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Sadhukhan S, Sinha T, Dey S, Panda AC. Subcellular localization of circular RNAs: Where and why. Biochem Biophys Res Commun 2024; 715:149937. [PMID: 38701688 DOI: 10.1016/j.bbrc.2024.149937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 04/02/2024] [Accepted: 04/11/2024] [Indexed: 05/05/2024]
Abstract
Localization of RNAs at specific subcellular locations regulating various local cellular events has gained much attention recently. Like most other classes of RNAs, the function of newly discovered circular RNAs (circRNAs) is predominantly determined by their association with different cellular factors in the cell. CircRNAs function as transcriptional and posttranscriptional regulators of gene expression by interacting with transcription factors, splicing regulators, RNA-binding proteins, and microRNAs or by translating into functional polypeptides. Hence, studying their subcellular localization to assess their function is essential. The discovery of more than a million circRNA and increasing evidence of their involvement in development and diseases require a thorough analysis of their subcellular localization linking to their biological functions. Here, we summarize current knowledge of circRNA localization in cells and extracellular vesicles, factors regulating their subcellular localization, and the implications of circRNA localization on their cellular functions. Given the discovery of many circRNAs in all life forms and their implications in pathophysiology, we discuss the challenges in studying circRNA localization and the opportunities for unlocking the mystery of circRNA functions.
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Affiliation(s)
- Susovan Sadhukhan
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India
| | - Tanvi Sinha
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India
| | - Suchanda Dey
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India
| | - Amaresh C Panda
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India.
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2
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Avolio R, Agliarulo I, Criscuolo D, Sarnataro D, Auriemma M, De Lella S, Pennacchio S, Calice G, Ng MY, Giorgi C, Pinton P, Cooperman BS, Landriscina M, Esposito F, Matassa DS. Cytosolic and mitochondrial translation elongation are coordinated through the molecular chaperone TRAP1 for the synthesis and import of mitochondrial proteins. Genome Res 2023; 33:1242-1257. [PMID: 37487647 PMCID: PMC10547376 DOI: 10.1101/gr.277755.123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 07/19/2023] [Indexed: 07/26/2023]
Abstract
A complex interplay between mRNA translation and cellular respiration has been recently unveiled, but its regulation in humans is poorly characterized in either health or disease. Cancer cells radically reshape both biosynthetic and bioenergetic pathways to sustain their aberrant growth rates. In this regard, we have shown that the molecular chaperone TRAP1 not only regulates the activity of respiratory complexes, behaving alternatively as an oncogene or a tumor suppressor, but also plays a concomitant moonlighting function in mRNA translation regulation. Herein, we identify the molecular mechanisms involved, showing that TRAP1 (1) binds both mitochondrial and cytosolic ribosomes, as well as translation elongation factors; (2) slows down translation elongation rate; and (3) favors localized translation in the proximity of mitochondria. We also provide evidence that TRAP1 is coexpressed in human tissues with the mitochondrial translational machinery, which is responsible for the synthesis of respiratory complex proteins. Altogether, our results show an unprecedented level of complexity in the regulation of cancer cell metabolism, strongly suggesting the existence of a tight feedback loop between protein synthesis and energy metabolism, based on the demonstration that a single molecular chaperone plays a role in both mitochondrial and cytosolic translation, as well as in mitochondrial respiration.
