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Pi Y, Huang Z, Xu X, Zhang H, Jin M, Zhang S, Lin G, Hu L. Increases in computationally predicted deleterious variants of unknown significance and sperm mtDNA copy numbers may be associated with semen quality. Andrology 2024; 12:585-598. [PMID: 37622679 DOI: 10.1111/andr.13521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 06/24/2023] [Accepted: 08/08/2023] [Indexed: 08/26/2023]
Abstract
BACKGROUND Mitochondria are essential for sperm motility because they provide the energy required for the movement. Changes in sperm mtDNA, such as point mutations, large-scale deletions, or copy number variations, may interfere with ATP production and reduce sperm motility. However, it is not clear if changes in mtDNA are linked to semen quality. OBJECTIVES To explore the association between sperm mitochondrial DNA (mtDNA) changes and semen quality. MATERIALS AND METHODS Sixty-five oligo and/or astheno and/or terato patients (O/A/T) patients and 41 controls were recruited from couples undergoing assisted reproduction. Semen and blood samples were collected from the same individual on the day of oocyte retrieval to extract, isolate and purify mtDNA for next-generation sequencing. mtDNA copy numbers were assessed in 64 patient and 39 control sperm DNA samples using quantitative real-time PCR. The 4977 bp deletion was assessed in 20 patient and 20 control sperm DNA samples using polymerase chain reaction. RESULTS The mtDNA of patients was more likely to carry pathogenic variants or variants of unknown significance (VUSs) (P = 0.091) with higher heteroplasmy levels (P < 0.05) than that of controls. Interestingly, 33.85% of O/A/T patients (22 out of 65) lacked unique variants in their spermatozoa. but presented an exceptionally high mtDNA copy number (P < 0.0001). Moreover, we observed a decrease in the heteroplasmy level of common mtDNA variants shared by somatic and gamete cells (P < 0.0001) and the emergence of a very large number of de novo mtDNA variants with low-level heteroplasmy in spermatozoa. DISCUSSION AND CONCLUSION The increases in the number of computationally predicted deleterious VUS and mtDNA copies in spermatozoa may be associated with semen quality. Exposure to environmental mutation pressure that causes novel mtDNA variants with low-level heteroplasmy may occur during spermatogenesis. Furthermore, when a certain harmful threshold is reached, male germ cells may degrade mtDNA with mutations and replicate the correct mtDNA sequence to maintain the mitochondrial function in spermatozoa.
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Affiliation(s)
- Yuze Pi
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Zhuo Huang
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Laboratory Medicine Centre, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital), Shenzhen, Guangdong, China
| | - Xilin Xu
- College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Huan Zhang
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Hunan, China
| | - Miao Jin
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Hunan, China
| | - Shuoping Zhang
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Hunan, China
| | - Ge Lin
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Hunan, China
- National Engineering and Research Center of Human Stem Cells, Changsha, Hunan, China
| | - Liang Hu
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Hunan, China
- National Engineering and Research Center of Human Stem Cells, Changsha, Hunan, China
- Hunan International Scientific and Technological Cooperation base of Development and Carcinogenesis, Changsha, Hunan, China
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Abstract
Mitochondria are multifunctional organelles that play a central role in a wide range of life-sustaining tasks in eukaryotic cells, including adenosine triphosphate (ATP) production, calcium storage and coenzyme generation pathways such as iron-sulfur cluster biosynthesis. The wide range of mitochondrial functions is carried out by a diverse array of proteins comprising approximately 1500 proteins or polypeptides. Degradation of these proteins is mainly performed by four AAA+ proteases localized in mitochondria. These AAA+ proteases play a quality control role in degrading damaged or misfolded proteins and perform various other functions. This chapter describes previously identified roles for these AAA+ proteases that are localized in the mitochondria of animal cells.
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Affiliation(s)
- Yuichi Matsushima
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan.
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3
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Kozal JS, Jayasundara N, Massarsky A, Lindberg CD, Oliveri AN, Cooper EM, Levin ED, Meyer JN, Giulio RTD. Mitochondrial dysfunction and oxidative stress contribute to cross-generational toxicity of benzo(a)pyrene in Danio rerio. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 263:106658. [PMID: 37722151 PMCID: PMC10591944 DOI: 10.1016/j.aquatox.2023.106658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/06/2023] [Accepted: 08/10/2023] [Indexed: 09/20/2023]
Abstract
The potential for polycyclic aromatic hydrocarbons (PAHs) to have adverse effects that persist across generations is an emerging concern for human and wildlife health. This study evaluated the role of mitochondria, which are maternally inherited, in the cross-generational toxicity of benzo(a)pyrene (BaP), a model PAH and known mitochondrial toxicant. Mature female zebrafish (F0) were fed diets containing 0, 12.5, 125, or 1250 μg BaP/g at a feed rate of 1% body weight twice/day for 21 days. These females were bred with unexposed males, and the embryos (F1) were collected for subsequent analyses. Maternally-exposed embryos exhibited altered mitochondrial function and metabolic partitioning (i.e. the portion of respiration attributable to different cellular processes), as evidenced by in vivo oxygen consumption rates (OCRs). F1 embryos had lower basal and mitochondrial respiration and ATP turnover-mediated OCR, and increased proton leak and reserve capacity. Reductions in mitochondrial DNA (mtDNA) copy number, increases in mtDNA damage, and alterations in biomarkers of oxidative stress were also found in maternally-exposed embryos. Notably, the mitochondrial effects in offspring occurred largely in the absence of effects in maternal ovaries, suggesting that PAH-induced mitochondrial dysfunction may manifest in subsequent generations. Maternally-exposed larvae also displayed swimming hypoactivity. The lowest observed effect level (LOEL) for maternal BaP exposure causing mitochondrial effects in offspring was 12.5 µg BaP/g diet (nominally equivalent to 250 ng BaP/g fish). It was concluded that maternal BaP exposure can cause significant mitochondrial impairments in offspring.
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Affiliation(s)
- Jordan S Kozal
- Nicholas School of the Environment, Duke University, Durham, NC, USA.
| | | | - Andrey Massarsky
- Nicholas School of the Environment, Duke University, Durham, NC, USA
| | - Casey D Lindberg
- Nicholas School of the Environment, Duke University, Durham, NC, USA
| | - Anthony N Oliveri
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Ellen M Cooper
- Nicholas School of the Environment, Duke University, Durham, NC, USA
| | - Edward D Levin
- Nicholas School of the Environment, Duke University, Durham, NC, USA; Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA; Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Joel N Meyer
- Nicholas School of the Environment, Duke University, Durham, NC, USA
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Mongelli A, Mengozzi A, Geiger M, Gorica E, Mohammed SA, Paneni F, Ruschitzka F, Costantino S. Mitochondrial epigenetics in aging and cardiovascular diseases. Front Cardiovasc Med 2023; 10:1204483. [PMID: 37522089 PMCID: PMC10382027 DOI: 10.3389/fcvm.2023.1204483] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/29/2023] [Indexed: 08/01/2023] Open
Abstract
Mitochondria are cellular organelles which generate adenosine triphosphate (ATP) molecules for the maintenance of cellular energy through the oxidative phosphorylation. They also regulate a variety of cellular processes including apoptosis and metabolism. Of interest, the inner part of mitochondria-the mitochondrial matrix-contains a circular molecule of DNA (mtDNA) characterised by its own transcriptional machinery. As with genomic DNA, mtDNA may also undergo nucleotide mutations that have been shown to be responsible for mitochondrial dysfunction. During physiological aging, the mitochondrial membrane potential declines and associates with enhanced mitophagy to avoid the accumulation of damaged organelles. Moreover, if the dysfunctional mitochondria are not properly cleared, this could lead to cellular dysfunction and subsequent development of several comorbidities such as cardiovascular diseases (CVDs), diabetes, respiratory and cardiovascular diseases as well as inflammatory disorders and psychiatric diseases. As reported for genomic DNA, mtDNA is also amenable to chemical modifications, namely DNA methylation. Changes in mtDNA methylation have shown to be associated with altered transcriptional programs and mitochondrial dysfunction during aging. In addition, other epigenetic signals have been observed in mitochondria, in particular the interaction between mtDNA methylation and non-coding RNAs. Mitoepigenetic modifications are also involved in the pathogenesis of CVDs where oxygen chain disruption, mitochondrial fission, and ROS formation alter cardiac energy metabolism leading to hypertrophy, hypertension, heart failure and ischemia/reperfusion injury. In the present review, we summarize current evidence on the growing importance of epigenetic changes as modulator of mitochondrial function in aging. A better understanding of the mitochondrial epigenetic landscape may pave the way for personalized therapies to prevent age-related diseases.
