201
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Anand A, Pandi G. Noncoding RNA: An Insight into Chloroplast and Mitochondrial Gene Expressions. Life (Basel) 2021; 11:life11010049. [PMID: 33450961 PMCID: PMC7828403 DOI: 10.3390/life11010049] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 12/28/2020] [Accepted: 01/05/2021] [Indexed: 12/22/2022] Open
Abstract
Regulation of gene expression in any biological system is a complex process with many checkpoints at the transcriptional, post-transcriptional and translational levels. The control mechanism is mediated by various protein factors, secondary metabolites and a newly included regulatory member, i.e., noncoding RNAs (ncRNAs). It is known that ncRNAs modulate the mRNA or protein profiles of the cell depending on the degree of complementary and context of the microenvironment. In plants, ncRNAs are essential for growth and development in normal conditions by controlling various gene expressions and have emerged as a key player to guard plants during adverse conditions. In order to have smooth functioning of the plants under any environmental pressure, two very important DNA-harboring semi-autonomous organelles, namely, chloroplasts and mitochondria, are considered as main players. These organelles conduct the most crucial metabolic pathways that are required to maintain cell homeostasis. Thus, it is imperative to explore and envisage the molecular machineries responsible for gene regulation within the organelles and their coordination with nuclear transcripts. Therefore, the present review mainly focuses on ncRNAs origination and their gene regulation in chloroplasts and plant mitochondria.
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Affiliation(s)
- Asha Anand
- Correspondence: (A.A.); (G.P.); Tel.: +91-452-245-8230 (G.P.)
| | - Gopal Pandi
- Correspondence: (A.A.); (G.P.); Tel.: +91-452-245-8230 (G.P.)
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202
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Mitochondrial Reactive Oxygen Species (ROS) Production Alters Sperm Quality. Antioxidants (Basel) 2021; 10:antiox10010092. [PMID: 33440836 PMCID: PMC7827812 DOI: 10.3390/antiox10010092] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/22/2020] [Accepted: 12/30/2020] [Indexed: 02/06/2023] Open
Abstract
Besides ATP production, mitochondria are key organelles in several cellular functions, such as steroid hormone biosynthesis, calcium homoeostasis, intrinsic apoptotic pathway, and the generation of reactive oxygen species (ROS). Despite the loss of the majority of the cytoplasm occurring during spermiogenesis, mammalian sperm preserves a number of mitochondria that rearrange in a tubular structure at the level of the sperm flagellum midpiece. Although sperm mitochondria are destroyed inside the zygote, the integrity and the functionality of these organelles seem to be critical for fertilization and embryo development. The aim of this review was to discuss the impact of mitochondria-produced ROS at multiple levels in sperm: the genome, proteome, lipidome, epigenome. How diet, aging and environmental pollution may affect sperm quality and offspring health—by exacerbating oxidative stress—will be also described.
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203
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Miller B, Silverstein A, Flores M, Cao K, Kumagai H, Mehta HH, Yen K, Kim SJ, Cohen P. Host mitochondrial transcriptome response to SARS-CoV-2 in multiple cell models and clinical samples. Sci Rep 2021; 11:3. [PMID: 33420163 PMCID: PMC7794290 DOI: 10.1038/s41598-020-79552-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/09/2020] [Indexed: 12/18/2022] Open
Abstract
SARS-CoV-2 induces a muted innate immune response compared to other respiratory viruses. Mitochondrial dynamics might partially mediate this effect of SARS-CoV-2 on innate immunity. Polypeptides encoded by open reading frames of SARS-CoV and SARS-CoV-2 have been shown to localize to mitochondria and disrupt Mitochondrial Antiviral Signaling (MAVS) protein signaling. Therefore, we hypothesized that SARS-CoV-2 would distinctly regulate the mitochondrial transcriptome. We analyzed multiple publicly available RNASeq data derived from primary cells, cell lines, and clinical samples (i.e., BALF and lung). We report that SARS-CoV-2 did not dramatically regulate (1) mtDNA-encoded gene expression or (2) MAVS expression, and (3) SARS-CoV-2 downregulated nuclear-encoded mitochondrial (NEM) genes related to cellular respiration and Complex I.
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Affiliation(s)
- Brendan Miller
- Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave, Los Angeles, CA, 90089, USA
| | - Ana Silverstein
- Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave, Los Angeles, CA, 90089, USA
| | - Melanie Flores
- Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave, Los Angeles, CA, 90089, USA
| | - Kevin Cao
- Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave, Los Angeles, CA, 90089, USA
| | - Hiroshi Kumagai
- Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave, Los Angeles, CA, 90089, USA
- Graduate School of Health and Sports Science, Juntendo University, Chiba, Japan
| | - Hemal H Mehta
- Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave, Los Angeles, CA, 90089, USA
| | - Kelvin Yen
- Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave, Los Angeles, CA, 90089, USA
| | - Su- Jeong Kim
- Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave, Los Angeles, CA, 90089, USA
| | - Pinchas Cohen
- Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave, Los Angeles, CA, 90089, USA.
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204
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Isokallio MA, Stewart JB. High-Throughput Detection of mtDNA Mutations Leading to tRNA Processing Errors. Methods Mol Biol 2021; 2192:117-132. [PMID: 33230770 DOI: 10.1007/978-1-0716-0834-0_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Some mutations in the tRNA genes of mitochondrial DNA (mtDNA) have been demonstrated to affect the processing of the mitochondrial transcriptome in human patients with mitochondrial disease. A recent analysis of mtDNA mutations in 527 human tumors revealed that approximately a quarter of the somatic mt-tRNA gene mutations lead to aberrant processing of the mitochondrial transcriptome in these tumors. Here, we describe a method, based on mtDNA mutations induced by the mtDNA mutator mouse, to map the sites that lead to transcript processing abnormalities. Mutations in the mtDNA are identified and quantified by amplicon-based mtDNA sequencing, and compared to the allelic ratios observed in matched RNASeq data. Strong deviation in the variant allele frequencies between the amplicon and RNASeq data suggests that such mutations lead to disruptions in mitochondrial transcript processing.
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205
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Sas-Chen A, Nir R, Schwartz S. mito-Ψ-Seq: A High-Throughput Method for Systematic Mapping of Pseudouridine Within Mitochondrial RNA. Methods Mol Biol 2021; 2192:103-115. [PMID: 33230769 DOI: 10.1007/978-1-0716-0834-0_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
RNA modifications are present in most cellular RNAs and are formed posttranscriptionally by enzymatic machineries that involve hundreds of enzymes and cofactors. RNA modifications impact the life cycle of the RNA, its stability, folding, cellular localization, as well as interactions with RNA and protein partners. RNA modifications are important for mitochondrial function and are required for proper processing and function of mitochondrial (mt) tRNA and rRNA. Underscoring their importance, several mitochondrial diseases are caused by defects in mt-RNA modifications, stemming from mutations in mtDNA at or near mt-RNA modification sites or in nuclear-encoded mt-RNA modifying enzymes. A highly abundant RNA modification, involved in mitochondrial physiology and pathology is pseudouridylation (Ψ), which is catalyzed by enzymes of the Pseudouridine Synthase (PUS) family. Although some Ψ sites in mt-rRNA and mt-tRNA have been identified, little is known about the functional role of these modifications. Furthermore, it is unknown which enzyme facilitates the modification of each site and it is likely that many yet undiscovered mt-RNA modifications exist, as is evidenced by recent work showing some Ψ sites on mRNA. Here, we present mito-Ψ-Seq, a high-throughput method for semiquantitative mapping of Ψ in mt-RNA.
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Affiliation(s)
- Aldema Sas-Chen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ronit Nir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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206
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Investigating Mitochondrial Transcriptomes and RNA Processing Using Circular RNA Sequencing. Methods Mol Biol 2021; 2192:43-57. [PMID: 33230764 DOI: 10.1007/978-1-0716-0834-0_4] [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: 01/13/2023]
Abstract
Transcriptomic technologies have revolutionized the study of gene expression and RNA biology. Different RNA sequencing methods enable the analyses of diverse species of transcripts, including their abundance, processing, stability, and other specific features. Mitochondrial transcriptomics has benefited from these technologies that have revealed the surprising complexity of its RNAs. Here we describe a method based upon cyclization of mitochondrial RNAs and next generation sequencing to analyze the steady-state levels and sizes of mitochondrial RNAs, their degradation products, as well as their processing intermediates by capturing both 5' and 3' ends of transcripts.
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207
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Sang L, Ju HQ, Yang Z, Ge Q, Zhang Z, Liu F, Yang L, Gong H, Shi C, Qu L, Chen H, Wu M, Chen H, Li R, Zhuang Q, Piao H, Yan Q, Yu W, Wang L, Shao J, Liu J, Wang W, Zhou T, Lin A. Mitochondrial long non-coding RNA GAS5 tunes TCA metabolism in response to nutrient stress. Nat Metab 2021; 3:90-106. [PMID: 33398195 DOI: 10.1038/s42255-020-00325-z] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 11/17/2020] [Indexed: 02/08/2023]
Abstract
Organelles use specialized molecules to regulate their essential cellular processes. However, systematically elucidating the subcellular distribution and function of molecules such as long non-coding RNAs (lncRNAs) in cellular homeostasis and diseases has not been fully achieved. Here, we reveal the diverse and abundant subcellular distribution of organelle-associated lncRNAs from mitochondria, lysosomes and endoplasmic reticulum. Among them, we identify the mitochondrially localized lncRNA growth-arrest-specific 5 (GAS5) as a tumour suppressor in maintaining cellular energy homeostasis. Mechanistically, energy-stress-induced GAS5 modulates mitochondrial tricarboxylic acid flux by disrupting metabolic enzyme tandem association of fumarate hydratase, malate dehydrogenase and citrate synthase, the canonical members of the tricarboxylic acid cycle. GAS5 negatively correlates with levels of its associated mitochondrial metabolic enzymes in tumours and benefits overall survival in individuals with breast cancer. Together, our detailed annotation of subcellular lncRNA distribution identifies a functional role for lncRNAs in regulating cellular metabolic homeostasis, highlighting organelle-associated lncRNAs as potential clinical targets to manipulate cellular metabolism and diseases.
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Affiliation(s)
- Lingjie Sang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Huai-Qiang Ju
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Zuozhen Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Qiwei Ge
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
- Department of Gastroenterology, The Second Affiliated Hospital, School of Medicine and Institute of Gastroenterology, Zhejiang University, Hangzhou, China
| | - Zhen Zhang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Fangzhou Liu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Luojia Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hangdi Gong
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chengyu Shi
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Lei Qu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hui Chen
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Minjie Wu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hao Chen
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ruihua Li
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Qianqian Zhuang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hailong Piao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Liaoning, China
| | - Qingfeng Yan
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Weishi Yu
- Cipher Gene, Beijing, China
- Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Liangjing Wang
- Department of Gastroenterology, The Second Affiliated Hospital, School of Medicine and Institute of Gastroenterology, Zhejiang University, Hangzhou, China
| | - Jianzhong Shao
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jian Liu
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, Haining, China
| | - Wenqi Wang
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Tianhua Zhou
- Department of Gastroenterology, The Second Affiliated Hospital, School of Medicine and Institute of Gastroenterology, Zhejiang University, Hangzhou, China
- Department of Cell Biology and Program in Molecular Cell Biology, Zhejiang University School of Medicine, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Aifu Lin
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China.
- Cancer Center, Zhejiang University, Hangzhou, China.
- Breast Center of the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang, China.
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208
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Abstract
Evidence accumulated over the past decade shows that long non-coding RNAs (lncRNAs) are widely expressed and have key roles in gene regulation. Recent studies have begun to unravel how the biogenesis of lncRNAs is distinct from that of mRNAs and is linked with their specific subcellular localizations and functions. Depending on their localization and their specific interactions with DNA, RNA and proteins, lncRNAs can modulate chromatin function, regulate the assembly and function of membraneless nuclear bodies, alter the stability and translation of cytoplasmic mRNAs and interfere with signalling pathways. Many of these functions ultimately affect gene expression in diverse biological and physiopathological contexts, such as in neuronal disorders, immune responses and cancer. Tissue-specific and condition-specific expression patterns suggest that lncRNAs are potential biomarkers and provide a rationale to target them clinically. In this Review, we discuss the mechanisms of lncRNA biogenesis, localization and functions in transcriptional, post-transcriptional and other modes of gene regulation, and their potential therapeutic applications.