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Affiliation(s)
- Rosario Avolio
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples 80131, Italy
| | - Ilenia Agliarulo
- Institute of Experimental Endocrinology and Oncology "G. Salvatore"-IEOS, National Research Council of Italy (CNR), Naples 80131, Italy
| | - Daniela Criscuolo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples 80131, Italy
| | - Daniela Sarnataro
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples 80131, Italy
| | - Margherita Auriemma
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples 80131, Italy
| | - Sabrina De Lella
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples 80131, Italy
| | - Sara Pennacchio
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples 80131, Italy
| | - Giovanni Calice
- Laboratory of Preclinical and Translational Research, IRCCS, Referral Cancer Center of Basilicata, Rionero in Vulture 85028, Italy
| | - Martin Y Ng
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
| | - Carlotta Giorgi
- Department of Medical Sciences, University of Ferrara, Ferrara 44121, Italy
| | - Paolo Pinton
- Department of Medical Sciences, University of Ferrara, Ferrara 44121, Italy
| | - Barry S Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
| | - Matteo Landriscina
- Institute of Experimental Endocrinology and Oncology "G. Salvatore"-IEOS, National Research Council of Italy (CNR), Naples 80131, Italy
- Department Medical and Surgical Science, University of Foggia, Foggia 71122, Italy
| | - Franca Esposito
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples 80131, Italy;
| | - Danilo Swann Matassa
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples 80131, Italy;
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3
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Smoniewski CM, Mirzavand Borujeni P, Petersen A, Hampton M, Salavati R, Zimmer SL. Circular mitochondrial-encoded mRNAs are a distinct subpopulation of mitochondrial mRNA in Trypanosoma brucei. Sci Rep 2023; 13:7825. [PMID: 37188727 PMCID: PMC10185552 DOI: 10.1038/s41598-023-34255-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/26/2023] [Indexed: 05/17/2023] Open
Abstract
Since the first identification of circular RNA (circRNA) in viral-like systems, reports of circRNAs and their functions in various organisms, cell types, and organelles have greatly expanded. Here, we report the first evidence, to our knowledge, of circular mRNA in the mitochondrion of the eukaryotic parasite, Trypanosoma brucei. While using a circular RT-PCR technique developed to sequence mRNA tails of mitochondrial transcripts, we found that some mRNAs are circularized without an in vitro circularization step normally required to produce PCR products. Starting from total in vitro circularized RNA and in vivo circRNA, we high-throughput sequenced three transcripts from the 3' end of the coding region, through the 3' tail, to the 5' start of the coding region. We found that fewer reads in the circRNA libraries contained tails than in the total RNA libraries. When tails were present on circRNAs, they were shorter and less adenine-rich than the total population of RNA tails of the same transcript. Additionally, using hidden Markov modelling we determined that enzymatic activity during tail addition is different for circRNAs than for total RNA. Lastly, circRNA UTRs tended to be shorter and more variable than those of the same transcript sequenced from total RNA. We propose a revised model of Trypanosome mitochondrial tail addition, in which a fraction of mRNAs is circularized prior to the addition of adenine-rich tails and may act as a new regulatory molecule or in a degradation pathway.
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Affiliation(s)
- Clara M Smoniewski
- Department of Biomedical Sciences, University of Minnesota Medical School Duluth Campus, Duluth, MN, USA
| | | | - Austin Petersen
- Department of Biology, University of Minnesota Duluth, Duluth, MN, USA
| | - Marshall Hampton
- Department of Mathematics and Statistics, University of Minnesota Duluth, Duluth, MN, USA
| | - Reza Salavati
- Institute of Parasitology, McGill University, Montreal, QC, Canada
| | - Sara L Zimmer
- Department of Biomedical Sciences, University of Minnesota Medical School Duluth Campus, Duluth, MN, USA.
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4
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Smoniewski CM, Borujeni PM, Petersen A, Hampton M, Salavati R, Zimmer SL. Circular mitochondrial-encoded mRNAs are a distinct subpopulation of mitochondrial mRNA in Trypanosoma brucei. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.10.528059. [PMID: 36798374 DOI: 10.1101/2023.01.18.524644] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Since the first identification of circular RNA (circRNA) in viral-like systems, reports of circRNAs and their functions in various organisms, cell types, and organelles have greatly expanded. Here, we report the first evidence of circular mRNA in the mitochondrion of the eukaryotic parasite, Trypanosoma brucei . While using a circular RT-PCR technique developed to sequence mRNA tails of mitochondrial transcripts, we found that some mRNAs are circularized without an in vitro circularization step normally required to produce PCR products. Starting from total in vitro circularized RNA and in vivo circRNA, we high-throughput sequenced three transcripts from the 3' end of the coding region, through the 3' tail, to the 5' start of the coding region. We found that fewer reads in the circRNA libraries contained tails than in the total RNA libraries. When tails were present on circRNAs, they were shorter and less adenine-rich than the total population of RNA tails of the same transcript. Additionally, using hidden Markov modelling we determined that enzymatic activity during tail addition is different for circRNAs than for total RNA. Lastly, circRNA UTRs tended to be shorter and more variable than those of the same transcript sequenced from total RNA. We propose a revised model of Trypanosome mitochondrial tail addition, in which a fraction of mRNAs is circularized prior to the addition of adenine-rich tails and may act as a new regulatory molecule or in a degradation pathway.
