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Box JM, Higgins ME, Stuart RA. Importance of conserved hydrophobic pocket region in yeast mitoribosomal mL44 protein for mitotranslation and transcript preference. J Biol Chem 2024; 300:107519. [PMID: 38950860 PMCID: PMC11345376 DOI: 10.1016/j.jbc.2024.107519] [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: 01/23/2024] [Revised: 06/14/2024] [Accepted: 06/19/2024] [Indexed: 07/03/2024] Open
Abstract
The mitochondrial ribosome (mitoribosome) is responsible for the synthesis of key oxidative phosphorylation subunits encoded by the mitochondrial genome. Defects in mitoribosomal function therefore can have serious consequences for the bioenergetic capacity of the cell. Mutation of the conserved mitoribosomal mL44 protein has been directly linked to childhood cardiomyopathy and progressive neurophysiology issues. To further explore the functional significance of the mL44 protein in supporting mitochondrial protein synthesis, we have performed a mutagenesis study of the yeast mL44 homolog, the MrpL3/mL44 protein. We specifically investigated the conserved hydrophobic pocket region of the MrpL3/mL44 protein, where the known disease-related residue in the human mL44 protein (L156R) is located. While our findings identify a number of residues in this region critical for MrpL3/mL44's ability to support the assembly of translationally active mitoribosomes, the introduction of the disease-related mutation into the equivalent position in the yeast protein (residue A186) was found to not have a major impact on function. The human and yeast mL44 proteins share many similarities in sequence and structure; however results presented here indicate that these two proteins have diverged somewhat in evolution. Finally, we observed that mutation of the MrpL3/mL44 does not impact the translation of all mitochondrial encoded proteins equally, suggesting the mitochondrial translation system may exhibit a transcript hierarchy and prioritization.
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Affiliation(s)
- Jodie M Box
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Margo E Higgins
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Rosemary A Stuart
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA.
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2
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Li X, Liu Q, Fu C, Li M, Li C, Li X, Zhao S, Zheng Z. Characterizing structural variants based on graph-genotyping provides insights into pig domestication and local adaption. J Genet Genomics 2024; 51:394-406. [PMID: 38056526 DOI: 10.1016/j.jgg.2023.11.005] [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: 07/14/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/08/2023]
Abstract
Structural variants (SVs), such as deletions (DELs) and insertions (INSs), contribute substantially to pig genetic diversity and phenotypic variation. Using a library of SVs discovered from long-read primary assemblies and short-read sequenced genomes, we map pig genomic SVs with a graph-based method for re-genotyping SVs in 402 genomes. Our results demonstrate that those SVs harboring specific trait-associated genes may greatly shape pig domestication and local adaptation. Further characterization of SVs reveals that some population-stratified SVs may alter the transcription of genes by affecting regulatory elements. We identify that the genotypes of two DELs (296-bp DEL, chr7: 52,172,101-52,172,397; 278-bp DEL, chr18: 23,840,143-23,840,421) located in muscle-specific enhancers are associated with the expression of target genes related to meat quality (FSD2) and muscle fiber hypertrophy (LMOD2 and WASL) in pigs. Our results highlight the role of SVs in domestic porcine evolution, and the identified candidate functional genes and SVs are valuable resources for future genomic research and breeding programs in pigs.
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Affiliation(s)
- Xin Li
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Quan Liu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Chong Fu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Mengxun Li
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Changchun Li
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China
| | - Xinyun Li
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Shuhong Zhao
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China.
| | - Zhuqing Zheng
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Institute of Agricultural Biotechnology, Jingchu University of Technology, Jingmen, Hubei 448000, China.
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3
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Roy S, Sheikh SZ, Furey TS. CoVar: A generalizable machine learning approach to identify the coordinated regulators driving variational gene expression. PLoS Comput Biol 2024; 20:e1012016. [PMID: 38630807 PMCID: PMC11057768 DOI: 10.1371/journal.pcbi.1012016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/29/2024] [Accepted: 03/22/2024] [Indexed: 04/19/2024] Open
Abstract
Network inference is used to model transcriptional, signaling, and metabolic interactions among genes, proteins, and metabolites that identify biological pathways influencing disease pathogenesis. Advances in machine learning (ML)-based inference models exhibit the predictive capabilities of capturing latent patterns in genomic data. Such models are emerging as an alternative to the statistical models identifying causative factors driving complex diseases. We present CoVar, an ML-based framework that builds upon the properties of existing inference models, to find the central genes driving perturbed gene expression across biological states. Unlike differentially expressed genes (DEGs) that capture changes in individual gene expression across conditions, CoVar focuses on identifying variational genes that undergo changes in their expression network interaction profiles, providing insights into changes in the regulatory dynamics, such as in disease pathogenesis. Subsequently, it finds core genes from among the nearest neighbors of these variational genes, which are central to the variational activity and influence the coordinated regulatory processes underlying the observed changes in gene expression. Through the analysis of simulated as well as yeast expression data perturbed by the deletion of the mitochondrial genome, we show that CoVar captures the intrinsic variationality and modularity in the expression data, identifying key driver genes not found through existing differential analysis methodologies.
