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Krieger MR, Abrahamian M, He KL, Atamdede S, Hakimjavadi H, Momcilovic M, Ostrow D, Maggo SD, Tsang YP, Gai X, Chanfreau GF, Shackelford DB, Teitell MA, Koehler CM. Trafficking of mitochondrial double-stranded RNA from mitochondria to the cytosol. Life Sci Alliance 2024; 7:e202302396. [PMID: 38955468 PMCID: PMC11220484 DOI: 10.26508/lsa.202302396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 06/25/2024] [Accepted: 06/25/2024] [Indexed: 07/04/2024] Open
Abstract
In addition to mitochondrial DNA, mitochondrial double-stranded RNA (mtdsRNA) is exported from mitochondria. However, specific channels for RNA transport have not been demonstrated. Here, we begin to characterize channel candidates for mtdsRNA export from the mitochondrial matrix to the cytosol. Down-regulation of SUV3 resulted in the accumulation of mtdsRNAs in the matrix, whereas down-regulation of PNPase resulted in the export of mtdsRNAs to the cytosol. Targeting experiments show that PNPase functions in both the intermembrane space and matrix. Strand-specific sequencing of the double-stranded RNA confirms the mitochondrial origin. Inhibiting or down-regulating outer membrane proteins VDAC1/2 and BAK/BAX or inner membrane proteins PHB1/2 strongly attenuated the export of mtdsRNAs to the cytosol. The cytosolic mtdsRNAs subsequently localized to large granules containing the stress protein TIA-1 and activated the type 1 interferon stress response pathway. Abundant mtdsRNAs were detected in a subset of non-small-cell lung cancer cell lines that were glycolytic, indicating relevance in cancer biology. Thus, we propose that mtdsRNA is a new damage-associated molecular pattern that is exported from mitochondria in a regulated manner.
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Affiliation(s)
- Matthew R Krieger
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
| | | | - Kevin L He
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
| | - Sean Atamdede
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
| | | | - Milica Momcilovic
- Pulmonary and Critical Care Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA
| | - Dejerianne Ostrow
- Department of Pathology, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Simran Ds Maggo
- Department of Pathology, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Yik Pui Tsang
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
| | - Xiaowu Gai
- Department of Pathology, Children's Hospital Los Angeles, Los Angeles, CA, USA
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Guillaume F Chanfreau
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
| | - David B Shackelford
- Pulmonary and Critical Care Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA
| | - Michael A Teitell
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, CA, USA
- Broad Stem Cell Research Center, UCLA, Los Angeles, CA, USA
- NanoSystems Institute, UCLA, Los Angeles, CA, USA
| | - Carla M Koehler
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
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2
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Begeman A, Smolka JA, Shami A, Waingankar TP, Lewis SC. A spatial atlas of mitochondrial gene expression reveals dynamic translation hubs and remodeling in stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.05.604215. [PMID: 39149346 PMCID: PMC11326164 DOI: 10.1101/2024.08.05.604215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Mitochondrial genome expression is important for cellular bioenergetics. How mitochondrial RNA processing and translation are spatially organized across dynamic mitochondrial networks is not well understood. Here, we report that processed mitochondrial RNAs are consolidated with mitoribosome components into translation hubs distal to either nucleoids or processing granules in human cells. During stress, these hubs are remodeled into translationally repressed mesoscale bodies containing messenger, ribosomal, and double-stranded RNA. We show that the highly conserved helicase SUV3 contributes to the distribution of processed RNA within mitochondrial networks, and that stress bodies form downstream of proteostatic stress in cells lacking SUV3 unwinding activity. We propose that the spatial organization of nascent chain synthesis into discrete domains serves to throttle the flow of genetic information in stress to ensure mitochondrial quality control.
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Affiliation(s)
- Adam Begeman
- Department of Molecular and Cell Biology, University of California, Berkeley, CA USA
| | - John A. Smolka
- Department of Molecular and Cell Biology, University of California, Berkeley, CA USA
| | - Ahmad Shami
- Department of Molecular and Cell Biology, University of California, Berkeley, CA USA
| | | | - Samantha C. Lewis
- Department of Molecular and Cell Biology, University of California, Berkeley, CA USA
- Innovative Genomics Institute, Berkeley, CA, USA
- Helen Wills Neuroscience Institute, Berkeley, CA USA
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA USA
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3
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Muneretto G, Plazzi F, Passamonti M. Mitochondrion-to-nucleus communication mediated by RNA export: a survey of potential mechanisms and players across eukaryotes. Biol Lett 2024; 20:20240147. [PMID: 38982851 PMCID: PMC11283861 DOI: 10.1098/rsbl.2024.0147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/16/2024] [Accepted: 06/06/2024] [Indexed: 07/11/2024] Open
Abstract
The nucleus interacts with the other organelles to perform essential functions of the eukaryotic cell. Mitochondria have their own genome and communicate back to the nucleus in what is known as mitochondrial retrograde response. Information is transferred to the nucleus in many ways, leading to wide-ranging changes in nuclear gene expression and culminating with changes in metabolic, regulatory or stress-related pathways. RNAs are emerging molecules involved in this signalling. RNAs encode precise information and are involved in highly target-specific signalling, through a wide range of processes known as RNA interference. RNA-mediated mitochondrial retrograde response requires these molecules to exit the mitochondrion, a process that is still mostly unknown. We suggest that the proteins/complexes translocases of the inner membrane, polynucleotide phosphorylase, mitochondrial permeability transition pore, and the subunits of oxidative phosphorylation complexes may be responsible for RNA export.
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Affiliation(s)
- Giorgio Muneretto
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Federico Plazzi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Marco Passamonti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
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4
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Głodowicz P, Kuczyński K, Val R, Dietrich A, Rolle K. Mitochondrial transport of catalytic RNAs and targeting of the organellar transcriptome in human cells. J Mol Cell Biol 2024; 15:mjad051. [PMID: 37591617 PMCID: PMC11148835 DOI: 10.1093/jmcb/mjad051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/19/2023] Open
Abstract
Mutations in the small genome present in mitochondria often result in severe pathologies. Different genetic strategies have been explored, aiming to rescue such mutations. A number of these strategies were based on the capacity of human mitochondria to import RNAs from the cytosol and designed to repress the replication of the mutated genomes or to provide the organelles with wild-type versions of mutant transcripts. However, the mutant RNAs present in mitochondria turned out to be an obstacle to therapy and little attention has been devoted so far to their elimination. Here, we present the development of a strategy to knockdown mitochondrial RNAs in human cells using the transfer RNA-like structure of Brome mosaic virus or Tobacco mosaic virus as a shuttle to drive trans-cleaving ribozymes into the organelles in human cell lines. We obtained a specific knockdown of the targeted mitochondrial ATP6 mRNA, followed by a deep drop in ATP6 protein and a functional impairment of the oxidative phosphorylation chain. Our strategy provides a powerful approach to eliminate mutant organellar transcripts and to analyse the control and communication of the human organellar genetic system.
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Affiliation(s)
- Paweł Głodowicz
- Department of Molecular Neurooncology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Z. Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Konrad Kuczyński
- Department of Molecular Neurooncology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Z. Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Romain Val
- Institute of Plant Molecular Biology, French National Center for Scientific Research (CNRS) and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - André Dietrich
- Institute of Plant Molecular Biology, French National Center for Scientific Research (CNRS) and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Katarzyna Rolle
- Department of Molecular Neurooncology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Z. Noskowskiego 12/14, 61-704 Poznan, Poland
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5
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Jasra IT, Cuesta-Gomez N, Verhoeff K, Marfil-Garza BA, Dadheech N, Shapiro AMJ. Mitochondrial regulation in human pluripotent stem cells during reprogramming and β cell differentiation. Front Endocrinol (Lausanne) 2023; 14:1236472. [PMID: 37929027 PMCID: PMC10623316 DOI: 10.3389/fendo.2023.1236472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/06/2023] [Indexed: 11/07/2023] Open
Abstract
Mitochondria are the powerhouse of the cell and dynamically control fundamental biological processes including cell reprogramming, pluripotency, and lineage specification. Although remarkable progress in induced pluripotent stem cell (iPSC)-derived cell therapies has been made, very little is known about the role of mitochondria and the mechanisms involved in somatic cell reprogramming into iPSC and directed reprogramming of iPSCs in terminally differentiated cells. Reprogramming requires changes in cellular characteristics, genomic and epigenetic regulation, as well as major mitochondrial metabolic changes to sustain iPSC self-renewal, pluripotency, and proliferation. Differentiation of autologous iPSC into terminally differentiated β-like cells requires further metabolic adaptation. Many studies have characterized these alterations in signaling pathways required for the generation and differentiation of iPSC; however, very little is known regarding the metabolic shifts that govern pluripotency transition to tissue-specific lineage differentiation. Understanding such metabolic transitions and how to modulate them is essential for the optimization of differentiation processes to ensure safe iPSC-derived cell therapies. In this review, we summarize the current understanding of mitochondrial metabolism during somatic cell reprogramming to iPSCs and the metabolic shift that occurs during directed differentiation into pancreatic β-like cells.
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Affiliation(s)
- Ila Tewari Jasra
- Clinical Islet Transplant Program, Department of Surgery, Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Nerea Cuesta-Gomez
- Clinical Islet Transplant Program, Department of Surgery, Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Kevin Verhoeff
- Clinical Islet Transplant Program, Department of Surgery, Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Braulio A. Marfil-Garza
- Clinical Islet Transplant Program, Department of Surgery, Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
- Tecnologico de Monterrey, The Institute for Obesity Research, Monterrey, Nuevo Leon, Mexico
| | - Nidheesh Dadheech
- Clinical Islet Transplant Program, Department of Surgery, Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - A. M. James Shapiro
- Clinical Islet Transplant Program, Department of Surgery, Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
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6
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Liu J, Li W, Li J, Song E, Liang H, Rong W, Jiang X, Xu N, Wang W, Qu S, Gu S, Zhang Y, Yu Zhang C, Zen K. A Novel Pathway of Functional microRNA Uptake and Mitochondria Delivery. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2300452. [PMID: 37357137 PMCID: PMC10460862 DOI: 10.1002/advs.202300452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/22/2023] [Indexed: 06/27/2023]
Abstract
Extracellular microRNAs (miRNAs) play a critical role in horizontal gene regulation. Uptake of extracellular miRNAs by recipient cells and their intracellular transport, however, remains elusive. Here RNA phase separation is shown as a novel pathway of miRNA uptake. In the presence of serum, synthetic miRNAs rapidly self-assembly into ≈110 nm discrete nanoparticles, which enable miRNAs' entry into different cells. Depleting serum cationic proteins prevents the formation of such nanoparticles and thus blocks miRNA uptake. Different from lipofectamine-mediated miRNA transfection in which majority of miRNAs are accumulated in lysosomes of transfected cells, nanoparticles-mediated miRNA uptake predominantly delivers miRNAs into mitochondria in a polyribonucleotide nucleotidyltransferase 1(PNPT1)-dependent manner. Functional assays further show that the internalized miR-21 via miRNA phase separation enhances mitochondrial translation of cytochrome b (CYB), leading to increase in adenosine triphosphate (ATP) and reactive oxygen species (ROS) reduction in HEK293T cells. The findings thus reveal a previously unrecognized mechanism for uptake and delivery functional extracellular miRNAs into mitochondria.