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Affiliation(s)
- Alessia Mongelli
- Center for Translational and Experimental Cardiology (CTEC), Department of Cardiology, Zurich University Hospital and University of Zürich, Zurich, Switzerland
| | - Alessandro Mengozzi
- Center for Translational and Experimental Cardiology (CTEC), Department of Cardiology, Zurich University Hospital and University of Zürich, Zurich, Switzerland
| | - Martin Geiger
- Center for Translational and Experimental Cardiology (CTEC), Department of Cardiology, Zurich University Hospital and University of Zürich, Zurich, Switzerland
| | - Era Gorica
- Center for Translational and Experimental Cardiology (CTEC), Department of Cardiology, Zurich University Hospital and University of Zürich, Zurich, Switzerland
| | - Shafeeq Ahmed Mohammed
- Center for Translational and Experimental Cardiology (CTEC), Department of Cardiology, Zurich University Hospital and University of Zürich, Zurich, Switzerland
| | - Francesco Paneni
- Center for Translational and Experimental Cardiology (CTEC), Department of Cardiology, Zurich University Hospital and University of Zürich, Zurich, Switzerland
- Department of Cardiology, University Heart Center, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Frank Ruschitzka
- Center for Translational and Experimental Cardiology (CTEC), Department of Cardiology, Zurich University Hospital and University of Zürich, Zurich, Switzerland
- Department of Cardiology, University Heart Center, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sarah Costantino
- Center for Translational and Experimental Cardiology (CTEC), Department of Cardiology, Zurich University Hospital and University of Zürich, Zurich, Switzerland
- Department of Cardiology, University Heart Center, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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Yuan Y, Tian Y, Jiang H, Cai LY, Song J, Peng R, Zhang XM. Mechanism of PGC-1α-mediated mitochondrial biogenesis in cerebral ischemia-reperfusion injury. Front Mol Neurosci 2023; 16:1224964. [PMID: 37492523 PMCID: PMC10363604 DOI: 10.3389/fnmol.2023.1224964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 06/21/2023] [Indexed: 07/27/2023] Open
Abstract
Cerebral ischemia-reperfusion injury (CIRI) is a series of cascade reactions that occur after blood flow recanalization in the ischemic zone in patients with cerebral infarction, causing an imbalance in intracellular homeostasis through multiple pathologies such as increased oxygen free radicals, inflammatory response, calcium overload, and impaired energy metabolism, leading to mitochondrial dysfunction and ultimately apoptosis. Rescue of reversibly damaged neurons in the ischemic hemispheric zone is the key to saving brain infarction and reducing neurological deficits. Complex and active neurological functions are highly dependent on an adequate energy supply from mitochondria. Mitochondrial biogenesis (MB), a process that generates new functional mitochondria and restores normal mitochondrial function by replacing damaged mitochondria, is a major mechanism for maintaining intra-mitochondrial homeostasis and is involved in mitochondrial quality control to ameliorate mitochondrial dysfunction and thus protects against CIRI. The main regulator of MB is peroxisome proliferator-activated receptor gamma coactivator-1α (PGC-1α), which improves mitochondrial function to protect against CIRI by activating its downstream nuclear respiratory factor 1 (NRF1) and mitochondrial transcription factor A (TFAM) to promote mitochondrial genome replication and transcription. This paper provides a theoretical reference for the treatment of neurological impairment caused by CIRI by discussing the mechanisms of mitochondrial biogenesis during cerebral ischemia-reperfusion injury.
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Affiliation(s)
- Ying Yuan
- School of Acupuncture-Moxibustion and Orthopedics, Hubei University of Chinese Medicine, Wuhan, China
| | - Yuan Tian
- School of Acupuncture-Moxibustion and Orthopedics, Hubei University of Chinese Medicine, Wuhan, China
| | - Hui Jiang
- School of Acupuncture-Moxibustion and Orthopedics, Hubei University of Chinese Medicine, Wuhan, China
| | - Luo-yang Cai
- School of Acupuncture-Moxibustion and Orthopedics, Hubei University of Chinese Medicine, Wuhan, China
| | - Jie Song
- School of Acupuncture-Moxibustion and Orthopedics, Hubei University of Chinese Medicine, Wuhan, China
| | - Rui Peng
- School of Acupuncture-Moxibustion and Orthopedics, Hubei University of Chinese Medicine, Wuhan, China
- Sub-Health Institute Hubei University of Chinese Medicine, Wuhan, China
| | - Xiao-ming Zhang
- School of Acupuncture-Moxibustion and Orthopedics, Hubei University of Chinese Medicine, Wuhan, China
- Sub-Health Institute Hubei University of Chinese Medicine, Wuhan, China
- Hubei Provincial Collaborative Innovation Center for Preventive Treatment of Disease by Acupuncture, Wuhan, China
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Kozhukhar N, Alexeyev MF. 35 Years of TFAM Research: Old Protein, New Puzzles. BIOLOGY 2023; 12:823. [PMID: 37372108 DOI: 10.3390/biology12060823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 05/29/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023]
Abstract
Transcription Factor A Mitochondrial (TFAM), through its contributions to mtDNA maintenance and expression, is essential for cellular bioenergetics and, therefore, for the very survival of cells. Thirty-five years of research on TFAM structure and function generated a considerable body of experimental evidence, some of which remains to be fully reconciled. Recent advancements allowed an unprecedented glimpse into the structure of TFAM complexed with promoter DNA and TFAM within the open promoter complexes. These novel insights, however, raise new questions about the function of this remarkable protein. In our review, we compile the available literature on TFAM structure and function and provide some critical analysis of the available data.
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Affiliation(s)
- Natalya Kozhukhar
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Mikhail F Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA
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7
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Chen PL. SUV3 Helicase and Mitochondrial Homeostasis. Int J Mol Sci 2023; 24:9233. [PMID: 37298184 PMCID: PMC10253155 DOI: 10.3390/ijms24119233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/21/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
SUV3 is a nuclear-encoded helicase that is highly conserved and localizes to the mitochondrial matrix. In yeast, loss of SUV3 function leads to the accumulation of group 1 intron transcripts, ultimately resulting in the loss of mitochondrial DNA, causing a petite phenotype. However, the mechanism leading to the loss of mitochondrial DNA remains unknown. SUV3 is essential for survival in higher eukaryotes, and its knockout in mice results in early embryonic lethality. Heterozygous mice exhibit a range of phenotypes, including premature aging and an increased cancer incidence. Furthermore, cells derived from SUV3 heterozygotes or knockdown cultural cells show a reduction in mtDNA. Transient downregulation of SUV3 leads to the formation of R-loops and the accumulation of double-stranded RNA in mitochondria. This review aims to provide an overview of the current knowledge regarding the SUV3-containing complex and discuss its potential mechanism for tumor suppression activity.
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Affiliation(s)
- Phang-Lang Chen
- Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
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8
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Chen M, Yan R, Luo J, Ning J, Zhou R, Ding L. The Role of PGC-1α-Mediated Mitochondrial Biogenesis in Neurons. Neurochem Res 2023:10.1007/s11064-023-03934-8. [PMID: 37097395 DOI: 10.1007/s11064-023-03934-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/28/2023] [Accepted: 03/31/2023] [Indexed: 04/26/2023]
Abstract
Neurons are highly dependent on mitochondrial ATP production and Ca2+ buffering. Neurons have unique compartmentalized anatomy and energy requirements, and each compartment requires continuously renewed mitochondria to maintain neuronal survival and activity. Peroxisome proliferator-activated receptor-gamma coactivator-1α (PGC-1α) is a key factor in the regulation of mitochondrial biogenesis. It is widely accepted that mitochondria are synthesized in the cell body and transported via axons to the distal end. However, axonal mitochondrial biogenesis is necessary to maintain axonal bioenergy supply and mitochondrial density due to limitations in mitochondrial axonal transport rate and mitochondrial protein lifespan. In addition, impaired mitochondrial biogenesis leading to inadequate energy supply and neuronal damage has been observed in neurological disorders. In this review, we focus on the sites where mitochondrial biogenesis occurs in neurons and the mechanisms by which it maintains axonal mitochondrial density. Finally, we summarize several neurological disorders in which mitochondrial biogenesis is affected.
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Affiliation(s)
- Mengjie Chen
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China
| | - Ruyu Yan
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China
| | - Jiansheng Luo
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China
| | - Jiaqi Ning
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China
| | - Ruiling Zhou
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China
| | - Lingling Ding
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China.