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209
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Hoser SM, Hoffmann A, Meindl A, Gamper M, Fallmann J, Bernhart SH, Müller L, Ploner M, Misslinger M, Kremser L, Lindner H, Geley S, Schaal H, Stadler PF, Huettenhofer A. Intronic tRNAs of mitochondrial origin regulate constitutive and alternative splicing. Genome Biol 2020; 21:299. [PMID: 33292386 PMCID: PMC7722341 DOI: 10.1186/s13059-020-02199-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 11/09/2020] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND The presence of nuclear mitochondrial DNA (numtDNA) has been reported within several nuclear genomes. Next to mitochondrial protein-coding genes, numtDNA sequences also encode for mitochondrial tRNA genes. However, the biological roles of numtDNA remain elusive. RESULTS Employing in silico analysis, we identify 281 mitochondrial tRNA homologs in the human genome, which we term nimtRNAs (nuclear intronic mitochondrial-derived tRNAs), being contained within introns of 76 nuclear host genes. Despite base changes in nimtRNAs when compared to their mtRNA homologs, a canonical tRNA cloverleaf structure is maintained. To address potential functions of intronic nimtRNAs, we insert them into introns of constitutive and alternative splicing reporters and demonstrate that nimtRNAs promote pre-mRNA splicing, dependent on the number and positioning of nimtRNA genes and splice site recognition efficiency. A mutational analysis reveals that the nimtRNA cloverleaf structure is required for the observed splicing increase. Utilizing a CRISPR/Cas9 approach, we show that a partial deletion of a single endogenous nimtRNALys within intron 28 of the PPFIBP1 gene decreases inclusion of the downstream-located exon 29 of the PPFIBP1 mRNA. By employing a pull-down approach followed by mass spectrometry, a 3'-splice site-associated protein network is identified, including KHDRBS1, which we show directly interacts with nimtRNATyr by an electrophoretic mobility shift assay. CONCLUSIONS We propose that nimtRNAs, along with associated protein factors, can act as a novel class of intronic splicing regulatory elements in the human genome by participating in the regulation of splicing.
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Affiliation(s)
- Simon M Hoser
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria.
| | - Anne Hoffmann
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Philipp-Rosenthal-Str. 27, 04103, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107, Leipzig, Germany
| | - Andreas Meindl
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Maximilian Gamper
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Jörg Fallmann
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107, Leipzig, Germany
| | - Stephan H Bernhart
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107, Leipzig, Germany
| | - Lisa Müller
- Institute for Virology, Medical Faculty Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Melanie Ploner
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Matthias Misslinger
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Leopold Kremser
- Division of Clinical Biochemistry, Protein Micro-Analysis Facility, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Herbert Lindner
- Division of Clinical Biochemistry, Protein Micro-Analysis Facility, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Stephan Geley
- Institute of Pathophysiology, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Heiner Schaal
- Institute for Virology, Medical Faculty Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107, Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04103, Leipzig, Germany
| | - Alexander Huettenhofer
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria.
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210
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Xiao Y, Wang M, He Q, Xu L, Zhang Q, Meng F, Jia Z, Zhang F, Wang H, Guan MX. Asymmetrical effects of deafness-associated mitochondrial DNA 7516delA mutation on the processing of RNAs in the H-strand and L-strand polycistronic transcripts. Nucleic Acids Res 2020; 48:11113-11129. [PMID: 33045734 PMCID: PMC7641755 DOI: 10.1093/nar/gkaa860] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/10/2020] [Accepted: 09/23/2020] [Indexed: 12/31/2022] Open
Abstract
In this report, we investigated the molecular mechanism underlying a deafness-associated m.7516delA mutation affecting the 5′ end processing sites of mitochondrial tRNAAsp and tRNASer(UCN). An in vitro processing experiment demonstrated that m.7516delA mutation caused the aberrant 5′ end processing of tRNASer(UCN) and tRNAAsp precursors, catalyzed by RNase P. Using cytoplasmic hybrids (cybrids) derived from one hearing-impaired Chinese family bearing the m.7516delA mutation and control, we demonstrated the asymmetrical effects of m.7516delA mutation on the processing of tRNAs in the heavy (H)-strand and light (L)-strand polycistronic transcripts. Specially, the m.7516delA mutation caused the decreased levels of tRNASer(UCN) and downstream five tRNAs, including tRNATyr from the L-strand transcripts and tRNAAsp from the H-strand transcripts. Strikingly, mutant cybrids exhibited the lower level of COX2 mRNA and accumulation of longer and uncleaved precursors of COX2 from the H-strand transcripts. Aberrant RNA metabolisms yielded variable reductions in the mitochondrial proteins, especially marked reductions in the levels of ND4, ND5, CO1, CO2 and CO3. The impairment of mitochondrial translation caused the proteostasis stress and respiratory deficiency, diminished ATP production and membrane potential, increased production of reactive oxygen species and promoted apoptosis. Our findings provide new insights into the pathophysiology of deafness arising from mitochondrial tRNA processing defects.
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Affiliation(s)
- Yun Xiao
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Shandong University, Jinan, Shandong 250022, China
| | - Meng Wang
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Qiufen He
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Lei Xu
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Shandong University, Jinan, Shandong 250022, China
| | - Qinghai Zhang
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Feilong Meng
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Zidong Jia
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310058, China
| | - Fengguo Zhang
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Shandong University, Jinan, Shandong 250022, China
| | - Haibo Wang
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Shandong University, Jinan, Shandong 250022, China
| | - Min-Xin Guan
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Key Lab of Reproductive Genetics, Ministry of Education of PRC, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Joint Institute of Genetics and Genome Medicine between Zhejiang University and University of Toronto, Hangzhou, Zhejiang 310058, China
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211
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Ji K, Lin Y, Xu X, Wang W, Wang D, Zhang C, Li W, Zhao Y, Yan C. MELAS-associated m.5541C>T mutation caused instability of mitochondrial tRNA Trp and remarkable mitochondrial dysfunction. J Med Genet 2020; 59:79-87. [PMID: 33208382 DOI: 10.1136/jmedgenet-2020-107323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/13/2020] [Accepted: 10/24/2020] [Indexed: 11/04/2022]
Abstract
BACKGROUND Mitochondrial encephalomyopathy with lactic acidosis and stroke-like episode (MELAS) is a group of genetic diseases caused by mutations in mitochondrial DNA and nuclear DNA. The causative mutations of MELAS have drawn much attention, among them, mutations in mitochondrial tRNA genes possessing prominent status. However, the detailed molecular pathogenesis of these tRNA gene mutations remains unclear and there are very few effective therapies available to date. METHODS We performed muscle histochemistry, genetic analysis, molecular dynamic stimulation and measurement of oxygen consumption rate and respiratory chain complex activities to demonstrate the molecular pathomechanisms of m.5541C>T mutation. Moreover, we use cybrid cells to investigate the potential of taurine to rescue mitochondrial dysfunction caused by this mutation. RESULTS We found a pathogenic m.5541C>T mutation in the tRNATrp gene in a large MELAS family. This mutation first affected the maturation and stability of tRNATrp and impaired mitochondrial respiratory chain complex activities, followed by remarkable mitochondrial dysfunction. Surprisingly, we identified that the supplementation of taurine almost completely restored mitochondrial tRNATrp levels and mitochondrial respiration deficiency at the in vitro cell level. CONCLUSION The m.5541C>T mutation disturbed the translation machinery of mitochondrial tRNATrp and taurine supplementation may be a potential treatment for patients with m.5541C>T mutation. Further studies are needed to explore the full potential of taurine supplementation as therapy for patients with this mutation.
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Affiliation(s)
- Kunqian Ji
- Department of Neurology, Qilu Hospital of Shandong University, Jinan, Shandong, China.,Department of Neurology, Research Institute of Neuromuscular and Neurodegenerative Diseases of Shandong University, Jinan, China
| | - Yan Lin
- Department of Neurology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Xuebi Xu
- Department of Neurology, Wenzhou Medical University First Affiliated Hospital, Wenzhou, Zhejiang, China
| | - Wei Wang
- Department of Neurology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Dongdong Wang
- Department of Neurology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Chen Zhang
- Mitochondrial Medicine Laboratory, Qilu Hospital (Qingdao), Shandong University, Qingda, China
| | - Wei Li
- Department of Neurology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Yuying Zhao
- Department of Neurology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Chuanzhu Yan
- Department of Neurology, Qilu Hospital of Shandong University, Jinan, Shandong, China .,Department of Neurology, Research Institute of Neuromuscular and Neurodegenerative Diseases of Shandong University, Jinan, China.,Brain Science Research Institute of Shandong University, Jinan, China
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212
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Guo Q, Yin X, Gao J, Wang X, Zhang S, Zhou X, Wang Z, Zhang Q. MiR-381-3p redistributes between cytosol and mitochondria and aggravates endothelial cell injury induced by reactive oxygen species. Tissue Cell 2020; 67:101451. [PMID: 33137708 DOI: 10.1016/j.tice.2020.101451] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 10/02/2020] [Accepted: 10/13/2020] [Indexed: 01/25/2023]
Abstract
MicroRNAs (miRNAs) are reported to play pivotal roles in reactive oxygen species (ROS)-induced endothelial cell injury and several studies have demonstrated the miRNA distribution in the mitochondria of various cells. However, very little is known about its changes and roles in ROS-induced endothelial cell injury. In the present study, we systematically revealed the distribution changes of miRNAs in mitochondria during ROS-induced endothelial cell injury and found that H2O2 obviously reduced the mitochondrial distribution of many miRNAs without affecting their expression levels in the whole endothelial cells. Most of these miRNAs showing reduced mitochondrial distribution were potentially involved in ROS-induced endothelial cell injury. MiR-381-3p was a typical representative of these miRNAs and its redistribution between mitochondria and cytosol regulated the network consisting of downstream molecules (P53, P21, CCND1, and MYC) by inhibiting its target genes (LRP6 and NFIA) to promote apoptosis and inhibit proliferation in endothelial cells. Our findings highlight the significance of redistribution of miRNAs between mitochondria and cytosol and improve our understanding of miRNA function regulation.
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Affiliation(s)
- Qianqian Guo
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, PR China
| | - Xianlun Yin
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, PR China
| | - Jing Gao
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, PR China
| | - Xiaowei Wang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, PR China
| | - Shucui Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, PR China
| | - Xiaoming Zhou
- Institute of Endocrinology, Shandong Academy of Clinical Medicine, Shandong Clinical Medical Center of Endocrinology and Metabolism, Jinan, 250021, PR China
| | - Zhe Wang
- Division of Endocrinology and Metabolism, Division of Geriatrics, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, 250021, PR China.
| | - Qunye Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, PR China.
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213
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Huang J, Zhao R, Qin S, Yang S, Li W, Mo J, Wang F, Du Y, Weng X, Zhou X. 4-Thiouridine-Enhanced Peroxidase-Generated Biotinylation of RNA. Chembiochem 2020; 22:212-216. [PMID: 32864814 DOI: 10.1002/cbic.202000567] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 08/28/2020] [Indexed: 12/21/2022]
Abstract
Peroxidase-generated proximity labeling is in widespread use to study subcellular proteomes and the protein interaction networks in living cells, but the development of subcellular RNA labeling is limited. APEX-seq has emerged as a new method to study subcellular RNA in living cells, but the labeling of RNA still has room to improve. In this work, we describe 4-thiouridine (s4 U)-enhanced peroxidase-generated biotinylation of RNA with high efficiency. The incorporation of s4 U could introduce additional sites for RNA labeling, enhanced biotinylation was observed on monomer, model oligo RNA and total RNA. Through the s4 U metabolic approach, the in vivo RNA biotinylation efficiency by peroxidase catalysis was also dramatically increased, which will benefit RNA isolation and study for the spatial transcriptome.
