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Vučković A, Freyer C, Wredenberg A, Hillen HS. The molecular machinery for maturation of primary mtDNA transcripts. Hum Mol Genet 2024; 33:R19-R25. [PMID: 38779769 PMCID: PMC11112384 DOI: 10.1093/hmg/ddae023] [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: 01/31/2024] [Revised: 01/31/2024] [Accepted: 02/08/2024] [Indexed: 05/25/2024] Open
Abstract
Human mitochondria harbour a circular, polyploid genome (mtDNA) encoding 11 messenger RNAs (mRNAs), two ribosomal RNAs (rRNAs) and 22 transfer RNAs (tRNAs). Mitochondrial transcription produces long, polycistronic transcripts that span almost the entire length of the genome, and hence contain all three types of RNAs. The primary transcripts then undergo a number of processing and maturation steps, which constitute key regulatory points of mitochondrial gene expression. The first step of mitochondrial RNA processing consists of the separation of primary transcripts into individual, functional RNA molecules and can occur by two distinct pathways. Both are carried out by dedicated molecular machineries that substantially differ from RNA processing enzymes found elsewhere. As a result, the underlying molecular mechanisms remain poorly understood. Over the last years, genetic, biochemical and structural studies have identified key players involved in both RNA processing pathways and provided the first insights into the underlying mechanisms. Here, we review our current understanding of RNA processing in mammalian mitochondria and provide an outlook on open questions in the field.
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MESH Headings
- Humans
- DNA, Mitochondrial/genetics
- RNA Processing, Post-Transcriptional
- Mitochondria/genetics
- Mitochondria/metabolism
- RNA, Mitochondrial/genetics
- RNA, Mitochondrial/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Animals
- Transcription, Genetic
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
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Affiliation(s)
- Ana Vučković
- Department of Cellular Biochemistry, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
- Research Group Structure and Function of Molecular Machines, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christoph Freyer
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Anna Steckséns gata 47, 171 64 Solna, Sweden
| | - Anna Wredenberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Anna Steckséns gata 47, 171 64 Solna, Sweden
| | - Hauke S Hillen
- Department of Cellular Biochemistry, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
- Research Group Structure and Function of Molecular Machines, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, Robert-Koch-Straße 40, 37073 Göttingen, Germany
- Research Group Structure and Function of Molecular Machines, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Justus-von-Liebig-Weg 11, Goettingen 37077, Germany
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2
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Khandibharad S, Singh S. Single-cell ATAC sequencing identifies sleepy macrophages during reciprocity of cytokines in L. major infection. Microbiol Spectr 2024; 12:e0347823. [PMID: 38299832 PMCID: PMC10913457 DOI: 10.1128/spectrum.03478-23] [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: 09/25/2023] [Accepted: 12/31/2023] [Indexed: 02/02/2024] Open
Abstract
The hallmark characteristic of macrophages lies in their inherent plasticity, allowing them to adapt to dynamic microenvironments. Leishmania strategically modulates the phenotypic plasticity of macrophages, creating a favorable environment for intracellular survival and persistent infection through regulatory cytokine such as interleukin (IL)-10. Nevertheless, these effector cells can counteract infection by modulating crucial cytokines like IL-12 and key components involved in its production. Using sophisticated tool of single-cell assay for transposase accessible chromatin (ATAC) sequencing, we systematically examined the regulatory axis of IL-10 and IL-12 in a time-dependent manner during Leishmania major infection in macrophages Our analysis revealed the cellular heterogeneity post-infection with the regulators of IL-10 and IL-12, unveiling a reciprocal relationship between these cytokines. Notably, our significant findings highlighted the presence of sleepy macrophages and their pivotal role in mediating reciprocity between IL-10 and IL-12. To summarize, the roles of cytokine expression, transcription factors, cell cycle, and epigenetics of host cell machinery were vital in identification of sleepy macrophages, which is a transient state where transcription factors controlled the epigenetic remodeling and expression of genes involved in pro-inflammatory cytokine expression and recruitment of immune cells.IMPORTANCELeishmaniasis is an endemic affecting 99 countries and territories globally, as outlined in the 2022 World Health Organization report. The disease's severity is compounded by compromised host immune systems, emphasizing the pivotal role of the interplay between parasite and host immune factors in disease regulation. In instances of cutaneous leishmaniasis induced by L. major, macrophages function as sentinel cells. Our findings indicate that the plasticity and phenotype of macrophages can be modulated to express a cytokine profile involving IL-10 and IL-12, mediated by the regulation of transcription factors and their target genes post-L. major infection in macrophages. Employing sophisticated methodologies such as single-cell ATAC sequencing and computational genomics, we have identified a distinctive subset of macrophages termed "sleepy macrophages." These macrophages exhibit downregulated housekeeping genes while expressing a unique set of variable features. This data set constitutes a valuable resource for comprehending the intricate host-parasite interplay during L. major infection.
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Affiliation(s)
- Shweta Khandibharad
- Systems Medicine Lab, National Centre for Cell Science, SP Pune University Campus, Pune, India
| | - Shailza Singh
- Systems Medicine Lab, National Centre for Cell Science, SP Pune University Campus, Pune, India
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3
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Tao S, Cui D, Cheng H, Liu X, Jiang Z, Chen H, Gao Y. High expression of TBRG4 in relation to unfavorable outcome and cell ferroptosis in hepatocellular carcinoma. BMC Cancer 2024; 24:194. [PMID: 38347489 PMCID: PMC10860303 DOI: 10.1186/s12885-024-11943-1] [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: 11/11/2023] [Accepted: 02/01/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the most common type of malignant liver tumor with poor prognosis. In this study, we investigated the expression of transforming growth factor beta regulator 4 (TBRG4) in HCC and its effects on the proliferation, invasion, and metastasis of HCC cells, and analyzed the possible molecular mechanisms. METHOD Downloading the expression and clinical information of HCC samples in the TCGA database, analyzing the expression differences of TBRG4 by bioinformatics methods, analyzing the clinical relevance and prognostic significance. Performing GO, KEGG and GSEA enrichment analysis on the TBRG4-related gene set in patient HCC tissues. Applying cell counting, scratch test and Transwell experiment to study the biological function of TBRG4 in HCC. Mitochondrial membrane potential, apoptosis and ROS levels were evaluated to assess cell iron death. Western blot, RT-PCR, laser confocal microscopy and co-immunoprecipitation were used to detect and analyze the downstream signaling pathways and interacting molecules of TBRG4. RESULTS Bioinformatics analysis revealed that TBRG4 was abnormally highly expressed in HCC tumor tissues and was associated with poor prognosis and metastasis in HCC patients. GO and KEGG functional enrichment analysis showed that TBRG4 was related to oxidative stress and NADH dehydrogenase (ubiquinone) activity. GSEA enrichment analysis showed that TBRG4 was associated with Beta catenin independent wnt signaling and B cell receptor. Functional experiments confirmed that knocking down TBRG4 could inhibit the proliferation, migration, and invasion of HCC cells. Mechanistically, TBRG4 inhibited the function of HCC cells through the DDX56/p-AKT/GSK3β signaling pathway. In addition, interference with TBRG4 expression could reduce the mitochondrial membrane potential and accumulate ROS in HCC cells, leading to increased ferroptosis. Co-IP analysis showed that TBRG4 specifically bound to Beclin1. CONCLUSION TBRG4 is highly expressed in HCC tumor tissues and is associated with poor prognosis. It may regulate the proliferation, invasion, and metastasis of HCC cells through the DDX56/p-AKT/GSK3β signaling pathway. TBRG4 may interact with Beclin1 to regulate the ferroptosis of HCC cells.
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Affiliation(s)
- Shanchun Tao
- Blood Transfusion Department, Fuyang Normal University Affiliated Second Hospital, Fuyang, Anhui, 236000, China
| | - Di Cui
- Fuyang Medical College, Fuyang Normal University, Fuyang, Anhui, 236037, China
| | - Huimin Cheng
- School of Biology and Food Engineering, Fuyang Normal University, Fuyang, Anhui, 236037, China
| | - Xiaofei Liu
- Fuyang Medical College, Fuyang Normal University, Fuyang, Anhui, 236037, China
| | - Zhaobin Jiang
- Fuyang Medical College, Fuyang Normal University, Fuyang, Anhui, 236037, China
| | - Hongwei Chen
- Fuyang Medical College, Fuyang Normal University, Fuyang, Anhui, 236037, China.
| | - Yong Gao
- Department of Clinical Laboratory, Fuyang Second People's Hospital, Fuyang Infectious Disease Clinical College, Anhui Medical University, Fuyang, Anhui, 236015, China.