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Xu S, Duan Y, Ma L, Song F, Tian L, Cai W, Li H. Full-Length Transcriptome Profiling of Coridius chinensis Mitochondrial Genome Reveals the Transcription of Genes with Ancestral Arrangement in Insects. Genes (Basel) 2023; 14:225. [PMID: 36672965 PMCID: PMC9859431 DOI: 10.3390/genes14010225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/13/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
Coridius chinensis (Hemiptera: Dinidoridae) is a medicinal insect. Its mitochondrial gene arrangement is consistent with that of Drosophila melanogaster and Erthesina fullo, the two insects with well-studied mitochondrial transcription. To investigate whether the structural consistency of mitochondrial genes leads to similarities in transcription and post-transcriptional processing, we improved the gene annotation and constructed a quantitative transcription map for the C. chinensis mitochondrial genome (mitogenome) using full-length transcriptome sequencing. The size of this mitogenome was 16,214 bp and the proposed model of mitochondrial transcription was similar to that of Drosophila. Both strands were nearly entirely transcribed except for the antisense genes downstream of trnS2 on N strand. The expression of cytochrome c subunit genes is higher than that of NADH-dehydrogenase subunit genes. The post-transcriptional cleavage process followed the "tRNA punctuation" model, and both the "reverse cleavage" model in Drosophila and "forward cleavage" model in E. fullo were found in C. chinensis. In addition, we found that long non-coding RNAs from the control region contained tandem repeats. Polyadenylation was performed after CCA triplet at the 3' end of tRNA. The isoform diversity of lrRNA was identified. Our study sheds light on the transcriptional regulation and RNA processing of insect mitogenomes with the putative ancestral gene arrangement.
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Affiliation(s)
| | | | | | | | | | | | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
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Gezen-Ak D, Yurttaş Z, Çamoǧlu T, Dursun E. Could Amyloid-β 1-42 or α-Synuclein Interact Directly with Mitochondrial DNA? A Hypothesis. ACS Chem Neurosci 2022; 13:2803-2812. [PMID: 36125124 PMCID: PMC9542719 DOI: 10.1021/acschemneuro.2c00512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The amyloid β (Aβ) and the α-synuclein (α-syn) are shown to be translocated into mitochondria. Even though their roles are widely investigated in pathological conditions, information on the presence and functions of Aβ and α-syn in mitochondria in endogenous levels is somewhat limited. We hypothesized that endogenous Aβ fragments or α-syn could interact with mitochondrial DNA (mtDNA) directly or influence RNAs or transcription factors in mitochondria and change the mtDNA transcription profile. In this review, we summarized clues of these possible interactions.
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Affiliation(s)
| | | | | | - Erdinç Dursun
- E.D.: email, ; phone, +90 212 414 30 00/68025, +90 533 339
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Chen K, Lu P, Beeraka NM, Sukocheva OA, Madhunapantula SV, Liu J, Sinelnikov MY, Nikolenko VN, Bulygin KV, Mikhaleva LM, Reshetov IV, Gu Y, Zhang J, Cao Y, Somasundaram SG, Kirkland CE, Fan R, Aliev G. Mitochondrial mutations and mitoepigenetics: Focus on regulation of oxidative stress-induced responses in breast cancers. Semin Cancer Biol 2022; 83:556-569. [PMID: 33035656 DOI: 10.1016/j.semcancer.2020.09.012] [Citation(s) in RCA: 113] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 02/08/2023]
Abstract
Epigenetic regulation of mitochondrial DNA (mtDNA) is an emerging and fast-developing field of research. Compared to regulation of nucler DNA, mechanisms of mtDNA epigenetic regulation (mitoepigenetics) remain less investigated. However, mitochondrial signaling directs various vital intracellular processes including aerobic respiration, apoptosis, cell proliferation and survival, nucleic acid synthesis, and oxidative stress. The later process and associated mismanagement of reactive oxygen species (ROS) cascade were associated with cancer progression. It has been demonstrated that cancer cells contain ROS/oxidative stress-mediated defects in mtDNA repair system and mitochondrial nucleoid protection. Furthermore, mtDNA is vulnerable to damage caused by somatic mutations, resulting in the dysfunction of the mitochondrial respiratory chain and energy production, which fosters further generation of ROS and promotes oncogenicity. Mitochondrial proteins are encoded by the collective mitochondrial genome that comprises both nuclear and mitochondrial genomes coupled by crosstalk. Recent reports determined the defects in the collective mitochondrial genome that are conducive to breast cancer initiation and progression. Mutational damage to mtDNA, as well as its overproliferation and deletions, were reported to alter the nuclear epigenetic landscape. Unbalanced mitoepigenetics and adverse regulation of oxidative phosphorylation (OXPHOS) can efficiently facilitate cancer cell survival. Accordingly, several mitochondria-targeting therapeutic agents (biguanides, OXPHOS inhibitors, vitamin-E analogues, and antibiotic bedaquiline) were suggested for future clinical trials in breast cancer patients. However, crosstalk mechanisms between altered mitoepigenetics and cancer-associated mtDNA mutations remain largely unclear. Hence, mtDNA mutations and epigenetic modifications could be considered as potential molecular markers for early diagnosis and targeted therapy of breast cancer. This review discusses the role of mitoepigenetic regulation in cancer cells and potential employment of mtDNA modifications as novel anti-cancer targets.
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Affiliation(s)
- Kuo Chen
- The First Affiliated Hospital of Zhengzhou University, 1 Jianshedong Street, Zhengzhou, 450052, China; Institue for Regenerative Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia
| | - Pengwei Lu
- The First Affiliated Hospital of Zhengzhou University, 1 Jianshedong Street, Zhengzhou, 450052, China
| | - Narasimha M Beeraka
- Center of Excellence in Regenerative Medicine and Molecular Biology (CEMR), Department of Biochemistry, JSS Academy of Higher Education and Research (JSS AHER), Mysuru, Karnataka, India
| | - Olga A Sukocheva
- Discipline of Health Sciences, College of Nursing and Health Sciences, Flinders University, Bedford Park, South Australia, 5042, Australia
| | - SubbaRao V Madhunapantula
- Center of Excellence in Regenerative Medicine and Molecular Biology (CEMR), Department of Biochemistry, JSS Academy of Higher Education and Research (JSS AHER), Mysuru, Karnataka, India
| | - Junqi Liu
- Cancer Center, The First Affiliated Hospital of Zhengzhou University, 1 Jianshedong Str., Zhengzhou, 450052, China
| | - Mikhail Y Sinelnikov
- Institue for Regenerative Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia
| | - Vladimir N Nikolenko
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia; Department of Normal and Topographic Anatomy, Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University (MSU), 31-5 Lomonosovsky Prospect, 117192, Moscow, Russia
| | - Kirill V Bulygin
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia; Department of Normal and Topographic Anatomy, Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University (MSU), 31-5 Lomonosovsky Prospect, 117192, Moscow, Russia
| | - Liudmila M Mikhaleva
- Research Institute of Human Morphology, 3 Tsyurupy Street, Moscow, 117418, Russian Federation
| | - Igor V Reshetov
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia
| | - Yuanting Gu
- The First Affiliated Hospital of Zhengzhou University, 1 Jianshedong Street, Zhengzhou, 450052, China
| | - Jin Zhang
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia
| | - Yu Cao
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia
| | - Siva G Somasundaram
- Department of Biological Sciences, Salem University, 223 West Main Street Salem, WV, 26426, USA
| | - Cecil E Kirkland
- Department of Biological Sciences, Salem University, 223 West Main Street Salem, WV, 26426, USA
| | - Ruitai Fan
- The First Affiliated Hospital of Zhengzhou University, 1 Jianshedong Street, Zhengzhou, 450052, China.
| | - Gjumrakch Aliev
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia; Research Institute of Human Morphology, 3 Tsyurupy Street, Moscow, 117418, Russian Federation; Institute of Physiologically Active Compounds of Russian Academy of Sciences, Severny pr. 1, Chernogolovka, Moscow Region, 142432, Russia; GALLY International Research Institute, 7733 Louis Pasteur Drive, #330, San Antonio, TX, 78229, USA
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Kozhukhar N, Spadafora D, Rodriguez YAR, Alexeyev MF. A Method for In Situ Reverse Genetic Analysis of Proteins Involved mtDNA Replication. Cells 2022; 11:2168. [PMID: 35883613 PMCID: PMC9316749 DOI: 10.3390/cells11142168] [Citation(s) in RCA: 1] [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: 06/09/2022] [Revised: 06/29/2022] [Accepted: 07/10/2022] [Indexed: 02/01/2023] Open
Abstract
The unavailability of tractable reverse genetic analysis approaches represents an obstacle to a better understanding of mitochondrial DNA replication. Here, we used CRISPR-Cas9 mediated gene editing to establish the conditional viability of knockouts in the key proteins involved in mtDNA replication. This observation prompted us to develop a set of tools for reverse genetic analysis in situ, which we called the GeneSwap approach. The technique was validated by identifying 730 amino acid (aa) substitutions in the mature human TFAM that are conditionally permissive for mtDNA replication. We established that HMG domains of TFAM are functionally independent, which opens opportunities for engineering chimeric TFAMs with customized properties for studies on mtDNA replication, mitochondrial transcription, and respiratory chain function. Finally, we present evidence that the HMG2 domain plays the leading role in TFAM species-specificity, thus indicating a potential pathway for TFAM-mtDNA evolutionary co-adaptations.
