonstrated that CLUH specifically binds a subset of mRNAs encoding mitochondrial proteins. CLUH depletion decreased the levels of proteins translated by target transcripts and caused mitochondrial clustering. A fraction of CLUH colocalizes with tyrosinated tubulin and can be detected close to mitochondria, suggesting a role in regulating transport or translation of target transcripts close to mitochondria. Our data unravel a novel mechanism linking mitochondrial biogenesis and distribution.
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Affiliation(s)
- Jie Gao
- Institute for Genetics, Center for Molecular Medicine, Cologne Center for Genomics, and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50923 Cologne, Germany Institute for Genetics, Center for Molecular Medicine, Cologne Center for Genomics, and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50923 Cologne, Germany
| | - Désirée Schatton
- Institute for Genetics, Center for Molecular Medicine, Cologne Center for Genomics, and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50923 Cologne, Germany
| | - Paola Martinelli
- Institute for Genetics, Center for Molecular Medicine, Cologne Center for Genomics, and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50923 Cologne, Germany
| | - Henriette Hansen
- Institute for Genetics, Center for Molecular Medicine, Cologne Center for Genomics, and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50923 Cologne, Germany
| | - David Pla-Martin
- Institute for Genetics, Center for Molecular Medicine, Cologne Center for Genomics, and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50923 Cologne, Germany
| | - Esther Barth
- Institute for Genetics, Center for Molecular Medicine, Cologne Center for Genomics, and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50923 Cologne, Germany
| | - Christian Becker
- Institute for Genetics, Center for Molecular Medicine, Cologne Center for Genomics, and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50923 Cologne, Germany
| | - Janine Altmueller
- Institute for Genetics, Center for Molecular Medicine, Cologne Center for Genomics, and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50923 Cologne, Germany
| | - Peter Frommolt
- Institute for Genetics, Center for Molecular Medicine, Cologne Center for Genomics, and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50923 Cologne, Germany
| | - Marco Sardiello
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030
| | - Elena I Rugarli
- Institute for Genetics, Center for Molecular Medicine, Cologne Center for Genomics, and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50923 Cologne, Germany Institute for Genetics, Center for Molecular Medicine, Cologne Center for Genomics, and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50923 Cologne, Germany Institute for Genetics, Center for Molecular Medicine, Cologne Center for Genomics, and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50923 Cologne, Germany
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In the right place at the right time: visualizing and understanding mRNA localization. Nat Rev Mol Cell Biol 2014; 16:95-109. [PMID: 25549890 DOI: 10.1038/nrm3918] [Citation(s) in RCA: 388] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The spatial regulation of protein translation is an efficient way to create functional and structural asymmetries in cells. Recent research has furthered our understanding of how individual cells spatially organize protein synthesis, by applying innovative technology to characterize the relationship between mRNAs and their regulatory proteins, single-mRNA trafficking dynamics, physiological effects of abrogating mRNA localization in vivo and for endogenous mRNA labelling. The implementation of new imaging technologies has yielded valuable information on mRNA localization, for example, by observing single molecules in tissues. The emerging movements and localization patterns of mRNAs in morphologically distinct unicellular organisms and in neurons have illuminated shared and specialized mechanisms of mRNA localization, and this information is complemented by transgenic and biochemical techniques that reveal the biological consequences of mRNA mislocalization.