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Affiliation(s)
- Jiachen Liu
- State Key Laboratory of Pharmaceutical BiotechnologyNanjing University School of Life SciencesNanjingJiangsu210093China
| | - Weili Li
- State Key Laboratory of Pharmaceutical BiotechnologyNanjing University School of Life SciencesNanjingJiangsu210093China
| | - Jianfeng Li
- State Key Laboratory of Pharmaceutical BiotechnologyNanjing University School of Life SciencesNanjingJiangsu210093China
| | - Eli Song
- The Laboratory of Biological Electron Microscopy and Structural Biology Centre for Biological ImagingInstitute of Biophysics ChineseAcademy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
| | - Hongwei Liang
- School of Life Science and TechnologyChina Pharmaceutical University639 Longmian AvenueNanjingJiangsu211198China
| | - Weiwei Rong
- State Key Laboratory of Pharmaceutical BiotechnologyNanjing University School of Life SciencesNanjingJiangsu210093China
| | - Xinli Jiang
- State Key Laboratory of Pharmaceutical BiotechnologyNanjing University School of Life SciencesNanjingJiangsu210093China
| | - Nuo Xu
- State Key Laboratory of Pharmaceutical BiotechnologyNanjing University School of Life SciencesNanjingJiangsu210093China
| | - Wei Wang
- State Key Laboratory of Pharmaceutical BiotechnologyNanjing University School of Life SciencesNanjingJiangsu210093China
| | - Shuang Qu
- School of Life Science and TechnologyChina Pharmaceutical University639 Longmian AvenueNanjingJiangsu211198China
| | - Shouyong Gu
- Institute of Geriatric MedicineJiangsu Province Geriatric HospitalNanjingJiangsuChina
| | - Yujing Zhang
- State Key Laboratory of Pharmaceutical BiotechnologyNanjing University School of Life SciencesNanjingJiangsu210093China
| | - Chen‐ Yu Zhang
- State Key Laboratory of Pharmaceutical BiotechnologyNanjing University School of Life SciencesNanjingJiangsu210093China
| | - Ke Zen
- State Key Laboratory of Pharmaceutical BiotechnologyNanjing University School of Life SciencesNanjingJiangsu210093China
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7
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Udroiu I, Marinaccio J, Sgura A. Many Functions of Telomerase Components: Certainties, Doubts, and Inconsistencies. Int J Mol Sci 2022; 23:ijms232315189. [PMID: 36499514 PMCID: PMC9736166 DOI: 10.3390/ijms232315189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/23/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
A growing number of studies have evidenced non-telomeric functions of "telomerase". Almost all of them, however, investigated the non-canonical effects of the catalytic subunit TERT, and not the telomerase ribonucleoprotein holoenzyme. These functions mainly comprise signal transduction, gene regulation and the increase of anti-oxidative systems. Although less studied, TERC (the RNA component of telomerase) has also been shown to be involved in gene regulation, as well as other functions. All this has led to the publication of many reviews on the subject, which, however, are often disseminating personal interpretations of experimental studies of other researchers as original proofs. Indeed, while some functions such as gene regulation seem ascertained, especially because mechanistic findings have been provided, other ones remain dubious and/or are contradicted by other direct or indirect evidence (e.g., telomerase activity at double-strand break site, RNA polymerase activity of TERT, translation of TERC, mitochondrion-processed TERC). In a critical study of the primary evidence so far obtained, we show those functions for which there is consensus, those showing contradictory results and those needing confirmation. The resulting picture, together with some usually neglected aspects, seems to indicate a link between TERT and TERC functions and cellular stemness and gives possible directions for future research.
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8
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How RNases Shape Mitochondrial Transcriptomes. Int J Mol Sci 2022; 23:ijms23116141. [PMID: 35682820 PMCID: PMC9181182 DOI: 10.3390/ijms23116141] [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: 05/02/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 11/17/2022] Open
Abstract
Mitochondria are the power houses of eukaryote cells. These endosymbiotic organelles of prokaryote origin are considered as semi-autonomous since they have retained a genome and fully functional gene expression mechanisms. These pathways are particularly interesting because they combine features inherited from the bacterial ancestor of mitochondria with characteristics that appeared during eukaryote evolution. RNA biology is thus particularly diverse in mitochondria. It involves an unexpectedly vast array of factors, some of which being universal to all mitochondria and others being specific from specific eukaryote clades. Among them, ribonucleases are particularly prominent. They play pivotal functions such as the maturation of transcript ends, RNA degradation and surveillance functions that are required to attain the pool of mature RNAs required to synthesize essential mitochondrial proteins such as respiratory chain proteins. Beyond these functions, mitochondrial ribonucleases are also involved in the maintenance and replication of mitochondrial DNA, and even possibly in the biogenesis of mitochondrial ribosomes. The diversity of mitochondrial RNases is reviewed here, showing for instance how in some cases a bacterial-type enzyme was kept in some eukaryotes, while in other clades, eukaryote specific enzymes were recruited for the same function.
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Yamada Y, Ishizuka S, Arai M, Maruyama M, Harashima H. Recent advances in delivering RNA-based therapeutics to mitochondria. Expert Opin Biol Ther 2022; 22:1209-1219. [PMID: 35543589 DOI: 10.1080/14712598.2022.2070427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION After the emergence of lipid nanoparticles (LNP) containing therapeutic mRNA as vaccines for use against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the clinical usefulness of nucleic acid-encapsulated LNPs is now a fact. In addition to the nucleus and cytoplasm, mitochondria, which have their own genome, are a site where nucleic acids function in the cell. Gene therapies targeting mitochondria are expected to pave the way for the next generation of therapies. AREAS COVERED Methods for delivering nucleic acids to mitochondria are needed in order to realize such innovative therapies. However, only a few reports on delivery systems targeting mitochondria have appeared. In this review, we summarize the current state of research on RNA-based therapeutics targeted to mitochondria, with emphasis on mitochondrial RNA delivery therapies and on therapies that involve the use of mitochondrial genome editing devices. EXPERT OPINION We hope that this review article will focus our attention to this area of research, stimulate more interest in this field of research, and lead to the development of mitochondria-targeted nucleic acid medicine. It has the potential to become a major weapon against urgent and unknown diseases, including SARS-CoV-2 infections.
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Affiliation(s)
- Yuma Yamada
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.,Fusion Oriented Research for Disruptive Science and Technology (FOREST) Program, Japan Science and Technology Agency (JST), Japan
| | - Sen Ishizuka
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Manae Arai
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Minako Maruyama
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
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10
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Yin T, Luo J, Huang D, Li H. Current Progress of Mitochondrial Genome Editing by CRISPR. Front Physiol 2022; 13:883459. [PMID: 35586709 PMCID: PMC9108280 DOI: 10.3389/fphys.2022.883459] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/18/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- Tao Yin
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Junjie Luo
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, China
| | - Danqiong Huang
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Hui Li
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- *Correspondence: Hui Li,
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11
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Falchi FA, Pizzoccheri R, Briani F. Activity and Function in Human Cells of the Evolutionary Conserved Exonuclease Polynucleotide Phosphorylase. Int J Mol Sci 2022; 23:ijms23031652. [PMID: 35163574 PMCID: PMC8836086 DOI: 10.3390/ijms23031652] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 01/28/2022] [Accepted: 01/28/2022] [Indexed: 02/04/2023] Open
Abstract
Polynucleotide phosphorylase (PNPase) is a phosphorolytic RNA exonuclease highly conserved throughout evolution. Human PNPase (hPNPase) is located in mitochondria and is essential for mitochondrial function and homeostasis. Not surprisingly, mutations in the PNPT1 gene, encoding hPNPase, cause serious diseases. hPNPase has been implicated in a plethora of processes taking place in different cell compartments and involving other proteins, some of which physically interact with hPNPase. This paper reviews hPNPase RNA binding and catalytic activity in relation with the protein structure and in comparison, with the activity of bacterial PNPases. The functions ascribed to hPNPase in different cell compartments are discussed, highlighting the gaps that still need to be filled to understand the physiological role of this ancient protein in human cells.
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12
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Giordani C, Silvestrini A, Giuliani A, Olivieri F, Rippo MR. MicroRNAs as Factors in Bidirectional Crosstalk Between Mitochondria and the Nucleus During Cellular Senescence. Front Physiol 2021; 12:734976. [PMID: 34566699 PMCID: PMC8458936 DOI: 10.3389/fphys.2021.734976] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/12/2021] [Indexed: 01/12/2023] Open
Abstract
Mitochondria are essential organelles that generate most of the chemical energy to power the cell through ATP production, thus regulating cell homeostasis. Although mitochondria have their own independent genome, most of the mitochondrial proteins are encoded by nuclear genes. An extensive bidirectional communication network between mitochondria and the nucleus has been discovered, thus making them semi-autonomous organelles. The nucleus-to-mitochondria signaling pathway, called Anterograde Signaling Pathway can be deduced, since the majority of mitochondrial proteins are encoded in the nucleus, less is known about the opposite pathway, the so-called mitochondria-to-nucleus retrograde signaling pathway. Several studies have demonstrated that non-coding RNAs are essential "messengers" of this communication between the nucleus and the mitochondria and that they might have a central role in the coordination of important mitochondrial biological processes. In particular, the finding of numerous miRNAs in mitochondria, also known as mitomiRs, enabled insights into their role in mitochondrial gene transcription. MitomiRs could act as important mediators of this complex crosstalk between the nucleus and the mitochondria. Mitochondrial homeostasis is critical for the physiological processes of the cell. Disruption at any stage in their metabolism, dynamics and bioenergetics could lead to the production of considerable amounts of reactive oxygen species and increased mitochondrial permeability, which are among the hallmarks of cellular senescence. Extensive changes in mitomiR expression and distribution have been demonstrated in senescent cells, those could possibly lead to an alteration in mitochondrial homeostasis. Here, we discuss the emerging putative roles of mitomiRs in the bidirectional communication pathways between mitochondria and the nucleus, with a focus on the senescence-associated mitomiRs.