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Affiliation(s)
- Clara M Smoniewski
- Department of Biomedical Sciences, University of Minnesota Medical School Duluth Campus, Duluth, MN, USA
| | | | - Austin Petersen
- Department of Biology, University of Minnesota Duluth, Duluth, MN, USA
| | - Marshall Hampton
- Department of Mathematics and Statistics, University of Minnesota Duluth, Duluth, MN, USA
| | - Reza Salavati
- Institute of Parasitology, McGill University, Quebec, Canada
| | - Sara L Zimmer
- Department of Biomedical Sciences, University of Minnesota Medical School Duluth Campus, Duluth, MN, USA
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5
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Smoniewski CM, Borujeni PM, Petersen A, Hampton M, Salavati R, Zimmer SL. Circular mitochondrial-encoded mRNAs are a distinct subpopulation of mitochondrial mRNA in Trypanosoma brucei. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.10.528059. [PMID: 36798374 PMCID: PMC9934643 DOI: 10.1101/2023.02.10.528059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Since the first identification of circular RNA (circRNA) in viral-like systems, reports of circRNAs and their functions in various organisms, cell types, and organelles have greatly expanded. Here, we report the first evidence of circular mRNA in the mitochondrion of the eukaryotic parasite, Trypanosoma brucei . While using a circular RT-PCR technique developed to sequence mRNA tails of mitochondrial transcripts, we found that some mRNAs are circularized without an in vitro circularization step normally required to produce PCR products. Starting from total in vitro circularized RNA and in vivo circRNA, we high-throughput sequenced three transcripts from the 3' end of the coding region, through the 3' tail, to the 5' start of the coding region. We found that fewer reads in the circRNA libraries contained tails than in the total RNA libraries. When tails were present on circRNAs, they were shorter and less adenine-rich than the total population of RNA tails of the same transcript. Additionally, using hidden Markov modelling we determined that enzymatic activity during tail addition is different for circRNAs than for total RNA. Lastly, circRNA UTRs tended to be shorter and more variable than those of the same transcript sequenced from total RNA. We propose a revised model of Trypanosome mitochondrial tail addition, in which a fraction of mRNAs is circularized prior to the addition of adenine-rich tails and may act as a new regulatory molecule or in a degradation pathway.