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Lesnik C, Cohen Y, Atir-Lande A, Schuldiner M, Arava Y. OM14 is a mitochondrial receptor for cytosolic ribosomes that supports co-translational import into mitochondria. Nat Commun 2014; 5:5711. [PMID: 25487825 PMCID: PMC4268710 DOI: 10.1038/ncomms6711] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 10/30/2014] [Indexed: 11/13/2022] Open
Abstract
It is well established that import of proteins into mitochondria can occur after their complete synthesis by cytosolic ribosomes. Recently, an additional model was revived, proposing that some proteins are imported co-translationally. This model entails association of ribosomes with the mitochondrial outer membrane, shown to be mediated through the ribosome-associated chaperone nascent chain-associated complex (NAC). However, the mitochondrial receptor of this complex is unknown. Here, we identify the Saccharomyces cerevisiae outer membrane protein OM14 as a receptor for NAC. OM14Δ mitochondria have significantly lower amounts of associated NAC and ribosomes, and ribosomes from NAC[Δ] cells have reduced levels of associated OM14. Importantly, mitochondrial import assays reveal a significant decrease in import efficiency into OM14Δ mitochondria, and OM14-dependent import necessitates NAC. Our results identify OM14 as the first mitochondrial receptor for ribosome-associated NAC and reveal its importance for import. These results provide a strong support for an additional, co-translational mode of import into mitochondria. Mitochondrial proteins can be imported post-translationally; however, a role for co-translational import has recently provoked renewed interest. Lesnik et al. identify OM14 as a mitochondrial ribosome receptor required for efficient co-translational import of mitochondrial proteins.
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Affiliation(s)
- Chen Lesnik
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Yifat Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Avigail Atir-Lande
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yoav Arava
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
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32
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Singer-Krüger B, Jansen RP. Here, there, everywhere. mRNA localization in budding yeast. RNA Biol 2014; 11:1031-9. [PMID: 25482891 DOI: 10.4161/rna.29945] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
mRNA localization and localized translation is a common mechanism that contributes to cell polarity and cellular asymmetry. In metazoan, mRNA transport participates in embryonic axis determination and neuronal plasticity. Since the mRNA localization process and its molecular machinery are rather complex in higher eukaryotes, the unicellular yeast Saccharomyces cerevisiae has become an attractive model to study mRNA localization. Although the focus has so far been on the mechanism of ASH1 mRNA transport, it has become evident that mRNA localization also assists in protein sorting to organelles, as well as in polarity establishment and maintenance. A diversity of different pathways has been identified that targets mRNA to their destination site, ranging from motor protein-dependent trafficking of translationally silenced mRNAs to co-translational targeting, in which mRNAs hitch-hike to organelles on ribosomes during nascent polypeptide chain elongation. The presence of these diverse pathways in yeast allows a systemic analysis of the contribution of mRNA localization to the physiology of a cell.
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Affiliation(s)
- Birgit Singer-Krüger
- a Interfaculty Institute of Biochemistry ; University of Tübingen ; Tübingen , Germany
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33
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Differential targeting of VDAC3 mRNA isoforms influences mitochondria morphology. Proc Natl Acad Sci U S A 2014; 111:8991-6. [PMID: 24889622 DOI: 10.1073/pnas.1402588111] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Intracellular targeting of mRNAs has recently emerged as a prevalent mechanism to control protein localization. For mitochondria, a cotranslational model of protein import is now proposed in parallel to the conventional posttranslational model, and mitochondrial targeting of mRNAs has been demonstrated in various organisms. Voltage-dependent anion channels (VDACs) are the most abundant proteins in the outer mitochondrial membrane and the major transport pathway for numerous metabolites. Four nucleus-encoded VDACs have been identified in Arabidopsis thaliana. Alternative cleavage and polyadenylation generate two VDAC3 mRNA isoforms differing by their 3' UTR. By using quantitative RT-PCR and in vivo mRNA visualization approaches, the two mRNA variants were shown differentially associated with mitochondria. The longest mRNA presents a 3' extension named alternative UTR (aUTR) that is necessary and sufficient to target VDAC3 mRNA to the mitochondrial surface. Moreover, aUTR is sufficient for the mitochondrial targeting of a reporter transcript, and can be used as a tool to target an unrelated mRNA to the mitochondrial surface. Finally, VDAC3-aUTR mRNA variant impacts mitochondria morphology and size, demonstrating the role of mRNA targeting in mitochondria biogenesis.