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Affiliation(s)
- Jinguo Huang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Ruiqi Zhao
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Shanshan Qin
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Shixi Yang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Wei Li
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Jing Mo
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Fang Wang
- Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, P. R. China
| | - Yuhao Du
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, 430072, P. R. China
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214
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Dorji J, Vander Jagt CJ, Garner JB, Marett LC, Mason BA, Reich CM, Xiang R, Clark EL, Cocks BG, Chamberlain AJ, MacLeod IM, Daetwyler HD. Expression of mitochondrial protein genes encoded by nuclear and mitochondrial genomes correlate with energy metabolism in dairy cattle. BMC Genomics 2020; 21:720. [PMID: 33076826 PMCID: PMC7574280 DOI: 10.1186/s12864-020-07018-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 08/20/2020] [Indexed: 12/21/2022] Open
Abstract
Background Mutations in the mitochondrial genome have been implicated in mitochondrial disease, often characterized by impaired cellular energy metabolism. Cellular energy metabolism in mitochondria involves mitochondrial proteins (MP) from both the nuclear (NuMP) and mitochondrial (MtMP) genomes. The expression of MP genes in tissues may be tissue specific to meet varying specific energy demands across the tissues. Currently, the characteristics of MP gene expression in tissues of dairy cattle are not well understood. In this study, we profile the expression of MP genes in 29 adult and six foetal tissues in dairy cattle using RNA sequencing and gene expression analyses: particularly differential gene expression and co-expression network analyses. Results MP genes were differentially expressed (DE; over-expressed or under-expressed) across tissues in cattle. All 29 tissues showed DE NuMP genes in varying proportions of over-expression and under-expression. On the other hand, DE of MtMP genes was observed in < 50% of tissues and notably MtMP genes within a tissue was either all over-expressed or all under-expressed. A high proportion of NuMP (up to 60%) and MtMP (up to 100%) genes were over-expressed in tissues with expected high metabolic demand; heart, skeletal muscles and tongue, and under-expressed (up to 45% of NuMP, 77% of MtMP genes) in tissues with expected low metabolic rates; leukocytes, thymus, and lymph nodes. These tissues also invariably had the expression of all MtMP genes in the direction of dominant NuMP genes expression. The NuMP and MtMP genes were highly co-expressed across tissues and co-expression of genes in a cluster were non-random and functionally enriched for energy generation pathway. The differential gene expression and co-expression patterns were validated in independent cow and sheep datasets. Conclusions The results of this study support the concept that there are biological interaction of MP genes from the mitochondrial and nuclear genomes given their over-expression in tissues with high energy demand and co-expression in tissues. This highlights the importance of considering MP genes from both genomes in future studies related to mitochondrial functions and traits related to energy metabolism.
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Affiliation(s)
- Jigme Dorji
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia. .,Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.
| | - Christy J Vander Jagt
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Josie B Garner
- Agriculture Victoria, Ellinbank Dairy Centre, Ellinbank, VIC, 3822, Australia
| | - Leah C Marett
- Agriculture Victoria, Ellinbank Dairy Centre, Ellinbank, VIC, 3822, Australia
| | - Brett A Mason
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Coralie M Reich
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Ruidong Xiang
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.,Faculty of Veterinary & Agricultural Science, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Emily L Clark
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, UK
| | - Benjamin G Cocks
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia.,Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Amanda J Chamberlain
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Iona M MacLeod
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Hans D Daetwyler
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia.,Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
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215
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Webb M, Sideris DP. Intimate Relations-Mitochondria and Ageing. Int J Mol Sci 2020; 21:ijms21207580. [PMID: 33066461 PMCID: PMC7589147 DOI: 10.3390/ijms21207580] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 12/14/2022] Open
Abstract
Mitochondrial dysfunction is associated with ageing, but the detailed causal relationship between the two is still unclear. We review the major phenomenological manifestations of mitochondrial age-related dysfunction including biochemical, regulatory and energetic features. We conclude that the complexity of these processes and their inter-relationships are still not fully understood and at this point it seems unlikely that a single linear cause and effect relationship between any specific aspect of mitochondrial biology and ageing can be established in either direction.
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Affiliation(s)
- Michael Webb
- Mitobridge Inc., an Astellas Company, 1030 Massachusetts Ave, Cambridge, MA 02138, USA
| | - Dionisia P Sideris
- Mitobridge Inc., an Astellas Company, 1030 Massachusetts Ave, Cambridge, MA 02138, USA
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216
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Girardin SE, Cuziol C, Philpott DJ, Arnoult D. The eIF2α kinase HRI in innate immunity, proteostasis, and mitochondrial stress. FEBS J 2020; 288:3094-3107. [DOI: 10.1111/febs.15553] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/09/2020] [Accepted: 09/01/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Stephen E. Girardin
- Department of Laboratory Medicine and Pathobiology University of Toronto ON Canada
| | - Camille Cuziol
- INSERM UMR_S 1197 Hôpital Paul Brousse Villejuif France
- Université Paris‐Saclay France
| | | | - Damien Arnoult
- INSERM UMR_S 1197 Hôpital Paul Brousse Villejuif France
- Université Paris‐Saclay France
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217
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Sural S, Liang CY, Wang FY, Ching TT, Hsu AL. HSB-1/HSF-1 pathway modulates histone H4 in mitochondria to control mtDNA transcription and longevity. SCIENCE ADVANCES 2020; 6:eaaz4452. [PMID: 33087356 PMCID: PMC7577724 DOI: 10.1126/sciadv.aaz4452] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 09/08/2020] [Indexed: 06/02/2023]
Abstract
Heat shock factor-1 (HSF-1) is a master regulator of stress responses across taxa. Overexpression of HSF-1 or genetic ablation of its conserved negative regulator, heat shock factor binding protein 1 (HSB-1), results in robust life-span extension in Caenorhabditis elegans Here, we found that increased HSF-1 activity elevates histone H4 levels in somatic tissues during development, while knockdown of H4 completely suppresses HSF-1-mediated longevity. Moreover, overexpression of H4 is sufficient to extend life span. Ablation of HSB-1 induces an H4-dependent increase in micrococcal nuclease protection of both nuclear chromatin and mitochondrial DNA (mtDNA), which consequently results in reduced transcription of mtDNA-encoded complex IV genes, decreased respiratory capacity, and a mitochondrial unfolded protein response-dependent life-span extension. Collectively, our findings reveal a previously unknown role of HSB-1/HSF-1 signaling in modulation of mitochondrial function via mediating histone H4-dependent regulation of mtDNA gene expression and concomitantly acting as a determinant of organismal longevity.
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Affiliation(s)
- Surojit Sural
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chung-Yi Liang
- Research Center for Healthy Aging, China Medical University, Taichung, 404, Taiwan
| | - Feng-Yung Wang
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 112, Taiwan
| | - Tsui-Ting Ching
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei 112, Taiwan.
| | - Ao-Lin Hsu
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA.
- Research Center for Healthy Aging, China Medical University, Taichung, 404, Taiwan
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 112, Taiwan
- Division of Geriatric and Palliative Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
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218
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Cao J, Cowan DB, Wang DZ. tRNA-Derived Small RNAs and Their Potential Roles in Cardiac Hypertrophy. Front Pharmacol 2020; 11:572941. [PMID: 33041815 PMCID: PMC7527594 DOI: 10.3389/fphar.2020.572941] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/28/2020] [Indexed: 12/21/2022] Open
Abstract
Transfer RNAs (tRNAs) are abundantly expressed, small non-coding RNAs that have long been recognized as essential components of the protein translation machinery. The tRNA-derived small RNAs (tsRNAs), including tRNA halves (tiRNAs), and tRNA fragments (tRFs), were unexpectedly discovered and have been implicated in a variety of important biological functions such as cell proliferation, cell differentiation, and apoptosis. Mechanistically, tsRNAs regulate mRNA destabilization and translation, as well as retro-element reverse transcriptional and post-transcriptional processes. Emerging evidence has shown that tsRNAs are expressed in the heart, and their expression can be induced by pathological stress, such as hypertrophy. Interestingly, cardiac pathophysiological conditions, such as oxidative stress, aging, and metabolic disorders can be viewed as inducers of tsRNA biogenesis, which further highlights the potential involvement of tsRNAs in these conditions. There is increasing enthusiasm for investigating the molecular and biological functions of tsRNAs in the heart and their role in cardiovascular disease. It is anticipated that this new class of small non-coding RNAs will offer new perspectives in understanding disease mechanisms and may provide new therapeutic targets to treat cardiovascular disease.
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Affiliation(s)
- Jun Cao
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Douglas B Cowan
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Da-Zhi Wang
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
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219
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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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220
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Zhao Q, Liu J, Deng H, Ma R, Liao JY, Liang H, Hu J, Li J, Guo Z, Cai J, Xu X, Gao Z, Su S. Targeting Mitochondria-Located circRNA SCAR Alleviates NASH via Reducing mROS Output. Cell 2020; 183:76-93.e22. [PMID: 32931733 DOI: 10.1016/j.cell.2020.08.009] [Citation(s) in RCA: 239] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 04/27/2020] [Accepted: 08/05/2020] [Indexed: 02/06/2023]
Abstract
Mitochondria, which play central roles in immunometabolic diseases, have their own genome. However, the functions of mitochondria-located noncoding RNAs are largely unknown due to the absence of a specific delivery system. By circular RNA (circRNA) expression profile analysis of liver fibroblasts from patients with nonalcoholic steatohepatitis (NASH), we observe that mitochondrial circRNAs account for a considerable fraction of downregulated circRNAs in NASH fibroblasts. By constructing mitochondria-targeting nanoparticles, we observe that Steatohepatitis-associated circRNA ATP5B Regulator (SCAR), which is located in mitochondria, inhibits mitochondrial ROS (mROS) output and fibroblast activation. circRNA SCAR, mediated by PGC-1α, binds to ATP5B and shuts down mPTP by blocking CypD-mPTP interaction. Lipid overload inhibits PGC-1α by endoplasmic reticulum (ER) stress-induced CHOP. In vivo, targeting circRNA SCAR alleviates high fat diet-induced cirrhosis and insulin resistance. Clinically, circRNA SCAR is associated with steatosis-to-NASH progression. Collectively, we identify a mitochondrial circRNA that drives metaflammation and serves as a therapeutic target for NASH.
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Affiliation(s)
- Qiyi Zhao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510630, China; Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China; Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong 510080, 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 510120, China; Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510630, China
| | - Hong Deng
- Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510630, China; Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Ruiying Ma
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510630, China
| | - Jian-You Liao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Huixin Liang
- Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510630, China; Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Jingxiong Hu
- Department of Hepatobiliary Surgery, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510630, China
| | - Jiaqian Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Zhiyong Guo
- Organ Transplant Center, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Junchao Cai
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Xiaoding Xu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China.
| | - Zhiliang Gao
- Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510630, China; Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China; Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong 510080, China.
| | - Shicheng Su
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510630, China; Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Department of Immunology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China.
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221
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PET Imaging for Oxidative Stress in Neurodegenerative Disorders Associated with Mitochondrial Dysfunction. Antioxidants (Basel) 2020; 9:antiox9090861. [PMID: 32937849 PMCID: PMC7554831 DOI: 10.3390/antiox9090861] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/11/2020] [Accepted: 09/12/2020] [Indexed: 02/07/2023] Open
Abstract
Oxidative stress based on mitochondrial dysfunction is assumed to be the principal molecular mechanism for the pathogenesis of many neurodegenerative disorders. However, the effects of oxidative stress on the neurodegeneration process in living patients remain to be elucidated. Molecular imaging with positron emission tomography (PET) can directly evaluate subtle biological changes, including the redox status. The present review focuses on recent advances in PET imaging for oxidative stress, in particular the use of the Cu-ATSM radioligand, in neurodegenerative disorders associated with mitochondrial dysfunction. Since reactive oxygen species are mostly generated by leakage of excess electrons from an over-reductive state due to mitochondrial respiratory chain impairment, PET with 62Cu-ATSM, the accumulation of which depends on an over-reductive state, is able to image oxidative stress. 62Cu-ATSM PET studies demonstrated enhanced oxidative stress in the disease-related brain regions of patients with mitochondrial disease, Parkinson’s disease, and amyotrophic lateral sclerosis. Furthermore, the magnitude of oxidative stress increased with disease severity, indicating that oxidative stress based on mitochondrial dysfunction contributes to promoting neurodegeneration in these diseases. Oxidative stress imaging has improved our insights into the pathological mechanisms of neurodegenerative disorders, and is a promising tool for monitoring further antioxidant therapies.