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Wang Q, Gao QC, Wang QC, Wu L, Yu Q, He PF. A compendium of mitochondrial molecular characteristics provides novel perspectives on the treatment of rheumatoid arthritis patients. J Transl Med 2023; 21:561. [PMID: 37608254 PMCID: PMC10463924 DOI: 10.1186/s12967-023-04426-7] [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: 06/08/2023] [Accepted: 08/06/2023] [Indexed: 08/24/2023] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease that exhibits a high degree of heterogeneity, marked by unpredictable disease flares and significant variations in the response to available treatments. The lack of optimal stratification for RA patients may be a contributing factor to the poor efficacy of current treatment options. The objective of this study is to elucidate the molecular characteristics of RA through the utilization of mitochondrial genes and subsequently construct and authenticate a diagnostic framework for RA. Mitochondrial proteins were obtained from the MitoCarta database, and the R package limma was employed to filter for differentially expressed mitochondrial genes (MDEGs). Metascape was utilized to perform enrichment analysis, followed by an unsupervised clustering algorithm using the ConsensuClusterPlus package to identify distinct subtypes based on MDEGs. The immune microenvironment, biological pathways, and drug response were further explored in these subtypes. Finally, a multi-biomarker-based diagnostic model was constructed using machine learning algorithms. Utilizing 88 MDEGs present in transcript profiles, it was possible to classify RA patients into three distinct subtypes, each characterized by unique molecular and cellular signatures. Subtype A exhibited a marked activation of inflammatory cells and pathways, while subtype C was characterized by the presence of specific innate lymphocytes. Inflammatory and immune cells in subtype B displayed a more modest level of activation (Wilcoxon test P < 0.05). Notably, subtype C demonstrated a stronger correlation with a superior response to biologics such as infliximab, anti-TNF, rituximab, and methotrexate/abatacept (P = 0.001) using the fisher test. Furthermore, the mitochondrial diagnosis SVM model demonstrated a high degree of discriminatory ability in distinguishing RA in both training (AUC = 100%) and validation sets (AUC = 80.1%). This study presents a pioneering analysis of mitochondrial modifications in RA, offering a novel framework for patient stratification and potentially enhancing therapeutic decision-making.
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Affiliation(s)
- Qi Wang
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China
| | - Qi-Chao Gao
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China
| | - Qi-Chuan Wang
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
| | - Li Wu
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
- Department of Anesthesiology, Shanxi Provincial People's Hospital (Fifth Hospital) of Shanxi Medical University, Taiyuan, China
| | - Qi Yu
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China
- School of Management, Shanxi Medical University, Taiyuan, China
| | - Pei-Feng He
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China.
- School of Management, Shanxi Medical University, Taiyuan, China.
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5
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Han H, McGivney BA, Allen L, Bai D, Corduff LR, Davaakhuu G, Davaasambuu J, Dorjgotov D, Hall TJ, Hemmings AJ, Holtby AR, Jambal T, Jargalsaikhan B, Jargalsaikhan U, Kadri NK, MacHugh DE, Pausch H, Readhead C, Warburton D, Dugarjaviin M, Hill EW. Common protein-coding variants influence the racing phenotype in galloping racehorse breeds. Commun Biol 2022; 5:1320. [PMID: 36513809 PMCID: PMC9748125 DOI: 10.1038/s42003-022-04206-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 11/01/2022] [Indexed: 12/14/2022] Open
Abstract
Selection for system-wide morphological, physiological, and metabolic adaptations has led to extreme athletic phenotypes among geographically diverse horse breeds. Here, we identify genes contributing to exercise adaptation in racehorses by applying genomics approaches for racing performance, an end-point athletic phenotype. Using an integrative genomics strategy to first combine population genomics results with skeletal muscle exercise and training transcriptomic data, followed by whole-genome resequencing of Asian horses, we identify protein-coding variants in genes of interest in galloping racehorse breeds (Arabian, Mongolian and Thoroughbred). A core set of genes, G6PC2, HDAC9, KTN1, MYLK2, NTM, SLC16A1 and SYNDIG1, with central roles in muscle, metabolism, and neurobiology, are key drivers of the racing phenotype. Although racing potential is a multifactorial trait, the genomic architecture shaping the common athletic phenotype in horse populations bred for racing provides evidence for the influence of protein-coding variants in fundamental exercise-relevant genes. Variation in these genes may therefore be exploited for genetic improvement of horse populations towards specific types of racing.
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Affiliation(s)
- Haige Han
- grid.411638.90000 0004 1756 9607Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018 China
| | - Beatrice A. McGivney
- grid.496984.ePlusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, A96 W5T3 Ireland
| | - Lucy Allen
- grid.417905.e0000 0001 2186 5933Royal Agricultural University, Cirencester, Gloucestershire GL7 6JS UK
| | - Dongyi Bai
- grid.411638.90000 0004 1756 9607Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018 China
| | - Leanne R. Corduff
- grid.496984.ePlusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, A96 W5T3 Ireland
| | - Gantulga Davaakhuu
- grid.425564.40000 0004 0587 3863Institute of Biology, Mongolian Academy of Sciences, Peace Avenue 54B, Ulaanbaatar, 13330 Mongolia
| | - Jargalsaikhan Davaasambuu
- Ajnai Sharga Horse Racing Team, Encanto Town 210-11, Ikh Mongol State Street, 26th Khoroo, Bayanzurkh district Ulaanbaatar, 13312 Mongolia
| | - Dulguun Dorjgotov
- grid.440461.30000 0001 2191 7895School of Industrial Technology, Mongolian University of Science and Technology, Ulaanbaatar, 661 Mongolia
| | - Thomas J. Hall
- grid.7886.10000 0001 0768 2743UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin D04 V1W8 Ireland
| | - Andrew J. Hemmings
- grid.417905.e0000 0001 2186 5933Royal Agricultural University, Cirencester, Gloucestershire GL7 6JS UK
| | - Amy R. Holtby
- grid.496984.ePlusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, A96 W5T3 Ireland
| | - Tuyatsetseg Jambal
- grid.440461.30000 0001 2191 7895School of Industrial Technology, Mongolian University of Science and Technology, Ulaanbaatar, 661 Mongolia
| | - Badarch Jargalsaikhan
- grid.444534.60000 0000 8485 883XDepartment of Obstetrics and Gynecology, Mongolian National University of Medical Sciences, Ulaanbaatar, 14210 Mongolia
| | - Uyasakh Jargalsaikhan
- Ajnai Sharga Horse Racing Team, Encanto Town 210-11, Ikh Mongol State Street, 26th Khoroo, Bayanzurkh district Ulaanbaatar, 13312 Mongolia
| | - Naveen K. Kadri
- grid.5801.c0000 0001 2156 2780Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - David E. MacHugh
- grid.7886.10000 0001 0768 2743UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin D04 V1W8 Ireland ,grid.7886.10000 0001 0768 2743UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin D04 V1W8 Ireland
| | - Hubert Pausch
- grid.5801.c0000 0001 2156 2780Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Carol Readhead
- grid.20861.3d0000000107068890Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125 USA
| | - David Warburton
- grid.42505.360000 0001 2156 6853The Saban Research Institute, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA 90027 USA
| | - Manglai Dugarjaviin
- grid.411638.90000 0004 1756 9607Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018 China
| | - Emmeline W. Hill
- grid.496984.ePlusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, A96 W5T3 Ireland ,grid.7886.10000 0001 0768 2743UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin D04 V1W8 Ireland
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Bharthur Sanjay A, Patania A, Yan X, Svaldi D, Duran T, Shah N, Nemes S, Chen E, Apostolova LG. Characterization of gene expression patterns in mild cognitive impairment using a transcriptomics approach and neuroimaging endophenotypes. Alzheimers Dement 2022; 18:2493-2508. [PMID: 35142026 PMCID: PMC10078657 DOI: 10.1002/alz.12587] [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: 04/11/2021] [Revised: 12/10/2021] [Accepted: 12/15/2021] [Indexed: 01/31/2023]
Abstract
INTRODUCTION Identification of novel therapeutics and risk assessment in early stages of Alzheimer's disease (AD) is a crucial aspect of addressing this complex disease. We characterized gene-expression patterns at the mild cognitive impairment (MCI) stage to identify critical mRNA measures and gene clusters associated with AD pathogenesis. METHODS We used a transcriptomics approach, integrating magnetic resonance imaging (MRI) and peripheral blood-based gene expression data using persistent homology (PH) followed by kernel-based clustering. RESULTS We identified three clusters of genes significantly associated with diagnosis of amnestic MCI. The biological processes associated with each cluster were mitochondrial function, NF-kB signaling, and apoptosis. Cluster-level associations with cortical thickness displayed canonical AD-like patterns. Driver genes from clusters were also validated in an external dataset for prediction of amyloidosis and clinical diagnosis. DISCUSSION We found a disease-relevant transcriptomic signature sensitive to prodromal AD and identified a subset of potential therapeutic targets associated with AD pathogenesis.