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Affiliation(s)
- Clara M. Smoniewski
- Department of Biomedical Sciences, University of Minnesota Medical School Duluth Campus, Duluth, MN, USA
| | | | - Austin Petersen
- Department of Biology, University of Minnesota Duluth, Duluth, MN, USA
| | - Marshall Hampton
- Department of Mathematics and Statistics, University of Minnesota Duluth, Duluth, MN, USA
| | - Reza Salavati
- Institute of Parasitology, McGill University, Quebec, Canada
| | - Sara L. Zimmer
- Department of Biomedical Sciences, University of Minnesota Medical School Duluth Campus, Duluth, MN, USA
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6
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Avolio R, Agliarulo I, Criscuolo D, Sarnataro D, Auriemma M, Pennacchio S, Calice G, Ng MY, Giorgi C, Pinton P, Cooperman B, Landriscina M, Esposito F, Matassa DS. Cytosolic and mitochondrial translation elongation are coordinated through the molecular chaperone TRAP1 for the synthesis and import of mitochondrial proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.19.524708. [PMID: 36712063 PMCID: PMC9882373 DOI: 10.1101/2023.01.19.524708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A complex interplay between mRNA translation and cellular respiration has been recently unveiled, but its regulation in humans is poorly characterized in either health or disease. Cancer cells radically reshape both biosynthetic and bioenergetic pathways to sustain their aberrant growth rates. In this regard, we have shown that the molecular chaperone TRAP1 not only regulates the activity of respiratory complexes, behaving alternatively as an oncogene or a tumor suppressor, but also plays a concomitant moonlighting function in mRNA translation regulation. Herein we identify the molecular mechanisms involved, demonstrating that TRAP1: i) binds both mitochondrial and cytosolic ribosomes as well as translation elongation factors, ii) slows down translation elongation rate, and iii) favors localized translation in the proximity of mitochondria. We also provide evidence that TRAP1 is coexpressed in human tissues with the mitochondrial translational machinery, which is responsible for the synthesis of respiratory complex proteins. Altogether, our results show an unprecedented level of complexity in the regulation of cancer cell metabolism, strongly suggesting the existence of a tight feedback loop between protein synthesis and energy metabolism, based on the demonstration that a single molecular chaperone plays a role in both mitochondrial and cytosolic translation, as well as in mitochondrial respiration.
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Affiliation(s)
- Rosario Avolio
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, 80131, Italy
| | - Ilenia Agliarulo
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” - IEOS, National Research Council of Italy (CNR), Naples, 80131, Italy
| | - Daniela Criscuolo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, 80131, Italy
| | - Daniela Sarnataro
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, 80131, Italy
| | - Margherita Auriemma
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, 80131, Italy
| | - Sara Pennacchio
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, 80131, Italy
| | - Giovanni Calice
- Laboratory of Pre-clinical and Translational Research, IRCCS, Referral Cancer Center of Basilicata, Rionero in Vulture, 85028, Italy
| | - Martin Y. Ng
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Carlotta Giorgi
- Dept. of Medical Sciences, University of Ferrara, Ferrara, 44121, Italy
| | - Paolo Pinton
- Dept. of Medical Sciences, University of Ferrara, Ferrara, 44121, Italy
| | - Barry Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Matteo Landriscina
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” - IEOS, National Research Council of Italy (CNR), Naples, 80131, Italy
- Department Medical and Surgical Science, University of Foggia, Foggia, 71122, Italy
| | - Franca Esposito
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, 80131, Italy
| | - Danilo Swann Matassa
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, 80131, Italy
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7
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circMTND5 Participates in Renal Mitochondrial Injury and Fibrosis by Sponging MIR6812 in Lupus Nephritis. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:2769487. [PMID: 36267809 PMCID: PMC9578797 DOI: 10.1155/2022/2769487] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 09/12/2022] [Accepted: 09/22/2022] [Indexed: 11/18/2022]
Abstract
Recent studies have focused on nuclear-encoded circular RNAs (circRNAs) in kidney diseases, but little is known about mitochondrial circRNAs. Differentially expressed circRNAs were analyzed by RNA deep sequencing from lupus nephritis (LN) biopsies and normal human kidneys. In LN renal biopsies, the most downregulated circRNA was circMTND5, which is encoded in the mitochondrial genome. We quantitated circMTND5 by qPCR and localized by fluorescence in situ hybridization (FISH). Mitochondrial abnormalities were identified by electron microscopy. The expression of mitochondrial genes was decreased, and the expression of profibrotic genes was increased on qPCR and immunostaining. RNA binding sites for MIR6812 and circMTND5 were predicted. MIR6812 expression was increased by FISH and qPCR. In HK-2 cells and its mitochondrial fraction, the role of circMTND5 sponging MIR6812 was assessed by their colocalization in mitochondria on FISH, RNA immunoprecipitation, and RNA pulldown coupled with luciferase reporter assay. circMTND5 knockdown upregulated MIR6812, decreased mitochondrial functional gene expression, and increased profibrotic gene expression. Overexpression of circMTND5 reversed these effects in hTGF-β stimulated HK-2 cells. Similar effects were observed in HK-2 cells with overexpression and with knockdown of MIR6812. We conclude that circMTND5 alleviates renal mitochondrial injury and kidney fibrosis by sponging MIR6812 in LN.