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Affiliation(s)
| | | | | | - Mikhail F. Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA; (N.K.); (D.S.); (Y.A.R.R.)
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13
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Miranda M, Bonekamp NA, Kühl I. Starting the engine of the powerhouse: mitochondrial transcription and beyond. Biol Chem 2022; 403:779-805. [PMID: 35355496 DOI: 10.1515/hsz-2021-0416] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 03/09/2022] [Indexed: 12/25/2022]
Abstract
Mitochondria are central hubs for cellular metabolism, coordinating a variety of metabolic reactions crucial for human health. Mitochondria provide most of the cellular energy via their oxidative phosphorylation (OXPHOS) system, which requires the coordinated expression of genes encoded by both the nuclear (nDNA) and mitochondrial genomes (mtDNA). Transcription of mtDNA is not only essential for the biogenesis of the OXPHOS system, but also generates RNA primers necessary to initiate mtDNA replication. Like the prokaryotic system, mitochondria have no membrane-based compartmentalization to separate the different steps of mtDNA maintenance and expression and depend entirely on nDNA-encoded factors imported into the organelle. Our understanding of mitochondrial transcription in mammalian cells has largely progressed, but the mechanisms regulating mtDNA gene expression are still poorly understood despite their profound importance for human disease. Here, we review mechanisms of mitochondrial gene expression with a focus on the recent findings in the field of mammalian mtDNA transcription and disease phenotypes caused by defects in proteins involved in this process.
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Affiliation(s)
- Maria Miranda
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, D-50931, Germany
| | - Nina A Bonekamp
- Department of Neuroanatomy, Mannheim Center for Translational Neurosciences (MCTN), Medical Faculty Mannheim, Heidelberg University, Mannheim, D-68167, Germany
| | - Inge Kühl
- Department of Cell Biology, Institute of Integrative Biology of the Cell (I2BC), UMR9198, CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, F-91190, France
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14
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Kong Q, Yan X, Cheng M, Jiang X, Xu L, Shen L, Yu H, Sun L. p62 Promotes the Mitochondrial Localization of p53 through Its UBA Domain and Participates in Regulating the Sensitivity of Ovarian Cancer Cells to Cisplatin. Int J Mol Sci 2022; 23:ijms23063290. [PMID: 35328718 PMCID: PMC8949157 DOI: 10.3390/ijms23063290] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/05/2022] [Accepted: 03/16/2022] [Indexed: 02/06/2023] Open
Abstract
Chemotherapeutic drug-induced p53-dependent crosstalk among tumor cells affects the sensitivity of tumor cells to chemotherapeutic drugs, contributing to chemoresistance. Therefore, pharmacological targeting of p53 may contribute to overcoming drug resistance. The localization of p53 is closely related to its function. Thus, we assessed the effect of p62 on the coordination of p53 mitochondrial localization under chemotherapeutic drug treatment in ovarian cancer cells. We found that the combined use of the proteasome inhibitor epoxomicin and cisplatin led to the accumulation of p53 and sequestosome1(p62) in the mitochondria, downregulated mitochondrial DNA (mtDNA) transcription, inhibited mitochondrial functions, and ultimately promoted apoptosis by enhancing cisplatin sensitivity in ovarian cancer cells. Moreover, the ubiquitin-associated (UBA) domain of p62 was involved in regulating the mitochondrial localization of p53. Our findings suggest that the interaction between p62 and p53 may be a mechanism that determines the fate of tumor cells. In conclusion, p62 coordinated the mitochondrial localization of p53 through its UBA domain, inhibited mtDNA transcription, downregulated mitochondrial function, and promoted ovarian cancer cell death. Our study demonstrates the important role of p53 localization in tumor cell survival and apoptosis, and provides new insights into understanding the anti-tumor mechanism of targeting the ubiquitin–proteasome system in tumor cells.
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Affiliation(s)
- Qinghuan Kong
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (Q.K.); (X.Y.); (M.C.); (L.X.); (L.S.)
| | - Xiaoyu Yan
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (Q.K.); (X.Y.); (M.C.); (L.X.); (L.S.)
| | - Meiyu Cheng
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (Q.K.); (X.Y.); (M.C.); (L.X.); (L.S.)
| | - Xin Jiang
- Department of Biochemistry, College of Basic Medical Sciences, Jilin University, Changchun 130021, China;
| | - Long Xu
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (Q.K.); (X.Y.); (M.C.); (L.X.); (L.S.)
| | - Luyan Shen
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (Q.K.); (X.Y.); (M.C.); (L.X.); (L.S.)
| | - Huimei Yu
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (Q.K.); (X.Y.); (M.C.); (L.X.); (L.S.)
- Correspondence: (H.Y.); (L.S.); Tel.: +86-0-431-8561-9485 or +86-0-431-8561-9110 (H.Y. & L.S.)
| | - Liankun Sun
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (Q.K.); (X.Y.); (M.C.); (L.X.); (L.S.)
- Correspondence: (H.Y.); (L.S.); Tel.: +86-0-431-8561-9485 or +86-0-431-8561-9110 (H.Y. & L.S.)
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15
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Guitton R, Dölle C, Alves G, Ole-Bjørn T, Nido GS, Tzoulis C. Ultra-deep whole genome bisulfite sequencing reveals a single methylation hotspot in human brain mitochondrial DNA. Epigenetics 2022; 17:906-921. [PMID: 35253628 PMCID: PMC9423827 DOI: 10.1080/15592294.2022.2045754] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
While DNA methylation is established as a major regulator of gene expression in the nucleus, the existence of mitochondrial DNA (mtDNA) methylation remains controversial. Here, we characterized the mtDNA methylation landscape in the prefrontal cortex of neurological healthy individuals (n=26) and patients with Parkinson’s disease (n=27), using a combination of whole-genome bisulphite sequencing (WGBS) and bisulphite-independent methods. Accurate mtDNA mapping from WGBS data required alignment to an mtDNA reference only, to avoid misalignment to nuclear mitochondrial pseudogenes. Once correctly aligned, WGBS data provided ultra-deep mtDNA coverage (16,723 ± 7,711) and revealed overall very low levels of cytosine methylation. The highest methylation levels (5.49 ± 0.97%) were found on CpG position m.545, located in the heavy-strand promoter 1 region. The m.545 methylation was validated using a combination of methylation-sensitive DNA digestion and quantitative PCR analysis. We detected no association between mtDNA methylation profile and Parkinson’s disease. Interestingly, m.545 methylation correlated with the levels of mtDNA transcripts, suggesting a putative role in regulating mtDNA gene expression. In addition, we propose a robust framework for methylation analysis of mtDNA from WGBS data, which is less prone to false-positive findings due to misalignment of nuclear mitochondrial pseudogene sequences.
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Affiliation(s)
- Romain Guitton
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Christian Dölle
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Guido Alves
- The Norwegian Centre for Movement Disorders and Department of Neurology, Stavanger University Hospital, Stavanger, Norway.,Department of Mathematics and Natural Sciences, University of Stavanger, University of Bergen, Stavanger, Norway
| | - Tysnes Ole-Bjørn
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Gonzalo S Nido
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Charalampos Tzoulis
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Medicine, University of Bergen, Bergen, Norway
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16
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Jerome MS, Kuthethur R, Kabekkodu SP, Chakrabarty S. Regulation of mitochondrial function by forkhead transcription factors. Biochimie 2022; 198:96-108. [PMID: 35367579 DOI: 10.1016/j.biochi.2022.03.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 03/09/2022] [Accepted: 03/29/2022] [Indexed: 02/06/2023]
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17
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Picca A, Guerra F, Calvani R, Romano R, Coelho-Junior HJ, Damiano FP, Bucci C, Marzetti E. Circulating Mitochondrial DNA and Inter-Organelle Contact Sites in Aging and Associated Conditions. Cells 2022; 11:cells11040675. [PMID: 35203322 PMCID: PMC8870554 DOI: 10.3390/cells11040675] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 02/07/2023] Open
Abstract
Mitochondria are primarily involved in cell bioenergetics, regulation of redox homeostasis, and cell death/survival signaling. An immunostimulatory property of mitochondria has also been recognized which is deployed through the extracellular release of entire or portioned organelle and/or mitochondrial DNA (mtDNA) unloading. Dynamic homo- and heterotypic interactions involving mitochondria have been described. Each type of connection has functional implications that eventually optimize mitochondrial activity according to the bioenergetic demands of a specific cell/tissue. Inter-organelle communications may also serve as molecular platforms for the extracellular release of mitochondrial components and subsequent ignition of systemic inflammation. Age-related chronic inflammation (inflamm-aging) has been associated with mitochondrial dysfunction and increased extracellular release of mitochondrial components—in particular, cell-free mtDNA. The close relationship between mitochondrial dysfunction and cellular senescence further supports the central role of mitochondria in the aging process and its related conditions. Here, we provide an overview of (1) the mitochondrial genetic system and the potential routes for generating and releasing mtDNA intermediates; (2) the pro-inflammatory pathways elicited by circulating mtDNA; (3) the participation of inter-organelle contacts to mtDNA homeostasis; and (4) the link of these processes with senescence and age-associated conditions.