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Affiliation(s)
| | - Alice Patania
- Indiana University Network Sciences InstituteIndiana UniversityBloomingtonIndianaUSA
| | - Xiaoran Yan
- Indiana University Network Sciences InstituteIndiana UniversityBloomingtonIndianaUSA
| | - Diana Svaldi
- Department of NeurologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Tugce Duran
- Department of Internal Medicine, Section of Gerontology & Geriatric MedicineWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Niraj Shah
- Department of NeurologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Sara Nemes
- Department of NeurologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Eric Chen
- Department of NeurologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Liana G. Apostolova
- Department of NeurologyIndiana University School of MedicineIndianapolisIndianaUSA
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Chu G, Li P, Wen J, Zheng G, Zhao Y, He R. Copy Number Variation Analysis of 5p Deletion Provides Accurate Prenatal Diagnosis and Reveals Candidate Pathogenic Genes. Front Med (Lausanne) 2022; 9:883565. [PMID: 35911393 PMCID: PMC9329539 DOI: 10.3389/fmed.2022.883565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/21/2022] [Indexed: 11/19/2022] Open
Abstract
Objective 5p deletion syndrome, that characterized by cat-like cry and peculiar timbre of voice, is believed to be one of the most common pathogenic copy number variations (CNVs). Variable critical regions on 5p involving a variety of genes contribute to the phenotypic heterogeneity without specific correlation. The objective of this study was to examine the genotype–phenotype correlation of 5p deletion syndrome, and to redefine 5p deletion syndrome relevant regions. In addition, we demonstrate the potential use of whole genome sequencing (WGS) to identify chromosomal breakpoints in prenatal diagnosis. Methods Three families with women undergoing prenatal diagnosis and two children were recruited. Karyotyping, CNV-seq, fluorescence in situ hybridization, WGS, and Sanger sequencing were performed to identify the chromosomal disorder. Results We reported three families and two children with CNVs of 5p deletion or combined 6p duplication. Five different sizes of 5p deletion were detected and their pathogenicity was determined, including 5p15.33-p15.31 [1–7,700,000, family1-variant of uncertain significance (VUS)], 5p15.33 (1–3,220,000, family 2-VUS), 5p15.33-p15.31 (1–7,040,000, family 3-VUS), 5p15.33-p15.31 (1–8,740,000, child 1-pathogenic) and 5p15.31-p15.1 (8,520,001–18,080,000, child 2-pathogenic). One duplication at 6p25.3-p24.3 (1–10,420,000) was detected and determined as likely pathogenic. The chromosomal breakpoints in family 3 were successfully identified by WGS. Conclusion Some critical genes that were supposed to be causative of the symptoms were identified. Relevant region in 5p deletion syndrome was redefined, and the chr5:7,700,000–8,740,000 region was supposed to be responsible for the cat-like cry. The great potential of WGS in detecting chromosomal translocations was demonstrated. Our findings may pave the way for further research on the prevention, diagnosis, and treatment of related diseases.
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Affiliation(s)
- Guoming Chu
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Pingping Li
- Department of Obstetrics and Gynecology, Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Juan Wen
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Gaoyan Zheng
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yanyan Zhao
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Rong He
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
- *Correspondence: Rong He,
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8
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Wu T, Mao L, Chen C, Yin F, Peng J. A novel homozygous missense mutation in the FASTKD2 gene leads to Lennox-Gastaut syndrome. J Hum Genet 2022; 67:589-594. [PMID: 35729327 DOI: 10.1038/s10038-022-01056-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/27/2022] [Accepted: 06/13/2022] [Indexed: 11/09/2022]
Abstract
FASTKD2 encodes an RNA-binding protein, which is a key post-transcriptional regulator of mitochondrial gene expression. Mutations in FASTKD2 have recently been found in mitochondrial encephalomyopathy, which is characterized by a deficiency in mitochondrial function. To date, seven patients have been reported. Six patients were identified with nonsense or frameshift mutations in the FASTKD2 gene, and only one patient harbored a missense mutation and a nonsense mutation. Here, we identified a novel FASTKD2 homozygous mutation, c.911 T > C, in a patient diagnosed with Lennox-Gastaut syndrome. We observed that the expression of FASTKD2 and the levels of mitochondrial 16 S rRNA were lower in the patient than in the unaffected controls. In conclusion, the missense mutation c.911 T > C caused loss of function in FASTKD2, which was associated with a new phenotype, Lennox-Gastaut syndrome.
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Affiliation(s)
- Tenghui Wu
- Department of Pediatrics, Xiangya Hospital Central South University, Changsha, 410008, China.,Hunan Children's Mental Disorders Research Center, XiangYa Hospital, Central South University, Changsha, 410008, China
| | - Leilei Mao
- Department of Pediatrics, Xiangya Hospital Central South University, Changsha, 410008, China.,Hunan Children's Mental Disorders Research Center, XiangYa Hospital, Central South University, Changsha, 410008, China
| | - Chen Chen
- Department of Pediatrics, Xiangya Hospital Central South University, Changsha, 410008, China.,Hunan Children's Mental Disorders Research Center, XiangYa Hospital, Central South University, Changsha, 410008, China
| | - Fei Yin
- Department of Pediatrics, Xiangya Hospital Central South University, Changsha, 410008, China.,Hunan Children's Mental Disorders Research Center, XiangYa Hospital, Central South University, Changsha, 410008, China
| | - Jing Peng
- Department of Pediatrics, Xiangya Hospital Central South University, Changsha, 410008, China. .,Hunan Children's Mental Disorders Research Center, XiangYa Hospital, Central South University, Changsha, 410008, China.
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9
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How RNases Shape Mitochondrial Transcriptomes. Int J Mol Sci 2022; 23:ijms23116141. [PMID: 35682820 PMCID: PMC9181182 DOI: 10.3390/ijms23116141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 11/17/2022] Open
Abstract
Mitochondria are the power houses of eukaryote cells. These endosymbiotic organelles of prokaryote origin are considered as semi-autonomous since they have retained a genome and fully functional gene expression mechanisms. These pathways are particularly interesting because they combine features inherited from the bacterial ancestor of mitochondria with characteristics that appeared during eukaryote evolution. RNA biology is thus particularly diverse in mitochondria. It involves an unexpectedly vast array of factors, some of which being universal to all mitochondria and others being specific from specific eukaryote clades. Among them, ribonucleases are particularly prominent. They play pivotal functions such as the maturation of transcript ends, RNA degradation and surveillance functions that are required to attain the pool of mature RNAs required to synthesize essential mitochondrial proteins such as respiratory chain proteins. Beyond these functions, mitochondrial ribonucleases are also involved in the maintenance and replication of mitochondrial DNA, and even possibly in the biogenesis of mitochondrial ribosomes. The diversity of mitochondrial RNases is reviewed here, showing for instance how in some cases a bacterial-type enzyme was kept in some eukaryotes, while in other clades, eukaryote specific enzymes were recruited for the same function.
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10
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Ramasubramanian A, Paramasivam A, Ramani P. FASTK family of genes linked to cancer. Bioinformation 2022; 18:206-213. [PMID: 36518140 PMCID: PMC9722426 DOI: 10.6026/97320630018206] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/25/2022] [Accepted: 03/31/2022] [Indexed: 02/05/2024] Open
Abstract
Fas Activated Serine/Threonine Kinase (FASTK) family is a protein family encoded in the nuclear genome that spans the mitochondria and executes numerous functions, and consists of FASTK, the founding member along with 5 homologous proteins FASTKD1-5. Up regulation of FASTK family members have not only been implicated in tumour progression and invasion but also in increased resistance to chemotherapy proven by their knockdown leading to increased sensitivity to drugs. Thus, this review reports the implication of FASTK proteins in cancer and hence provides a scope to emphasise the role of these proteins in Oral Cancer.
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Affiliation(s)
- Abilasha Ramasubramanian
- Department of Oral Pathology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Poonamallee High Road, Chennai, Tamilnadu - 600077, India
| | - A Paramasivam
- Department of Dental Research Cell- Blue Lab, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Poonamallee High Road, Chennai, Tamilnadu - 600077, India
| | - Pratibha Ramani
- Department of Oral Pathology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Poonamallee High Road, Chennai, Tamilnadu - 600077, India
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11
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Hollin T, Abel S, Falla A, Pasaje CFA, Bhatia A, Hur M, Kirkwood JS, Saraf A, Prudhomme J, De Souza A, Florens L, Niles JC, Le Roch KG. Functional genomics of RAP proteins and their role in mitoribosome regulation in Plasmodium falciparum. Nat Commun 2022; 13:1275. [PMID: 35277503 PMCID: PMC8917122 DOI: 10.1038/s41467-022-28981-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 02/14/2022] [Indexed: 12/31/2022] Open
Abstract
The RAP (RNA-binding domain abundant in Apicomplexans) protein family has been identified in various organisms. Despite expansion of this protein family in apicomplexan parasites, their main biological functions remain unknown. In this study, we use inducible knockdown studies in the human malaria parasite, Plasmodium falciparum, to show that two RAP proteins, PF3D7_0105200 (PfRAP01) and PF3D7_1470600 (PfRAP21), are essential for parasite survival and localize to the mitochondrion. Using transcriptomics, metabolomics, and proteomics profiling experiments, we further demonstrate that these RAP proteins are involved in mitochondrial RNA metabolism. Using high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (eCLIP-seq), we validate that PfRAP01 and PfRAP21 are true RNA-binding proteins and interact specifically with mitochondrial rRNAs. Finally, mitochondrial enrichment experiments followed by deep sequencing of small RNAs demonstrate that PfRAP21 controls mitochondrial rRNA expression. Collectively, our results establish the role of these RAP proteins in mitoribosome activity and contribute to further understanding this protein family in malaria parasites.