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8
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Wang Y, Wu C, Du Y, Li Z, Li M, Hou P, Shen Z, Chu S, Zheng J, Bai J. Expanding uncapped translation and emerging function of circular RNA in carcinomas and noncarcinomas. Mol Cancer 2022; 21:13. [PMID: 34996480 PMCID: PMC8740365 DOI: 10.1186/s12943-021-01484-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/16/2021] [Indexed: 02/07/2023] Open
Abstract
Circular RNAs (circRNAs) are classified as noncoding RNAs because they are devoid of a 5' end cap and a 3' end poly (A) tail necessary for cap-dependent translation. However, increasing numbers of translated circRNAs identified through high-throughput RNA sequencing overlapping with polysome profiling indicate that this rule is being broken. CircRNAs can be translated in cap-independent mechanism, including IRES (internal ribosome entry site)-initiated pattern, MIRES (m6A internal ribosome entry site) -initiated patterns, and rolling translation mechanism (RCA). CircRNA-encoded proteins harbour diverse functions similar to or different from host proteins. In addition, they are linked to the modulation of human disease including carcinomas and noncarcinomas. CircRNA-related translatomics and proteomics have attracted increasing attention. This review discusses the progress and exclusive characteristics of circRNA translation and highlights the latest mechanisms and regulation of circRNA translatomics. Furthermore, we summarize the extensive functions and mechanisms of circRNA-derived proteins in human diseases, which contribute to a better understanding of intricate noncanonical circRNA translatomics and proteomics and their therapeutic potential in human diseases.
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Affiliation(s)
- Yan Wang
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China
- Center of Clinical Oncology, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Department of Pharmacy, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Chunjie Wu
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China
- Department of Pharmacy, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yu Du
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China
- Department of Pharmacy, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Zhongwei Li
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China
| | - Minle Li
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China
| | - Pingfu Hou
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China
| | - Zhigang Shen
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China
| | - Sufang Chu
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China
| | - Junnian Zheng
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China.
- Center of Clinical Oncology, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.
| | - Jin Bai
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China.
- Center of Clinical Oncology, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.
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9
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Liu X, Shan G. Mitochondria Encoded Non-coding RNAs in Cell Physiology. Front Cell Dev Biol 2021; 9:713729. [PMID: 34395442 PMCID: PMC8362354 DOI: 10.3389/fcell.2021.713729] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/12/2021] [Indexed: 01/05/2023] Open
Abstract
Mitochondria are the powerhouses of mammalian cells, which participate in series of metabolic processes and cellular events. Mitochondria have their own genomes, and it is generally acknowledged that human mitochondrial genome encodes 13 proteins, 2 rRNAs and 22 tRNAs. However, the complexity of mitochondria derived transcripts is just starting to be envisaged. Currently, there are at least 8 lncRNAs, some dsRNAs, various small RNAs, and hundreds of circRNAs known to be generated from mitochondrial genome. These non-coding RNAs either translocate into cytosol/nucleus or reside in mitochondria to play various biological functions. Here we present an overview of regulatory non-coding RNAs encoded by the mammalian mitochondria genome. For overall understandings of non-coding RNAs in mitochondrial function, a brief summarization of nuclear-encoded non-coding RNAs in mitochondria is also included. We discuss about roles of these non-coding RNAs in cellular physiology and the communication between mitochondria and the nucleus.