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Affiliation(s)
- Anna Picca
- Fondazione Policlinico Universitario “Agostino Gemelli” IRCCS, 00168 Rome, Italy; (A.P.); (F.P.D.); (E.M.)
| | - Flora Guerra
- Department of Biological and Environmental Sciences and Technologies, Università del Salento, 73100 Lecce, Italy; (F.G.); (R.R.); (C.B.)
| | - Riccardo Calvani
- Fondazione Policlinico Universitario “Agostino Gemelli” IRCCS, 00168 Rome, Italy; (A.P.); (F.P.D.); (E.M.)
- Correspondence: ; Tel.: +39-06-3015-5559; Fax: +39-06-3051-911
| | - Roberta Romano
- Department of Biological and Environmental Sciences and Technologies, Università del Salento, 73100 Lecce, Italy; (F.G.); (R.R.); (C.B.)
| | - Hélio José Coelho-Junior
- Department of Geriatrics and Orthopedics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy;
| | - Francesco P. Damiano
- Fondazione Policlinico Universitario “Agostino Gemelli” IRCCS, 00168 Rome, Italy; (A.P.); (F.P.D.); (E.M.)
| | - Cecilia Bucci
- Department of Biological and Environmental Sciences and Technologies, Università del Salento, 73100 Lecce, Italy; (F.G.); (R.R.); (C.B.)
| | - Emanuele Marzetti
- Fondazione Policlinico Universitario “Agostino Gemelli” IRCCS, 00168 Rome, Italy; (A.P.); (F.P.D.); (E.M.)
- Department of Geriatrics and Orthopedics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy;
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18
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Ruple BA, Godwin JS, Mesquita PHC, Osburn SC, Vann CG, Lamb DA, Sexton CL, Candow DG, Forbes SC, Frugé AD, Kavazis AN, Young KC, Seaborne RA, Sharples AP, Roberts MD. Resistance training rejuvenates the mitochondrial methylome in aged human skeletal muscle. FASEB J 2021; 35:e21864. [PMID: 34423880 DOI: 10.1096/fj.202100873rr] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 11/11/2022]
Abstract
Resistance training (RT) dynamically alters the skeletal muscle nuclear DNA methylome. However, no study has examined if RT affects the mitochondrial DNA (mtDNA) methylome. Herein, ten older, Caucasian untrained males (65 ± 7 y.o.) performed six weeks of full-body RT (twice weekly). Body composition and knee extensor torque were assessed prior to and 72 h following the last RT session. Vastus lateralis (VL) biopsies were also obtained. VL DNA was subjected to reduced representation bisulfite sequencing providing excellent coverage across the ~16-kilobase mtDNA methylome (254 CpG sites). Biochemical assays were also performed, and older male data were compared to younger trained males (22 ± 2 y.o., n = 7, n = 6 Caucasian & n = 1 African American). RT increased whole-body lean tissue mass (p = .017), VL thickness (p = .012), and knee extensor torque (p = .029) in older males. RT also affected the mtDNA methylome, as 63% (159/254) of the CpG sites demonstrated reduced methylation (p < .05). Several mtDNA sites presented a more "youthful" signature in older males after RT in comparison to younger males. The 1.12 kilobase mtDNA D-loop/control region, which regulates replication and transcription, possessed enriched hypomethylation in older males following RT. Enhanced expression of mitochondrial H- and L-strand genes and complex III/IV protein levels were also observed (p < .05). While limited to a shorter-term intervention, this is the first evidence showing that RT alters the mtDNA methylome in skeletal muscle. Observed methylome alterations may enhance mitochondrial transcription, and RT evokes mitochondrial methylome profiles to mimic younger men. The significance of these findings relative to broader RT-induced epigenetic changes needs to be elucidated.
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Affiliation(s)
- Bradley A Ruple
- School of Kinesiology, Auburn University, Auburn, Alabama, USA
| | - Joshua S Godwin
- School of Kinesiology, Auburn University, Auburn, Alabama, USA
| | | | - Shelby C Osburn
- School of Kinesiology, Auburn University, Auburn, Alabama, USA
| | | | - Donald A Lamb
- Department of Nutrition, Dietetics and Hospitality Management, Auburn University, Auburn, Alabama, USA
| | - Casey L Sexton
- School of Kinesiology, Auburn University, Auburn, Alabama, USA
| | - Darren G Candow
- Faculty of Kinesiology and Health Studies, University of Regina, Regina, Saskatchewan, Canada
| | - Scott C Forbes
- Faculty of Education, Department of Physical Education Studies, Brandon University, Brandon, Manitoba, Canada
| | - Andrew D Frugé
- Department of Nutrition, Dietetics and Hospitality Management, Auburn University, Auburn, Alabama, USA
| | | | - Kaelin C Young
- School of Kinesiology, Auburn University, Auburn, Alabama, USA.,Edward Via College of Osteopathic Medicine, Auburn, Alabama, USA
| | - Robert A Seaborne
- Centre for Genomics and Child Health, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Adam P Sharples
- Institute for Physical Performance, Norwegian School of Sport Sciences, Olso, Norway
| | - Michael D Roberts
- School of Kinesiology, Auburn University, Auburn, Alabama, USA.,Edward Via College of Osteopathic Medicine, Auburn, Alabama, USA
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19
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Exploring the Ability of LARS2 Carboxy-Terminal Domain in Rescuing the MELAS Phenotype. Life (Basel) 2021; 11:life11070674. [PMID: 34357047 PMCID: PMC8303833 DOI: 10.3390/life11070674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 12/25/2022] Open
Abstract
The m.3243A>G mutation within the mitochondrial mt-tRNALeu(UUR) gene is the most prevalent variant linked to mitochondrial encephalopathy with lactic acidosis and stroke-like episodes (MELAS) syndrome. This pathogenic mutation causes severe impairment of mitochondrial protein synthesis due to alterations of the mutated tRNA, such as reduced aminoacylation and a lack of post-transcriptional modification. In transmitochondrial cybrids, overexpression of human mitochondrial leucyl-tRNA synthetase (LARS2) has proven effective in rescuing the phenotype associated with m.3243A>G substitution. The rescuing activity resides in the carboxy-terminal domain (Cterm) of the enzyme; however, the precise molecular mechanisms underlying this process have not been fully elucidated. To deepen our knowledge on the rescuing mechanisms, we demonstrated the interactions of the Cterm with mutated mt-tRNALeu(UUR) and its precursor in MELAS cybrids. Further, the effect of Cterm expression on mitochondrial functions was evaluated. We found that Cterm ameliorates de novo mitochondrial protein synthesis, whilst it has no effect on mt-tRNALeu(UUR) steady-state levels and aminoacylation. Despite the complete recovery of cell viability and the increase in mitochondrial translation, Cterm-overexpressing cybrids were not able to recover bioenergetic competence. These data suggest that, in our MELAS cell model, the beneficial effect of Cterm may be mediated by factors that are independent of the mitochondrial bioenergetics.
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20
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Moorey SE, Monnig JM, Smith MF, Ortega MS, Green JA, Pohler KG, Bridges GA, Behura SK, Geary TW. Differential Transcript Profiles in Cumulus-Oocyte Complexes Originating from Pre-Ovulatory Follicles of Varied Physiological Maturity in Beef Cows. Genes (Basel) 2021; 12:genes12060893. [PMID: 34200628 PMCID: PMC8227736 DOI: 10.3390/genes12060893] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 05/27/2021] [Accepted: 05/27/2021] [Indexed: 12/13/2022] Open
Abstract
Small dominant follicle diameter at induced ovulation, but not at spontaneous ovulation, decreased pregnancy rate, fertilization rate, and day seven embryo quality in beef cows. We hypothesized that the physiological status of the follicle at GnRH-induced ovulation has a direct effect on the transcriptome of the Cumulus-Oocyte complex, thereby affecting oocyte competence and subsequent embryo development. The objective of this study was to determine if the transcriptome of oocytes and associated cumulus cells (CC) differed among small (≤11.7 mm) and large follicles (≥12.7 mm) exposed to a GnRH-induced gonadotropin surge and follicles (11.7–14.0 mm) exposed to an endogenous gonadotropin surge (spontaneous follicles). RNA sequencing data, from pools of four oocytes or their corresponding CC, revealed 69, 94, and 83 differentially expressed gene transcripts (DEG) among oocyte pools from small versus large, small versus spontaneous, and large versus spontaneous follicle classifications, respectively. An additional 128, 98, and 80 DEG were identified among small versus large, small versus spontaneous, and large versus spontaneous follicle CC pools, respectively. The biological pathway “oxidative phosphorylation” was significantly enriched with DEG from small versus spontaneous follicle oocyte pools (FDR < 0.01); whereas the glycolytic pathway was significantly enriched with DEG from CC pools obtained from large versus small follicles (FDR < 0.01). These findings collectively suggest that altered carbohydrate metabolism within the Cumulus-Oocyte complex likely contributes to the decreased competency of oocytes from small pre-ovulatory follicles exposed to an exogenous GnRH-induced gonadotropin surge.