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Affiliation(s)
- Thomas Hollin
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Alejandra Falla
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Anil Bhatia
- Metabolomics Core Facility, University of California, Riverside, CA, 92521, USA
| | - Manhoi Hur
- Metabolomics Core Facility, University of California, Riverside, CA, 92521, USA
| | - Jay S Kirkwood
- Metabolomics Core Facility, University of California, Riverside, CA, 92521, USA
| | - Anita Saraf
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA
| | - Jacques Prudhomme
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Amancio De Souza
- Metabolomics Core Facility, University of California, Riverside, CA, 92521, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA.
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12
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Ohkubo A, Van Haute L, Rudler DL, Stentenbach M, Steiner FA, Rackham O, Minczuk M, Filipovska A, Martinou JC. The FASTK family proteins fine-tune mitochondrial RNA processing. PLoS Genet 2021; 17:e1009873. [PMID: 34748562 PMCID: PMC8601606 DOI: 10.1371/journal.pgen.1009873] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 11/18/2021] [Accepted: 10/11/2021] [Indexed: 12/28/2022] Open
Abstract
Transcription of the human mitochondrial genome and correct processing of the two long polycistronic transcripts are crucial for oxidative phosphorylation. According to the tRNA punctuation model, nucleolytic processing of these large precursor transcripts occurs mainly through the excision of the tRNAs that flank most rRNAs and mRNAs. However, some mRNAs are not punctuated by tRNAs, and it remains largely unknown how these non-canonical junctions are resolved. The FASTK family proteins are emerging as key players in non-canonical RNA processing. Here, we have generated human cell lines carrying single or combined knockouts of several FASTK family members to investigate their roles in non-canonical RNA processing. The most striking phenotypes were obtained with loss of FASTKD4 and FASTKD5 and with their combined double knockout. Comprehensive mitochondrial transcriptome analyses of these cell lines revealed a defect in processing at several canonical and non-canonical RNA junctions, accompanied by an increase in specific antisense transcripts. Loss of FASTKD5 led to the most severe phenotype with marked defects in mitochondrial translation of key components of the electron transport chain complexes and in oxidative phosphorylation. We reveal that the FASTK protein family members are crucial regulators of non-canonical junction and non-coding mitochondrial RNA processing. As a legacy of their bacterial origin, mitochondria have retained their own genome with a unique gene expression system. All mitochondrially encoded proteins are essential components of the respiratory chain. Therefore, the mitochondrial gene expression is crucial for their iconic role as the ‘powerhouse of the cell’–ATP synthesis through oxidative phosphorylation. Consistently, defects in enzymes involved in this gene expression system are a common source of incurable inherited metabolic disorders, called mitochondrial diseases. The human mitochondrial transcription generates long polycistronic transcripts that carry information for multiple genes, so that the expression level of each gene is mainly regulated through post-transcriptional events. The polycistronic transcript first undergoes RNA processing, where individual mRNA, rRNA, and tRNA are cleaved off. However, its entire molecular mechanism remains unclear, and in particular, ‘non-canonical’ RNA processing has been poorly understood. To address this question, we studied the FASTK family proteins, emerging key mitochondrial post-transcriptional regulators. We generated different human cell lines carrying single or combined disruption of FASTKD3, FASTKD4, and FASTKD5 genes, and analyzed them using biochemical and genetic approaches. We show that the FASTK family members fine-tune the processing of both ‘canonical’ and ‘non-canonical’ mitochondrial RNA junctions.
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Affiliation(s)
- Akira Ohkubo
- Department of Cell Biology, University of Geneva, Geneva, Switzerland
| | - Lindsey Van Haute
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Danielle L. Rudler
- Harry Perkins Institute of Medical Research, Queen Elizabeth II Medical Centre, Perth, Australia
- ARC Centre of Excellence in Synthetic Biology, Queen Elizabeth II Medical Centre, Perth, Australia
- Centre for Medical Research, The University of Western Australia, Queen Elizabeth II Medical Centre, Perth, Australia
| | - Maike Stentenbach
- Harry Perkins Institute of Medical Research, Queen Elizabeth II Medical Centre, Perth, Australia
- ARC Centre of Excellence in Synthetic Biology, Queen Elizabeth II Medical Centre, Perth, Australia
- Centre for Medical Research, The University of Western Australia, Queen Elizabeth II Medical Centre, Perth, Australia
| | - Florian A. Steiner
- Department of Molecular Biology, University of Geneva, Geneva, Switzerland
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, Queen Elizabeth II Medical Centre, Perth, Australia
- ARC Centre of Excellence in Synthetic Biology, Queen Elizabeth II Medical Centre, Perth, Australia
- School of Pharmacy and Biomedical Sciences, Curtin University, Perth, Australia
- Curtin Health Innovation Research Institute, Curtin University, Perth, Australia
- Telethon Kids Institute, Perth Children’s Hospital, Perth, Australia
| | - Michal Minczuk
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, Queen Elizabeth II Medical Centre, Perth, Australia
- ARC Centre of Excellence in Synthetic Biology, Queen Elizabeth II Medical Centre, Perth, Australia
- Centre for Medical Research, The University of Western Australia, Queen Elizabeth II Medical Centre, Perth, Australia
- Telethon Kids Institute, Perth Children’s Hospital, Perth, Australia
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
- * E-mail: (AF); (J-CM)
| | - Jean-Claude Martinou
- Department of Cell Biology, University of Geneva, Geneva, Switzerland
- * E-mail: (AF); (J-CM)
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13
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Xavier VJ, Martinou JC. RNA Granules in the Mitochondria and Their Organization under Mitochondrial Stresses. Int J Mol Sci 2021; 22:9502. [PMID: 34502411 PMCID: PMC8431320 DOI: 10.3390/ijms22179502] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 12/25/2022] Open
Abstract
The human mitochondrial genome (mtDNA) regulates its transcription products in specialised and distinct ways as compared to nuclear transcription. Thanks to its mtDNA mitochondria possess their own set of tRNAs, rRNAs and mRNAs that encode a subset of the protein subunits of the electron transport chain complexes. The RNA regulation within mitochondria is organised within specialised, membraneless, compartments of RNA-protein complexes, called the Mitochondrial RNA Granules (MRGs). MRGs were first identified to contain nascent mRNA, complexed with many proteins involved in RNA processing and maturation and ribosome assembly. Most recently, double-stranded RNA (dsRNA) species, a hybrid of the two complementary mRNA strands, were found to form granules in the matrix of mitochondria. These RNA granules are therefore components of the mitochondrial post-transcriptional pathway and as such play an essential role in mitochondrial gene expression. Mitochondrial dysfunctions in the form of, for example, RNA processing or RNA quality control defects, or inhibition of mitochondrial fission, can cause the loss or the aberrant accumulation of these RNA granules. These findings underline the important link between mitochondrial maintenance and the efficient expression of its genome.
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Affiliation(s)
| | - Jean-Claude Martinou
- Department of Cell Biology, Faculty of Sciences, University of Geneva, 1205 Geneva, Switzerland;
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14
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Autophagy and Mitophagy-Related Pathways at the Crossroads of Genetic Pathways Involved in Familial Sarcoidosis and Host-Pathogen Interactions Induced by Coronaviruses. Cells 2021; 10:cells10081995. [PMID: 34440765 PMCID: PMC8393644 DOI: 10.3390/cells10081995] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/16/2021] [Accepted: 07/29/2021] [Indexed: 12/12/2022] Open
Abstract
Sarcoidosis is a multisystem disease characterized by the development and accumulation of granulomas, the hallmark of an inflammatory process induced by environmental and/or infectious and or genetic factors. This auto-inflammatory disease mainly affects the lungs, the gateway to environmental aggressions and viral infections. We have shown previously that genetic predisposition to sarcoidosis occurring in familial cases is related to a large spectrum of pathogenic variants with, however, a clustering around mTOR (mammalian Target Of Rapamycin)-related pathways and autophagy regulation. The context of the COVID-19 pandemic led us to evaluate whether such genetic defects may increase the risk of a severe course of SARS-CoV2 infection in patients with sarcoidosis. We extended a whole exome screening to 13 families predisposed to sarcoidosis and crossed the genes sharing mutations with the list of genes involved in the SARS-CoV2 host-pathogen protein-protein interactome. A similar analysis protocol was applied to a series of 100 healthy individuals. Using ENRICH.R, a comprehensive gene set enrichment web server, we identified the functional pathways represented in the set of genes carrying deleterious mutations and confirmed the overrepresentation of autophagy- and mitophagy-related functions in familial cases of sarcoidosis. The same protocol was applied to the set of genes common to sarcoidosis and the SARS-CoV2-host interactome and found a significant enrichment of genes related to mitochondrial factors involved in autophagy, mitophagy, and RIG-I-like (Retinoic Acid Inducible Gene 1) Receptor antiviral response signaling. From these results, we discuss the hypothesis according to which sarcoidosis is a model for studying genetic abnormalities associated with host response to viral infections as a consequence of defects in autophagy and mitophagy processes.