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222
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Elmorsy E, Alelwani W, Kattan S, Babteen N, Alnajeebi A, Ghulam J, Mosad S. Antipsychotics inhibit the mitochondrial bioenergetics of pancreatic beta cells isolated from CD1 mice. Basic Clin Pharmacol Toxicol 2020; 128:154-168. [PMID: 32860481 DOI: 10.1111/bcpt.13484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/21/2020] [Accepted: 08/23/2020] [Indexed: 01/14/2023]
Abstract
Antipsychotics (APs) are widely used medications with reported diabetogenic side effects. This study investigated the effect of commonly used APs, namely chlorpromazine (CPZ), haloperidol (HAL) and clozapine, on the bioenergetics of male CD1 mice isolated pancreatic beta cells as an underlying mechanism of their diabetogenic effects. The effect of APs on Alamar blue reduction, adenosine triphosphate (ATP) production and glucose-stimulated insulin secretion (GSIS) of isolated beta cells was evaluated. Then, the effects of APs on the activities of mitochondrial complexes and their common coding genes expression, oxygen consumption rate (OCR), mitochondrial membrane potential (MMP) and lactate production were investigated. The effects of APs on the mitochondrial membrane fluidity (MMF) and mitochondrial membrane fatty acid composition were also examined. Results showed that the tested APs significantly decreased cellular ATP production and GSIS of the beta cells. The APs significantly inhibited the activities of mitochondrial complexes and their coding gene expression, MMP and OCR of the treated cells, with a parallel increase in lactate production to different extents with the different APs. CPZ and HAL showed increased MMF and mitochondrial membrane polyunsaturated fatty acid content. In conclusion, the tested APs-induced mitochondrial disruption can play a role in their diabetogenic side effect.
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Affiliation(s)
- Ekramy Elmorsy
- Department of Forensic Medicine and Clinical Toxicology, Faculty of Medicine, Mansoura University, Mansoura, Egypt.,Pathology Department, Faculty of Medicine, Northern Border University, Arar, Saudi Arabia
| | - Walla Alelwani
- Department of Biochemistry, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Shahad Kattan
- Medical Laboratory Department, College of Applied Medical Sciences, Taibah University, Yanbu, Saudi Arabia
| | - Nouf Babteen
- Department of Biochemistry, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Afnan Alnajeebi
- Department of Biochemistry, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Jihan Ghulam
- General Education Department, Dar Al-Hekma University, Jeddah, Saudi Arabia
| | - Soad Mosad
- Department of Forensic Medicine and Clinical Toxicology, Faculty of Medicine, Mansoura University, Mansoura, Egypt.,Pathology Department, Faculty of Medicine, King Khalid University, Abha, Saudi Arabia
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223
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Adekunle DA, Wang ET. Transcriptome-wide organization of subcellular microenvironments revealed by ATLAS-Seq. Nucleic Acids Res 2020; 48:5859-5872. [PMID: 32421779 PMCID: PMC7293051 DOI: 10.1093/nar/gkaa334] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 04/20/2020] [Accepted: 05/07/2020] [Indexed: 12/22/2022] Open
Abstract
Subcellular organization of RNAs and proteins is critical for cell function, but we still lack global maps and conceptual frameworks for how these molecules are localized in cells and tissues. Here, we introduce ATLAS-Seq, which generates transcriptomes and proteomes from detergent-free tissue lysates fractionated across a sucrose gradient. Proteomic analysis of fractions confirmed separation of subcellular compartments. Unexpectedly, RNAs tended to co-sediment with other RNAs in similar protein complexes, cellular compartments, or with similar biological functions. With the exception of those encoding secreted proteins, most RNAs sedimented differently than their encoded protein counterparts. To identify RNA binding proteins potentially driving these patterns, we correlated their sedimentation profiles to all RNAs, confirming known interactions and predicting new associations. Hundreds of alternative RNA isoforms exhibited distinct sedimentation patterns across the gradient, despite sharing most of their coding sequence. These observations suggest that transcriptomes can be organized into networks of co-segregating mRNAs encoding functionally related proteins and provide insights into the establishment and maintenance of subcellular organization.
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Affiliation(s)
- Danielle A Adekunle
- Department of Molecular Genetics & Microbiology, UF Genetics Institute, Center for NeuroGenetics, University of Florida, USA.,Department of Biology, Massachusetts Institute of Technology, USA
| | - Eric T Wang
- Department of Molecular Genetics & Microbiology, UF Genetics Institute, Center for NeuroGenetics, University of Florida, USA
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224
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Razgonova MP, Zakharenko AM, Golokhvast KS, Thanasoula M, Sarandi E, Nikolouzakis K, Fragkiadaki P, Tsoukalas D, Spandidos DA, Tsatsakis A. Telomerase and telomeres in aging theory and chronographic aging theory (Review). Mol Med Rep 2020; 22:1679-1694. [PMID: 32705188 PMCID: PMC7411297 DOI: 10.3892/mmr.2020.11274] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/24/2020] [Indexed: 01/03/2023] Open
Abstract
The current review focuses on the connection of telomerase and telomeres with aging. In this review, we describe the changes in telomerase and telomere length (TEL) during development, their role in carcinogenesis processes, and the consequences of reduced telomerase activity. More specifically, the connection of TEL in peripheral blood cells with the development of aging‑associated diseases is discussed. The review provides systematic data on the role of telomerase in mitochondria, the biology of telomeres in stem cells, as well as the consequences of the forced expression of telomerase (telomerization) in human cells. Additionally, it presents the effects of chronic stress exposure on telomerase activity, the effect of TEL on fertility, and the effect of nutraceutical supplements on TEL. Finally, a comparative review of the chronographic theory of aging, presented by Olovnikov is provided based on currently available scientific research on telomere, telomerase activity, and the nature of aging by multicellular organisms.
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Affiliation(s)
- Mayya P. Razgonova
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190000 Saint-Petersburg, Russia
- Far Eastern Federal University, 690950 Vladivostok, Russia
| | - Alexander M. Zakharenko
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190000 Saint-Petersburg, Russia
- Far Eastern Federal University, 690950 Vladivostok, Russia
| | - Kirill S. Golokhvast
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190000 Saint-Petersburg, Russia
- Far Eastern Federal University, 690950 Vladivostok, Russia
- Pacific Geographical Institute, Far Eastern Branch of The Russian Academy of Sciences, 690041 Vladivostok, Russia
| | - Maria Thanasoula
- Metabolomic Μedicine, Health Clinics for Autoimmune and Chronic Diseases, 10674 Athens, Greece
| | - Evangelia Sarandi
- Metabolomic Μedicine, Health Clinics for Autoimmune and Chronic Diseases, 10674 Athens, Greece
| | | | - Persefoni Fragkiadaki
- Laboratory of Toxicology, Medical School, University of Crete, 71003 Heraklion, Greece
- Spin-Off Toxplus S.A., 71601 Heraklion, Greece
| | - Dimitris Tsoukalas
- Metabolomic Μedicine, Health Clinics for Autoimmune and Chronic Diseases, 10674 Athens, Greece
| | - Demetrios A. Spandidos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, Heraklion 71003, Greece
| | - Aristidis Tsatsakis
- Laboratory of Toxicology, Medical School, University of Crete, 71003 Heraklion, Greece
- Spin-Off Toxplus S.A., 71601 Heraklion, Greece
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225
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Reading the heart at single-cell resolution. J Mol Cell Cardiol 2020; 148:34-45. [PMID: 32871159 DOI: 10.1016/j.yjmcc.2020.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/04/2020] [Accepted: 08/20/2020] [Indexed: 12/21/2022]
Abstract
The burgeoning field of single-cell transcriptomics augments our ability to scrutinize organ systems at unprecedented resolutions. Single-cell RNA sequencing (scRNA-seq) and analytical techniques have shed light on the cellular heterogeneity, developmental trajectories, intercellular communications of the cardiac system, and thus contributed much to the understanding of cardiac development, homeostasis and disorders. Although generalized protocols are well established for scRNA-seq pipelines, customized sample preparation, quality control, and data interpretation are still needed in cardiac research. In this article, we highlight major steps that impact data quality in scRNA-seq experiments, with particular focus on sample and data processing of cardiomyocytes. We also summarize popular applications of scRNA-seq, outlining general tools, caveats and examples in cardiac research.
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226
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Medini H, Cohen T, Mishmar D. Mitochondria Are Fundamental for the Emergence of Metazoans: On Metabolism, Genomic Regulation, and the Birth of Complex Organisms. Annu Rev Genet 2020; 54:151-166. [PMID: 32857636 DOI: 10.1146/annurev-genet-021920-105545] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Out of many intracellular bacteria, only the mitochondria and chloroplasts abandoned their independence billions of years ago and became endosymbionts within the host eukaryotic cell. Consequently, one cannot grow eukaryotic cells without their mitochondria, and the mitochondria cannot divide outside of the cell, thus reflecting interdependence. Here, we argue that such interdependence underlies the fundamental role of mitochondrial activities in the emergence of metazoans. Several lines of evidence support our hypothesis: (a) Differentiation and embryogenesis rely on mitochondrial function; (b) mitochondrial metabolites are primary precursors for epigenetic modifications (such as methyl and acetyl), which are critical for chromatin remodeling and gene expression, particularly during differentiation and embryogenesis; and (c) mitonuclear coregulation adapted to accommodate both housekeeping and tissue-dependent metabolic needs. We discuss the evolution of the unique mitochondrial genetic system, mitochondrial metabolites, mitonuclear coregulation, and their critical roles in the emergence of metazoans and in human disorders.
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Affiliation(s)
- Hadar Medini
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501 Israel;
| | - Tal Cohen
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501 Israel;
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501 Israel;
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227
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Sohn BK, Basu U, Lee SW, Cho H, Shen J, Deshpande A, Johnson LC, Das K, Patel SS, Kim H. The dynamic landscape of transcription initiation in yeast mitochondria. Nat Commun 2020; 11:4281. [PMID: 32855416 PMCID: PMC7452894 DOI: 10.1038/s41467-020-17793-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 07/14/2020] [Indexed: 01/24/2023] Open
Abstract
Controlling efficiency and fidelity in the early stage of mitochondrial DNA transcription is crucial for regulating cellular energy metabolism. Conformational transitions of the transcription initiation complex must be central for such control, but how the conformational dynamics progress throughout transcription initiation remains unknown. Here, we use single-molecule fluorescence resonance energy transfer techniques to examine the conformational dynamics of the transcriptional system of yeast mitochondria with single-base resolution. We show that the yeast mitochondrial transcriptional complex dynamically transitions among closed, open, and scrunched states throughout the initiation stage. Then abruptly at position +8, the dynamic states of initiation make a sharp irreversible transition to an unbent conformation with associated promoter release. Remarkably, stalled initiation complexes remain in dynamic scrunching and unscrunching states without dissociating the RNA transcript, implying the existence of backtracking transitions with possible regulatory roles. The dynamic landscape of transcription initiation suggests a kinetically driven regulation of mitochondrial transcription.
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Affiliation(s)
- Byeong-Kwon Sohn
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Urmimala Basu
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Seung-Won Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Hayoon Cho
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Jiayu Shen
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Aishwarya Deshpande
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Laura C Johnson
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Kalyan Das
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA.
| | - Hajin Kim
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea.
- Institute for Basic Science, Ulsan, Republic of Korea.
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228
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Szewczyk M, Malik D, Borowski LS, Czarnomska SD, Kotrys AV, Klosowska-Kosicka K, Nowotny M, Szczesny RJ. Human REXO2 controls short mitochondrial RNAs generated by mtRNA processing and decay machinery to prevent accumulation of double-stranded RNA. Nucleic Acids Res 2020; 48:5572-5590. [PMID: 32365187 PMCID: PMC7261184 DOI: 10.1093/nar/gkaa302] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 03/31/2020] [Accepted: 04/22/2020] [Indexed: 12/15/2022] Open
Abstract
RNA decay is a key element of mitochondrial RNA metabolism. To date, the only well-documented machinery that plays a role in mtRNA decay in humans is the complex of polynucleotide phosphorylase (PNPase) and SUV3 helicase, forming the degradosome. REXO2, a homolog of prokaryotic oligoribonucleases present in humans both in mitochondria and the cytoplasm, was earlier shown to be crucial for maintaining mitochondrial homeostasis, but its function in mitochondria has not been fully elucidated. In the present study, we created a cellular model that enables the clear dissection of mitochondrial and non-mitochondrial functions of human REXO2. We identified a novel mitochondrial short RNA, referred to as ncH2, that massively accumulated upon REXO2 silencing. ncH2 degradation occurred independently of the mitochondrial degradosome, strongly supporting the hypothesis that ncH2 is a primary substrate of REXO2. We also investigated the global impact of REXO2 depletion on mtRNA, revealing the importance of the protein for maintaining low steady-state levels of mitochondrial antisense transcripts and double-stranded RNA. Our detailed biochemical and structural studies provide evidence of sequence specificity of the REXO2 oligoribonuclease. We postulate that REXO2 plays dual roles in human mitochondria, ‘scavenging’ nanoRNAs that are produced by the degradosome and clearing short RNAs that are generated by RNA processing.