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Affiliation(s)
- Sarah E. Moorey
- Department of Animal Science, University of Tennessee, Knoxville, TN 37996, USA
- Correspondence:
| | - Jenna M. Monnig
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA; (J.M.M.); (M.F.S.); (M.S.O.); (J.A.G.); (S.K.B.)
| | - Michael F. Smith
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA; (J.M.M.); (M.F.S.); (M.S.O.); (J.A.G.); (S.K.B.)
| | - M. Sofia Ortega
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA; (J.M.M.); (M.F.S.); (M.S.O.); (J.A.G.); (S.K.B.)
| | - Jonathan A. Green
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA; (J.M.M.); (M.F.S.); (M.S.O.); (J.A.G.); (S.K.B.)
| | - Ky G. Pohler
- Department of Animal Science, Texas A&M University, College Station, TX 77843, USA;
| | - G. Alan Bridges
- Department of Animal Science, University of Minnesota, St. Paul, MN 55108, USA;
| | - Susanta K. Behura
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA; (J.M.M.); (M.F.S.); (M.S.O.); (J.A.G.); (S.K.B.)
| | - Thomas W. Geary
- USDA-ARS Fort Keogh Livestock and Range Research Lab, Miles City, MT 59301, USA;
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21
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Jamwal S, Blackburn JK, Elsworth JD. PPARγ/PGC1α signaling as a potential therapeutic target for mitochondrial biogenesis in neurodegenerative disorders. Pharmacol Ther 2021; 219:107705. [PMID: 33039420 PMCID: PMC7887032 DOI: 10.1016/j.pharmthera.2020.107705] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022]
Abstract
Neurodegenerative diseases represent some of the most devastating neurological disorders, characterized by progressive loss of the structure and function of neurons. Current therapy for neurodegenerative disorders is limited to symptomatic treatment rather than disease modifying interventions, emphasizing the desperate need for improved approaches. Abundant evidence indicates that impaired mitochondrial function plays a crucial role in pathogenesis of many neurodegenerative diseases and so biochemical factors in mitochondria are considered promising targets for pharmacological-based therapies. Peroxisome proliferator-activated receptors-γ (PPARγ) are ligand-inducible transcription factors involved in regulating various genes including peroxisome proliferator-activated receptor gamma co-activator-1 alpha (PGC1α). This review summarizes the evidence supporting the ability of PPARγ-PGC1α to coordinately up-regulate the expression of genes required for mitochondrial biogenesis in neurons and provide directions for future work to explore the potential benefit of targeting mitochondrial biogenesis in neurodegenerative disorders. We have highlighted key roles of NRF2, uncoupling protein-2 (UCP2), and paraoxonase-2 (PON2) signaling in mediating PGC1α-induced mitochondrial biogenesis. In addition, the status of PPARγ modulators being used in clinical trials for Parkinson's disease (PD), Alzheimer's disease (AD) and Huntington's disease (HD) has been compiled. The overall purpose of this review is to update and critique our understanding of the role of PPARγ-PGC1α-NRF2 in the induction of mitochondrial biogenesis together with suggestions for strategies to target PPARγ-PGC1α-NRF2 signaling in order to combat mitochondrial dysfunction in neurodegenerative disorders.
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Affiliation(s)
- Sumit Jamwal
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Jennifer K Blackburn
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06511, USA
| | - John D Elsworth
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06511, USA.
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22
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Kim J, Choi JW, Namkung J. Expression Profile of Mouse Gm20594, Nuclear-Encoded Humanin-Like Gene. J Lifestyle Med 2021; 11:13-22. [PMID: 33763338 PMCID: PMC7957044 DOI: 10.15280/jlm.2021.11.1.13] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 11/29/2020] [Indexed: 12/21/2022] Open
Abstract
Background Mitochondrial-derived peptides (MDPs) such as MOTS-c and humanin have been studied for their cytoprotective functions. In mice, humanin-encoding Mtrnr2 is a mitochondrial pseudogene, and the humanin-like peptide is encoded by the nuclear Gm20594 gene. However, endogenous tissue-specific expression profiles of Gm20594 have not yet been identified. Methods Mtrnr1 and Gm20594 expression was profiled via reverse transcription using only oligo(dT) primers from tissues of C57BL6/J mice. To analyze altered expression upon mitochondrial biogenesis, C2C12 myocytes and brown adipocytes were differentiated. Mitochondrial DNA copy numbers were quantified for normalization. Results Both Mtrnr1 and Gm20594 were highly expressed in brown adipose tissue. When normalized against mitochondrial content, Mtrnr1 was identified as being highly expressed in the duodenum, followed by the jejunum. In models of mitochondrial biogenesis, both Mtrnr1 and Gm20594 were upregulated during myocyte and brown adipocyte differentiation. Increased Mtrnr1 expression during brown adipocyte differentiation remained significant after normalization against mitochondrial DNA copy number, whereas myocyte differentiation exhibited biphasic upregulation and downregulation in early and late phases, respectively. Conclusion Nuclear-encoded Gm20594 showed similar expression patterns of mitochondrial-encoded Mtrnr1. Brown adipose tissue presented the highest basal expression levels of Gm20594 and Mtrnr1. When normalized against mitochondrial DNA copy number, gut tissues exhibited the highest expression of Mtrnr1. Upregulation of Mtrnr1 during mitochondrial biogenesis is independent of mitochondrial content.
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Affiliation(s)
- Jihye Kim
- Department of Biochemistry, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Jong-Whan Choi
- Department of Biochemistry, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Jun Namkung
- Department of Biochemistry, Yonsei University Wonju College of Medicine, Wonju, Korea
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23
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Oliveira GL, Coelho AR, Marques R, Oliveira PJ. Cancer cell metabolism: Rewiring the mitochondrial hub. Biochim Biophys Acta Mol Basis Dis 2020; 1867:166016. [PMID: 33246010 DOI: 10.1016/j.bbadis.2020.166016] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/12/2020] [Accepted: 11/15/2020] [Indexed: 12/15/2022]
Abstract
To adapt to tumoral environment conditions or even to escape chemotherapy, cells rapidly reprogram their metabolism to handle adversities and survive. Given the rapid rise of studies uncovering novel insights and therapeutic opportunities based on the role of mitochondria in tumor metabolic programing and therapeutics, this review summarizes most significant developments in the field. Taking in mind the key role of mitochondria on carcinogenesis and tumor progression due to their involvement on tumor plasticity, metabolic remodeling, and signaling re-wiring, those organelles are also potential therapeutic targets. Among other topics, we address the recent data intersecting mitochondria as of prognostic value and staging in cancer, by mitochondrial DNA (mtDNA) determination, and current inhibitors developments targeting mtDNA, OXPHOS machinery and metabolic pathways. We contribute for a holistic view of the role of mitochondria metabolism and directed therapeutics to understand tumor metabolism, to circumvent therapy resistance, and to control tumor development.
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Affiliation(s)
- Gabriela L Oliveira
- CNC-Center for Neuroscience and Cell Biology, UC-Biotech, University of Coimbra, Biocant Park, Cantanhede, Portugal
| | - Ana R Coelho
- CNC-Center for Neuroscience and Cell Biology, UC-Biotech, University of Coimbra, Biocant Park, Cantanhede, Portugal
| | - Ricardo Marques
- CNC-Center for Neuroscience and Cell Biology, UC-Biotech, University of Coimbra, Biocant Park, Cantanhede, Portugal
| | - Paulo J Oliveira
- CNC-Center for Neuroscience and Cell Biology, UC-Biotech, University of Coimbra, Biocant Park, Cantanhede, Portugal.