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15
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Human Mitochondrial RNA Processing and Modifications: Overview. Int J Mol Sci 2021; 22:ijms22157999. [PMID: 34360765 PMCID: PMC8348895 DOI: 10.3390/ijms22157999] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 01/29/2023] Open
Abstract
Mitochondria, often referred to as the powerhouses of cells, are vital organelles that are present in almost all eukaryotic organisms, including humans. They are the key energy suppliers as the site of adenosine triphosphate production, and are involved in apoptosis, calcium homeostasis, and regulation of the innate immune response. Abnormalities occurring in mitochondria, such as mitochondrial DNA (mtDNA) mutations and disturbances at any stage of mitochondrial RNA (mtRNA) processing and translation, usually lead to severe mitochondrial diseases. A fundamental line of investigation is to understand the processes that occur in these organelles and their physiological consequences. Despite substantial progress that has been made in the field of mtRNA processing and its regulation, many unknowns and controversies remain. The present review discusses the current state of knowledge of RNA processing in human mitochondria and sheds some light on the unresolved issues.
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16
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Hollin T, Jaroszewski L, Stajich JE, Godzik A, Le Roch KG. Identification and phylogenetic analysis of RNA binding domain abundant in apicomplexans or RAP proteins. Microb Genom 2021; 7. [PMID: 33656416 PMCID: PMC8190603 DOI: 10.1099/mgen.0.000541] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The RNA binding domain abundant in apicomplexans (RAP) is a protein domain identified in a diverse group of proteins, called RAP proteins, many of which have been shown to be involved in RNA binding. To understand the expansion and potential function of the RAP proteins, we conducted a hidden Markov model based screen among the proteomes of 54 eukaryotes, 17 bacteria and 12 archaea. We demonstrated that the domain is present in closely and distantly related organisms with particular expansions in Alveolata and Chlorophyta, and are not unique to Apicomplexa as previously believed. All RAP proteins identified can be decomposed into two parts. In the N-terminal region, the presence of variable helical repeats seems to participate in the specific targeting of diverse RNAs, while the RAP domain is mostly identified in the C-terminal region and is highly conserved across the different phylogenetic groups studied. Several conserved residues defining the signature motif could be crucial to ensure the function(s) of the RAP proteins. Modelling of RAP domains in apicomplexan parasites confirmed an ⍺/β structure of a restriction endonuclease-like fold. The phylogenetic trees generated from multiple alignment of RAP domains and full-length proteins from various distantly related eukaryotes indicated a complex evolutionary history of this family. We further discuss these results to assess the potential function of this protein family in apicomplexan parasites.
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Affiliation(s)
- Thomas Hollin
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Avenue, Riverside, CA 92521, USA
| | - Lukasz Jaroszewski
- Department of Biomedical Sciences, University of California Riverside School of Medicine, 900 University Avenue, Riverside, CA 92521, USA
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California Riverside, 900 University Avenue, Riverside, CA 92521, USA
| | - Adam Godzik
- Department of Biomedical Sciences, University of California Riverside School of Medicine, 900 University Avenue, Riverside, CA 92521, USA
| | - Karine G. Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Avenue, Riverside, CA 92521, USA
- *Correspondence: Karine G. Le Roch,
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17
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Mechanisms and regulation of protein synthesis in mitochondria. Nat Rev Mol Cell Biol 2021; 22:307-325. [PMID: 33594280 DOI: 10.1038/s41580-021-00332-2] [Citation(s) in RCA: 140] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2021] [Indexed: 02/06/2023]
Abstract
Mitochondria are cellular organelles responsible for generation of chemical energy in the process called oxidative phosphorylation. They originate from a bacterial ancestor and maintain their own genome, which is expressed by designated, mitochondrial transcription and translation machineries that differ from those operating for nuclear gene expression. In particular, the mitochondrial protein synthesis machinery is structurally and functionally very different from that governing eukaryotic, cytosolic translation. Despite harbouring their own genetic information, mitochondria are far from being independent of the rest of the cell and, conversely, cellular fitness is closely linked to mitochondrial function. Mitochondria depend heavily on the import of nuclear-encoded proteins for gene expression and function, and hence engage in extensive inter-compartmental crosstalk to regulate their proteome. This connectivity allows mitochondria to adapt to changes in cellular conditions and also mediates responses to stress and mitochondrial dysfunction. With a focus on mammals and yeast, we review fundamental insights that have been made into the biogenesis, architecture and mechanisms of the mitochondrial translation apparatus in the past years owing to the emergence of numerous near-atomic structures and a considerable amount of biochemical work. Moreover, we discuss how cellular mitochondrial protein expression is regulated, including aspects of mRNA and tRNA maturation and stability, roles of auxiliary factors, such as translation regulators, that adapt mitochondrial translation rates, and the importance of inter-compartmental crosstalk with nuclear gene expression and cytosolic translation and how it enables integration of mitochondrial translation into the cellular context.
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18
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Oberleitner L, Poschmann G, Macorano L, Schott-Verdugo S, Gohlke H, Stühler K, Nowack ECM. The Puzzle of Metabolite Exchange and Identification of Putative Octotrico Peptide Repeat Expression Regulators in the Nascent Photosynthetic Organelles of Paulinella chromatophora. Front Microbiol 2020; 11:607182. [PMID: 33329499 PMCID: PMC7729196 DOI: 10.3389/fmicb.2020.607182] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/05/2020] [Indexed: 12/12/2022] Open
Abstract
The endosymbiotic acquisition of mitochondria and plastids more than one billion years ago was central for the evolution of eukaryotic life. However, owing to their ancient origin, these organelles provide only limited insights into the initial stages of organellogenesis. The cercozoan amoeba Paulinella chromatophora contains photosynthetic organelles-termed chromatophores-that evolved from a cyanobacterium ∼100 million years ago, independently from plastids in plants and algae. Despite the more recent origin of the chromatophore, it shows tight integration into the host cell. It imports hundreds of nucleus-encoded proteins, and diverse metabolites are continuously exchanged across the two chromatophore envelope membranes. However, the limited set of chromatophore-encoded solute transporters appears insufficient for supporting metabolic connectivity or protein import. Furthermore, chromatophore-localized biosynthetic pathways as well as multiprotein complexes include proteins of dual genetic origin, suggesting that mechanisms evolved that coordinate gene expression levels between chromatophore and nucleus. These findings imply that similar to the situation in mitochondria and plastids, also in P. chromatophora nuclear factors evolved that control metabolite exchange and gene expression in the chromatophore. Here we show by mass spectrometric analyses of enriched insoluble protein fractions that, unexpectedly, nucleus-encoded transporters are not inserted into the chromatophore inner envelope membrane. Thus, despite the apparent maintenance of its barrier function, canonical metabolite transporters are missing in this membrane. Instead we identified several expanded groups of short chromatophore-targeted orphan proteins. Members of one of these groups are characterized by a single transmembrane helix, and others contain amphipathic helices. We hypothesize that these proteins are involved in modulating membrane permeability. Thus, the mechanism generating metabolic connectivity of the chromatophore fundamentally differs from the one for mitochondria and plastids, but likely rather resembles the poorly understood mechanism in various bacterial endosymbionts in plants and insects. Furthermore, our mass spectrometric analysis revealed an expanded family of chromatophore-targeted helical repeat proteins. These proteins show similar domain architectures as known organelle-targeted expression regulators of the octotrico peptide repeat type in algae and plants. Apparently these chromatophore-targeted proteins evolved convergently to plastid-targeted expression regulators and are likely involved in gene expression control in the chromatophore.