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Affiliation(s)
- Maciej Szewczyk
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw 02-106, Poland.,Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw 02-106, Poland
| | - Deepshikha Malik
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
| | - Lukasz S Borowski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw 02-106, Poland.,Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw 02-106, Poland
| | - Sylwia D Czarnomska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Anna V Kotrys
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw 02-106, Poland
| | | | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
| | - Roman J Szczesny
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw 02-106, Poland
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229
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Mitochondria, the gut microbiome and ROS. Cell Signal 2020; 75:109737. [PMID: 32810578 DOI: 10.1016/j.cellsig.2020.109737] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/11/2020] [Accepted: 08/11/2020] [Indexed: 12/11/2022]
Abstract
In this review, we discuss the connections between mitochondria and the gut microbiome provided by reactive oxygen species (ROS). We examine the mitochondrion as an endosymbiotic organelle that is a hub for energy production, signaling, and cell homeostasis. Maintaining a diverse gut microbiome is generally associated with organismal fitness, intestinal health and resistance to environmental stress. In contrast, gut microbiome imbalance, termed dysbiosis, is linked to a reduction in organismal well-being. ROS are essential signaling molecules but can be damaging when present in excess. Increasing ROS levels have been shown to influence human health, homeostasis of gut cells, and the gastrointestinal microbial community's biodiversity. Reciprocally, gut microbes can affect ROS levels, mitochondrial homeostasis, and host health. We propose that mechanistic understanding of the suite of bi-directional interactions between mitochondria and the gut microbiome will facilitate innovative interdisciplinary studies examining evolutionary divergence and provide novel treatments and therapeutics for disease. GLOSS: In this review, we focus on the nexus between mitochondria and the gut microbiome provided by reactive oxygen species (ROS). Mitochondria are a cell organelle that is derived from an ancestral alpha-proteobacteria. They generate around 80% of the adenosine triphosphate that an organism needs to function and release a range of signaling molecules essential for cellular homeostasis. The gut microbiome is a suite of microorganisms that are commensal, symbiotic and pathogenic to their host. ROS are one predominant group of essential signaling molecules that can be harmful in excess. We suggest that the mitochondria- microbiome nexus is a frontier of research that has cross-disciplinary benefits in understanding genetic divergence and human well-being.
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230
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Miller B, Kim SJ, Kumagai H, Mehta HH, Xiang W, Liu J, Yen K, Cohen P. Peptides derived from small mitochondrial open reading frames: Genomic, biological, and therapeutic implications. Exp Cell Res 2020; 393:112056. [PMID: 32387288 PMCID: PMC7778388 DOI: 10.1016/j.yexcr.2020.112056] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 04/20/2020] [Accepted: 05/02/2020] [Indexed: 12/15/2022]
Abstract
Mitochondrial-derived peptides (MDPs) are a novel class of bioactive microproteins that modify cell metabolism. The the eight MDPs that been characterized (e.g., humanin, MOTS-c, SHLPs1-6) attenuate disease pathology including Alzheimer's disease, prostate cancer, macular degeneration, cardiovascular disease, and diabetes. The association between disease and human genetic variation in MDPs is underexplored, although two polymorphisms in humanin and MOTS-c associate with cognitive decline and diabetes, respectively, suggesting a precise role for MDPs in disease-modification. There could be hundreds of additional MDPs that have yet to be discovered. Altogether, MDPs could explain unanswered biological and metabolic questions and are part of a growing field of novel microproteins encoded by small open reading frames. In this review, the current state of MDPs are summarized with an emphasis on biological and therapeutic implications.
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Affiliation(s)
- Brendan Miller
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Su-Jeong Kim
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Hiroshi Kumagai
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA; Graduate School of Health and Sports Science, Juntendo University, Chiba, Japan
| | - Hemal H Mehta
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Wang Xiang
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Jiali Liu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Kelvin Yen
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Pinchas Cohen
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA.
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231
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Zhou Y, Zou P. The evolving capabilities of enzyme-mediated proximity labeling. Curr Opin Chem Biol 2020; 60:30-38. [PMID: 32801087 DOI: 10.1016/j.cbpa.2020.06.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 12/22/2022]
Abstract
The subcellular organization of proteins and RNA molecules is crucial for their proper functions. Over the past decade, both ligase-mediated and peroxidase-mediated proximity labeling (PL) techniques have been developed to map biomolecules at near-nanometer spatial resolution and subminute temporal resolution. These methods are shedding light on the spatial arrangement of proteome and transcriptome in their native context. Here, we review the recent evolution and applications of PL techniques, compare and contrast the two classes of methods, and highlight emerging trends and future opportunities.
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Affiliation(s)
- Ying Zhou
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Peng Zou
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China; Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, 100871, China.
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232
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Lee JH, Shim YR, Seo W, Kim MH, Choi WM, Kim HH, Kim YE, Yang K, Ryu T, Jeong JM, Choi HG, Eun HS, Kim SH, Mun H, Yoon JH, Jeong WI. Mitochondrial Double-Stranded RNA in Exosome Promotes Interleukin-17 Production Through Toll-Like Receptor 3 in Alcohol-associated Liver Injury. Hepatology 2020; 72:609-625. [PMID: 31849082 PMCID: PMC7297661 DOI: 10.1002/hep.31041] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 11/07/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS Mitochondrial double-stranded RNA (mtdsRNA) and its innate immune responses have been reported previously; however, mtdsRNA generation and its effects on alcohol-associated liver disease (ALD) remain unclear. Here, we report that hepatic mtdsRNA stimulates toll-like receptor 3 (TLR3) in Kupffer cells through the exosome (Exo) to enhance interleukin (IL)-17A (IL-17A) production in ALD. APPROACH AND RESULTS Following binge ethanol (EtOH) drinking, IL-17A production primarily increased in γδ T cells of wild-type (WT) mice, whereas the production of IL-17A was mainly facilitated by CD4+ T cells in acute-on-chronic EtOH consumption. These were not observed in TLR3 knockout (KO) or Kupffer cell-depleted WT mice. The expression of polynucleotide phosphorylase, an mtdsRNA-restricting enzyme, was significantly decreased in EtOH-exposed livers and hepatocytes of WT mice. Immunostaining revealed that mtdsRNA colocalized with the mitochondria in EtOH-treated hepatocytes from WT mice and healthy humans. Bioanalyzer analysis revealed that small-sized RNAs were enriched in EtOH-treated Exos (EtOH-Exos) rather than EtOH-treated microvesicles in hepatocytes of WT mice and humans. Quantitative real-time PCR and RNA sequencing analyses indicated that mRNA expression of mitochondrial genes encoded by heavy and light strands was robustly increased in EtOH-Exos from mice and humans. After direct treatment with EtOH-Exos, IL-1β expression was significantly increased in WT Kupffer cells but not in TLR3 KO Kupffer cells, augmenting IL-17A production of γδ T cells in mice and humans. CONCLUSIONS EtOH-mediated generation of mtdsRNA contributes to TLR3 activation in Kupffer cells through exosomal delivery. Consequently, increased IL-1β expression in Kupffer cells triggers IL-17A production in γδ T cells at the early stage that may accelerate IL-17A expression in CD4+ T cells in the later stage of ALD. Therefore, mtdsRNA and TLR3 may function as therapeutic targets in ALD.
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Affiliation(s)
- Jun-Hee Lee
- Laboratory of Liver Research, Graduate School of Medical Science and Engineering, KAIST, Daejeon 34141, Republic of Korea
| | - Young-Ri Shim
- Laboratory of Liver Research, Graduate School of Medical Science and Engineering, KAIST, Daejeon 34141, Republic of Korea
| | - Wonhyo Seo
- Laboratory of Liver Research, Graduate School of Medical Science and Engineering, KAIST, Daejeon 34141, Republic of Korea
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Myung-Ho Kim
- Laboratory of Liver Research, Graduate School of Medical Science and Engineering, KAIST, Daejeon 34141, Republic of Korea
| | - Won-Mook Choi
- Laboratory of Liver Research, Graduate School of Medical Science and Engineering, KAIST, Daejeon 34141, Republic of Korea
| | - Hee-Hoon Kim
- Laboratory of Liver Research, Graduate School of Medical Science and Engineering, KAIST, Daejeon 34141, Republic of Korea
| | - Ye-Eun Kim
- Laboratory of Liver Research, Graduate School of Medical Science and Engineering, KAIST, Daejeon 34141, Republic of Korea
| | - Keungmo Yang
- Laboratory of Liver Research, Graduate School of Medical Science and Engineering, KAIST, Daejeon 34141, Republic of Korea
| | - Tom Ryu
- Laboratory of Liver Research, Graduate School of Medical Science and Engineering, KAIST, Daejeon 34141, Republic of Korea
| | - Jong-Min Jeong
- Laboratory of Liver Research, Graduate School of Medical Science and Engineering, KAIST, Daejeon 34141, Republic of Korea
| | - Hei-Gwon Choi
- Department of Internal Medicine, Chungnam National University, School of Medicine, Daejeon 35015, Republic of Korea
| | - Hyuk Soo Eun
- Department of Internal Medicine, Chungnam National University, School of Medicine, Daejeon 35015, Republic of Korea
| | - Seok-Hwan Kim
- Department of Surgery, Chungnam National University, College of Medicine, Daejeon 35015, Republic of Korea
| | - Hyejin Mun
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Je-Hyun Yoon
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Won-Il Jeong
- Laboratory of Liver Research, Graduate School of Medical Science and Engineering, KAIST, Daejeon 34141, Republic of Korea
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233
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Sreekumar PG, Kannan R. Mechanisms of protection of retinal pigment epithelial cells from oxidant injury by humanin and other mitochondrial-derived peptides: Implications for age-related macular degeneration. Redox Biol 2020; 37:101663. [PMID: 32768357 PMCID: PMC7767738 DOI: 10.1016/j.redox.2020.101663] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 07/18/2020] [Accepted: 07/26/2020] [Indexed: 02/06/2023] Open
Abstract
The mitochondrial-derived peptides (MDPs) are a new class of small open reading frame encoded polypeptides with pleiotropic properties. The prominent members are Humanin (HN) and small HN-like peptide (SHLP) 2, which encode 16S rRNA, while mitochondrial open reading frame of the twelve S c (MOTS-c) encodes 12S rRNA of the mitochondrial genome. While the multifunctional properties of HN and its analog 14-HNG have been well documented, their protective role in the retinal pigment epithelium (RPE)/retina has been investigated only recently. In this review, we have summarized the multiple effects of HN and its analogs, SHLP2 and MOTS-c in oxidatively stressed human RPE and the regulatory pathways of signaling, mitochondrial function, senescence, and inter-organelle crosstalk. Emphasis is given to the mitochondrial functions such as biogenesis, bioenergetics, and autophagy in RPE undergoing oxidative stress. Further, the potential use of HN and its analogs in the prevention of age-related macular degeneration (AMD) are also presented. In addition, the role of novel, long-acting HN elastin-like polypeptides in nanotherapy of AMD and other ocular diseases stemming from oxidative damage is discussed. It is expected MDPs will become a promising group of mitochondrial peptides with valuable therapeutic applications in the treatment of retinal diseases.