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24
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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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25
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Mitochondrial OXPHOS Biogenesis: Co-Regulation of Protein Synthesis, Import, and Assembly Pathways. Int J Mol Sci 2020; 21:ijms21113820. [PMID: 32481479 PMCID: PMC7312649 DOI: 10.3390/ijms21113820] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/21/2020] [Accepted: 05/25/2020] [Indexed: 02/07/2023] Open
Abstract
The assembly of mitochondrial oxidative phosphorylation (OXPHOS) complexes is an intricate process, which—given their dual-genetic control—requires tight co-regulation of two evolutionarily distinct gene expression machineries. Moreover, fine-tuning protein synthesis to the nascent assembly of OXPHOS complexes requires regulatory mechanisms such as translational plasticity and translational activators that can coordinate mitochondrial translation with the import of nuclear-encoded mitochondrial proteins. The intricacy of OXPHOS complex biogenesis is further evidenced by the requirement of many tightly orchestrated steps and ancillary factors. Early-stage ancillary chaperones have essential roles in coordinating OXPHOS assembly, whilst late-stage assembly factors—also known as the LYRM (leucine–tyrosine–arginine motif) proteins—together with the mitochondrial acyl carrier protein (ACP)—regulate the incorporation and activation of late-incorporating OXPHOS subunits and/or co-factors. In this review, we describe recent discoveries providing insights into the mechanisms required for optimal OXPHOS biogenesis, including the coordination of mitochondrial gene expression with the availability of nuclear-encoded factors entering via mitochondrial protein import systems.
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26
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Stotland AB, Spivia W, Orosco A, Andres AM, Gottlieb RA, Van Eyk JE, Parker SJ. MitoPlex: A targeted multiple reaction monitoring assay for quantification of a curated set of mitochondrial proteins. J Mol Cell Cardiol 2020; 142:1-13. [PMID: 32234390 PMCID: PMC7347090 DOI: 10.1016/j.yjmcc.2020.03.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 12/21/2022]
Abstract
Mitochondria are the major source of cellular energy (ATP), as well as critical mediators of widespread functions such as cellular redox balance, apoptosis, and metabolic flux. The organelles play an especially important role in the maintenance of cardiac homeostasis; their inability to generate ATP following impairment due to ischemic damage has been directly linked to organ failure. Methods to quantify mitochondrial content are limited to low throughput immunoassays, measurement of mitochondrial DNA, or relative quantification by untargeted mass spectrometry. Here, we present a high throughput, reproducible and quantitative mass spectrometry multiple reaction monitoring based assay of 37 proteins critical to central carbon chain metabolism and overall mitochondrial function termed 'MitoPlex'. We coupled this protein multiplex with a parallel analysis of the central carbon chain metabolites (219 metabolite assay) extracted in tandem from the same sample, be it cells or tissue. In tests of its biological applicability in cells and tissues, "MitoPlex plus metabolites" indicated profound effects of HMG-CoA Reductase inhibition (e.g., statin treatment) on mitochondria of i) differentiating C2C12 skeletal myoblasts, as well as a clear opposite trend of statins to promote mitochondrial protein expression and metabolism in heart and liver, while suppressing mitochondrial protein and ii) aspects of metabolism in the skeletal muscle obtained from C57Bl6 mice. Our results not only reveal new insights into the metabolic effect of statins in skeletal muscle, but present a new high throughput, reliable MS-based tool to study mitochondrial dynamics in both cell culture and in vivo models.
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Affiliation(s)
- Aleksandr B Stotland
- Molecular Cardiobiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Weston Spivia
- Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Amanda Orosco
- Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Allen M Andres
- Molecular Cardiobiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Roberta A Gottlieb
- Molecular Cardiobiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Sarah J Parker
- Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America.
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27
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Reynolds JC, Bwiza CP, Lee C. Mitonuclear genomics and aging. Hum Genet 2020; 139:381-399. [PMID: 31997134 PMCID: PMC7147958 DOI: 10.1007/s00439-020-02119-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 01/17/2020] [Indexed: 12/25/2022]
Abstract
Our cells operate based on two distinct genomes that are enclosed in the nucleus and mitochondria. The mitochondrial genome presumably originates from endosymbiotic bacteria. With time, a large portion of the original genes in the bacterial genome is considered to have been lost or transferred to the nuclear genome, leaving a reduced 16.5 Kb circular mitochondrial DNA (mtDNA). Traditionally only 37 genes, including 13 proteins, were thought to be encoded within mtDNA, its genetic repertoire is expanding with the identification of mitochondrial-derived peptides (MDPs). The biology of aging has been largely unveiled to be regulated by genes that are encoded in the nuclear genome, whereas the mitochondrial genome remained more cryptic. However, recent studies position mitochondria and mtDNA as an important counterpart to the nuclear genome, whereby the two organelles constantly regulate each other. Thus, the genomic network that regulates lifespan and/or healthspan is likely constituted by two unique, yet co-evolved, genomes. Here, we will discuss aspects of mitochondrial biology, especially mitochondrial communication that may add substantial momentum to aging research by accounting for both mitonuclear genomes to more comprehensively and inclusively map the genetic and molecular networks that govern aging and age-related diseases.
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Affiliation(s)
- Joseph C Reynolds
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Conscience P Bwiza
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Changhan Lee
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA.
- USC Norris Comprehensive Cancer Center, Los Angeles, CA, 90089, USA.
- Biomedical Sciences, Graduate School, Ajou University, Suwon, 16499, South Korea.
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28
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Alexeyev M. On separation and coding capacity of mtDNA strands. Protein Sci 2020; 29:1070. [PMID: 32057149 DOI: 10.1002/pro.3840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 02/12/2020] [Indexed: 11/06/2022]
Affiliation(s)
- Mikhail Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, Alabama
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29
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Dong Z, Pu L, Cui H. Mitoepigenetics and Its Emerging Roles in Cancer. Front Cell Dev Biol 2020; 8:4. [PMID: 32039210 PMCID: PMC6989428 DOI: 10.3389/fcell.2020.00004] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/08/2020] [Indexed: 12/11/2022] Open
Abstract
In human beings, there is a ∼16,569 bp circular mitochondrial DNA (mtDNA) encoding 22 tRNAs, 12S and 16S rRNAs, 13 polypeptides that constitute the central core of ETC/OxPhos complexes, and some non-coding RNAs. Recently, mtDNA has been shown to have some covalent modifications such as methylation or hydroxylmethylation, which play pivotal epigenetic roles in mtDNA replication and transcription. Post-translational modifications of proteins in mitochondrial nucleoids such as mitochondrial transcription factor A (TFAM) also emerge as essential epigenetic modulations in mtDNA replication and transcription. Post-transcriptional modifications of mitochondrial RNAs (mtRNAs) including mt-rRNAs, mt-tRNAs and mt-mRNAs are important epigenetic modulations. Besides, mtDNA or nuclear DNA (n-DNA)-derived non-coding RNAs also play important roles in the regulation of translation and function of mitochondrial genes. These evidences introduce a novel concept of mitoepigenetics that refers to the study of modulations in the mitochondria that alter heritable phenotype in mitochondria itself without changing the mtDNA sequence. Since mitochondrial dysfunction contributes to carcinogenesis and tumor development, mitoepigenetics is also essential for cancer. Understanding the mode of actions of mitoepigenetics in cancers may shade light on the clinical diagnosis and prevention of these diseases. In this review, we summarize the present study about modifications in mtDNA, mtRNA and nucleoids and modulations of mtDNA/nDNA-derived non-coding RNAs that affect mtDNA translation/function, and overview recent studies of mitoepigenetic alterations in cancer.
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Affiliation(s)
- Zhen Dong
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China.,Cancer Center, Medical Research Institute, Southwest University, Chongqing, China.,Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, China.,Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Chongqing, China
| | - Longjun Pu
- Umeå Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China.,Cancer Center, Medical Research Institute, Southwest University, Chongqing, China.,Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, China.,Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Chongqing, China
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30
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Sharma A, Smith HJ, Yao P, Mair WB. Causal roles of mitochondrial dynamics in longevity and healthy aging. EMBO Rep 2019; 20:e48395. [PMID: 31667999 DOI: 10.15252/embr.201948395] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 07/24/2019] [Accepted: 10/09/2019] [Indexed: 12/14/2022] Open
Abstract
Mitochondria are organized in the cell in the form of a dynamic, interconnected network. Mitochondrial dynamics, regulated by mitochondrial fission, fusion, and trafficking, ensure restructuring of this complex reticulum in response to nutrient availability, molecular signals, and cellular stress. Aberrant mitochondrial structures have long been observed in aging and age-related diseases indicating that mitochondrial dynamics are compromised as cells age. However, the specific mechanisms by which aging affects mitochondrial dynamics and whether these changes are causally or casually associated with cellular and organismal aging is not clear. Here, we review recent studies that show specifically how mitochondrial fission, fusion, and trafficking are altered with age. We discuss factors that change with age to directly or indirectly influence mitochondrial dynamics while examining causal roles for altered mitochondrial dynamics in healthy aging and underlying functional outputs that might affect longevity. Lastly, we propose that altered mitochondrial dynamics might not just be a passive consequence of aging but might constitute an adaptive mechanism to mitigate age-dependent cellular impairments and might be targeted to increase longevity and promote healthy aging.