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Affiliation(s)
- Linda Oberleitner
- Department of Biology, Institute of Microbial Cell Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Gereon Poschmann
- Medical Faculty, Institute for Molecular Medicine, Proteome Research, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Luis Macorano
- Department of Biology, Institute of Microbial Cell Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Stephan Schott-Verdugo
- Department of Pharmacy, Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Faculty of Engineering, Centro de Bioinformática y Simulación Molecular, Universidad de Talca, Talca, Chile
| | - Holger Gohlke
- Department of Pharmacy, Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Jülich Supercomputing Centre, John von Neumann Institute for Computing, Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Kai Stühler
- Medical Faculty, Institute for Molecular Medicine, Proteome Research, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Molecular Proteomics Laboratory, Biologisch-Medizinisches Forschungszentrum, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Eva C. M. Nowack
- Department of Biology, Institute of Microbial Cell Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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19
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Zhang F, Wang K, Zhang S, Li J, Fan R, Chen X, Pei J. Accelerated FASTK mRNA degradation induced by oxidative stress is responsible for the destroyed myocardial mitochondrial gene expression and respiratory function in alcoholic cardiomyopathy. Redox Biol 2020; 38:101778. [PMID: 33197770 PMCID: PMC7677712 DOI: 10.1016/j.redox.2020.101778] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/07/2020] [Accepted: 10/26/2020] [Indexed: 01/25/2023] Open
Abstract
Chronic alcoholism disrupts mitochondrial function and often results in alcoholic cardiomyopathy (ACM). Fas-activated serine/threonine kinase (FASTK) is newly recognized as a key post-transcriptional regulator of mitochondrial gene expression. However, the modulatory role of FASTK in cardiovascular pathophysiology remains totally unknown. In experimental ACM models, cardiac FASTK expression markedly declined. Ethanol directly suppressed FASTK expression at post-transcriptional level through NADPH oxidase-derived reactive oxygen species (ROS). Ethanol destabilized FASTK mRNA 3'-untranslated region (3'-UTR) and accelerated its decay, which was blocked by the clearance of ROS. Regnase-1 (Reg1), a ribonuclease regulating mRNA stability, was induced by ROS in ethanol-stimulated cardiomyocytes. Reg1 directly bound to FASTK mRNA 3'-UTR and promoted its degradation, whereas silencing of Reg1 reversed ethanol-induced FASTK downregulation. Compared to wild type control, alcohol-related myocardial morphological (hypertrophy, fibrosis and cardiomyocyte apoptosis) and functional (reduced ejection fraction and compromised cardiomyocyte contraction) anomalies were worsened in FASTK deficient mice. Mechanistically, FASTK ablation repressed NADH dehydrogenase subunit 6 (MTND6, a mitochondrial gene encoding a subunit of complex I) mRNA production and reduced complex I-supported respiration. Importantly, cardiomyocyte-specific upregulation of FASTK through intra-cardiac AAV9-cTNT injection mitigated myocardial mitochondrial dysfunction and restrained ACM progression. In vitro study showed that overexpression of FASTK ameliorated ethanol-induced MTND6 mRNA downregulation, complex I inactivation, and cardiomyocyte death, whereas these beneficial effects were counteracted by rotenone, a complex I inhibitor. Collectively, ROS-accelerated FASTK mRNA degradation via Reg1 underlies chronic ethanol ingestion-associated mitochondrial dysfunction and cardiomyopathy. Restoration of FASTK expression through genetic approaches might be a promising therapeutic strategy for ACM.
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Affiliation(s)
- Fuyang Zhang
- Department of Physiology and Pathophysiology, Basic Medicine School, National Key Discipline of Cell Biology, Air Force Medical University, China; Department of Cardiology, Xijing Hospital, Air Force Medical University, China
| | - Kai Wang
- Department of Physiology and Pathophysiology, Basic Medicine School, National Key Discipline of Cell Biology, Air Force Medical University, China
| | - Shumiao Zhang
- Department of Physiology and Pathophysiology, Basic Medicine School, National Key Discipline of Cell Biology, Air Force Medical University, China
| | - Juan Li
- Department of Physiology and Pathophysiology, Basic Medicine School, National Key Discipline of Cell Biology, Air Force Medical University, China
| | - Rong Fan
- Department of Physiology and Pathophysiology, Basic Medicine School, National Key Discipline of Cell Biology, Air Force Medical University, China
| | - Xiyao Chen
- Department of Geriatrics, Xijing Hospital, Air Force Medical University, China.
| | - Jianming Pei
- Department of Physiology and Pathophysiology, Basic Medicine School, National Key Discipline of Cell Biology, Air Force Medical University, China.
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20
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Arévalo-Martínez M, Cidad P, García-Mateo N, Moreno-Estar S, Serna J, Fernández M, Swärd K, Simarro M, de la Fuente MA, López-López JR, Pérez-García MT. Myocardin-Dependent Kv1.5 Channel Expression Prevents Phenotypic Modulation of Human Vessels in Organ Culture. Arterioscler Thromb Vasc Biol 2019; 39:e273-e286. [DOI: 10.1161/atvbaha.119.313492] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Objective:
We have previously described that changes in the expression of Kv channels associate to phenotypic modulation (PM), so that Kv1.3/Kv1.5 ratio is a landmark of vascular smooth muscle cells phenotype. Moreover, we demonstrated that the Kv1.3 functional expression is relevant for PM in several types of vascular lesions. Here, we explore the efficacy of Kv1.3 inhibition for the prevention of remodeling in human vessels, and the mechanisms linking the switch in Kv1.3 /Kv1.5 ratio to PM.
Approach and Results:
Vascular remodeling was explored using organ culture and primary cultures of vascular smooth muscle cells obtained from human vessels. We studied the effects of Kv1.3 inhibition on serum-induced remodeling, as well as the impact of viral vector-mediated overexpression of Kv channels or myocardin knock-down. Kv1.3 blockade prevented remodeling by inhibiting proliferation, migration, and extracellular matrix secretion. PM activated Kv1.3 via downregulation of Kv1.5. Hence, both Kv1.3 blockers and Kv1.5 overexpression inhibited remodeling in a nonadditive fashion. Finally, myocardin knock-down induced vessel remodeling and Kv1.5 downregulation and myocardin overexpression increased Kv1.5, while Kv1.5 overexpression inhibited PM without changing myocardin expression.
Conclusions:
We demonstrate that Kv1.5 channel gene is a myocardin-regulated, vascular smooth muscle cells contractile marker. Kv1.5 downregulation upon PM leaves Kv1.3 as the dominant Kv1 channel expressed in dedifferentiated cells. We demonstrated that the inhibition of Kv1.3 channel function with selective blockers or by preventing Kv1.5 downregulation can represent an effective, novel strategy for the prevention of intimal hyperplasia and restenosis of the human vessels used for coronary angioplasty procedures.
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Affiliation(s)
- Marycarmen Arévalo-Martínez
- From the Departamento de Bioquímica y Biología Molecular y Fisiología, Universidad de Valladolid, Spain (M.A.-M., P.C., N.G.-M., S.M.-E., J.S., J.R.L.-L., M.T.P.-G.)
- Instituto de Biología y Genética Molecular (IBGM), CSIC, Universidad de Valladolid, Spain (M.A.-M., P.C., N.G.-M., S.M.-E., J.S., M.S., M.A.d.l.F.)
| | - Pilar Cidad
- From the Departamento de Bioquímica y Biología Molecular y Fisiología, Universidad de Valladolid, Spain (M.A.-M., P.C., N.G.-M., S.M.-E., J.S., J.R.L.-L., M.T.P.-G.)
- Instituto de Biología y Genética Molecular (IBGM), CSIC, Universidad de Valladolid, Spain (M.A.-M., P.C., N.G.-M., S.M.-E., J.S., M.S., M.A.d.l.F.)
| | - Nadia García-Mateo
- From the Departamento de Bioquímica y Biología Molecular y Fisiología, Universidad de Valladolid, Spain (M.A.-M., P.C., N.G.-M., S.M.-E., J.S., J.R.L.-L., M.T.P.-G.)
- Instituto de Biología y Genética Molecular (IBGM), CSIC, Universidad de Valladolid, Spain (M.A.-M., P.C., N.G.-M., S.M.-E., J.S., M.S., M.A.d.l.F.)
| | - Sara Moreno-Estar
- From the Departamento de Bioquímica y Biología Molecular y Fisiología, Universidad de Valladolid, Spain (M.A.-M., P.C., N.G.-M., S.M.-E., J.S., J.R.L.-L., M.T.P.-G.)
- Instituto de Biología y Genética Molecular (IBGM), CSIC, Universidad de Valladolid, Spain (M.A.-M., P.C., N.G.-M., S.M.-E., J.S., M.S., M.A.d.l.F.)
| | - Julia Serna
- From the Departamento de Bioquímica y Biología Molecular y Fisiología, Universidad de Valladolid, Spain (M.A.-M., P.C., N.G.-M., S.M.-E., J.S., J.R.L.-L., M.T.P.-G.)
- Instituto de Biología y Genética Molecular (IBGM), CSIC, Universidad de Valladolid, Spain (M.A.-M., P.C., N.G.-M., S.M.-E., J.S., M.S., M.A.d.l.F.)
| | - Mirella Fernández
- Cardiovascular Surgery Department, Hospital Clínico Universitario de Valladolid, Spain (M.F.)
| | - Karl Swärd
- Department of Experimental Medical Science, University of Lund, Sweden (K.S.)
| | - María Simarro
- Instituto de Biología y Genética Molecular (IBGM), CSIC, Universidad de Valladolid, Spain (M.A.-M., P.C., N.G.-M., S.M.-E., J.S., M.S., M.A.d.l.F.)