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34
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Lesnik C, Arava Y. Isolation of mRNAs associated with yeast mitochondria to study mechanisms of localized translation. J Vis Exp 2014. [PMID: 24686138 DOI: 10.3791/51265] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Most of mitochondrial proteins are encoded in the nucleus and need to be imported into the organelle. Import may occur while the protein is synthesized near the mitochondria. Support for this possibility is derived from recent studies, in which many mRNAs encoding mitochondrial proteins were shown to be localized to the mitochondria vicinity. Together with earlier demonstrations of ribosomes' association with the outer membrane, these results suggest a localized translation process. Such localized translation may improve import efficiency, provide unique regulation sites and minimize cases of ectopic expression. Diverse methods have been used to characterize the factors and elements that mediate localized translation. Standard among these is subcellular fractionation by differential centrifugation. This protocol has the advantage of isolation of mRNAs, ribosomes and proteins in a single procedure. These can then be characterized by various molecular and biochemical methods. Furthermore, transcriptomics and proteomics methods can be applied to the resulting material, thereby allow genome-wide insights. The utilization of yeast as a model organism for such studies has the advantages of speed, costs and simplicity. Furthermore, the advanced genetic tools and available deletion strains facilitate verification of candidate factors.
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Affiliation(s)
- Chen Lesnik
- Department of Biology, Technion - Israel Institute of Technology
| | - Yoav Arava
- Department of Biology, Technion - Israel Institute of Technology;
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35
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Kar AN, Sun CY, Reichard K, Gervasi NM, Pickel J, Nakazawa K, Gioio AE, Kaplan BB. Dysregulation of the axonal trafficking of nuclear-encoded mitochondrial mRNA alters neuronal mitochondrial activity and mouse behavior. Dev Neurobiol 2013; 74:333-50. [PMID: 24151253 DOI: 10.1002/dneu.22141] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 09/03/2013] [Accepted: 10/16/2013] [Indexed: 01/22/2023]
Abstract
Local translation of nuclear-encoded mitochondrial mRNAs is essential for mitochondrial activity, yet there is little insight into the role that axonal trafficking of these transcripts play in neuronal function and behavior. Previously, we identified a 38 nucleotide stem-loop structure (zipcode) in the 3' untranslated region of the Cytochrome C oxidase IV (COXIV) mRNA that directs the transport of a reporter mRNA to the axon of superior cervical ganglion neurons (SCG). Overexpression of a chimeric reporter mRNA with the COXIV zipcode competed with the axonal trafficking of endogenous COXIV mRNA, and led to attenuated axon growth in SCG neurons. Here, we show that exogenous expression of the COXIV zipcode in cultured SCG neurons also results in the reduction of local ATP levels and increases levels of reactive oxygen species (ROS) in the axon. We took advantage of this "competition" phenotype to investigate the in vivo significance of axonal transport of COXIV mRNA. Toward this end, we generated transgenic mice expressing a fluorescent reporter fused to COXIV zipcode under a forebrain-specific promoter. Immunohistological analyses and RT-PCR analyses of RNA from the transgenic mouse brain showed expression of the reporter in the deep layer neurons in the pre-frontal and frontal cortex. Consistent with the in vitro studies, we observed increased ROS levels in neurons of these transgenic animals. A battery of behavioral tests on transgenic mice expressing the COXIV zipcode revealed an "anxiety-like" behavioral phenotype, suggesting an important role for axonal trafficking of nuclear-encoded mitochondrial mRNAs in neuronal physiology and animal behavior.
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Affiliation(s)
- Amar N Kar
- Laboratory of Molecular Biology, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, 20892
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36
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Abstract
The mitochondrion is arguably the most complex organelle in the budding yeast cell cytoplasm. It is essential for viability as well as respiratory growth. Its innermost aqueous compartment, the matrix, is bounded by the highly structured inner membrane, which in turn is bounded by the intermembrane space and the outer membrane. Approximately 1000 proteins are present in these organelles, of which eight major constituents are coded and synthesized in the matrix. The import of mitochondrial proteins synthesized in the cytoplasm, and their direction to the correct soluble compartments, correct membranes, and correct membrane surfaces/topologies, involves multiple pathways and macromolecular machines. The targeting of some, but not all, cytoplasmically synthesized mitochondrial proteins begins with translation of messenger RNAs localized to the organelle. Most proteins then pass through the translocase of the outer membrane to the intermembrane space, where divergent pathways sort them to the outer membrane, inner membrane, and matrix or trap them in the intermembrane space. Roughly 25% of mitochondrial proteins participate in maintenance or expression of the organellar genome at the inner surface of the inner membrane, providing 7 membrane proteins whose synthesis nucleates the assembly of three respiratory complexes.