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Affiliation(s)
- Chiara Giordani
- Department of Clinical and Molecular Sciences, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy
| | - Andrea Silvestrini
- Department of Clinical and Molecular Sciences, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy
| | - Angelica Giuliani
- Department of Clinical and Molecular Sciences, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy
| | - Fabiola Olivieri
- Department of Clinical and Molecular Sciences, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy
- Center of Clinical Pathology and Innovative Therapy, IRCCS INRCA, Ancona, Italy
| | - Maria Rita Rippo
- Department of Clinical and Molecular Sciences, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy
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13
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Tarasenko TA, Klimenko ES, Tarasenko VI, Koulintchenko MV, Dietrich A, Weber-Lotfi F, Konstantinov YM. Plant mitochondria import DNA via alternative membrane complexes involving various VDAC isoforms. Mitochondrion 2021; 60:43-58. [PMID: 34303006 DOI: 10.1016/j.mito.2021.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/17/2021] [Accepted: 07/19/2021] [Indexed: 12/23/2022]
Abstract
Mitochondria possess transport mechanisms for import of RNA and DNA. Based on import into isolated Solanum tuberosum mitochondria in the presence of competitors, inhibitors or effectors, we show that DNA fragments of different size classes are taken up into plant organelles through distinct channels. Alternative channels can also be activated according to the amount of DNA substrate of a given size class. Analyses of Arabidopsis thaliana knockout lines pointed out a differential involvement of individual voltage-dependent anion channel (VDAC) isoforms in the formation of alternative channels. We propose several outer and inner membrane proteins as VDAC partners in these pathways.
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Affiliation(s)
- Tatiana A Tarasenko
- Siberian Institute of Plant Physiology and Biochemistry, SB RAS, 132 Lermontov St, Irkutsk 664033, Russia
| | - Ekaterina S Klimenko
- Siberian Institute of Plant Physiology and Biochemistry, SB RAS, 132 Lermontov St, Irkutsk 664033, Russia
| | - Vladislav I Tarasenko
- Siberian Institute of Plant Physiology and Biochemistry, SB RAS, 132 Lermontov St, Irkutsk 664033, Russia
| | - Milana V Koulintchenko
- Siberian Institute of Plant Physiology and Biochemistry, SB RAS, 132 Lermontov St, Irkutsk 664033, Russia.
| | - André Dietrich
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 Rue du Général Zimmer, 67084 Strasbourg, France
| | - Frédérique Weber-Lotfi
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 Rue du Général Zimmer, 67084 Strasbourg, France
| | - Yuri M Konstantinov
- Siberian Institute of Plant Physiology and Biochemistry, SB RAS, 132 Lermontov St, Irkutsk 664033, Russia; Irkutsk State University, 1 Karl Marx St, Irkutsk 664003, Russia
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14
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Jang YH, Ahn SR, Shim JY, Lim KI. Engineering Genetic Systems for Treating Mitochondrial Diseases. Pharmaceutics 2021; 13:810. [PMID: 34071708 PMCID: PMC8227772 DOI: 10.3390/pharmaceutics13060810] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/23/2021] [Accepted: 05/24/2021] [Indexed: 12/13/2022] Open
Abstract
Mitochondria are intracellular energy generators involved in various cellular processes. Therefore, mitochondrial dysfunction often leads to multiple serious diseases, including neurodegenerative and cardiovascular diseases. A better understanding of the underlying mitochondrial dysfunctions of the molecular mechanism will provide important hints on how to mitigate the symptoms of mitochondrial diseases and eventually cure them. In this review, we first summarize the key parts of the genetic processes that control the physiology and functions of mitochondria and discuss how alterations of the processes cause mitochondrial diseases. We then list up the relevant core genetic components involved in these processes and explore the mutations of the components that link to the diseases. Lastly, we discuss recent attempts to apply multiple genetic methods to alleviate and further reverse the adverse effects of the core component mutations on the physiology and functions of mitochondria.
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Affiliation(s)
- Yoon-ha Jang
- Department of Chemical and Biological Engineering, Sookmyung Women’s University, Yongsan-gu, Seoul 04310, Korea; (Y.-h.J.); (J.-y.S.)
| | - Sae Ryun Ahn
- Industry Collaboration Center, Industry-Academic Cooperation Foundation, Sookmyung Women’s University, Yongsan-gu, Seoul 04310, Korea;
| | - Ji-yeon Shim
- Department of Chemical and Biological Engineering, Sookmyung Women’s University, Yongsan-gu, Seoul 04310, Korea; (Y.-h.J.); (J.-y.S.)
| | - Kwang-il Lim
- Department of Chemical and Biological Engineering, Sookmyung Women’s University, Yongsan-gu, Seoul 04310, Korea; (Y.-h.J.); (J.-y.S.)
- Industry Collaboration Center, Industry-Academic Cooperation Foundation, Sookmyung Women’s University, Yongsan-gu, Seoul 04310, Korea;
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15
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Hussain SRA, Yalvac ME, Khoo B, Eckardt S, McLaughlin KJ. Adapting CRISPR/Cas9 System for Targeting Mitochondrial Genome. Front Genet 2021; 12:627050. [PMID: 33889176 PMCID: PMC8055930 DOI: 10.3389/fgene.2021.627050] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 03/01/2021] [Indexed: 12/21/2022] Open
Abstract
Gene editing of the mitochondrial genome using the CRISPR-Cas9 system is highly challenging mainly due to sub-efficient delivery of guide RNA and Cas9 enzyme complexes into the mitochondria. In this study, we were able to perform gene editing in the mitochondrial DNA by appending an NADH-ubiquinone oxidoreductase chain 4 (ND4) targeting guide RNA to an RNA transport-derived stem loop element (RP-loop) and expressing the Cas9 enzyme with a preceding mitochondrial localization sequence. We observe mitochondrial colocalization of RP-loop gRNA and a marked reduction of ND4 expression in the cells carrying a 11205G variant in their ND4 sequence coincidently decreasing the mtDNA levels. This proof-of-concept study suggests that a stem-loop element added sgRNA can be transported to the mitochondria and functionally interact with Cas9 to mediate sequence-specific mtDNA cleavage. Using this novel approach to target the mtDNA, our results provide further evidence that CRISPR-Cas9-mediated gene editing might potentially be used to treat mitochondrial-related diseases.
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Affiliation(s)
- Syed-Rehan A Hussain
- Center for Molecular and Human Genetics, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States.,Center for Clinical and Translational Research, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States
| | - Mehmet E Yalvac
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Benedict Khoo
- Center for Molecular and Human Genetics, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States
| | - Sigrid Eckardt
- Center for Molecular and Human Genetics, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States
| | - K John McLaughlin
- Center for Molecular and Human Genetics, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States
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16
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Li L, Miao H, Chang Y, Yao H, Zhao Y, Wu F, Song X. Multidimensional crosstalk between RNA-binding proteins and noncoding RNAs in cancer biology. Semin Cancer Biol 2021; 75:84-96. [PMID: 33722631 DOI: 10.1016/j.semcancer.2021.03.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 03/07/2021] [Accepted: 03/09/2021] [Indexed: 02/09/2023]
Abstract
RNA-binding proteins (RBPs) are well-known to bind RNA via a set of RNA-binding domains (RBDs) and determine the fate and function of their RNA targets; inversely, some RBPs, in certain cases, may be modulated by the bound RNAs rather than regulate their RNA partners. Current proteome-wide studies reveal that almost half of RBPs have no canonical RBDs, and the discovery of tens of thousands of noncoding RNAs (ncRNAs), especially those with the size larger than 200 nt (namely long noncoding RNAs, lncRNAs), makes the crosstalk between RBPs and RNAs more complicated. It is clear that macromolecular complexes formed by RBP and RNA are not only a form of existence of their RBP and RNA components in cells, but also represent a functional entity through which those RBPs and regulatory ncRNAs participate in the construction of regulatory networks in organism. In this review, we summarize the multidimensional crosstalk between RBPs and ncRNAs in cancer and discuss how RBPs achieve their function via the bound ncRNAs in different aspects of gene expression as well as how RBPs direct modification and processing of ncRNAs, in order to better understand tumor biology and provide new insights into development of strategies for cancer therapy and early detection.
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Affiliation(s)
- Ling Li
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China.
| | - Hui Miao
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yanbo Chang
- Sichuan Institute for Food and Drug Control, Department of Forensic Analytical Toxicology, West China School of Basic Medical and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Hong Yao
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yongyun Zhao
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Fan Wu
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Xu Song
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China.
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17
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Antón Z, Mullally G, Ford HC, van der Kamp MW, Szczelkun MD, Lane JD. Mitochondrial import, health and mtDNA copy number variability seen when using type II and type V CRISPR effectors. J Cell Sci 2020; 133:jcs.248468. [PMID: 32843580 DOI: 10.1242/jcs.248468] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/10/2020] [Indexed: 12/18/2022] Open
Abstract
Current methodologies for targeting the mitochondrial genome for research and/or therapy development in mitochondrial diseases are restricted by practical limitations and technical inflexibility. A molecular toolbox for CRISPR-mediated mitochondrial genome editing is desirable, as this could enable targeting of mtDNA haplotypes using the precision and tuneability of CRISPR enzymes. Such 'MitoCRISPR' systems described to date lack reproducibility and independent corroboration. We have explored the requirements for MitoCRISPR in human cells by CRISPR nuclease engineering, including the use of alternative mitochondrial protein targeting sequences and smaller paralogues, and the application of guide (g)RNA modifications for mitochondrial import. We demonstrate varied mitochondrial targeting efficiencies and effects on mitochondrial dynamics/function of different CRISPR nucleases, with Lachnospiraceae bacterium ND2006 (Lb) Cas12a being better targeted and tolerated than Cas9 variants. We also provide evidence of Cas9 gRNA association with mitochondria in HeLa cells and isolated yeast mitochondria, even in the absence of a targeting RNA aptamer. Our data link mitochondrial-targeted LbCas12a/crRNA with increased mtDNA copy number dependent upon DNA binding and cleavage activity. We discuss reproducibility issues and the future steps necessary for MitoCRISPR.