- Departamento de Enfermería, Universidad de Valladolid, Spain (M.S.)
| | - Miguel A. de la Fuente
- Instituto de Biología y Genética Molecular (IBGM), CSIC, Universidad de Valladolid, Spain (M.A.-M., P.C., N.G.-M., S.M.-E., J.S., M.S., M.A.d.l.F.)
- Departamento de Biología Celular, Universidad de Valladolid, Spain (M.A.d.l.F.)
| | - José R. López-López
- From the Departamento de Bioquímica y Biología Molecular y Fisiología, Universidad de Valladolid, Spain (M.A.-M., P.C., N.G.-M., S.M.-E., J.S., J.R.L.-L., M.T.P.-G.)
| | - M. Teresa Pérez-García
- From the Departamento de Bioquímica y Biología Molecular y Fisiología, Universidad de Valladolid, Spain (M.A.-M., P.C., N.G.-M., S.M.-E., J.S., J.R.L.-L., M.T.P.-G.)
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21
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Fang R, Zhang B, Lu X, Jin X, Liu T. FASTKD2 promotes cancer cell progression through upregulating Myc expression in pancreatic ductal adenocarcinoma. J Cell Biochem 2019; 121:2458-2466. [PMID: 31692063 DOI: 10.1002/jcb.29468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/10/2019] [Indexed: 12/30/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most fatal cancers of the digestive system. Despite the development of novel therapeutic methods, including chemotherapy, radiotherapy, and molecular targeted therapy, the incidence rate of PDAC is almost equal to the mortality rate with 5-year overall survival rate less than 5%. Kras mutation is found in 95% of patient with PDAC specimens, but targeting Kras mutation do not benefit patients with pancreatic cancer in preclinical trials. c-Myc is one of the main effector molecules of the Kras signaling pathway. In this study, we found that dysregulation of FAST kinase-domain-containing protein 2 (FASTKD2) resulted in the poor prognosis of patients with PDAC. Then, we showed that FASTKD2 promoted pancreatic cancer cell proliferation and invasion. Importantly, we demonstrated that c-Myc was transcriptionally increased by FASTKD2/BRD4 axis and responsible for FASTKD2-mediated tumor growth and invasion in pancreatic cancer cells. Collectively, this study uncovered that FASTKD2 promoted cancer cell progression through upregulating Myc expression in pancreatic cancer. FASTKD2 might be a potential target for pancreatic cancer therapy.
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Affiliation(s)
- Rui Fang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bin Zhang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoming Lu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xin Jin
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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22
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Marshall KD, Klutho PJ, Song L, Krenz M, Baines CP. The novel cyclophilin-D-interacting protein FASTKD1 protects cells against oxidative stress-induced cell death. Am J Physiol Cell Physiol 2019; 317:C584-C599. [PMID: 31268778 DOI: 10.1152/ajpcell.00471.2018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Opening of the mitochondrial permeability transition (MPT) pore leads to necrotic cell death. Excluding cyclophilin D (CypD), the makeup of the MPT pore remains conjecture. The purpose of these experiments was to identify novel MPT modulators by analyzing proteins that associate with CypD. We identified Fas-activated serine/threonine phosphoprotein kinase domain-containing protein 1 (FASTKD1) as a novel CypD interactor. Overexpression of FASTKD1 protected mouse embryonic fibroblasts (MEFs) against oxidative stress-induced reactive oxygen species (ROS) production and cell death, whereas depletion of FASTKD1 sensitized them. However, manipulation of FASTKD1 levels had no effect on MPT responsiveness, Ca2+-induced cell death, or antioxidant capacity. Moreover, elevated FASTKD1 levels still protected against oxidative stress in CypD-deficient MEFs. FASTKD1 overexpression decreased Complex-I-dependent respiration and ΔΨm in MEFs, effects that were abrogated in CypD-null cells. Additionally, overexpression of FASTKD1 in MEFs induced mitochondrial fragmentation independent of CypD, activation of Drp1, and inhibition of autophagy/mitophagy, whereas knockdown of FASTKD1 had the opposite effect. Manipulation of FASTKD1 expression also modified oxidative stress-induced caspase-3 cleavage yet did not alter apoptotic death. Finally, the effects of FASTKD1 overexpression on oxidative stress-induced cell death and mitochondrial morphology were recapitulated in cultured cardiac myocytes. Together, these data indicate that FASTKD1 supports mitochondrial homeostasis and plays a critical protective role against oxidant-induced death.
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Affiliation(s)
- Kurt D Marshall
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri
| | - Paula J Klutho
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri
| | - Lihui Song
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri
| | - Maike Krenz
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri.,Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, Missouri
| | - Christopher P Baines
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri.,Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri.,Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, Missouri
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23
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Transcription, Processing, and Decay of Mitochondrial RNA in Health and Disease. Int J Mol Sci 2019; 20:ijms20092221. [PMID: 31064115 PMCID: PMC6540609 DOI: 10.3390/ijms20092221] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/01/2019] [Accepted: 05/03/2019] [Indexed: 12/16/2022] Open
Abstract
Although the large majority of mitochondrial proteins are nuclear encoded, for their correct functioning mitochondria require the expression of 13 proteins, two rRNA, and 22 tRNA codified by mitochondrial DNA (mtDNA). Once transcribed, mitochondrial RNA (mtRNA) is processed, mito-ribosomes are assembled, and mtDNA-encoded proteins belonging to the respiratory chain are synthesized. These processes require the coordinated spatio-temporal action of several enzymes, and many different factors are involved in the regulation and control of protein synthesis and in the stability and turnover of mitochondrial RNA. In this review, we describe the essential steps of mitochondrial RNA synthesis, maturation, and degradation, the factors controlling these processes, and how the alteration of these processes is associated with human pathologies.
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24
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García Del Río A, Delmiro A, Martín MA, Cantalapiedra R, Carretero R, Durántez C, Menegotto F, Morán M, Serrano-Lorenzo P, De la Fuente MA, Orduña A, Simarro M. The Mitochondrial Isoform of FASTK Modulates Nonopsonic Phagocytosis of Bacteria by Macrophages via Regulation of Respiratory Complex I. THE JOURNAL OF IMMUNOLOGY 2018; 201:2977-2985. [PMID: 30322967 DOI: 10.4049/jimmunol.1701075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/10/2018] [Indexed: 12/18/2022]
Abstract
Phagocytosis is a pivotal process by which innate immune cells eliminate bacteria. In this study, we explore novel regulatory mechanisms of phagocytosis driven by the mitochondria. Fas-activated serine/threonine kinase (FASTK) is an RNA-binding protein with two isoforms, one localized to the mitochondria (mitoFASTK) and the other isoform to cytosol and nucleus. The mitoFASTK isoform has been reported to be necessary for the biogenesis of the mitochondrial ND6 mRNA, which encodes an essential subunit of mitochondrial respiratory complex I (CI, NADH:ubiquinone oxidoreductase). This study investigates the role and the mechanisms of action of FASTK in phagocytosis. Macrophages from FASTK─/─ mice exhibited a marked increase in nonopsonic phagocytosis of bacteria. As expected, CI activity was specifically reduced by almost 50% in those cells. To explore if decreased CI activity could underlie the phagocytic phenotype, we tested the effect of CI inhibition on phagocytosis. Indeed, treatment with CI inhibitor rotenone or short hairpin RNAs against two CI subunits (NDUFS3 and NDUFS4) resulted in a marked increase in nonopsonic phagocytosis of bacteria. Importantly, re-expression of mitoFASTK in FASTK-depleted macrophages was sufficient to rescue the phagocytic phenotype. In addition, we also report that the decrease in CI activity in FASTK─/─ macrophages is associated with an increase in phosphorylation of the energy sensor AMP-activated protein kinase (AMPK) and that its inhibition using Compound C reverted the phagocytosis phenotype. Taken together, our results clearly demonstrate for the first time, to our knowledge, that mitoFASTK plays a negative regulatory role on nonopsonic phagocytosis of bacteria in macrophages through its action on CI activity.