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37
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Weis BL, Schleiff E, Zerges W. Protein targeting to subcellular organelles via MRNA localization. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:260-73. [PMID: 23457718 DOI: 10.1016/j.bbamcr.2012.04.004] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Cells have complex membranous organelles for the compartmentalization and the regulation of most intracellular processes. Organelle biogenesis and maintenance requires newly synthesized proteins, each of which needs to go from the ribosome translating its mRNA to the correct membrane for insertion or transclocation to an a organellar subcompartment. Decades of research have revealed how proteins are targeted to the correct organelle and translocated across one or more organelle membranes ro the compartment where they function. The paradigm examples involve interactions between a peptide sequence in the protein, localization factors, and various membrane embedded translocation machineries. Membrane translocation is either cotranslational or posttranslational depending on the protein and target organelle. Meanwhile research in embryos, neurons and yeast revealed an alternative targeting mechanism in which the mRNA is localized and only then translated to synthesize the protein in the correct location. In these cases, the targeting information is coded by the cis-acting sequences in the mRNA ("Zipcodes") that interact with localization factors and, in many cases, are transported by the molecular motors on the cytoskeletal filaments. Recently, evidence has been found for this "mRNA based" mechanism in organelle protein targeting to endoplasmic reticulum, mitochondria, and the photosynthetic membranes within chloroplasts. Here we review known and potential roles of mRNA localization in protein targeting to and within organelles. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.
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Affiliation(s)
- Benjamin L Weis
- Goether University, Cluster of Excellence Macromolecular Complexes, Institute for Molecular Biosciences, Max-von-Laue Str. 9, D-60438 Frankfort, Germany
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38
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McNally MA, Soane L, Roelofs BA, Hartman AL, Hardwick JM. The N-terminal helix of Bcl-xL targets mitochondria. Mitochondrion 2013; 13:119-24. [PMID: 23333404 DOI: 10.1016/j.mito.2013.01.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2012] [Revised: 12/16/2012] [Accepted: 01/07/2013] [Indexed: 11/26/2022]
Abstract
Anti- and pro-apoptotic Bcl-2 family members regulate the mitochondrial phase of apoptotic cell death. The mitochondrial targeting mechanisms of Bcl-2 family proteins are tightly regulated. Known outer mitochondrial membrane targeting sequences include the C-terminal tail and central helical hairpin. Bcl-xL also localizes to the inner mitochondrial membrane, but these targeting sequences are unknown. Here we investigate the possibility that the N-terminus of Bcl-xL also contains mitochondrial targeting information. Amino acid residues 1-28 of Bcl-xL fused to EGFP are sufficient to target mitochondria. Although positive charges and helical propensity are required for targeting, similar to import sequences the N-terminus is not sufficient for efficient mitochondrial import.
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Affiliation(s)
- Melanie A McNally
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD 21205, USA.
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Blower MD. Molecular insights into intracellular RNA localization. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2013; 302:1-39. [PMID: 23351709 DOI: 10.1016/b978-0-12-407699-0.00001-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Localization of mRNAs to specific destinations within a cell or an embryo is important for local control of protein synthesis. mRNA localization is well known to function in very large and polarized cells such as neurons, and to facilitate embryonic patterning during early development. However, recent genome-wide studies have revealed that mRNA localization is more widely utilized than previously thought to control gene expression. Not only can transcripts be localized asymmetrically within the cytoplasm, they are often also localized to symmetrically distributed organelles. Recent genetic, cytological, and biochemical studies have begun to provide molecular insight into how cells select RNAs for transport, move them to specific destinations, and control their translation. This chapter will summarize recent insights into the mechanisms and function of RNA localization with a specific emphasis on molecular insights into each step in the mRNA localization process.