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Affiliation(s)
- Zuriñe Antón
- Cell Biology Laboratories, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Grace Mullally
- DNA-Protein Interactions Unit, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Holly C Ford
- DNA-Protein Interactions Unit, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Marc W van der Kamp
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK.,Centre for Computational Chemistry, School of Chemistry, Faculty of Science, University of Bristol, Bristol BS8 1TD, UK.,BrisSynBio, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol BS8 1TQ, UK
| | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK .,BrisSynBio, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol BS8 1TQ, UK
| | - Jon D Lane
- Cell Biology Laboratories, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK .,BrisSynBio, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol BS8 1TQ, UK
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18
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Mullally G, van Aelst K, Naqvi MM, Diffin FM, Karvelis T, Gasiunas G, Siksnys V, Szczelkun MD. 5' modifications to CRISPR-Cas9 gRNA can change the dynamics and size of R-loops and inhibit DNA cleavage. Nucleic Acids Res 2020; 48:6811-6823. [PMID: 32496535 PMCID: PMC7337959 DOI: 10.1093/nar/gkaa477] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/21/2020] [Accepted: 05/26/2020] [Indexed: 12/26/2022] Open
Abstract
A key aim in exploiting CRISPR-Cas is gRNA engineering to introduce additional functionalities, ranging from individual nucleotide changes that increase efficiency of on-target binding to the inclusion of larger functional RNA aptamers or ribonucleoproteins (RNPs). Cas9-gRNA interactions are crucial for complex assembly, but several distinct regions of the gRNA are amenable to modification. We used in vitro ensemble and single-molecule assays to assess the impact of gRNA structural alterations on RNP complex formation, R-loop dynamics, and endonuclease activity. Our results indicate that RNP formation was unaffected by any of our modifications. R-loop formation and DNA cleavage activity were also essentially unaffected by modification of the Upper Stem, first Hairpin and 3' end. In contrast, we found that 5' additions of only two or three nucleotides could reduce R-loop formation and cleavage activity of the RuvC domain relative to a single nucleotide addition. Such modifications are a common by-product of in vitro transcribed gRNA. We also observed that addition of a 20 nt RNA hairpin to the 5' end of a gRNA still supported RNP formation but produced a stable ∼9 bp R-loop that could not activate DNA cleavage. Consideration of these observations will assist in successful gRNA design.
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Affiliation(s)
- Grace Mullally
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
- BrisSynBio, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol BS8 1TQ, UK
| | - Kara van Aelst
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Mohsin M Naqvi
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Fiona M Diffin
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | | | - Giedrius Gasiunas
- Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
- CasZyme, Vilnius, Lithuania
| | | | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
- BrisSynBio, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol BS8 1TQ, UK
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19
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Gusic M, Prokisch H. ncRNAs: New Players in Mitochondrial Health and Disease? Front Genet 2020; 11:95. [PMID: 32180794 PMCID: PMC7059738 DOI: 10.3389/fgene.2020.00095] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/28/2020] [Indexed: 12/19/2022] Open
Abstract
The regulation of mitochondrial proteome is unique in that its components have origins in both mitochondria and nucleus. With the development of OMICS technologies, emerging evidence indicates an interaction between mitochondria and nucleus based not only on the proteins but also on the non-coding RNAs (ncRNAs). It is now accepted that large parts of the non‐coding genome are transcribed into various ncRNA species. Although their characterization has been a hot topic in recent years, the function of the majority remains unknown. Recently, ncRNA species microRNA (miRNA) and long-non coding RNAs (lncRNA) have been gaining attention as direct or indirect modulators of the mitochondrial proteome homeostasis. These ncRNA can impact mitochondria indirectly by affecting transcripts encoding for mitochondrial proteins in the cytoplasm. Furthermore, reports of mitochondria-localized miRNAs, termed mitomiRs, and lncRNAs directly regulating mitochondrial gene expression suggest the import of RNA to mitochondria, but also transcription from the mitochondrial genome. Interestingly, ncRNAs have been also shown to hide small open reading frames (sORFs) encoding for small functional peptides termed micropeptides, with several examples reported with a role in mitochondria. In this review, we provide a literature overview on ncRNAs and micropeptides found to be associated with mitochondrial biology in the context of both health and disease. Although reported, small study overlap and rare replications by other groups make the presence, transport, and role of ncRNA in mitochondria an attractive, but still challenging subject. Finally, we touch the topic of their potential as prognosis markers and therapeutic targets.
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Affiliation(s)
- Mirjana Gusic
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.,Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technical University of Munich, Munich, Germany
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20
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Zheng Q, Huang J, Wang G. Mitochondria, Telomeres and Telomerase Subunits. Front Cell Dev Biol 2019; 7:274. [PMID: 31781563 PMCID: PMC6851022 DOI: 10.3389/fcell.2019.00274] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 10/24/2019] [Indexed: 12/11/2022] Open
Abstract
Mitochondrial functions and telomere functions have mostly been studied independently. In recent years, it, however, has become clear that there are intimate links between mitochondria, telomeres, and telomerase subunits. Mitochondrial dysfunctions cause telomere attrition, while telomere damage leads to reprogramming of mitochondrial biosynthesis and mitochondrial dysfunctions, which has important implications in aging and diseases. In addition, evidence has accumulated that telomere-independent functions of telomerase also exist and that the protein component of telomerase TERT shuttles between the nucleus and mitochondria under oxidative stress. Our previously published data show that the RNA component of telomerase TERC is also imported into mitochondria, processed, and exported back to the cytosol. These data show a complex regulation network where telomeres, nuclear genome, and mitochondria are co-regulated by multi-localization and multi-function proteins and RNAs. This review summarizes the connections between mitochondria and telomeres, the mitochondrion-related functions of telomerase subunits, and how they play a role in crosstalk between mitochondria and the nucleus.
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Affiliation(s)
- Qian Zheng
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Jinliang Huang
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Geng Wang
- School of Life Sciences, Tsinghua University, Beijing, China.,School of Life Sciences, Xiamen University, Xiamen, China
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21
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Malla S, Li Z. Functions of Conserved Domains of Human Polynucleotide Phosphorylase on RNA Oxidation. ACTA ACUST UNITED AC 2019; 3:62-67. [PMID: 32123871 PMCID: PMC7051052 DOI: 10.36959/584/448] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human polynucleotide phosphorylase (hPNPase), an exoribonuclease that is primarily localized in mitochondria, plays an important role in reducing oxidized RNA and protecting cells under oxidative stress conditions. hPNPase contains two catalytic domains (RPH1 and RPH2) and two RNA binding domains (KH and S1), and an N-terminal mitochondrial translocation signal (MTS). In this study, we examined the potential roles of each domain in hPNPase function on controlling RNA oxidative damage. DNA encoding full-length hPNPase and its domain-deletion mutants were introduced into HeLa cells, and the levels of an oxidized RNA lesion, 8-hydroxyguanosine (8-oxo-Guo) were determined in mitochondrial and cytoplasmic RNA under oxidative stress conditions. Our study showed that the S1 RNA binding domain is crucial for reducing 8-oxo-Guo in both cytoplasm and mitochondria, while the MTS is required for 8-oxo-Guo reduction in mitochondria.
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Affiliation(s)
- Sulochan Malla
- Department of Biomedical Science, Florida Atlantic University, USA
| | - Zhongwei Li
- Department of Biomedical Science, Florida Atlantic University, USA
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22
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Golzarroshan B, Lin CL, Li CL, Yang WZ, Chu LY, Agrawal S, Yuan HS. Crystal structure of dimeric human PNPase reveals why disease-linked mutants suffer from low RNA import and degradation activities. Nucleic Acids Res 2018; 46:8630-8640. [PMID: 30020492 PMCID: PMC6144817 DOI: 10.1093/nar/gky642] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/13/2018] [Accepted: 07/16/2018] [Indexed: 11/13/2022] Open
Abstract
Human polynucleotide phosphorylase (PNPase) is an evolutionarily conserved 3'-to-5' exoribonuclease principally located in mitochondria where it is responsible for RNA turnover and import. Mutations in PNPase impair structured RNA transport into mitochondria, resulting in mitochondrial dysfunction and disease. PNPase is a trimeric protein with a doughnut-shaped structure hosting a central channel for single-stranded RNA binding and degradation. Here, we show that the disease-linked human PNPase mutants, Q387R and E475G, form dimers, not trimers, and have significantly lower RNA binding and degradation activities compared to wild-type trimeric PNPase. Moreover, S1 domain-truncated PNPase binds single-stranded RNA but not the stem-loop signature motif of imported structured RNA, suggesting that the S1 domain is responsible for binding structured RNAs. We further determined the crystal structure of dimeric PNPase at a resolution of 2.8 Å and, combined with small-angle X-ray scattering, show that the RNA-binding K homology and S1 domains are relatively inaccessible in the dimeric assembly. Taken together, these results show that mutations at the interface of the trimeric PNPase tend to produce a dimeric protein with destructive RNA-binding surfaces, thus impairing both of its RNA import and degradation activities and leading to mitochondria disorders.
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Affiliation(s)
- Bagher Golzarroshan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan 30013, Republic of China
| | - Chia-Liang Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
| | - Chia-Lung Li
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
| | - Wei-Zen Yang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
| | - Lee-Ya Chu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan 30013, Republic of China
| | - Sashank Agrawal
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Molecular and Cell Biology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan 11490, Republic of China
| | - Hanna S Yuan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Molecular and Cell Biology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan 11529, Republic of China
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23
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Dos Santos RF, Quendera AP, Boavida S, Seixas AF, Arraiano CM, Andrade JM. Major 3'-5' Exoribonucleases in the Metabolism of Coding and Non-coding RNA. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 159:101-155. [PMID: 30340785 DOI: 10.1016/bs.pmbts.2018.07.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
3'-5' exoribonucleases are key enzymes in the degradation of superfluous or aberrant RNAs and in the maturation of precursor RNAs into their functional forms. The major bacterial 3'-5' exoribonucleases responsible for both these activities are PNPase, RNase II and RNase R. These enzymes are of ancient nature with widespread distribution. In eukaryotes, PNPase and RNase II/RNase R enzymes can be found in the cytosol and in mitochondria and chloroplasts; RNase II/RNase R-like enzymes are also found in the nucleus. Humans express one PNPase (PNPT1) and three RNase II/RNase R family members (Dis3, Dis3L and Dis3L2). These enzymes take part in a multitude of RNA surveillance mechanisms that are critical for translation accuracy. Although active against a wide range of both coding and non-coding RNAs, the different 3'-5' exoribonucleases exhibit distinct substrate affinities. The latest studies on these RNA degradative enzymes have contributed to the identification of additional homologue proteins, the uncovering of novel RNA degradation pathways, and to a better comprehension of several disease-related processes and response to stress, amongst many other exciting findings. Here, we provide a comprehensive and up-to-date overview on the function, structure, regulation and substrate preference of the key 3'-5' exoribonucleases involved in RNA metabolism.