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Affiliation(s)
- Xu Liu
- Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Science and Medicine, Department of Clinical Laboratory, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, University of Science and Technology of China, Hefei, China
| | - Ge Shan
- Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Science and Medicine, Department of Clinical Laboratory, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, University of Science and Technology of China, Hefei, China
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10
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Liang H, Liu J, Su S, Zhao Q. Mitochondrial noncoding RNAs: new wine in an old bottle. RNA Biol 2021; 18:2168-2182. [PMID: 34110970 DOI: 10.1080/15476286.2021.1935572] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Mitochondrial noncoding RNAs (mt-ncRNAs) include noncoding RNAs inside the mitochondria that are transcribed from the mitochondrial genome or nuclear genome, and noncoding RNAs transcribed from the mitochondrial genome that are transported to the cytosol or nucleus. Recent findings have revealed that mt-ncRNAs play important roles in not only mitochondrial functions, but also other cellular activities. This review proposes a classification of mt-ncRNAs and outlines the emerging understanding of mitochondrial circular RNAs (mt-circRNAs), mitochondrial microRNAs (mitomiRs), and mitochondrial long noncoding RNAs (mt-lncRNAs), with an emphasis on their identification and functions.
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Affiliation(s)
- Huixin Liang
- Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Jiayu Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Shicheng Su
- Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Department of Immunology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Qiyi Zhao
- Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
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11
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Proulex GCR, Meade MJ, Manoylov KM, Cahoon AB. Mitochondrial mRNA Processing in the Chlorophyte Alga Pediastrum duplex and Streptophyte Alga Chara vulgaris Reveals an Evolutionary Branch in Mitochondrial mRNA Processing. PLANTS (BASEL, SWITZERLAND) 2021; 10:576. [PMID: 33803683 PMCID: PMC8003010 DOI: 10.3390/plants10030576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/12/2021] [Accepted: 03/13/2021] [Indexed: 11/17/2022]
Abstract
Mitochondria carry the remnant of an ancestral bacterial chromosome and express those genes with a system separate and distinct from the nucleus. Mitochondrial genes are transcribed as poly-cistronic primary transcripts which are post-transcriptionally processed to create individual translationally competent mRNAs. Algae post-transcriptional processing has only been explored in Chlamydomonas reinhardtii (Class: Chlorophyceae) and the mature mRNAs are different than higher plants, having no 5' UnTranslated Regions (UTRs), much shorter and more variable 3' UTRs and polycytidylated mature mRNAs. In this study, we analyzed transcript termini using circular RT-PCR and PacBio Iso-Seq to survey the 3' and 5' UTRs and termini for two green algae, Pediastrum duplex (Class: Chlorophyceae) and Chara vulgaris (Class: Charophyceae). This enabled the comparison of processing in the chlorophyte and charophyte clades of green algae to determine if the differences in mitochondrial mRNA processing pre-date the invasion of land by embryophytes. We report that the 5' mRNA termini and non-template 3' termini additions in P. duplex resemble those of C. reinhardtii, suggesting a conservation of mRNA processing among the chlorophyceae. We also report that C. vulgaris mRNA UTRs are much longer than chlorophytic examples, lack polycytidylation, and are polyadenylated similar to embryophytes. This demonstrates that some mitochondrial mRNA processing events diverged with the split between chlorophytic and streptophytic algae.
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Affiliation(s)
- Grayson C. R. Proulex
- Department of Natural Sciences, The University of Virginia’s College at Wise, 1 College Ave., Wise, VA 24293, USA; (G.C.R.P.); (M.J.M.)
| | - Marcus J. Meade
- Department of Natural Sciences, The University of Virginia’s College at Wise, 1 College Ave., Wise, VA 24293, USA; (G.C.R.P.); (M.J.M.)
| | - Kalina M. Manoylov
- Department of Biological and Environmental Sciences, Georgia College and State University, Milledgeville, GA 31061, USA;
| | - A. Bruce Cahoon
- Department of Natural Sciences, The University of Virginia’s College at Wise, 1 College Ave., Wise, VA 24293, USA; (G.C.R.P.); (M.J.M.)