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Affiliation(s)
- Michael D Blower
- Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA, USA.
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40
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Abstract
Reprogramming of energetic metabolism is a phenotypic trait of cancer in which mitochondrial dysfunction represents a key event in tumour progression. In the present study, we show that the acquisition of the tumour-promoting phenotype in colon cancer HCT116 cells treated with oligomycin to inhibit ATP synthase is exerted by repression of the synthesis of nuclear-encoded mitochondrial proteins in a process that is regulated at the level of translation. Remarkably, the synthesis of glycolytic proteins is not affected in this situation. Changes in translational control of mitochondrial proteins are signalled by the activation of AMPK (AMP-activated protein kinase) and the GCN2 (general control non-derepressible 2) kinase, leading also to the activation of autophagy. Changes in the bioenergetic function of mitochondria are mimicked by the activation of AMPK and the silencing of ATF4 (activating transcription factor 4). These findings emphasize the relevance of translational control for normal mitochondrial function and for the progression of cancer. Moreover, they demonstrate that glycolysis and oxidative phosphorylation are controlled at different levels of gene expression, offering the cell a mechanistic safeguard strategy for metabolic adaptation under stressful conditions.
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Dudek J, Rehling P, van der Laan M. Mitochondrial protein import: common principles and physiological networks. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1833:274-85. [PMID: 22683763 DOI: 10.1016/j.bbamcr.2012.05.028] [Citation(s) in RCA: 186] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 05/24/2012] [Accepted: 05/28/2012] [Indexed: 11/28/2022]
Abstract
Most mitochondrial proteins are encoded in the nucleus. They are synthesized as precursor forms in the cytosol and must be imported into mitochondria with the help of different protein translocases. Distinct import signals within precursors direct each protein to the mitochondrial surface and subsequently onto specific transport routes to its final destination within these organelles. In this review we highlight common principles of mitochondrial protein import and address different mechanisms of protein integration into mitochondrial membranes. Over the last years it has become clear that mitochondrial protein translocases are not independently operating units, but in fact closely cooperate with each other. We discuss recent studies that indicate how the pathways for mitochondrial protein biogenesis are embedded into a functional network of various other physiological processes, such as energy metabolism, signal transduction, and maintenance of mitochondrial morphology. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.
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Affiliation(s)
- Jan Dudek
- Abteilung Biochemie II, Universität Göttingen, 37073 Göttingen, Germany
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42
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Localization of mRNAs encoding human mitochondrial oxidative phosphorylation proteins. Mitochondrion 2012; 12:391-8. [DOI: 10.1016/j.mito.2012.02.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 02/01/2012] [Accepted: 02/20/2012] [Indexed: 11/21/2022]
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Willers IM, Martínez-Reyes I, Martínez-Diez M, Cuezva JM. miR-127-5p targets the 3'UTR of human β-F1-ATPase mRNA and inhibits its translation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:838-48. [PMID: 22433606 DOI: 10.1016/j.bbabio.2012.03.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 03/01/2012] [Accepted: 03/02/2012] [Indexed: 12/30/2022]
Abstract
The mitochondrial H(+)-ATP synthase is a bottleneck component in the provision of metabolic energy by oxidative phosphorylation. The expression of its catalytic subunit (β-F1-ATPase) is stringently controlled at post-transcriptional levels during oncogenesis, the cell cycle and in development. Here we show that miR-127-5p targets the 3'UTR of β-F1-ATPase mRNA (β-mRNA) significantly reducing its translational efficiency without affecting β-mRNA abundance. Despite the reduced expression of β-F1-ATPase in most human carcinomas, we observed no expression of miR-127-5p in different human cancer cell lines, minimizing the potential role of miR-127-5p as a regulator of the bioenergetic activity of mitochondria in cancer. In contrast, miR-127-5p is highly over-expressed in the human fetal liver. Consistent with previous findings in the rat, the expression of β-F1-ATPase in the human liver also seems to be controlled at post-transcriptional levels during development, what might suggest a role for miR-127-5p in controlling β-mRNA translation and thus in defining the bioenergetic activity of human liver mitochondria. Moreover, immunolocalization techniques and subcellular fractionation experiments using different antibodies against β-F1-ATPase reveal that the ectopic expression of β-F1-ATPase at the cell surface of the hepatocytes and HepG2 cells is negligible or stands for scrutiny.