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Affiliation(s)
- Ricardo F Dos Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ana P Quendera
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sofia Boavida
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - André F Seixas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - José M Andrade
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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24
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Abstract
MicroRNAs (miRNAs) are known as the master regulators of gene expression, and for the last two decades our knowledge of their functional reach keeps expanding. Recent studies have shown that a miRNA’s role in regulation extends to extracellular and intracellular organelles. Several studies have shown a role for miRNA in regulating the mitochondrial genome in normal and disease conditions. Mitochondrial dysfunction occurs in many human pathologies, such as cardiovascular disease, diabetes, cancer, and neurological diseases. These studies have shed some light on regulation of the mitochondrial genome as well as helped to explain the role of miRNA in altering mitochondrial function and the ensuing effects on cells. Although the field has grown in recent years, many questions still remain. For example, little is known about how nuclear-encoded miRNAs translocate to the mitochondrial matrix. Knowledge of the mechanisms of miRNA transport into the mitochondrial matrix is likely to provide important insights into our understanding of disease pathophysiology and could represent new targets for therapeutic intervention. For this review, our focus will be on the role of a subset of miRNAs, known as MitomiR, in mitochondrial function. We also discuss the potential mechanisms used by these nuclear-encoded miRNAs for import into the mitochondrial compartment. Listen to this article’s corresponding podcast at http://ajpheart.podbean.com/e/microrna-translocation-into-the-mitochondria/ .
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Affiliation(s)
| | - Samarjit Das
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland
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25
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Markantone DM, Towheed A, Crain AT, Collins JM, Celotto AM, Palladino MJ. Protein coding mitochondrial-targeted RNAs rescue mitochondrial disease in vivo. Neurobiol Dis 2018; 117:203-210. [PMID: 29908326 DOI: 10.1016/j.nbd.2018.06.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/08/2018] [Accepted: 06/12/2018] [Indexed: 11/28/2022] Open
Abstract
Mitochondrial encephalomyopathies (MEs) result from mutations in mitochondrial genes critical to oxidative phosphorylation. Severe and untreatable ME results from mutations affecting each endogenous mitochondrial encoded gene, including all 13 established protein coding genes. Effective techniques to manipulate mitochondrial genome are limited and targeted mitochondrial protein expression is currently unavailable. Here we report the development of a mitochondrial-targeted RNA expression (mtTRES) vector capable of protein expression within mitochondria (mtTRESPro). We demonstrate that mtTRESPro expressed RNAs are targeted to mitochondria and are capable of being translated using EGFP encoded constructs in vivo. We additionally test mtTRESPro constructs encoding wild type ATP6 for their ability to rescue an established ATP61Drosophila model of ME. Genetic rescue is examined including tests with co-expression of mitochondrial targeted translational inhibitors TLI-NCL::ATP6 RNAs that function to reduce expression of the endogenous mutant protein. The data demonstrate allotopic RNA expression of mitochondrial targeted wild type ATP6 coding RNAs are sufficient to partially rescue a severe and established animal model of ME but only when combined with a method to inhibit mutant protein expression, which likely competes for incorporation into complex V.
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Affiliation(s)
- Desiree M Markantone
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Atif Towheed
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Aaron T Crain
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Jessica M Collins
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Alicia M Celotto
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Michael J Palladino
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.
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Khacho M, Slack RS. Mitochondrial and Reactive Oxygen Species Signaling Coordinate Stem Cell Fate Decisions and Life Long Maintenance. Antioxid Redox Signal 2018; 28:1090-1101. [PMID: 28657337 DOI: 10.1089/ars.2017.7228] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Significance: Recent discoveries in mitochondrial biology have transformed and further solidified the importance of mitochondria in development, aging, and disease. Within the realm of regenerative and stem cell research, these recent advances have brought forth new concepts that revolutionize our understanding of metabolic and redox states in the establishment of cellular identity and fate decisions. Recent Advances: Mitochondrial metabolism, morphology, and cellular redox states are dynamic characteristics that undergo shifts during stem cell differentiation. Although it was once thought that this was solely because of changing metabolic needs of differentiating cells, it is now clear that these events are driving forces in the regulation of stem cell identity and fate decisions. Critical Issues: Although recent discoveries have placed mitochondrial function and physiological reactive oxygen species (ROS) at the forefront for the regulation of stem cell self-renewal, how this may impact tissue homeostasis and regenerative capacity is poorly understood. In addition, the role of mitochondria and ROS on the maintenance of a stem cell population in many degenerative diseases and during aging is not clear, despite the fact that mitochondrial dysfunction and elevated ROS levels are commonly observed in these conditions. Future Directions: Given the newly established role for mitochondria and ROS in stem cell self-renewal capacity, special attention should now be directed in understanding how this would impact the development and progression of aging and diseases, whereby mitochondrial and ROS defects are a prominent factor. Antioxid. Redox Signal. 28, 1090-1101.
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Affiliation(s)
- Mireille Khacho
- Department of Cellular and Molecular Medicine, Brain and Mind Research Institute, University of Ottawa, Ottawa, Canada
| | - Ruth S Slack
- Department of Cellular and Molecular Medicine, Brain and Mind Research Institute, University of Ottawa, Ottawa, Canada
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27
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Khacho M, Slack RS. Mitochondrial activity in the regulation of stem cell self-renewal and differentiation. Curr Opin Cell Biol 2017; 49:1-8. [DOI: 10.1016/j.ceb.2017.11.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 10/25/2017] [Accepted: 11/01/2017] [Indexed: 12/19/2022]
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Singh B, Modica-Napolitano JS, Singh KK. Defining the momiome: Promiscuous information transfer by mobile mitochondria and the mitochondrial genome. Semin Cancer Biol 2017; 47:1-17. [PMID: 28502611 PMCID: PMC5681893 DOI: 10.1016/j.semcancer.2017.05.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 04/20/2017] [Accepted: 05/07/2017] [Indexed: 12/30/2022]
Abstract
Mitochondria are complex intracellular organelles that have long been identified as the powerhouses of eukaryotic cells because of the central role they play in oxidative metabolism. A resurgence of interest in the study of mitochondria during the past decade has revealed that mitochondria also play key roles in cell signaling, proliferation, cell metabolism and cell death, and that genetic and/or metabolic alterations in mitochondria contribute to a number of diseases, including cancer. Mitochondria have been identified as signaling organelles, capable of mediating bidirectional intracellular information transfer: anterograde (from nucleus to mitochondria) and retrograde (from mitochondria to nucleus). More recently, evidence is now building that the role of mitochondria extends to intercellular communication as well, and that the mitochondrial genome (mtDNA) and even whole mitochondria are indeed mobile and can mediate information transfer between cells. We define this promiscuous information transfer function of mitochondria and mtDNA as "momiome" to include all mobile functions of mitochondria and the mitochondrial genome. Herein, we review the "momiome" and explore its role in cancer development, progression, and treatment.
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Affiliation(s)
- Bhupendra Singh
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Keshav K Singh
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA; Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA; Department of Environmental Health, Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, USA; Center for Aging, University of Alabama at Birmingham, Birmingham, AL, USA; UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA; Birmingham Veterans Affairs Medical Center, Birmingham, AL, USA.
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29
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Hathaway QA, Pinti MV, Durr AJ, Waris S, Shepherd DL, Hollander JM. Regulating microRNA expression: at the heart of diabetes mellitus and the mitochondrion. Am J Physiol Heart Circ Physiol 2017; 314:H293-H310. [PMID: 28986361 DOI: 10.1152/ajpheart.00520.2017] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Type 2 diabetes mellitus is a major risk factor for cardiovascular disease and mortality. Uncontrolled type 2 diabetes mellitus results in a systemic milieu of increased circulating glucose and fatty acids. The development of insulin resistance in cardiac tissue decreases cellular glucose import and enhances mitochondrial fatty acid uptake. While triacylglycerol and cytotoxic lipid species begin to accumulate in the cardiomyocyte, the energy substrate utilization ratio of free fatty acids to glucose changes to almost entirely free fatty acids. Accumulating evidence suggests a role of miRNA in mediating this metabolic transition. Energy substrate metabolism, apoptosis, and the production and response to excess reactive oxygen species are regulated by miRNA expression. The current momentum for understanding the dynamics of miRNA expression is limited by a lack of understanding of how miRNA expression is controlled. While miRNAs are important regulators in both normal and pathological states, an additional layer of complexity is added when regulation of miRNA regulators is considered. miRNA expression is known to be regulated through a number of mechanisms, which include, but are not limited to, epigenetics, exosomal transport, processing, and posttranscriptional sequestration. The purpose of this review is to outline how mitochondrial processes are regulated by miRNAs in the diabetic heart. Furthermore, we will highlight the regulatory mechanisms, such as epigenetics, exosomal transport, miRNA processing, and posttranslational sequestration, that participate as regulators of miRNA expression. Additionally, current and future treatment strategies targeting dysfunctional mitochondrial processes in the diseased myocardium, as well as emerging miRNA-based therapies, will be summarized.