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12
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Meade MJ, Proulex GCR, Manoylov KM, Cahoon AB. Chloroplast mRNAs are 3' polyuridylylated in the Green Alga Pithophora roettleri (Cladophorales). JOURNAL OF PHYCOLOGY 2020; 56:1124-1134. [PMID: 32464681 DOI: 10.1111/jpy.13033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/14/2020] [Indexed: 06/11/2023]
Abstract
Species within the green algal order Cladophorales have an unconventional plastome structure where individual coding regions or small numbers of genes occur as linear single-stranded DNAs folded into hairpin structures. Another group of photosynthetic organisms with an equivalently reduced chloroplast genome are the peridinin dinoflagellates of the Alveolata eukaryotic lineage whose plastomes are mini-circles carrying one or a few genes required for photosynthesis. One unusual aspect of the Alveolata is the polyuridylylation of mRNA 3' ends among peridinin dinoflagellates and the chromerid algae. This study was conducted to understand if an unconventional highly reduced plastome structure co-occurs with unconventional RNA processing. To address this, the 5' and 3' mRNA termini of the known chloroplast genes of Pithophora roettleri (order Cladophorales) were analyzed for evidence of post-transcriptional processing. Circular Reverse Transcriptase PCR (cRT-PCR) followed by deep sequencing of the amplicons was used to analyze 5' and 3' mRNA termini. Evidence of several processing events were collected, most notably the 3' termini of six of the eight genes were polyuridylylated, which has not been reported for any lineage outside of the Alveolata. Other processing events include poly(A) and heteropolymeric 3' additions, 5' primary transcript start sites, as well as the presence of circularized RNAs. Five other species representing other green algal lineages were also tested and poly(U) additions appear to be limited to the order Cladophorales. These results demonstrate that chloroplast mRNA polyuridylylation is not the sole provenance of photosynthetic alveolates and may have convergently evolved in two distinct photosynthetic lineages.
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Affiliation(s)
- Marcus J Meade
- Department of Natural Sciences, The University of Virginia's College at Wise, 1 College Ave., Wise, Virginia, 24293, USA
| | - Grayson C R Proulex
- Department of Natural Sciences, The University of Virginia's College at Wise, 1 College Ave., Wise, Virginia, 24293, USA
| | - Kalina M Manoylov
- Department of Biological and Environmental Sciences, Georgia College and State University, Milledgeville, Georgia, 31061, USA
| | - A Bruce Cahoon
- Department of Natural Sciences, The University of Virginia's College at Wise, 1 College Ave., Wise, Virginia, 24293, USA
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13
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Ottesen EW, Singh RN. Characteristics of circular RNAs generated by human Survival Motor Neuron genes. Cell Signal 2020; 73:109696. [PMID: 32553550 PMCID: PMC7387165 DOI: 10.1016/j.cellsig.2020.109696] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/12/2020] [Indexed: 02/06/2023]
Abstract
Circular RNAs (circRNAs) belong to a diverse class of stable RNAs expressed in all cell types. Their proposed functions include sponging of microRNAs (miRNAs), sequestration and trafficking of proteins, assembly of multimeric complexes, production of peptides, and regulation of transcription. Backsplicing due to RNA structures formed by an exceptionally high number of Alu repeats lead to the production of a vast repertoire of circRNAs by human Survival Motor Neuron genes, SMN1 and SMN2, that code for SMN, an essential multifunctional protein. Low levels of SMN due to deletion or mutation of SMN1 result in spinal muscular atrophy (SMA), a major genetic disease of infants and children. Mild SMA is also recorded in adult population, expanding the spectrum of the disease. Here we review SMN circRNAs with respect to their biogenesis, sequence features, and potential functions. We also discuss how SMN circRNAs could be exploited for diagnostic and therapeutic purposes.
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Affiliation(s)
- Eric W Ottesen
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, United States of America
| | - Ravindra N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, United States of America.