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Affiliation(s)
- Imke M Willers
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Instituto de Investigación Hospital 12 de Octubre, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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Haim-Vilmovsky L, Gadir N, Herbst RH, Gerst JE. A genomic integration method for the simultaneous visualization of endogenous mRNAs and their translation products in living yeast. RNA (NEW YORK, N.Y.) 2011; 17:2249-2255. [PMID: 22025736 PMCID: PMC3222136 DOI: 10.1261/rna.029637.111] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 09/13/2011] [Indexed: 05/31/2023]
Abstract
Protein localization within cells can be achieved by the targeting and localized translation of mRNA. Yet, our understanding of the dynamics of mRNA targeting and protein localization, and of how general this phenomenon is, is not clear. Plasmid-based expression systems have been used to visualize exogenously expressed mRNAs and proteins; however, these methods typically produce them at levels greater than endogenous and can result in mislocalization. Hence, a method that allows for the simultaneous visualization of endogenous mRNAs and their translation products in living cells is needed. We previously developed a method (m-TAG) to localize endogenously expressed mRNAs in yeast by chromosomal insertion of the MS2 aptamer sequence between the open-reading frame (ORF) and 3' UTR of any gene. Upon coexpression with the MS2 RNA-binding coat protein (MS2-CP) fused with GFP, the aptamer-tagged mRNAs bearing their 3' UTRs are localized using fluorescence microscopy. Here we describe an advanced method (mp-TAG) that allows for the simultaneous visualization of both endogenously expressed mRNAs and their translation products in living yeast for the first time. Homologous recombination is used to insert the mCherry gene and MS2-CP binding sites downstream from any ORF, in order to localize protein and mRNA, respectively. As proof of the concept, we tagged ATP2 as a representative gene and demonstrated that endogenous ATP2 mRNA and protein localize to mitochondria, as shown previously. In addition, we demonstrate that tagged proteins like Hhf2, Vph1, and Yef3 localize to their expected subcellular location, while the localization of their mRNAs is revealed for the first time.
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Affiliation(s)
- Liora Haim-Vilmovsky
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Noga Gadir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rebecca H. Herbst
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Jeffrey E. Gerst
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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Gadir N, Haim-Vilmovsky L, Kraut-Cohen J, Gerst JE. Localization of mRNAs coding for mitochondrial proteins in the yeast Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2011; 17:1551-65. [PMID: 21705432 PMCID: PMC3153978 DOI: 10.1261/rna.2621111] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Targeted mRNA localization is a likely determinant of localized protein synthesis. To investigate whether mRNAs encoding mitochondrial proteins (mMPs) localize to mitochondria and, thus, might confer localized protein synthesis and import, we visualized endogenously expressed mMPs in vivo for the first time. We determined the localization of 24 yeast mMPs encoding proteins of the mitochondrial matrix, outer and inner membrane, and intermembrane space and found that many mMPs colocalize with mitochondria in vivo. This supports earlier cell fractionation and microarray-based studies that proposed mMP association with the mitochondrial fraction. Interestingly, a number of mMPs showed a dependency on the mitochondrial Puf3 RNA-binding protein, as well as nonessential proteins of the translocase of the outer membrane (TOM) complex import machinery, for normal colocalization with mitochondria. We examined the specific determinants of ATP2 and OXA1 mRNA localization and found a mutual dependency on the 3' UTR, Puf3, Tom7, and Tom70, but not Tom20, for localization. Tom6 may facilitate the localization of specific mRNAs as OXA1, but not ATP2, mRNA was mislocalized in tom6Δ cells. Interestingly, a substantial fraction of OXA1 and ATP2 RNA granules colocalized with the endoplasmic reticulum (ER) and a deletion in MDM10, which mediates mitochondria-ER tethering, resulted in a significant loss of OXA1 mRNA localization with ER. Finally, neither ATP2 nor OXA1 mRNA targeting was affected by a block in translation initiation, indicating that translation may not be essential for mRNA anchoring. Thus, endogenously expressed mRNAs are targeted to the mitochondria in vivo, and multiple factors contribute to mMP localization.