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Affiliation(s)
- Parameswaran G Sreekumar
- The Stephen J. Ryan Initiative for Macular Research (RIMR), Doheny Eye Institute, Los Angeles, CA, 90033, USA
| | - Ram Kannan
- The Stephen J. Ryan Initiative for Macular Research (RIMR), Doheny Eye Institute, Los Angeles, CA, 90033, USA; Stein Eye Institute, Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
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Thakur N, Sharma AK, Singh H, Singh S. Role of Mitochondrial DNA (mtDNA) Variations in Cancer Development: A Systematic Review. Cancer Invest 2020; 38:375-393. [PMID: 32673136 DOI: 10.1080/07357907.2020.1797768] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
mtDNA is the closed circular, ds-DNA present in mitochondria of eukaryotic cells and are inherited maternally. Besides being the power house of the cell, mitochondria are also responsible for the regulation of redox homeostasis, signaling, metabolism, immunity, survival and apoptosis. Lack of a 'Systematic Review' on mtDNA variations and cancers encouraged us to perform the present study. Pubmed', 'Embase' and 'Cochrane Library' databases were searched using keywords 'Mitochondrial DNA' OR 'mtDNA' OR 'mDNA' AND 'polymorphism' AND 'cancer' AND 'risk' to retrieve literature. Polymorphisms occupy first rank among mtDNA variations followed by CNV, MSI, mutations and hold a great potential to emerge as key predictors for human cancers.
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Affiliation(s)
- Nisha Thakur
- Division of Molecular Diagnostics, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Ministry of Health & Family Welfare (Govt. of India), Noida, India
| | - Amitesh Kumar Sharma
- Division of Informatics, Systems Research and Management, Indian Council of Medical Research (ICMR), Ministry of Health & Family Welfare (Govt. of India), New Delhi, India
| | - Harpreet Singh
- Division of Informatics, Systems Research and Management, Indian Council of Medical Research (ICMR), Ministry of Health & Family Welfare (Govt. of India), New Delhi, India
| | - Shalini Singh
- Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Ministry of Health & Family Welfare (Govt. of India), Noida, India
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235
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Grassi L, Izuogu OG, Jorge NA, Seyres D, Bustamante M, Burden F, Farrow S, Farahi N, Martin FJ, Frankish A, Mudge JM, Kostadima M, Petersen R, Lambourne JJ, Rowlston S, Martin-Rendon E, Clarke L, Downes K, Estivill X, Flicek P, Martens JH, Yaspo ML, Stunnenberg HG, Ouwehand WH, Passetti F, Turro E, Frontini M. Cell type-specific novel long non-coding RNA and circular RNA in the BLUEPRINT hematopoietic transcriptomes atlas. Haematologica 2020; 106:2613-2623. [PMID: 32703790 PMCID: PMC8485671 DOI: 10.3324/haematol.2019.238147] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Indexed: 12/15/2022] Open
Abstract
Transcriptional profiling of hematopoietic cell subpopulations has helped to characterize the developmental stages of the hematopoietic system and the molecular bases of malignant and non-malignant blood diseases. Previously, only the genes targeted by expression microarrays could be profiled genome-wide. High-throughput RNA sequencing, however, encompasses a broader repertoire of RNA molecules, without restriction to previously annotated genes. We analyzed the BLUEPRINT consortium RNA-sequencing data for mature hematopoietic cell types. The data comprised 90 total RNA-sequencing samples, each composed of one of 27 cell types, and 32 small RNA-sequencing samples, each composed of one of 11 cell types. We estimated gene and isoform expression levels for each cell type using existing annotations from Ensembl. We then used guided transcriptome assembly to discover unannotated transcripts. We identified hundreds of novel non-coding RNA genes and showed that the majority have cell type-dependent expression. We also characterized the expression of circular RNA and found that these are also cell type-specific. These analyses refine the active transcriptional landscape of mature hematopoietic cells, highlight abundant genes and transcriptional isoforms for each blood cell type, and provide a valuable resource for researchers of hematologic development and diseases. Finally, we made the data accessible via a web-based interface: https://blueprint.haem.cam.ac.uk/bloodatlas/.
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Affiliation(s)
- Luigi Grassi
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
- National Institute for Health Research BioResource, Rare Diseases, Cambridge University Hospitals, Cambridge, UK
- *LG and OGI contributed equally as co-first authors
| | - Osagie G. Izuogu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- *LG and OGI contributed equally as co-first authors
| | - Natasha A.N. Jorge
- Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Denis Seyres
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
- National Institute for Health Research BioResource, Rare Diseases, Cambridge University Hospitals, Cambridge, UK
| | - Mariona Bustamante
- ISGlobal, Institute for Global Health, Barcelona, Spain
- Center for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Frances Burden
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
- National Institute for Health Research BioResource, Rare Diseases, Cambridge University Hospitals, Cambridge, UK
| | - Samantha Farrow
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
- National Institute for Health Research BioResource, Rare Diseases, Cambridge University Hospitals, Cambridge, UK
| | - Neda Farahi
- Division of Respiratory Medicine, Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Fergal J. Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Jonathan M. Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Myrto Kostadima
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Romina Petersen
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
| | - John J. Lambourne
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
| | - Sophia Rowlston
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
| | - Enca Martin-Rendon
- R&D Division, National Health Service (NHS)-Blood and Transplant, Oxford Centre, Oxford, UK
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
- National Institute for Health Research BioResource, Rare Diseases, Cambridge University Hospitals, Cambridge, UK
| | - Xavier Estivill
- Genes and Disease Research Group, Genetics and Genomics Program, Sidra Research Department, Sidra Medicine, Doha, Qatar
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Joost H.A. Martens
- Radboud University, Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | | | - Hendrik G. Stunnenberg
- Radboud University, Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Willem H. Ouwehand
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
- National Institute for Health Research BioResource, Rare Diseases, Cambridge University Hospitals, Cambridge, UK
- Department of Human Genetics, the Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- British Heart Foundation Centre of Excellence, Cambridge Biomedical Campus, Cambridge, UK
| | - Fabio Passetti
- Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratory of Gene Expression Regulation, Carlos Chagas Institute, Fundação Oswaldo Cruz, Curitiba, Brazil
| | - Ernest Turro
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
- National Institute for Health Research BioResource, Rare Diseases, Cambridge University Hospitals, Cambridge, UK
- Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK
- ERNEST TURRO
| | - Mattia Frontini
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
- British Heart Foundation Centre of Excellence, Cambridge Biomedical Campus, Cambridge, UK
- Institute of Biomedical & Clinical Science, College of Medicine and Health, University of Exeter Medical School, Exeter, UK
- MATTIA FRONTINI
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236
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Lopez Sanchez MIG, Cipullo M, Gopalakrishna S, Khawaja A, Rorbach J. Methylation of Ribosomal RNA: A Mitochondrial Perspective. Front Genet 2020; 11:761. [PMID: 32765591 PMCID: PMC7379855 DOI: 10.3389/fgene.2020.00761] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/26/2020] [Indexed: 01/02/2023] Open
Abstract
Ribosomal RNA (rRNA) from all organisms undergoes post-transcriptional modifications that increase the diversity of its composition and activity. In mitochondria, specialized mitochondrial ribosomes (mitoribosomes) are responsible for the synthesis of 13 oxidative phosphorylation proteins encoded by the mitochondrial genome. Mitoribosomal RNA is also modified, with 10 modifications thus far identified and all corresponding modifying enzymes described. This form of epigenetic regulation of mitochondrial gene expression affects mitoribosome biogenesis and function. Here, we provide an overview on rRNA methylation and highlight critical work that is beginning to elucidate its role in mitochondrial gene expression. Given the similarities between bacterial and mitochondrial ribosomes, we focus on studies involving Escherichia coli and human models. Furthermore, we highlight the use of state-of-the-art technologies, such as cryoEM in the study of rRNA methylation and its biological relevance. Understanding the mechanisms and functional relevance of this process represents an exciting frontier in the RNA biology and mitochondrial fields.
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Affiliation(s)
- M Isabel G Lopez Sanchez
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden.,Centre for Eye Research Australia, Melbourne, VIC, Australia
| | - Miriam Cipullo
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden.,Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Shreekara Gopalakrishna
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden.,Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Anas Khawaja
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden.,Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Joanna Rorbach
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden.,Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
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237
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Held JP, Patel MR. Functional conservation of mitochondrial RNA levels despite divergent mtDNA organization. BMC Res Notes 2020; 13:334. [PMID: 32653018 PMCID: PMC7353721 DOI: 10.1186/s13104-020-05177-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/07/2020] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVE Mitochondria-encoded ribosomal RNA (rRNA) genes in humans are expressed at a higher rate than protein coding genes of the mitochondria. The organization of the human mitochondrial genome (mtDNA) is amenable to differential expression of rRNAs as the rRNA encoding genes lie in tandem immediately downstream of the promoter-containing region. However, mtDNA is not organized in the same way as humans in all metazoans. In the nematode, Caenorhabditis elegans, the rRNA genes are on opposite sides of the mtDNA molecule and there are no obvious promoter sequences specific to the rRNA genes. Thus, we asked whether rRNA levels are higher relative to mRNAs in mitochondria of C. elegans as they are in humans. RESULTS Using droplet digital PCR, we discovered that steady-state mitochondrial rRNA transcript levels are approximately 120 times higher than the levels of mitochondrial mRNAs. These data demonstrate that despite the lack of conservation in mitochondrial genome organization, a high mitochondrial rRNA-to-mRNA ratio is a conserved feature of metazoans.
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Affiliation(s)
- James P Held
- Interdisciplinary Graduate Program, Vanderbilt University, Nashville, TN, 37232, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA
| | - Maulik R Patel
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA.
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA.
- Diabetes Research and Training Center, Vanderbilt University, Nashville, TN, 37232, USA.
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238
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Toren D, Kulaga A, Jethva M, Rubin E, Snezhkina AV, Kudryavtseva AV, Nowicki D, Tacutu R, Moskalev AA, Fraifeld VE. Gray whale transcriptome reveals longevity adaptations associated with DNA repair and ubiquitination. Aging Cell 2020; 19:e13158. [PMID: 32515539 PMCID: PMC7433004 DOI: 10.1111/acel.13158] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 03/16/2020] [Accepted: 04/09/2020] [Indexed: 12/29/2022] Open
Abstract
One important question in aging research is how differences in genomics and transcriptomics determine the maximum lifespan in various species. Despite recent progress, much is still unclear on the topic, partly due to the lack of samples in nonmodel organisms and due to challenges in direct comparisons of transcriptomes from different species. The novel ranking‐based method that we employ here is used to analyze gene expression in the gray whale and compare its de novo assembled transcriptome with that of other long‐ and short‐lived mammals. Gray whales are among the top 1% longest‐lived mammals. Despite the extreme environment, or maybe due to a remarkable adaptation to its habitat (intermittent hypoxia, Arctic water, and high pressure), gray whales reach at least the age of 77 years. In this work, we show that long‐lived mammals share common gene expression patterns between themselves, including high expression of DNA maintenance and repair, ubiquitination, apoptosis, and immune responses. Additionally, the level of expression for gray whale orthologs of pro‐ and anti‐longevity genes found in model organisms is in support of their alleged role and direction in lifespan determination. Remarkably, among highly expressed pro‐longevity genes many are stress‐related, reflecting an adaptation to extreme environmental conditions. The conducted analysis suggests that the gray whale potentially possesses high resistance to cancer and stress, at least in part ensuring its longevity. This new transcriptome assembly also provides important resources to support the efforts of maintaining the endangered population of gray whales.