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Affiliation(s)
- Quincy A Hathaway
- Division of Exercise Physiology, West Virginia University School of Medicine , Morgantown, West Virginia.,Mitochondria, Metabolism, and Bioenergetics Working Group, West Virginia University School of Medicine , Morgantown, West Virginia.,Toxicology Working Group, West Virginia University School of Medicine , Morgantown, West Virginia
| | - Mark V Pinti
- Division of Pharmaceutical and Pharmacological Sciences, West Virginia School of Pharmacy , Morgantown, West Virginia
| | - Andrya J Durr
- Division of Exercise Physiology, West Virginia University School of Medicine , Morgantown, West Virginia.,Mitochondria, Metabolism, and Bioenergetics Working Group, West Virginia University School of Medicine , Morgantown, West Virginia
| | - Shanawar Waris
- Department of Biomedical Engineering, West Virginia College of Engineering , Morgantown, West Virginia
| | - Danielle L Shepherd
- Division of Exercise Physiology, West Virginia University School of Medicine , Morgantown, West Virginia
| | - John M Hollander
- Division of Exercise Physiology, West Virginia University School of Medicine , Morgantown, West Virginia.,Mitochondria, Metabolism, and Bioenergetics Working Group, West Virginia University School of Medicine , Morgantown, West Virginia.,Toxicology Working Group, West Virginia University School of Medicine , Morgantown, West Virginia
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30
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Baudier J. ATAD3 proteins: brokers of a mitochondria-endoplasmic reticulum connection in mammalian cells. Biol Rev Camb Philos Soc 2017; 93:827-844. [PMID: 28941010 DOI: 10.1111/brv.12373] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/22/2017] [Accepted: 08/25/2017] [Indexed: 12/25/2022]
Abstract
In yeast, a sequence of physical and genetic interactions termed the endoplasmic reticulum (ER)-mitochondria organizing network (ERMIONE) controls mitochondria-ER interactions and mitochondrial biogenesis. Several functions that characterize ERMIONE complexes are conserved in mammalian cells, suggesting that a similar tethering complex must exist in metazoans. Recent studies have identified a new family of nuclear-encoded ATPases associated with diverse cellular activities (AAA+-ATPase) mitochondrial membrane proteins specific to multicellular eukaryotes, called the ATPase family AAA domain-containing protein 3 (ATAD3) proteins (ATAD3A and ATAD3B). These proteins are crucial for normal mitochondrial-ER interactions and lie at the heart of processes underlying mitochondrial biogenesis. ATAD3A orthologues have been studied in flies, worms, and mammals, highlighting the widespread importance of this gene during embryonic development and in adulthood. ATAD3A is a downstream effector of target of rapamycin (TOR) signalling in Drosophila and exhibits typical features of proteins from the ERMIONE-like complex in metazoans. In humans, mutations in the ATAD3A gene represent a new link between altered mitochondrial-ER interaction and recognizable neurological syndromes. The primate-specific ATAD3B protein is a biomarker of pluripotent embryonic stem cells. Through negative regulation of ATAD3A function, ATAD3B supports mitochondrial stemness properties.
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Affiliation(s)
- Jacques Baudier
- Aix Marseille Université, CNRS, IBDM, 13284, Marseille Cedex 07, France.,Institut de Biologie du Développement de Marseille-UMR CNRS 7288, 13288, Marseille Cedex 9, France
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31
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Shepherd DL, Hathaway QA, Pinti MV, Nichols CE, Durr AJ, Sreekumar S, Hughes KM, Stine SM, Martinez I, Hollander JM. Exploring the mitochondrial microRNA import pathway through Polynucleotide Phosphorylase (PNPase). J Mol Cell Cardiol 2017; 110:15-25. [PMID: 28709769 PMCID: PMC5854179 DOI: 10.1016/j.yjmcc.2017.06.012] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 06/20/2017] [Accepted: 06/27/2017] [Indexed: 01/01/2023]
Abstract
Cardiovascular disease is the primary cause of mortality for individuals with type 2 diabetes mellitus. During the diabetic condition, cardiovascular dysfunction can be partially attributed to molecular changes in the tissue, including alterations in microRNA (miRNA) interactions. MiRNAs have been reported in the mitochondrion and their presence may influence cellular bioenergetics, creating decrements in functional capacity. In this study, we examined the roles of Argonaute 2 (Ago2), a protein associated with cytosolic and mitochondrial miRNAs, and Polynucleotide Phosphorylase (PNPase), a protein found in the inner membrane space of the mitochondrion, to determine their role in mitochondrial miRNA import. In cardiac tissue from human and mouse models of type 2 diabetes mellitus, Ago2 protein levels were unchanged while PNPase protein expression levels were increased; also, there was an increase in the association between both proteins in the diabetic state. MiRNA-378 was found to be significantly increased in db/db mice, leading to decrements in ATP6 levels and ATP synthase activity, which was also exhibited when overexpressing PNPase in HL-1 cardiomyocytes and in HL-1 cells with stable miRNA-378 overexpression (HL-1-378). To assess potential therapeutic interventions, flow cytometry evaluated the capacity for targeting miRNA-378 species in mitochondria through antimiR treatment, revealing miRNA-378 level-dependent inhibition. Our study establishes PNPase as a contributor to mitochondrial miRNA import through the transport of miRNA-378, which may regulate bioenergetics during type 2 diabetes mellitus. Further, our data provide evidence that manipulation of PNPase levels may enhance the delivery of antimiR therapeutics to mitochondria in physiological and pathological conditions.
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Affiliation(s)
- Danielle L Shepherd
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV 26506, United States; Mitochondria, Metabolism & Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV 26506, United States
| | - Quincy A Hathaway
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV 26506, United States; Mitochondria, Metabolism & Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV 26506, United States
| | - Mark V Pinti
- Mitochondria, Metabolism & Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV 26506, United States
| | - Cody E Nichols
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV 26506, United States
| | - Andrya J Durr
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV 26506, United States; Mitochondria, Metabolism & Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV 26506, United States
| | - Shruthi Sreekumar
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV 26506, United States
| | - Kristen M Hughes
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV 26506, United States
| | - Seth M Stine
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV 26506, United States
| | - Ivan Martinez
- Cancer Cell Biology, West Virginia University School of Medicine, Morgantown, WV 26506, United States
| | - John M Hollander
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV 26506, United States; Mitochondria, Metabolism & Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV 26506, United States.
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32
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tRNAs and proteins use the same import channel for translocation across the mitochondrial outer membrane of trypanosomes. Proc Natl Acad Sci U S A 2017; 114:E7679-E7687. [PMID: 28847952 DOI: 10.1073/pnas.1711430114] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial tRNA import is widespread, but the mechanism by which tRNAs are imported remains largely unknown. The mitochondrion of the parasitic protozoan Trypanosoma brucei lacks tRNA genes, and thus imports all tRNAs from the cytosol. Here we show that in T. brucei in vivo import of tRNAs requires four subunits of the mitochondrial outer membrane protein translocase but not the two receptor subunits, one of which is essential for protein import. The latter shows that it is possible to uncouple mitochondrial tRNA import from protein import. Ablation of the intermembrane space domain of the translocase subunit, archaic translocase of the outer membrane (ATOM)14, on the other hand, while not affecting the architecture of the translocase, impedes both protein and tRNA import. A protein import intermediate arrested in the translocation channel prevents both protein and tRNA import. In the presence of tRNA, blocking events of single-channel currents through the pore formed by recombinant ATOM40 were detected in electrophysiological recordings. These results indicate that both types of macromolecules use the same import channel across the outer membrane. However, while tRNA import depends on the core subunits of the protein import translocase, it does not require the protein import receptors, indicating that the two processes are not mechanistically linked.
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33
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Dong Y, Yoshitomi T, Hu JF, Cui J. Long noncoding RNAs coordinate functions between mitochondria and the nucleus. Epigenetics Chromatin 2017; 10:41. [PMID: 28835257 PMCID: PMC5569521 DOI: 10.1186/s13072-017-0149-x] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 08/17/2017] [Indexed: 11/23/2022] Open
Abstract
In animal cells, mitochondria are the primary powerhouses and metabolic factories. They also contain genomes and can produce mitochondrial-specific nucleic acids and proteins. To maintain homeostasis of the entire cell, an intense cross-talk between mitochondria and the nucleus, mediated by encoded noncoding RNAs (ncRNAs), as well as proteins, is required. Long ncRNAs (lncRNAs) contain characteristic structures, and they are involved in the regulation of almost every stage of gene expression, as well as being implicated in a variety of disease states, such as cancer. In the coordinated signaling system, several lncRNAs, transcribed in the nucleus but residing in mitochondria, play a key role in regulating mitochondrial functions or dynamics. For example, RMRP, a component of the mitochondrial RNase MRP, is important for mitochondrial DNA replication and RNA processing, and the steroid receptor RNA activator, SRA, is a key modulator of hormone signaling and is present in both the nucleus and mitochondria. Some RNA-binding proteins maybe play a role in the lncRNAs transport system, such as HuR, GRSF1, SHARP, SLIRP, PPR, and PNPASE. Furthermore, a series of nuclear DNA-encoded lncRNAs were implicated in mitochondria-mediated apoptosis, mitochondrial bioenergetics and biosynthesis, and glutamine metabolism. The mitochondrial genome can also encode a set of lncRNAs, and they are divided into three categories: (1) lncND5, lncND6, and lncCyt b RNA; (2) chimeric mitochondrial DNA-encoded lncRNAs; and (3) putative mitochondrial DNA-encoded lncRNAs. It has been reported that the mitochondrial DNA-encoded lncRNAs appear to operate in the nucleus. The molecular mechanisms underlying trafficking of the mitochondrial DNA-encoded lncRNAs to the nucleus in mammals are only now beginning to emerge. In conclusion, both nuclear- and mitochondrial DNA-encoded lncRNAs mediate an intense intercompartmental cross-talk, which opens a rich field for investigation of the mechanism underlying the intercompartmental coordination and the maintenance of whole cell homeostasis.
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Affiliation(s)
- Yaru Dong
- Department of Ophthalmology, The Second Hospital of Jilin University, 218 Ziqiang Street, Changchun, 130041, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, CA, 94304, USA
| | - Takeshi Yoshitomi
- Department of Ophthalmology, Akita University School of Medicine, 1-1-1 Hondo, Akita, 010-8543, Japan
| | - Ji-Fan Hu
- Stanford University Medical School, VA Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, CA, 94304, USA. .,Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, 130061, Jilin, China.
| | - Jizhe Cui
- Department of Ophthalmology, The Second Hospital of Jilin University, 218 Ziqiang Street, Changchun, 130041, Jilin, China.
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Abstract
The report in 1988 that Leber Hereditary Optic Neuropathy (LHON) was the product of mitochondrial DNA (mtDNA) mutations provided the first demonstration of the clinical relevance of inherited mtDNA variation. From LHON studies, the medical importance was demonstrated for the mtDNA showing its coding for the most important energy genes, its maternal inheritance, its high mutation rate, its presence in hundreds to thousands of copies per cell, its quantitatively segregation of biallelic genotypes during both mitosis and meiosis, its preferential effect on the most energetic tissues including the eye and brain, its wide range of functional polymorphisms that predispose to common diseases, and its accumulation of mutations within somatic tissues providing the aging clock. These features of mtDNA genetics, in combination with the genetics of the 1-2000 nuclear DNA (nDNA) coded mitochondrial genes, is not only explaining the genetics of LHON but also providing a model for understanding the complexity of many common diseases. With the maturation of LHON biology and genetics, novel animal models for complex disease have been developed and new therapeutic targets and strategies envisioned, both pharmacological and genetic. Multiple somatic gene therapy approaches are being developed for LHON which are applicable to other mtDNA diseases. Moreover, the unique cytoplasmic genetics of the mtDNA has permitted the first successful human germline gene therapy via spindle nDNA transfer from mtDNA mutant oocytes to enucleated normal mtDNA oocytes. Such LHON lessons are actively being applied to common ophthalmological diseases like glaucoma and neurological diseases like Parkinsonism.