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Affiliation(s)
- Noga Gadir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Liora Haim-Vilmovsky
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Judith Kraut-Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Jeffrey E. Gerst
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
- Corresponding author.E-mail
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Cwerman-Thibault H, Sahel JA, Corral-Debrinski M. Mitochondrial medicine: to a new era of gene therapy for mitochondrial DNA mutations. J Inherit Metab Dis 2011; 34:327-44. [PMID: 20571866 DOI: 10.1007/s10545-010-9131-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Revised: 05/12/2010] [Accepted: 05/17/2010] [Indexed: 01/01/2023]
Abstract
Mitochondrial disorders can no longer be ignored in most medical disciplines. Such disorders include specific and widespread organ involvement, with tissue degeneration or tumor formation. Primary or secondary actors, mitochondrial dysfunctions also play a role in the aging process. Despite progresses made in identification of their molecular bases, nearly everything remains to be done as regards therapy. Research dealing with mitochondrial physiology and pathology has >20 years of history around the world. We are involved, as are many other laboratories, in the challenge of finding ways to fight these diseases. However, our main limitation is the scarcety of animal models required for both understanding the molecular mechanisms underlying the diseases and evaluating therapeutic strategies. This is especially true for diseases due to mutations in mitochondrial DNA (mtDNA), since an authentic genetic model of mtDNA mutations is technically a very difficult task due to both the inability of manipulating the mitochondrial genome of living mammalian cells and to its multicopy nature. This has led researchers in the field to consider the prospect of gene therapy approaches that can roughly be divided into three groups: (1) import of wild-type copies or relevant sections of DNA or RNA into mitochondria, (2) manipulation of mitochondrial genetic content, and (3) rescue of a defect by expression of an engineered gene product from the nucleus (allotopic or xenotropic expression). We briefly introduce these concepts and indicate where promising progress has been made in the last decade.
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Mitochondrial RNA import: from diversity of natural mechanisms to potential applications. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2011; 287:145-90. [PMID: 21414588 DOI: 10.1016/b978-0-12-386043-9.00004-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mitochondria, owing to their bacterial origin, still contain their own DNA. However, the majority of bacterial genes were lost or transferred to the nuclear genome and the biogenesis of the "present-day" mitochondria mainly depends on the expression of the nuclear genome. Thus, most mitochondrial proteins and a small number of mitochondrial RNAs (mostly tRNAs) expressed from nuclear genes need to be imported into the organelle. During evolution, macromolecule import systems were universally established. The processes of protein mitochondrial import are very well described in the literature. By contrast, deciphering the mitochondrial RNA import phenomenon is still a real challenge. The purpose of this review is to present a general survey of our present knowledge in this field in different model organisms, protozoa, plants, yeast, and mammals. Questions still under debate and major challenges are discussed. Mitochondria are involved in numerous human diseases. The targeting of macromolecule to mitochondria represents a promising way to fight mitochondrial disorders and recent developments in this area of research are presented.