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Affiliation(s)
| | - Aitor Delmiro
- Laboratorio de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación del Hospital 12 de Octubre, 28041 Madrid, Spain.,Spanish Network for Biomedical Research in Rare Diseases, U723, 28029 Madrid, Spain
| | - Miguel Angel Martín
- Laboratorio de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación del Hospital 12 de Octubre, 28041 Madrid, Spain.,Spanish Network for Biomedical Research in Rare Diseases, U723, 28029 Madrid, Spain
| | | | - Raquel Carretero
- Department of Microbiology, University of Valladolid, Valladolid, Spain
| | - Carlos Durántez
- Department of Microbiology, University of Valladolid, Valladolid, Spain
| | - Fabiola Menegotto
- Department of Microbiology, University of Valladolid, Valladolid, Spain
| | - María Morán
- Laboratorio de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación del Hospital 12 de Octubre, 28041 Madrid, Spain.,Spanish Network for Biomedical Research in Rare Diseases, U723, 28029 Madrid, Spain
| | - Pablo Serrano-Lorenzo
- Laboratorio de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación del Hospital 12 de Octubre, 28041 Madrid, Spain
| | - Miguel Angel De la Fuente
- Department of Cell Biology, Histology and Pharmacology, University of Valladolid, 47005 Valladolid, Spain; .,Institute of Biology and Molecular Genetics, 47003 Valladolid, Spain
| | - Antonio Orduña
- Department of Microbiology, University of Valladolid, Valladolid, Spain.,Departamento de Microbiología e Inmunología, Hospital Clínico Universitario, 47003 Valladolid, Spain; and
| | - María Simarro
- Department of Nursing, University of Valladolid, 47005 Valladolid, Spain
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25
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Is mitochondrial gene expression coordinated or stochastic? Biochem Soc Trans 2018; 46:1239-1246. [PMID: 30301847 DOI: 10.1042/bst20180174] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 08/29/2018] [Accepted: 08/30/2018] [Indexed: 12/25/2022]
Abstract
Mitochondrial biogenesis is intimately dependent on the coordinated expression of the nuclear and mitochondrial genomes that is necessary for the assembly and function of the respiratory complexes to produce most of the energy required by cells. Although highly compacted in animals, the mitochondrial genome and its expression are essential for survival, development, and optimal energy production. The machinery that regulates gene expression within mitochondria is localised within the same compartment and, like in their ancestors, the bacteria, this machinery does not use membrane-based compartmentalisation to order the gene expression pathway. Therefore, the lifecycle of mitochondrial RNAs from transcription through processing, maturation, translation to turnover is mediated by a gamut of RNA-binding proteins (RBPs), all contained within the mitochondrial matrix milieu. Recent discoveries indicate that multiple processes regulating RNA metabolism occur at once but since mitochondria have a new complement of RBPs, many evolved de novo from nuclear genes, we are left wondering how co-ordinated are these processes? Here, we review recently identified examples of the co-ordinated and stochastic processes that govern the mitochondrial transcriptome. These new discoveries reveal the complexity of mitochondrial gene expression and the need for its in-depth exploration to understand how these organelles can respond to the energy demands of the cell.
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26
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Khan NS, Khan P, Ansari MF, Srivastava S, Hasan GM, Husain M, Hassan MI. Thienopyrimidine-Chalcone Hybrid Molecules Inhibit Fas-Activated Serine/Threonine Kinase: An Approach To Ameliorate Antiproliferation in Human Breast Cancer Cells. Mol Pharm 2018; 15:4173-4189. [PMID: 30040903 DOI: 10.1021/acs.molpharmaceut.8b00566] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Apoptotic evasion by cancerous cells being one of the striking hallmarks of cancer has turned into a new arena of drug discovery. A large number of pathways reported that govern the apoptotic evasion have been reported. Fas-activated serine/threonine kinase (FASTK) is a member of Ser/Thr kinase family, and it has been implicated in the apoptotic evasion and, hence, the development of cancer. Keeping this in view, a series of novel thienopyrimidine-based chalcones have been synthesized and evaluated to modulate the FASTK mediated apoptotic evasion. Initial screening was done by enzyme inhibition assay and binding studies, which showed that out of 15 synthesized compounds, 3 thienopyrimidine-based chalcone derivatives possess considerably high binding affinity and enzyme inhibitory potential (nM range) for FASTK. Cell proliferation assessment of selected compounds was performed on HEK-293 and MCF-7 cells. For MCF-7 cells, compounds 2, 10, and 12 show IC50 values of 20.22 ± 1.50, 6.52 ± 0.82, and 8.20 ± 0.61 μM, respectively. Annexin-V and PI staining suggested that these molecules induce apoptosis in MCF-7 cells, arrest the cell cycle in the G0/G1 phase, and subsequently inhibit cell migration presumably by inhibiting FASTK and reactive oxygen species production. In conclusion, we have successfully designed, synthesized, and characterized thienopyrimidine-based chalcones that inhibit FASTK and induce apoptosis. These compounds may be exploited as potential anticancer agents.
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Affiliation(s)
| | | | | | | | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine , Prince Sattam Bin Abdulaziz University , Al-Kharj 11942 , Saudi Arabia
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27
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Singh K, Sripada L, Lipatova A, Roy M, Prajapati P, Gohel D, Bhatelia K, Chumakov PM, Singh R. NLRX1 resides in mitochondrial RNA granules and regulates mitochondrial RNA processing and bioenergetic adaptation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1865:1260-1276. [PMID: 29932989 DOI: 10.1016/j.bbamcr.2018.06.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/10/2018] [Accepted: 06/17/2018] [Indexed: 12/26/2022]
Abstract
The role of mitochondria is emerging in regulation of innate immunity, inflammation and cell death beyond its primary role in energy metabolism. Mitochondria act as molecular platform for immune adaptor protein complexes, which participate in innate immune signaling. The mitochondrial localized immune adaptors are widely expressed in non-immune cells, however their role in regulation of mitochondrial function and metabolic adaption is not well understood. NLRX1, a member of NOD family receptor proteins, localizes to mitochondria and is a negative regulator of anti-viral signaling. However, the submitochondrial localization of NLRX1 and its implication in regulation of mitochondrial functions remains elusive. Here, we confirm that NLRX1 translocates to mitochondrial matrix and associates with mitochondrial FASTKD5 (Fas-activated serine-threonine kinase family protein-5), a bonafide component of mitochondrial RNA granules (MRGs). The association of NLRX1 with FASTKD5 negatively regulates the processing of mitochondrial genome encoded transcripts for key components of complex-I and complex-IV, to modulate its activity and supercomplexes formation. The evidences, here, suggest an important role of NLRX1 in regulating the post-transcriptional processing of mitochondrial RNA, which may have an important implication in bioenergetic adaptation during metabolic stress, oncogenic transformation and innate immunity.
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Affiliation(s)
- Kritarth Singh
- Department of Biochemistry, Faculty of Science, The M.S. University of Baroda, Vadodara, 390002, Gujarat, India
| | - Lakshmi Sripada
- Department of Biochemistry, Faculty of Science, The M.S. University of Baroda, Vadodara, 390002, Gujarat, India
| | - Anastasia Lipatova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, 119991 Moscow, Russia
| | - Milton Roy
- Department of Biochemistry, Faculty of Science, The M.S. University of Baroda, Vadodara, 390002, Gujarat, India
| | - Paresh Prajapati
- SCoBIRC Department of Neuroscience, University of Kentucky, 741S.Limestone, BBSRB, Lexington, KY 40536, USA
| | - Dhruv Gohel
- Department of Biochemistry, Faculty of Science, The M.S. University of Baroda, Vadodara, 390002, Gujarat, India
| | - Khyati Bhatelia
- Department of Biochemistry, Faculty of Science, The M.S. University of Baroda, Vadodara, 390002, Gujarat, India
| | - Peter M Chumakov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, 119991 Moscow, Russia; Chumakov Institute of Poliomyelitis and Viral Encephalitides, Federal Scientific Center on Research and Development of Immunobiology Products, Russian Academy of Sciences, 142782 Moscow, Russia
| | - Rajesh Singh
- Department of Biochemistry, Faculty of Science, The M.S. University of Baroda, Vadodara, 390002, Gujarat, India.
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28
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Jourdain AA, Popow J, de la Fuente MA, Martinou JC, Anderson P, Simarro M. The FASTK family of proteins: emerging regulators of mitochondrial RNA biology. Nucleic Acids Res 2017; 45:10941-10947. [PMID: 29036396 PMCID: PMC5737537 DOI: 10.1093/nar/gkx772] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 09/14/2017] [Indexed: 12/22/2022] Open
Abstract
The FASTK family proteins have recently emerged as key post-transcriptional regulators of mitochondrial gene expression. FASTK, the founding member and its homologs FASTKD1-5 are architecturally related RNA-binding proteins, each having a different function in the regulation of mitochondrial RNA biology, from mRNA processing and maturation to ribosome assembly and translation. In this review, we outline the structure, evolution and function of these FASTK proteins and discuss the individual role that each has in mitochondrial RNA biology. In addition, we highlight the aspects of FASTK research that still require more attention.
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Affiliation(s)
- Alexis A Jourdain
- Department of Cell Biology, University of Geneva, 1211 Geneva 4, Switzerland
| | - Johannes Popow
- Department of Cancer Cell Signalling, Boehringer-Ingelheim Regional Center Vienna, 1121 Vienna, Austria
| | - Miguel A de la Fuente
- Departamento de Biología, Histología y Farmacología, Universidad de Valladolid, Instituto de Biología y Genética Molecular, Valladolid 47003, Spain
| | | | - Paul Anderson
- Division of Rheumatology, Immunology and Allergy, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Maria Simarro
- Departamento de Enfermería, Universidad de Valladolid, Instituto de Biología y Genética Molecular, Valladolid 47003, Spain
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29
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Srivastava S, Syed SB, Kumar V, Islam A, Ahmad F, Hassan MI. Fas-activated serine/threonine kinase: Structure and function. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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