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Affiliation(s)
- Dmitri Toren
- The Shraga Segal Department of Microbiology, Immunology and Genetics Center for Multidisciplinary Research on Aging Ben‐Gurion University of the Negev Beer Sheva Israel
- Systems Biology of Aging Group Institute of Biochemistry of the Romanian Academy Bucharest Romania
| | - Anton Kulaga
- Systems Biology of Aging Group Institute of Biochemistry of the Romanian Academy Bucharest Romania
- Humenhance OÜ Tallinn Estonia
| | - Mineshbhai Jethva
- The Shraga Segal Department of Microbiology, Immunology and Genetics Center for Multidisciplinary Research on Aging Ben‐Gurion University of the Negev Beer Sheva Israel
| | - Eitan Rubin
- The Shraga Segal Department of Microbiology, Immunology and Genetics Center for Multidisciplinary Research on Aging Ben‐Gurion University of the Negev Beer Sheva Israel
| | | | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences Moscow Russia
| | - Dmitry Nowicki
- Center for Cybernetics Institute of MMS of NASU Kiev Ukraine
| | - Robi Tacutu
- Systems Biology of Aging Group Institute of Biochemistry of the Romanian Academy Bucharest Romania
- Chronos Biosystems SRL Bucharest Romania
| | - Alexey A. Moskalev
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences Moscow Russia
- Institute of Biology of Komi Science Center of Ural Branch of RAS Syktyvkar Russia
| | - Vadim E. Fraifeld
- The Shraga Segal Department of Microbiology, Immunology and Genetics Center for Multidisciplinary Research on Aging Ben‐Gurion University of the Negev Beer Sheva Israel
- 8IVAO LLC Saint Petersburg Russia
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239
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Chen J, Zheng Q, Peiffer LB, Hicks JL, Haffner MC, Rosenberg AZ, Levi M, Wang XX, Ozbek B, Baena-Del Valle J, Yegnasubramanian S, De Marzo AM. An in Situ Atlas of Mitochondrial DNA in Mammalian Tissues Reveals High Content in Stem and Proliferative Compartments. THE AMERICAN JOURNAL OF PATHOLOGY 2020; 190:1565-1579. [PMID: 32304697 PMCID: PMC7338910 DOI: 10.1016/j.ajpath.2020.03.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 02/25/2020] [Accepted: 03/19/2020] [Indexed: 02/07/2023]
Abstract
Mitochondria regulate ATP production, metabolism, and cell death. Alterations in mitochondrial DNA (mtDNA) sequence and copy number are implicated in aging and organ dysfunction in diverse inherited and sporadic diseases. Because most measurements of mtDNA use homogenates of complex tissues, little is known about cell-type-specific mtDNA copy number heterogeneity in normal physiology, aging, and disease. Thus, the precise cell types whose loss of mitochondrial activity and altered mtDNA copy number that result in organ dysfunction in aging and disease have often not been clarified. Here, an in situ hybridization approach to generate a single-cell-resolution atlas of mtDNA content in mammalian tissues was validated. In hierarchically organized self-renewing tissues, higher levels of mtDNA were observed in stem/proliferative compartments compared with differentiated compartments. Striking zonal patterns of mtDNA levels in the liver reflected the known oxygen tension gradient. In the kidney, proximal and distal tubules had markedly higher mtDNA levels compared with cells within glomeruli and collecting duct epithelial cells. In mice, decreased mtDNA levels were visualized in renal tubules as a function of aging, which was prevented by calorie restriction. This study provides a novel approach for quantifying species- and cell-type-specific mtDNA copy number and dynamics in any normal or diseased tissue that can be used for monitoring the effects of interventions in animal and human studies.
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Affiliation(s)
- Jiayu Chen
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Qizhi Zheng
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lauren B Peiffer
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jessica L Hicks
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Michael C Haffner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Avi Z Rosenberg
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Moshe Levi
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC
| | - Xiaoxin X Wang
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC
| | - Busra Ozbek
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Javier Baena-Del Valle
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Srinivasan Yegnasubramanian
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Urology and Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Angelo M De Marzo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Urology and Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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240
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Bravo JI, Nozownik S, Danthi PS, Benayoun BA. Transposable elements, circular RNAs and mitochondrial transcription in age-related genomic regulation. Development 2020; 147:dev175786. [PMID: 32527937 PMCID: PMC10680986 DOI: 10.1242/dev.175786] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Our understanding of the molecular regulation of aging and age-related diseases is still in its infancy, requiring in-depth characterization of the molecular landscape shaping these complex phenotypes. Emerging classes of molecules with promise as aging modulators include transposable elements, circRNAs and the mitochondrial transcriptome. Analytical complexity means that these molecules are often overlooked, even though they exhibit strong associations with aging and, in some cases, may directly contribute to its progress. Here, we review the links between these novel factors and age-related phenotypes, and we suggest tools that can be easily incorporated into existing pipelines to better understand the aging process.
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Affiliation(s)
- Juan I Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Graduate Program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | - Séverine Nozownik
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Magistère européen de Génétique, Université Paris Diderot-Paris 7, Paris 75014, France
| | - Prakroothi S Danthi
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA
- USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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241
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Lv L, Zhao Y, Wei Q, Zhao Y, Yi Q. Downexpression of HSD17B6 correlates with clinical prognosis and tumor immune infiltrates in hepatocellular carcinoma. Cancer Cell Int 2020; 20:210. [PMID: 32514254 PMCID: PMC7268300 DOI: 10.1186/s12935-020-01298-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 05/27/2020] [Indexed: 12/24/2022] Open
Abstract
Background Hydroxysteroid 17-Beta Dehydrogenase 6 (HSD17B6), a key protein involved in synthetizing dihydrotestosterone, is abundant in the liver. Previous studies have suggested a role for dihydrotestosterone in modulating progress of various malignancies, and HSD17B6 dysfunction was associated with lung cancer and prostate cancer. However, little is known about the detailed role of HSD17B6 in hepatocellular carcinoma (HCC). Methods Clinical implication and survival data related to HSD17B6 expression in patients with HCC were obtained through TCGA, ICGC, ONCOMINE, GEO and HPA databases. Survival analysis plots were drawn with Kaplan–Meier Plotter. The ChIP-seq data were obtained from Cistrome DB. Protein–Protein Interaction and gene functional enrichment analyses were performed in STRING database. The correlations between HSD17B6 and tumor immune infiltrates was investigated via TIMER and xCell. The proliferation, migration and invasion of liver cancer cells transfected with HSD17B6 were evaluated by the CCK8 assay, wound healing test and transwell assay respectively. Expression of HSD17B6, TGFB1 and PD-L1 were assessed by quantitative RT-PCR. Results HSD17B6 expression was lower in HCC compared to normal liver and correlated with tumor stage and grade. Lower expression of HSD17B6 was associated with worse OS, PFS, RFS and DSS in HCC patients. HNF4A bound to enhancer and promoter regions of HSD17B6 gene, activating its transcription, and DNA methylation of HSD17B6 promoter negatively controlled the expression. HSD17B6 and its interaction partners were involved in androgen metabolism and biosynthesis in liver. HSD17B6 inhibited tumor cell proliferation, migration and invasion in liver cancer cells and low expression of HSD17B6 correlated with high immune cells infiltration, relative reduction of immune responses and multiple immune checkpoint genes expression in HCC, probably by regulating the expression of TGFB1. Conclusions This study indicate that HSD17B6 could be a new biomarker for the prognosis of HCC and an important negative regulator of immune responses in HCC.
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Affiliation(s)
- Lei Lv
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230031 Anhui People's Republic of China
| | - Yujia Zhao
- Teaching and Research Section of Nuclear Medicine, Anhui Medical University, 81 Meishan Road, Hefei, 230032 Anhui People's Republic of China
| | - Qinqin Wei
- Teaching and Research Section of Nuclear Medicine, Anhui Medical University, 81 Meishan Road, Hefei, 230032 Anhui People's Republic of China
| | - Ye Zhao
- Teaching and Research Section of Nuclear Medicine, Anhui Medical University, 81 Meishan Road, Hefei, 230032 Anhui People's Republic of China
| | - Qiyi Yi
- Teaching and Research Section of Nuclear Medicine, Anhui Medical University, 81 Meishan Road, Hefei, 230032 Anhui People's Republic of China
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242
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Clues of in vivo nuclear gene regulation by mitochondrial short non-coding RNAs. Sci Rep 2020; 10:8219. [PMID: 32427953 PMCID: PMC7237437 DOI: 10.1038/s41598-020-65084-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 04/22/2020] [Indexed: 12/15/2022] Open
Abstract
Gene expression involves multiple processes, from transcription to translation to the mature, functional peptide, and it is regulated at multiple levels. Small RNA molecules are known to bind RNA messengers affecting their fate in the cytoplasm (a process generically termed ‘RNA interference’). Such small regulatory RNAs are well-known to be originated from the nuclear genome, while the role of mitochondrial genome in RNA interference was largely overlooked. However, evidence is growing that mitochondrial DNA does provide the cell a source of interfering RNAs. Small mitochondrial highly transcribed RNAs (smithRNAs) have been proposed to be transcribed from the mitochondrion and predicted to regulate nuclear genes. Here, for the first time, we show in vivo clues of the activity of two smithRNAs in the Manila clam, Ruditapes philippinarum. Moreover, we show that smithRNAs are present and can be annotated in representatives of the three main bilaterian lineages; in some cases, they were already described and assigned to a small RNA category (e.g., piRNAs) given their biogenesis, while in other cases their biogenesis remains unclear. If mitochondria may affect nuclear gene expression through RNA interference, this opens a plethora of new possibilities for them to interact with the nucleus and makes metazoan mitochondrial DNA a much more complex genome than previously thought.
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243
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Silzer TK, Pathak GA, Phillips NR. Mitochondrial tRNA methylation in Alzheimer's disease and progressive supranuclear palsy. BMC Med Genomics 2020; 13:71. [PMID: 32429992 PMCID: PMC7236490 DOI: 10.1186/s12920-020-0727-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/29/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Methylation of mitochondrial tRNAs (mt-tRNA) at the 9th position ("p9 site") is known to impact translational efficiency and downstream mitochondrial function; however, direct assessment of mt-RNA methylation is challenging. Recent RNA sequence-based methods have been developed to reliably identify post-transcriptional methylation. Though p9 methylation has been studied in healthy human populations and in the context of cancer, it has not yet been analyzed in neurodegenerative disease, where mitochondrial dysfunction is a prominent and early hallmark of disease progression. METHODS Mitochondrial p9 methylation was inferred from multi-allelic calls in RNA-seq data. Gene-based association studies were performed in FUMA. Correlations between nuclear gene expression and p9 methylation were tested using Spearman's rho. Fisher's Exact test was used in PANTHER and IPA to test for overrepresentation and enrichment of biological processes and pathways in the top nuclear genes correlated with p9 methylation. RESULTS Variable methylation was observed at 11 p9 sites in post-mortem cerebellar tissue of elderly subjects who were either healthy or diagnosed with Alzheimer's disease (AD), progressive supranuclear palsy (PSP) or pathological aging (PA). Similarities in degree of methylation were observed between AD and PSP. Certain nuclear encoded genes were identified as significantly associated with p9 methylation. Expression of 5300 nuclear encoded genes was significantly correlated with p9 methylation, with AD and PSP subjects exhibiting similar expression profiles. Overrepresentation and enrichment testing using the top transcripts revealed enrichment for a number of molecular processes, terms and pathways including many of which that were mitochondrial-related. CONCLUSION With mitochondrial dysfunction being an established hallmark of neurodegenerative disease pathophysiology, this work sheds light on the potential molecular underpinnings of this dysfunction. Here we show overlap in cerebellar pathophysiology between common tauopathies such as Alzheimer's disease and progressive supranuclear palsy. Whether p9 hypermethylation is a cause or consequence of pathology remains an area of focus.
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Affiliation(s)
- Talisa K Silzer
- Department of Microbiology, Immunology and Genetics; Graduate School of Biomedical Science, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, USA
| | - Gita A Pathak
- Department of Microbiology, Immunology and Genetics; Graduate School of Biomedical Science, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, USA
| | - Nicole R Phillips
- Department of Microbiology, Immunology and Genetics; Graduate School of Biomedical Science, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, USA.
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244
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Abstract
Mitochondria are essential organelles in eukaryotes. Most mitochondrial proteins are encoded by the nuclear genome and translated in the cytosol. Nuclear-encoded mitochondrial proteins need to be imported, processed, folded, and assembled into their functional states. To maintain protein homeostasis (proteostasis), mitochondria are equipped with a distinct set of quality control machineries. Deficiencies in such systems lead to mitochondrial dysfunction, which is a hallmark of aging and many human diseases, such as neurodegenerative diseases, cardiovascular diseases, and cancer. In this review, we discuss the unique challenges and solutions of proteostasis in mitochondria. The import machinery coordinates with mitochondrial proteases and chaperones to maintain the mitochondrial proteome. Moreover, mitochondrial proteostasis depends on cytosolic protein quality control mechanisms during crises. In turn, mitochondria facilitate cytosolic proteostasis. Increasing evidence suggests that enhancing mitochondrial proteostasis may hold therapeutic potential to protect against protein aggregation-associated cellular defects.