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Affiliation(s)
- Arpit Sharma
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Hannah J Smith
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Pallas Yao
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - William B Mair
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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31
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Sharma N, Pasala MS, Prakash A. Mitochondrial DNA: Epigenetics and environment. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2019; 60:668-682. [PMID: 31335990 PMCID: PMC6941438 DOI: 10.1002/em.22319] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/08/2019] [Accepted: 07/11/2019] [Indexed: 05/22/2023]
Abstract
Maintenance of the mitochondrial genome is essential for proper cellular function. For this purpose, mitochondrial DNA (mtDNA) needs to be faithfully replicated, transcribed, translated, and repaired in the face of constant onslaught from endogenous and environmental agents. Although only 13 polypeptides are encoded within mtDNA, the mitochondrial proteome comprises over 1500 proteins that are encoded by nuclear genes and translocated to the mitochondria for the purpose of maintaining mitochondrial function. Regulation of mtDNA and mitochondrial proteins by epigenetic changes and post-translational modifications facilitate crosstalk between the nucleus and the mitochondria and ultimately lead to the maintenance of cellular health and homeostasis. DNA methyl transferases have been identified in the mitochondria implicating that methylation occurs within this organelle; however, the extent to which mtDNA is methylated has been debated for many years. Mechanisms of demethylation within this organelle have also been postulated, but the exact mechanisms and their outcomes is still an active area of research. Mitochondrial dysfunction in the form of altered gene expression and ATP production, resulting from epigenetic changes, can lead to various conditions including aging-related neurodegenerative disorders, altered metabolism, changes in circadian rhythm, and cancer. Here, we provide an overview of the epigenetic regulation of mtDNA via methylation, long and short noncoding RNAs, and post-translational modifications of nucleoid proteins (as mitochondria lack histones). We also highlight the influence of xenobiotics such as airborne environmental pollutants, contamination from heavy metals, and therapeutic drugs on mtDNA methylation. Environ. Mol. Mutagen., 60:668-682, 2019. © 2019 Wiley Periodicals, Inc.
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32
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Niazi AK, Delannoy E, Iqbal RK, Mileshina D, Val R, Gabryelska M, Wyszko E, Soubigou-Taconnat L, Szymanski M, Barciszewski J, Weber-Lotfi F, Gualberto JM, Dietrich A. Mitochondrial Transcriptome Control and Intercompartment Cross-Talk During Plant Development. Cells 2019; 8:E583. [PMID: 31200566 PMCID: PMC6627697 DOI: 10.3390/cells8060583] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 06/03/2019] [Accepted: 06/11/2019] [Indexed: 01/17/2023] Open
Abstract
We address here organellar genetic regulation and intercompartment genome coordination. We developed earlier a strategy relying on a tRNA-like shuttle to mediate import of nuclear transgene-encoded custom RNAs into mitochondria in plants. In the present work, we used this strategy to drive trans-cleaving hammerhead ribozymes into the organelles, to knock down specific mitochondrial RNAs and analyze the regulatory impact. In a similar approach, the tRNA mimic was used to import into mitochondria in Arabidopsis thaliana the orf77, an RNA associated with cytoplasmic male sterility in maize and possessing sequence identities with the atp9 mitochondrial RNA. In both cases, inducible expression of the transgenes allowed to characterise early regulation and signaling responses triggered by these respective manipulations of the organellar transcriptome. The results imply that the mitochondrial transcriptome is tightly controlled by a "buffering" mechanism at the early and intermediate stages of plant development, a control that is released at later stages. On the other hand, high throughput analyses showed that knocking down a specific mitochondrial mRNA triggered a retrograde signaling and an anterograde nuclear transcriptome response involving a series of transcription factor genes and small RNAs. Our results strongly support transcriptome coordination mechanisms within the organelles and between the organelles and the nucleus.
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Affiliation(s)
- Adnan Khan Niazi
- Institute of Plant Molecular Biology (IBMP), CNRS and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38000, Pakistan.
| | - Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France.
| | - Rana Khalid Iqbal
- Institute of Plant Molecular Biology (IBMP), CNRS and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
| | - Daria Mileshina
- Institute of Plant Molecular Biology (IBMP), CNRS and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
| | - Romain Val
- Institute of Plant Molecular Biology (IBMP), CNRS and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
| | - Marta Gabryelska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Ul. Z. Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Eliza Wyszko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Ul. Z. Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Ludivine Soubigou-Taconnat
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France.
| | - Maciej Szymanski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, A. Mickiewicz University Poznan, Ul. Umultowska 89, 61-614 Poznan, Poland.
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Ul. Z. Noskowskiego 12/14, 61-704 Poznan, Poland.
- NanoBioMedical Centre of the Adam Mickiewicz University, Umultowska 85, 61614 Poznan, Poland.
| | - Frédérique Weber-Lotfi
- Institute of Plant Molecular Biology (IBMP), CNRS and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
| | - José Manuel Gualberto
- Institute of Plant Molecular Biology (IBMP), CNRS and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
| | - André Dietrich
- Institute of Plant Molecular Biology (IBMP), CNRS and University of Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
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33
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Mitochondrial DNA Integrity: Role in Health and Disease. Cells 2019; 8:cells8020100. [PMID: 30700008 PMCID: PMC6406942 DOI: 10.3390/cells8020100] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 01/06/2023] Open
Abstract
As the primary cellular location for respiration and energy production, mitochondria serve in a critical capacity to the cell. Yet, by virtue of this very function of respiration, mitochondria are subject to constant oxidative stress that can damage one of the unique features of this organelle, its distinct genome. Damage to mitochondrial DNA (mtDNA) and loss of mitochondrial genome integrity is increasingly understood to play a role in the development of both severe early-onset maladies and chronic age-related diseases. In this article, we review the processes by which mtDNA integrity is maintained, with an emphasis on the repair of oxidative DNA lesions, and the cellular consequences of diminished mitochondrial genome stability.
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34
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Cameron TA, Matz LM, De Lay NR. Polynucleotide phosphorylase: Not merely an RNase but a pivotal post-transcriptional regulator. PLoS Genet 2018; 14:e1007654. [PMID: 30307990 PMCID: PMC6181284 DOI: 10.1371/journal.pgen.1007654] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Almost 60 years ago, Severo Ochoa was awarded the Nobel Prize in Physiology or Medicine for his discovery of the enzymatic synthesis of RNA by polynucleotide phosphorylase (PNPase). Although this discovery provided an important tool for deciphering the genetic code, subsequent work revealed that the predominant function of PNPase in bacteria and eukaryotes is catalyzing the reverse reaction, i.e., the release of ribonucleotides from RNA. PNPase has a crucial role in RNA metabolism in bacteria and eukaryotes mainly through its roles in processing and degrading RNAs, but additional functions in RNA metabolism have recently been reported for this enzyme. Here, we discuss these established and noncanonical functions for PNPase and the possibility that the major impact of PNPase on cell physiology is through its unorthodox roles.
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Affiliation(s)
- Todd A. Cameron
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Lisa M. Matz
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Nicholas R. De Lay
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, United States of America
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, Texas, United States of America
- * E-mail:
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35
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Weinhouse C. Mitochondrial-epigenetic crosstalk in environmental toxicology. Toxicology 2017; 391:5-17. [PMID: 28855114 DOI: 10.1016/j.tox.2017.08.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 08/20/2017] [Accepted: 08/22/2017] [Indexed: 12/18/2022]
Abstract
Crosstalk between the nuclear epigenome and mitochondria, both in normal physiological function and in responses to environmental toxicant exposures, is a developing sub-field of interest in environmental and molecular toxicology. The majority (∼99%) of mitochondrial proteins are encoded in the nuclear genome, so programmed communication among nuclear, cytoplasmic, and mitochondrial compartments is essential for maintaining cellular health. In this review, we will focus on correlative and mechanistic evidence for direct impacts of each system on the other, discuss demonstrated or potential crosstalk in the context of chemical insult, and highlight biological research questions for future study. We will first review the two main signaling systems: nuclear signaling to the mitochondria [anterograde signaling], best described in regulation of oxidative phosphorylation (OXPHOS) and mitochondrial biogenesis in response to environmental signals received by the nucleus, and mitochondrial signals to the nucleus [retrograde signaling]. Both signaling systems can communicate intracellular energy needs or a need to compensate for dysfunction to maintain homeostasis, but both can also relay inappropriate signals in the presence of dysfunction in either system and contribute to adverse health outcomes. We will first review these two signaling systems and highlight known or biologically feasible epigenetic contributions to both, then briefly discuss the emerging field of epigenetic regulation of the mitochondrial genome, and finally discuss putative "crosstalk phenotypes", including biological phenomena, such as caloric restriction, maintenance of stemness, and circadian rhythm, and states of disease or loss of function, such as cancer and aging, in which both the nuclear epigenome and mitochondria are strongly implicated.
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Affiliation(s)
- Caren Weinhouse
- Duke Global Health Institute, Duke University, Durham, NC 27708, United States.
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