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Banerjee Mustafi S, Aznar N, Dwivedi SKD, Chakraborty PK, Basak R, Mukherjee P, Ghosh P, Bhattacharya R. Mitochondrial BMI1 maintains bioenergetic homeostasis in cells. FASEB J 2016; 30:4042-4055. [PMID: 27613804 PMCID: PMC5102112 DOI: 10.1096/fj.201600321r] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 08/15/2016] [Indexed: 12/14/2022]
Abstract
The polycomb complex proto-oncogene BMI1 [B lymphoma Mo-MLV insertion region 1 homolog (mouse)] is essential for self-renewal of normal and cancer stem cells. BMI1-null mice show severe defects in growth, development, and survival. Although BMI1 is known to exert its effect in the nucleus via repression of 2 potent cell-cycle regulators that are encoded by the Ink4a/Arf locus, deletion of this locus only partially rescues BMI1-null phenotypes, which is indicative of alternate mechanisms of action of BMI1. Here, we show that an extranuclear pool of BMI1 localizes to inner mitochondrial membrane and directly regulates mitochondrial RNA (mtRNA) homeostasis and bioenergetics. These mitochondrial functions of BMI1 are independent of its previously described nuclear functions because a nuclear localization-defective mutant BMI1 rescued several bioenergetic defects that we observed in BMI1-depleted cells, for example, mitochondrial respiration, cytochrome c oxidase activity, and ATP production. Mechanistically, BMI1 coprecipitated with polynucleotide phosphorylase, a ribonuclease that is responsible for decay of mtRNA transcripts. Loss of BMI1 enhanced ribonuclease activity of polynucleotide phosphorylase and reduced mtRNA stability. These findings not only establish a novel extranuclear role of BMI1 in the regulation of mitochondrial bioenergetics, but also provide new mechanistic insights into the role of this proto-oncogene in stem cell differentiation, neuronal aging, and cancer.-Banerjee Mustafi, S., Aznar, N., Dwivedi, S. K. D., Chakraborty, P. K., Basak, R., Mukherjee, P., Ghosh, P., Bhattacharya, R. Mitochondrial BMI1 maintains bioenergetic homeostasis in cells.
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Affiliation(s)
- Soumyajit Banerjee Mustafi
- Department of Obstetrics and Gynecology, Stephenson Cancer Center, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma, USA
| | - Nicolas Aznar
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Shailendra Kumar Dhar Dwivedi
- Department of Obstetrics and Gynecology, Stephenson Cancer Center, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma, USA
| | - Prabir Kumar Chakraborty
- Department of Pathology, Stephenson Cancer Center, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma, USA; and
| | - Rumki Basak
- Department of Obstetrics and Gynecology, Stephenson Cancer Center, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma, USA
| | - Priyabrata Mukherjee
- Department of Pathology, Stephenson Cancer Center, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma, USA; and
| | - Pradipta Ghosh
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Resham Bhattacharya
- Department of Obstetrics and Gynecology, Stephenson Cancer Center, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma, USA;
- Department of Cell Biology, University of Oklahoma College of Medicine, Oklahoma City, Oklahoma, USA
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Pinti MV, Hathaway QA, Hollander JM. Role of microRNA in metabolic shift during heart failure. Am J Physiol Heart Circ Physiol 2016; 312:H33-H45. [PMID: 27742689 DOI: 10.1152/ajpheart.00341.2016] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 10/07/2016] [Accepted: 10/08/2016] [Indexed: 12/16/2022]
Abstract
Heart failure (HF) is an end point resulting from a number of disease states. The prognosis for HF patients is poor with survival rates precipitously low. Energy metabolism is centrally linked to the development of HF, and it involves the proteomic remodeling of numerous pathways, many of which are targeted to the mitochondrion. microRNAs (miRNA) are noncoding RNAs that influence posttranscriptional gene regulation. miRNA have garnered considerable attention for their ability to orchestrate changes to the transcriptome, and ultimately the proteome, during HF. Recently, interest in the role played by miRNA in the regulation of energy metabolism at the mitochondrion has emerged. Cardiac proteome remodeling during HF includes axes impacting hypertrophy, oxidative stress, calcium homeostasis, and metabolic fuel transition. Although it is established that the pathological environment of hypoxia and hemodynamic stress significantly contribute to the HF phenotype, it remains unclear as to the mechanistic underpinnings driving proteome remodeling. The aim of this review is to present evidence highlighting the role played by miRNA in these processes as a means for linking pathological stimuli with proteomic alteration. The differential expression of proteins of substrate transport, glycolysis, β-oxidation, ketone metabolism, the citric acid cycle (CAC), and the electron transport chain (ETC) are paralleled by the differential expression of miRNA species that modulate these processes. Identification of miRNAs that translocate to cardiomyocyte mitochondria (miR-181c, miR-378) influencing the expression of the mitochondrial genome-encoded transcripts as well as suggested import modulators are discussed. Current insights, applications, and challenges of miRNA-based therapeutics are also described.
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Affiliation(s)
- Mark V Pinti
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia; and Mitochondria, Metabolism, and Bioenergentics Working Group, Morgantown, West Virginia
| | - Quincy A Hathaway
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia; and Mitochondria, Metabolism, and Bioenergentics Working Group, Morgantown, West Virginia
| | - John M Hollander
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia; and Mitochondria, Metabolism, and Bioenergentics Working Group, Morgantown, West Virginia
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Sen A, Cox RT. Fly Models of Human Diseases: Drosophila as a Model for Understanding Human Mitochondrial Mutations and Disease. Curr Top Dev Biol 2016; 121:1-27. [PMID: 28057297 DOI: 10.1016/bs.ctdb.2016.07.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mitochondrial diseases are a prevalent, heterogeneous class of diseases caused by defects in oxidative phosphorylation, whose severity depends upon particular genetic mutations. These diseases can be difficult to diagnose, and current therapeutics have limited efficacy, primarily treating only symptoms. Because mitochondria play a pivotal role in numerous cellular functions, especially ATP production, their diminished activity has dramatic physiological consequences. While this in and of itself makes treating mitochondrial disease complex, these organelles contain their own DNA, mtDNA, whose products are required for ATP production, in addition to the hundreds of nucleus-encoded proteins. Drosophila offers a tractable whole-animal model to understand the mechanisms underlying loss of mitochondrial function, the subsequent cellular and tissue damage that results, and how these organelles are inherited. Human and Drosophila mtDNAs encode the same set of products, and the homologous nucleus-encoded genes required for mitochondrial function are conserved. In addition, Drosophila contain sufficiently complex organ systems to effectively recapitulate many basic symptoms of mitochondrial diseases, yet are relatively easy and fast to genetically manipulate. There are several Drosophila models for specific mitochondrial diseases, which have been recently reviewed (Foriel, Willems, Smeitink, Schenck, & Beyrath, 2015). In this review, we highlight the conservation between human and Drosophila mtDNA, the present and future techniques for creating mtDNA mutations for further study, and how Drosophila has contributed to our current understanding of mitochondrial inheritance.
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Affiliation(s)
- A Sen
- Uniformed Services University, Bethesda, MD, United States
| | - R T Cox
- Uniformed Services University, Bethesda, MD, United States.
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Highly Multiplexed RNA Aptamer Selection using a Microplate-based Microcolumn Device. Sci Rep 2016; 6:29771. [PMID: 27432610 PMCID: PMC4949599 DOI: 10.1038/srep29771] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/17/2016] [Indexed: 02/07/2023] Open
Abstract
We describe a multiplexed RNA aptamer selection to 19 different targets simultaneously using a microcolumn-based device, MEDUSA (Microplate-based Enrichment Device Used for the Selection of Aptamers), as well as a modified selection process, that significantly reduce the time and reagents needed for selections. We exploited MEDUSA’s reconfigurable design between parallel and serially-connected microcolumns to enable the use of just 2 aliquots of starting library, and its 96-well microplate compatibility to enable the continued use of high-throughput techniques in downstream processes. Our modified selection protocol allowed us to perform the equivalent of a 10-cycle selection in the time it takes for 4 traditional selection cycles. Several aptamers were discovered with nanomolar dissociation constants. Furthermore, aptamers were identified that not only bound with high affinity, but also acted as inhibitors to significantly reduce the activity of their target protein, mouse decapping exoribonuclease (DXO). The aptamers resisted DXO’s exoribonuclease activity, and in studies monitoring DXO’s degradation of a 30-nucleotide substrate, less than 1 μM of aptamer demonstrated significant inhibition of DXO activity. This aptamer selection method using MEDUSA helps to overcome some of the major challenges with traditional aptamer selections, and provides a platform for high-throughput selections that lends itself to process automation.
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Revisiting trends on mitochondrial mega-channels for the import of proteins and nucleic acids. J Bioenerg Biomembr 2016; 49:75-99. [DOI: 10.1007/s10863-016-9662-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/25/2016] [Indexed: 12/14/2022]
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Abstract
Methods of in vivo visualization and manipulation of mitochondrial genetic machinery are limited due to the need to surpass not only the cytoplasmic membrane but also two mitochondrial membranes. Here, we employ the matrix-addressing sequence of mitochondrial ribosomal 5S-rRNA (termed MAM), which is naturally imported into mammalian mitochondria, to construct an import system for in vivo targeting of mitochondrial (mt) DNA or mtRNA, in order to provide fluorescence hybridization of the desired sequences.
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Affiliation(s)
- Jaroslav Zelenka
- Department No. 75, Membrane Transprot Biophysics, Institute of Physiology, Academy of Sciences of the Czech Republic, Videnska 1084, Prague 4, 14220, Czech Republic
| | - Petr Ježek
- Department No. 75, Membrane Transprot Biophysics, Institute of Physiology, Academy of Sciences of the Czech Republic, Videnska 1084, Prague 4, 14220, Czech Republic.