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Affiliation(s)
- Linhao Ruan
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; , , , , ,
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Yuhao Wang
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; , , , , ,
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Xi Zhang
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; , , , , ,
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Alexis Tomaszewski
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; , , , , ,
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Joshua T McNamara
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; , , , , ,
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Rong Li
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; , , , , ,
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
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Kawamura E, Maruyama M, Abe J, Sudo A, Takeda A, Takada S, Yokota T, Kinugawa S, Harashima H, Yamada Y. Validation of Gene Therapy for Mutant Mitochondria by Delivering Mitochondrial RNA Using a MITO-Porter. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 20:687-698. [PMID: 32388194 PMCID: PMC7210581 DOI: 10.1016/j.omtn.2020.04.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/10/2020] [Accepted: 04/15/2020] [Indexed: 10/29/2022]
Abstract
Here, we report on validating a mitochondrial gene therapy by delivering nucleic acids to mitochondria of diseased cells by a MITO-Porter, a liposome-based carrier for mitochondrial delivery. We used cells derived from a patient with a mitochondrial disease with a G625A heteroplasmic mutation in the tRNAPhe of the mitochondrial DNA (mtDNA). It has been reported that some mitochondrial gene diseases are caused by heteroplasmic mutations, in which both mutated and wild-type (WT) genes are present, and the accumulation of pathological mutations leads to serious, intractable, multi-organ diseases. Therefore, the decrease of the mutated gene rate is considered to be a useful gene therapy strategy. To accomplish this, wild-type mitochondrial pre-tRNAPhe (pre-WT-tRNAPhe), prepared by in vitro transcription, was encapsulated in the MITO-Porter. The pre-WT-tRNAPhe encapsulated in the MITO-Porter was transfected into diseased mitochondrial cells, and the resulting mutant levels were examined by an amplification refractory mutation system (ARMS)-quantitative PCR. The mutation rate of tRNAPhe was decreased, and this therapeutic effect was sustained even on the 8th day after transfection. Furthermore, mitochondrial respiratory activity of the disease cells was increased after the transfection of therapeutic pre-WT-tRNAPhe. These results support the conclusion that the mitochondrial delivery of therapeutic nucleic acids represents a viable strategy for mitochondrial gene therapy.
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Affiliation(s)
- Eriko Kawamura
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Minako Maruyama
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Jiro Abe
- Department of Pediatrics, Hokkaido University Hospital, Kita-15, Nishi-7, Kita-ku, Sapporo 060-8638, Japan
| | - Akira Sudo
- Nire-no-kai Children's Clinic, Atsubetsu-cho Shimonopporo-49, Atsubetsu-ku, Sapporo 004-0007, Japan; Department of Pediatrics, Sapporo City General Hospital, Kita-11, Nishi-13, Chuo-ku, Sapporo 060-8604, Japan
| | - Atsuhito Takeda
- Department of Pediatrics, Hokkaido University Hospital, Kita-15, Nishi-7, Kita-ku, Sapporo 060-8638, Japan
| | - Shingo Takada
- Department of Cardiovascular Medicine, Graduate School of Medicine, Hokkaido University, Kita-15, Nishi-7, Kita-ku, Sapporo 060-8638, Japan
| | - Takashi Yokota
- Department of Cardiovascular Medicine, Graduate School of Medicine, Hokkaido University, Kita-15, Nishi-7, Kita-ku, Sapporo 060-8638, Japan
| | - Shintaro Kinugawa
- Department of Cardiovascular Medicine, Graduate School of Medicine, Hokkaido University, Kita-15, Nishi-7, Kita-ku, Sapporo 060-8638, Japan
| | - Hideyoshi Harashima
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Yuma Yamada
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.
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246
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Tsagakis I, Douka K, Birds I, Aspden JL. Long non-coding RNAs in development and disease: conservation to mechanisms. J Pathol 2020; 250:480-495. [PMID: 32100288 PMCID: PMC8638664 DOI: 10.1002/path.5405] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/05/2020] [Accepted: 02/18/2020] [Indexed: 12/22/2022]
Abstract
Our genomes contain the blueprint of what makes us human and many indications as to why we develop disease. Until the last 10 years, most studies had focussed on protein-coding genes, more specifically DNA sequences coding for proteins. However, this represents less than 5% of our genomes. The other 95% is referred to as the 'dark matter' of our genomes, our understanding of which is extremely limited. Part of this 'dark matter' includes regions that give rise to RNAs that do not code for proteins. A subset of these non-coding RNAs are long non-coding RNAs (lncRNAs), which in particular are beginning to be dissected and their importance to human health revealed. To improve our understanding and treatment of disease it is vital that we understand the molecular and cellular function of lncRNAs, and how their misregulation can contribute to disease. It is not yet clear what proportion of lncRNAs is actually functional; conservation during evolution is being used to understand the biological importance of lncRNA. Here, we present key themes within the field of lncRNAs, emphasising the importance of their roles in both the nucleus and the cytoplasm of cells, as well as patterns in their modes of action. We discuss their potential functions in development and disease using examples where we have the greatest understanding. Finally, we emphasise why lncRNAs can serve as biomarkers and discuss their emerging potential for therapy. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Ioannis Tsagakis
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of LeedsLeedsUK
- LeedsOmicsUniversity of LeedsLeedsUK
| | - Katerina Douka
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of LeedsLeedsUK
- LeedsOmicsUniversity of LeedsLeedsUK
| | - Isabel Birds
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of LeedsLeedsUK
- LeedsOmicsUniversity of LeedsLeedsUK
| | - Julie L Aspden
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of LeedsLeedsUK
- LeedsOmicsUniversity of LeedsLeedsUK
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247
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Analysis of mitochondrial m1A/G RNA modification reveals links to nuclear genetic variants and associated disease processes. Commun Biol 2020; 3:147. [PMID: 32221480 PMCID: PMC7101319 DOI: 10.1038/s42003-020-0879-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 03/06/2020] [Indexed: 12/13/2022] Open
Abstract
RNA modifications affect the stability and function of RNA species, regulating important downstream processes. Modification levels are often dynamic, varying between tissues and individuals, although it is not always clear what modulates this or what impact it has on biological systems. Here, we quantify variation in m1A/G RNA modification levels at functionally important positions in the human mitochondrial genome across 11,552 samples from 39 tissue/cell types and find that modification levels are associated with mitochondrial transcript processing. We identify links between mitochondrial RNA modification levels and genetic variants in the nuclear genome, including a missense mutation in LONP1, and find that genetic variants within MRPP3 and TRMT61B are associated with RNA modification levels across a large number of tissues. Genetic variants linked to RNA modification levels are associated with multiple disease/disease-related phenotypes, including blood pressure, breast cancer and psoriasis, suggesting a role for mitochondrial RNA modification in complex disease. Ali et al. analyze publicly available RNA-seq data from different tissues to quantify variation in m1A/G methylation levels in mitochondrial RNAs. They show a link between mitochondrial m1A/G modification levels and nuclear genetic variants, many of which are associated with disease.
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248
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Hao Z, Wu T, Cui X, Zhu P, Tan C, Dou X, Hsu KW, Lin YT, Peng PH, Zhang LS, Gao Y, Hu L, Sun HL, Zhu A, Liu J, Wu KJ, He C. N 6-Deoxyadenosine Methylation in Mammalian Mitochondrial DNA. Mol Cell 2020; 78:382-395.e8. [PMID: 32183942 DOI: 10.1016/j.molcel.2020.02.018] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 02/03/2020] [Accepted: 02/20/2020] [Indexed: 12/12/2022]
Abstract
N6-Methyldeoxyadenosine (6mA) has recently been shown to exist and play regulatory roles in eukaryotic genomic DNA (gDNA). However, the biological functions of 6mA in mammals have yet to be adequately explored, largely due to its low abundance in most mammalian genomes. Here, we report that mammalian mitochondrial DNA (mtDNA) is enriched for 6mA. The level of 6mA in HepG2 mtDNA is at least 1,300-fold higher than that in gDNA under normal growth conditions, corresponding to approximately four 6mA modifications on each mtDNA molecule. METTL4, a putative mammalian methyltransferase, can mediate mtDNA 6mA methylation, which contributes to attenuated mtDNA transcription and a reduced mtDNA copy number. Mechanistically, the presence of 6mA could repress DNA binding and bending by mitochondrial transcription factor (TFAM). Under hypoxia, the 6mA level in mtDNA could be further elevated, suggesting regulatory roles for 6mA in mitochondrial stress response. Our study reveals DNA 6mA as a regulatory mark in mammalian mtDNA.
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Affiliation(s)
- Ziyang Hao
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Tong Wu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Xiaolong Cui
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Pingping Zhu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; School of Life Science, Zhengzhou University, Zhengzhou 450001, China
| | - Caiping Tan
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Xiaoyang Dou
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Kai-Wen Hsu
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan
| | - Yueh-Te Lin
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan
| | - Pei-Hua Peng
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan
| | - Li-Sheng Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Yawei Gao
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Lulu Hu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Hui-Lung Sun
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Allen Zhu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Jianzhao Liu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Kou-Juey Wu
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
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249
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Eldarov CM, Vangely IM, Vays VB, Sheval EV, Holtze S, Hildebrandt TB, Kolosova NG, Popkov VA, Plotnikov EY, Zorov DB, Bakeeva LE, Skulachev VP. Mitochondria in the Nuclei of Rat Myocardial Cells. Cells 2020; 9:E712. [PMID: 32183238 PMCID: PMC7140638 DOI: 10.3390/cells9030712] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 03/03/2020] [Accepted: 03/05/2020] [Indexed: 01/01/2023] Open
Abstract
Electron microscopic study of cardiomyocytes taken from healthy Wistar and OXYS rats and naked mole rats (Heterocephalus glaber) revealed mitochondria in nuclei that lacked part of the nuclear envelope. The direct interaction of mitochondria with nucleoplasm is shown. The statistical analysis of the occurrence of mitochondria in cardiomyocyte nuclei showed that the percentage of nuclei with mitochondria was roughly around 1%, and did not show age and species dependency. Confocal microscopy of normal rat cardiac myocytes revealed a branched mitochondrial network in the vicinity of nuclei with an organization different than that of interfibrillar mitochondria. This mitochondrial network was energetically functional because it carried the membrane potential that responded by oscillatory mode after photodynamic challenge. We suggest that the presence of functional mitochondria in the nucleus is not only a consequence of certain pathologies but rather represents a normal biological phenomenon involved in mitochondrial/nuclear interactions.
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Affiliation(s)
- Chupalav M Eldarov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Irina M Vangely
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Valeriya B Vays
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Eugene V Sheval
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Susanne Holtze
- Department of Reproduction Management, Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Thomas B Hildebrandt
- Department of Reproduction Management, Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Natalia G Kolosova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Vasily A Popkov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Egor Y Plotnikov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Dmitry B Zorov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Lora E Bakeeva
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vladimir P Skulachev
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia
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250
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Warren JM, Sloan DB. Interchangeable parts: The evolutionarily dynamic tRNA population in plant mitochondria. Mitochondrion 2020; 52:144-156. [PMID: 32184120 DOI: 10.1016/j.mito.2020.03.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 03/06/2020] [Accepted: 03/11/2020] [Indexed: 01/31/2023]
Abstract
Transfer RNAs (tRNAs) remain one of the very few classes of genes still encoded in the mitochondrial genome. These key components of the protein translation system must interact with a large enzymatic network of nuclear-encoded gene products to maintain mitochondrial function. Plants have an evolutionarily dynamic mitochondrial tRNA population, including ongoing tRNA gene loss and replacement by both horizontal gene transfer from diverse sources and import of nuclear-expressed tRNAs from the cytosol. Thus, plant mitochondria represent an excellent model for understanding how anciently divergent genes can act as "interchangeable parts" during the evolution of complex molecular systems. In particular, understanding the integration of the mitochondrial translation system with elements of the corresponding machinery used in cytosolic protein synthesis is a key area for eukaryotic cellular evolution. Here, we review the increasingly detailed phylogenetic data about the evolutionary history of mitochondrial tRNA gene loss, transfer, and functional replacement that has created extreme variation in mitochondrial tRNA populations across plant species. We describe emerging tRNA-seq methods with promise for refining our understanding of the expression and subcellular localization of tRNAs. Finally, we summarize current evidence and identify open questions related to coevolutionary changes in nuclear-encoded enzymes that have accompanied turnover in mitochondrial tRNA populations.
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Affiliation(s)
- Jessica M Warren
- Department of Biology, Colorado State University, Fort Collins, CO, USA.
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, USA
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