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Post-transcriptional regulation of the mitochondrial H(+)-ATP synthase: a key regulator of the metabolic phenotype in cancer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1807:543-51. [PMID: 21035425 DOI: 10.1016/j.bbabio.2010.10.016] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Revised: 10/19/2010] [Accepted: 10/20/2010] [Indexed: 12/12/2022]
Abstract
A distinctive metabolic trait of tumors is their enforced aerobic glycolysis. This phenotype was first reported by Otto Warburg, who suggested that the increased glucose consumption of cancer cells under aerobic conditions might result from an impaired bioenergetic activity of their mitochondria. A central player in defining the bioenergetic activity of the cell is the mitochondrial H(+)-ATP synthase. The expression of its catalytic subunit β-F1-ATPase is tightly regulated at post-transcriptional levels during mammalian development and in the cell cycle. Moreover, the down-regulation of β-F1-ATPase is a hallmark of most human carcinomas. In this review we summarize our present understanding of the molecular mechanisms that participate in promoting the "abnormal" aerobic glycolysis of prevalent human carcinomas. The role of the ATPase Inhibitor Factor 1 (IF1) and of Ras-GAP SH3 binding protein 1 (G3BP1), controlling the activity of the H(+)-ATP synthase and the translation of β-F1-ATPase mRNA respectively in cancer cells is emphasized. Furthermore, we underline the role of mitochondrial dysfunction as a pivotal player of tumorigenesis.
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Michaud M, Maréchal-Drouard L, Duchêne AM. RNA trafficking in plant cells: targeting of cytosolic mRNAs to the mitochondrial surface. PLANT MOLECULAR BIOLOGY 2010; 73:697-704. [PMID: 20506035 DOI: 10.1007/s11103-010-9650-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Accepted: 05/07/2010] [Indexed: 05/06/2023]
Abstract
Subcellular localization of mRNA is a widespread and efficient way for targeting proteins to specific regions of a cell. Messenger RNA sorting appears as a key mechanism for posttranscriptional gene regulation, and its involvement in organelle biogenesis has been described in different organisms. Here we demonstrate that mRNA targeting to the surface of mitochondria occurs in higher plants. Cytosolic mRNAs corresponding to mitochondrial proteins, but also to some particular cytosolic proteins, were found associated to mitochondria, offering new perspectives for mitochondria biogenesis in plant cells.
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Affiliation(s)
- Morgane Michaud
- Institut de Biologie Moléculaire des Plantes, UPR 2357 du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
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Ortega AD, Willers IM, Sala S, Cuezva JM. Human G3BP1 interacts with beta-F1-ATPase mRNA and inhibits its translation. J Cell Sci 2010; 123:2685-96. [PMID: 20663914 DOI: 10.1242/jcs.065920] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The post-transcriptional regulation of nuclear mRNAs that encode core components of mitochondria has relevant implications in cell physiology. The mRNA that encodes the catalytic subunit of the mitochondrial H(+)-ATP synthase subunit beta (ATP5B, beta-F1-ATPase) is localized in a large ribonucleoprotein (RNP) complex (beta-F1-RNP), which is subjected to stringent translational control during development and the cell cycle, and in carcinogenesis. Because downregulation of beta-F1-ATPase is a conserved feature of most prevalent human carcinomas, we have investigated the molecular composition of the human beta-F1-RNP. By means of an improved affinity-chromatography procedure and protein sequencing we have identified nine RNA-binding proteins (RNABPs) of the beta-F1-RNP. Immunoprecipitation assays of Ras-GAP SH3 binding protein 1 (G3BP1) and fluorescent in-situ hybridization of mRNA indicate a direct interaction of the endogenous G3BP1 with mRNA of beta-F1-ATPase (beta-F1 mRNA). RNA-bridged trimolecular fluorescence complementation (TriFC) assays confirm the interaction of G3BP1 with the 3'-UTR of beta-F1 mRNA in cytoplasmic RNA-granules. Confocal and high-resolution immunoelectron-microscopy experiments suggest that the beta-F1-RNP is sorted to the periphery of mitochondria. Molecular and functional studies indicate that the interaction of G3BP1 with beta-F1 mRNA inhibits its translation at the initiation level, supporting a role for G3BP1 in the glycolytic switch that occurs in cancer.
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Affiliation(s)
- Alvaro D Ortega
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC-UAM, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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