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14
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Xu X, Zhou X, Gao C, Cui Y. Hsa_circ_0018818 knockdown suppresses tumorigenesis in non-small cell lung cancer by sponging miR-767-3p. Aging (Albany NY) 2020; 12:7774-7785. [PMID: 32357143 PMCID: PMC7244049 DOI: 10.18632/aging.103089] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/09/2020] [Indexed: 02/07/2023]
Abstract
To identify potential therapeutic targets in non-small cell lung cancer NSCLC, we conducted a bioinformatics analysis of circRNAs differentially expressed between NSCLC tissues and adjacent normal tissues. Cell proliferation and apoptosis was assessed using CCK-8 and flow cytometry, respectively. A connection between hsa_circ_0018818 and miR-767-3p was confirmed in dual luciferase reporter assays. Gene and protein expression in NSCLC cells were measured using quantitative PCR and Western-blotting, respectively. And a xenograft tumor model was established to assess the function of hsa_circ_0018818 in NSCLC in vivo. Hsa_circ_0018818 was greatly upregulated in NSCLC tumor tissues. Knocking down hsa_circ_0018818 using a targeted shRNA inhibited the proliferation and invasiveness of NSCLC cells and induced their apoptosis via the miR-767-3p/Nidogen 1 (NID1) signaling axis. Hsa_circ_0018818 knockdown also inactivated Epithelial-mesenchymal transition (EMT) process and PI3K/Akt signaling. In summary, hsa_circ_0018818 knockdown inhibited NSCLC tumorigenesis in vitro and in vivo, which suggests it could potentially serve as a target for the treatment of NSCLC.
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Affiliation(s)
- Xiaohui Xu
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Beijing 100730, China.,Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xiaoyun Zhou
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Beijing 100730, China.,Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Chao Gao
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Beijing 100730, China.,Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Yushang Cui
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Beijing 100730, China.,Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
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15
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Jusic A, Devaux Y. Mitochondrial noncoding RNA-regulatory network in cardiovascular disease. Basic Res Cardiol 2020; 115:23. [PMID: 32140778 DOI: 10.1007/s00395-020-0783-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 02/17/2020] [Indexed: 12/22/2022]
Abstract
Mitochondrial function and integrity are vital for the maintenance of cellular homeostasis, particularly in high-energy demanding cells. Cardiomyocytes have a large number of mitochondria, which provide a continuous and bulk supply of the ATP necessary for cardiac mechanical function. More than 90% of the ATP consumed by the heart is derived from the mitochondrial oxidative metabolism. Decreased energy supply as the main consequence of mitochondrial dysfunction is closely linked to cardiovascular disease (CVD). The discovery of noncoding RNA (ncRNAs) in the mitochondrial compartment has changed the traditional view of molecular pathways involved in the regulatory network of CVD. Mitochondrial ncRNAs participate in controlling cardiovascular pathogenesis by regulating glycolysis, mitochondrial energy status, and the expression of genes involved in mitochondrial metabolism. Understanding the underlying mechanisms of the association between impaired mitochondrial function resulting from fluctuation in expression levels of ncRNAs and specific disease phenotype can aid in preventing and treating CVD. This review presents an overview of the role of mitochondrial ncRNAs in the complex regulatory network of the cardiovascular pathology. We will summarize and discuss (1) mitochondrial microRNAs (mitomiRs) and long noncoding RNAs (lncRNAs) encoded either by nuclear or mitochondrial genome which are involved in the regulation of mitochondrial metabolism; (2) the role of mitomiRs and lncRNAs in the pathogenesis of several CVD such as hypertension, cardiac hypertrophy, acute myocardial infarction and heart failure; (3) the biomarker and therapeutic potential of mitochondrial ncRNAs in CVD; (4) and the challenges inherent to their translation into clinical application.
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Affiliation(s)
- Amela Jusic
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Tuzla, Tuzla, Bosnia and Herzegovina
| | - Yvan Devaux
- Cardiovascular Research Unit, Luxembourg Institute of Health, 1A-B rue Edison, 1445, Strassen, Luxembourg.
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