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Nucleic acid import into mitochondria: New insights into the translocation pathways. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:3165-81. [DOI: 10.1016/j.bbamcr.2015.09.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 08/16/2015] [Accepted: 09/10/2015] [Indexed: 11/18/2022]
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42
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Wang G, Shimada E, Nili M, Koehler CM, Teitell MA. Mitochondria-targeted RNA import. Methods Mol Biol 2015; 1264:107-16. [PMID: 25631008 DOI: 10.1007/978-1-4939-2257-4_11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The import of a modest number of nucleus-encoded RNAs into mitochondria has been reported in species ranging from yeast to human. With the advent of high-throughput RNA sequencing, additional nucleus-encoded mitochondrial RNAs are being identified. Confirming the mitochondrial localization of candidate RNAs of interest (e.g., small noncoding RNAs, miRNAs, tRNAs, and possibly lncRNAs and viral RNAs) and understanding their function within the mitochondrion is assisted by in vitro and in vivo import assay systems. Here we describe these two systems for studying mitochondrial RNA import, processing, and functions.
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Affiliation(s)
- Geng Wang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
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43
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Dietrich A, Wallet C, Iqbal RK, Gualberto JM, Lotfi F. Organellar non-coding RNAs: Emerging regulation mechanisms. Biochimie 2015; 117:48-62. [DOI: 10.1016/j.biochi.2015.06.027] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/29/2015] [Indexed: 02/06/2023]
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Mayr JA, Haack TB, Freisinger P, Karall D, Makowski C, Koch J, Feichtinger RG, Zimmermann FA, Rolinski B, Ahting U, Meitinger T, Prokisch H, Sperl W. Spectrum of combined respiratory chain defects. J Inherit Metab Dis 2015; 38:629-40. [PMID: 25778941 PMCID: PMC4493854 DOI: 10.1007/s10545-015-9831-y] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 02/20/2015] [Accepted: 02/23/2015] [Indexed: 01/22/2023]
Abstract
Inherited disorders of mitochondrial energy metabolism form a large and heterogeneous group of metabolic diseases. More than 250 gene defects have been reported to date and this number continues to grow. Mitochondrial diseases can be grouped into (1) disorders of oxidative phosphorylation (OXPHOS) subunits and their assembly factors, (2) defects of mitochondrial DNA, RNA and protein synthesis, (3) defects in the substrate-generating upstream reactions of OXPHOS, (4) defects in relevant cofactors and (5) defects in mitochondrial homeostasis. Deficiency of more than one respiratory chain enzyme is a common finding. Combined defects are found in 49 % of the known disease-causing genes of mitochondrial energy metabolism and in 57 % of patients with OXPHOS defects identified in our diagnostic centre. Combined defects of complexes I, III, IV and V are typically due to deficiency of mitochondrial DNA replication, RNA metabolism or translation. Defects in cofactors can result in combined defects of various combinations, and defects of mitochondrial homeostasis can result in a generalised decrease of all OXPHOS enzymes. Noteworthy, identification of combined defects can be complicated by different degrees of severity of each affected enzyme. Furthermore, even defects of single respiratory chain enzymes can result in combined defects due to aberrant formation of respiratory chain supercomplexes. Combined OXPHOS defects have a great variety of clinical manifestations in terms of onset, course severity and tissue involvement. They can present as classical encephalomyopathy but also with hepatopathy, nephropathy, haematologic findings and Perrault syndrome in a subset of disorders.
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Affiliation(s)
- Johannes A Mayr
- Department of Paediatrics, Paracelsus Medical University, SALK Salzburg, Salzburg, 5020, Austria,
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45
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RNase III-Independent Autogenous Regulation of Escherichia coli Polynucleotide Phosphorylase via Translational Repression. J Bacteriol 2015; 197:1931-8. [PMID: 25825432 DOI: 10.1128/jb.00105-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 03/23/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The complex posttranscriptional regulation mechanism of the Escherichia coli pnp gene, which encodes the phosphorolytic exoribonuclease polynucleotide phosphorylase (PNPase), involves two endoribonucleases, namely, RNase III and RNase E, and PNPase itself, which thus autoregulates its own expression. The models proposed for pnp autoregulation posit that the target of PNPase is a mature pnp mRNA previously processed at its 5' end by RNase III, rather than the primary pnp transcript (RNase III-dependent models), and that PNPase activity eventually leads to pnp mRNA degradation by RNase E. However, some published data suggest that pnp expression may also be regulated through a PNPase-dependent, RNase III-independent mechanism. To address this issue, we constructed isogenic Δpnp rnc(+) and Δpnp Δrnc strains with a chromosomal pnp-lacZ translational fusion and measured β-galactosidase activity in the absence and presence of PNPase expressed by a plasmid. Our results show that PNPase also regulates its own expression via a reversible RNase III-independent pathway acting upstream from the RNase III-dependent branch. This pathway requires the PNPase RNA binding domains KH and S1 but not its phosphorolytic activity. We suggest that the RNase III-independent autoregulation of PNPase occurs at the level of translational repression, possibly by competition for pnp primary transcript between PNPase and the ribosomal protein S1. IMPORTANCE In Escherichia coli, polynucleotide phosphorylase (PNPase, encoded by pnp) posttranscriptionally regulates its own expression. The two models proposed so far posit a two-step mechanism in which RNase III, by cutting the leader region of the pnp primary transcript, creates the substrate for PNPase regulatory activity, eventually leading to pnp mRNA degradation by RNase E. In this work, we provide evidence supporting an additional pathway for PNPase autogenous regulation in which PNPase acts as a translational repressor independently of RNase III cleavage. Our data make a new contribution to the understanding of the regulatory mechanism of pnp mRNA, a process long since considered a paradigmatic example of posttranscriptional regulation at the level of mRNA stability.
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46
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Wang X, Yu X, Vaughan W, Liu M, Guan Y. Novel drug-delivery approaches to the blood-brain barrier. Neurosci Bull 2015; 31:257-64. [PMID: 25595370 DOI: 10.1007/s12264-014-1498-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 07/21/2014] [Indexed: 11/30/2022] Open
Abstract
The blood-brain barrier (BBB) maintains homeostasis by blocking toxic molecules from the circulation, but drugs are blocked at the same time. When the dose is increased to enhance the drug concentration in the central nervous system, there are side-effects on peripheral organs. In recent years, genetic therapeutic agents and small molecules have been used in various strategies to penetrate the BBB while minimizing the damage to systemic organs. In this review, we describe several representative methods to circumvent or cross the BBB, including chemical and physical strategies.
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Affiliation(s)
- Xiaoqing Wang
- Department of Neurology, Changhai Hospital, Second Military Medical University, Shanghai, 200433, China
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47
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Borralho PM, Rodrigues CMP, Steer CJ. microRNAs in Mitochondria: An Unexplored Niche. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 887:31-51. [PMID: 26662985 DOI: 10.1007/978-3-319-22380-3_3] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mitochondria are pivotal organelles involved in the regulation of a myriad of crucial biological processes, including cell survival and cell death, rendering mitochondrial dysfunction a relevant step in numerous pathophysiological processes. MicroRNAs (miRNAs) are endogenous small noncoding RNAs that add a new layer of complexity to the control of gene expression. miRNAs function as master regulators and fine-tuners of gene expression, primarily via posttranscriptional mechanisms, and are increasingly demonstrated as a paramount class of endogenous molecules with relevant diagnostic, prognostic, and therapeutic applications. miRNAs and other RNA interference have recently been reported to be present in mitochondria from several species, and we are now beginning to unveil mitochondrial miRNA transport mechanisms, biological function and targets to ascertain their role in this unexplored niche. Here, we describe miRNA biogenesis and present key findings regarding miRNA localization to mitochondria, origin, putative biological function, and implications for human disease.
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Affiliation(s)
- Pedro M Borralho
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Cecília M P Rodrigues
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Clifford J Steer
- Departments of Medicine, and Genetics, Cell Biology and Development, University of Minnesota Medical School, VFW Cancer Research Center, 406 Harvard Street S.E., Minneapolis, MN, 55455, USA.
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Sokhi UK, Bacolod MD, Emdad L, Das SK, Dumur CI, Miles MF, Sarkar D, Fisher PB. Analysis of global changes in gene expression induced by human polynucleotide phosphorylase (hPNPase(old-35)). J Cell Physiol 2014; 229:1952-62. [PMID: 24729470 PMCID: PMC4149605 DOI: 10.1002/jcp.24645] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 04/09/2014] [Indexed: 01/19/2023]
Abstract
As a strategy to identify gene expression changes affected by human polynucleotide phosphorylase (hPNPase(old-35)), we performed gene expression analysis of HeLa cells in which hPNPase(old-35) was overexpressed. The observed changes were then compared to those of HO-1 melanoma cells in which hPNPase(old-35) was stably knocked down. Through this analysis, 90 transcripts, which positively or negatively correlated with hPNPase(old-35) expression, were identified. The majority of these genes were associated with cell communication, cell cycle, and chromosomal organization gene ontology categories. For a number of these genes, the positive or negative correlations with hPNPase(old-35) expression were consistent with transcriptional data extracted from the TCGA (The Cancer Genome Atlas) expression datasets for colon adenocarcinoma (COAD), skin cutaneous melanoma (SKCM), ovarian serous cyst adenocarcinoma (OV), and prostate adenocarcinoma (PRAD). Further analysis comparing the gene expression changes between Ad.hPNPase(old-35) infected HO-1 melanoma cells and HeLa cells overexpressing hPNPase(old-35) under the control of a doxycycline-inducible promoter, revealed global changes in genes involved in cell cycle and mitosis. Overall, this study provides further evidence that hPNPase(old-35) is associated with global changes in cell cycle-associated genes and identifies potential gene targets for future investigation.
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Affiliation(s)
- Upneet K. Sokhi
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
| | - Manny D. Bacolod
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
| | - Luni Emdad
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
- VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
| | - Swadesh K. Das
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
| | - Catherine I. Dumur
- Department of Pathology, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
| | - Michael F. Miles
- VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
- Department of Neurology, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
| | - Devanand Sarkar
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
- VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
| | - Paul B. Fisher
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
- VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298
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Rosenkranz AA, Ulasov AV, Slastnikova TA, Khramtsov YV, Sobolev AS. Use of intracellular transport processes for targeted drug delivery into a specified cellular compartment. BIOCHEMISTRY (MOSCOW) 2014; 79:928-46. [DOI: 10.1134/s0006297914090090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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50
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Mitochondrial MicroRNAs and Their Potential Role in Cell Function. CURRENT PATHOBIOLOGY REPORTS 2014. [DOI: 10.1007/s40139-014-0047-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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