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Affiliation(s)
- Satyaki Roy
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Shehzad Z. Sheikh
- Departments of Medicine and Genetics, Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Terrence S. Furey
- Departments of Genetics and Biology, Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina, United States of America
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4
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Del Giudice L, Pontieri P, Aletta M, Calcagnile M. Mitochondrial Neurodegenerative Diseases: Three Mitochondrial Ribosomal Proteins as Intermediate Stage in the Pathway That Associates Damaged Genes with Alzheimer's and Parkinson's. BIOLOGY 2023; 12:972. [PMID: 37508402 PMCID: PMC10376763 DOI: 10.3390/biology12070972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023]
Abstract
Currently, numerous research endeavors are dedicated to unraveling the intricate nature of neurodegenerative diseases. These conditions are characterized by the gradual and progressive impairment of specific neuronal systems that exhibit anatomical or physiological connections. In particular, in the last twenty years, remarkable efforts have been made to elucidate neurodegenerative disorders such as Alzheimer's disease and Parkinson's disease. However, despite extensive research endeavors, no cure or effective treatment has been discovered thus far. With the emergence of studies shedding light on the contribution of mitochondria to the onset and advancement of mitochondrial neurodegenerative disorders, researchers are now directing their investigations toward the development of therapies. These therapies include molecules designed to protect mitochondria and neurons from the detrimental effects of aging, as well as mutant proteins. Our objective is to discuss and evaluate the recent discovery of three mitochondrial ribosomal proteins linked to Alzheimer's and Parkinson's diseases. These proteins represent an intermediate stage in the pathway connecting damaged genes to the two mitochondrial neurological pathologies. This discovery potentially could open new avenues for the production of medicinal substances with curative potential for the treatment of these diseases.
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Affiliation(s)
- Luigi Del Giudice
- Istituto di Bioscienze e BioRisorse-UOS Napoli-CNR c/o Dipartimento di Biologia, Sezione di Igiene, 80134 Napoli, Italy
| | - Paola Pontieri
- Istituto di Bioscienze e BioRisorse-UOS Napoli-CNR c/o Dipartimento di Biologia, Sezione di Igiene, 80134 Napoli, Italy
| | | | - Matteo Calcagnile
- Dipartimento di Scienze e Tecnologie Biologiche e Ambientali, Università del Salento, 73100 Lecce, Italy
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5
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Roy S, Sheikh SZ, Furey TS. CoVar: A generalizable machine learning approach to identify the coordinated regulators driving variational gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.12.523808. [PMID: 36712050 PMCID: PMC9882103 DOI: 10.1101/2023.01.12.523808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Network inference is used to model transcriptional, signaling, and metabolic interactions among genes, proteins, and metabolites that identify biological pathways influencing disease pathogenesis. Advances in machine learning (ML)-based inference models exhibit the predictive capabilities of capturing latent patterns in genomic data. Such models are emerging as an alternative to the statistical models identifying causative factors driving complex diseases. We present CoVar, an inference framework that builds upon the properties of existing inference models, to find the central genes driving perturbed gene expression across biological states. We leverage ML-based network inference to find networks that capture the strength of regulatory interactions. Our model first pinpoints a subset of genes, termed variational, whose expression variabilities typify the differences in network connectivity between the control and perturbed data. Variational genes, by being differentially expressed themselves or possessing differentially expressed neighbor genes, capture gene expression variability. CoVar then creates subnetworks comprising variational genes and their strongly connected neighbor genes and identifies core genes central to these subnetworks that influence the bulk of the variational activity. Through the analysis of yeast expression data perturbed by the deletion of the mitochondrial genome, we show that CoVar identifies key genes not found through independent differential expression analysis.
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6
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Shu Y, Hao Y, Feng J, Liu H, Li S, Feng J, Jiang Z, Ye L, Zhou Y, Sun Y, Zhou Z, Wei H, Gao P, Zhang H, Sun L. Non-canonical phosphoglycerate dehydrogenase activity promotes liver cancer growth via mitochondrial translation and respiratory metabolism. EMBO J 2022; 41:e111550. [PMID: 36314841 PMCID: PMC9713714 DOI: 10.15252/embj.2022111550] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 11/07/2022] Open
Abstract
Phosphoglycerate dehydrogenase (PHGDH) is a key serine biosynthesis enzyme whose aberrant expression promotes various types of tumors. Recently, PHGDH has been found to have some non-canonical functions beyond serine biosynthesis, but its specific mechanisms in tumorigenesis remain unclear. Here, we show that PHGDH localizes to the inner mitochondrial membrane and promotes the translation of mitochondrial DNA (mtDNA)-encoded proteins in liver cancer cells. Mechanistically, we demonstrate that mitochondrial PHGDH directly interacts with adenine nucleotide translocase 2 (ANT2) and then recruits mitochondrial elongation factor G2 (mtEFG2) to promote mitochondrial ribosome recycling efficiency, thereby promoting mtDNA-encoded protein expression and subsequent mitochondrial respiration. Moreover, we show that treatment with a mitochondrial translation inhibitor or depletion of mtEFG2 diminishes PHGDH-mediated tumor growth. Collectively, our findings uncover a previously unappreciated function of PHGDH in tumorigenesis acting via promotion of mitochondrial translation and bioenergetics.
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Affiliation(s)
- Ying Shu
- Division of Life Science and Medicine, Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, The First Affiliated Hospital of USTCUniversity of Science and Technology of ChinaHefeiChina
- Division of Life Science and Medicine, The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical SciencesUniversity of Science and Technology of ChinaHefeiChina
- Division of Life Science and Medicine, Anhui Province Key Laboratory of Biomedical Aging ResearchUniversity of Science and Technology of ChinaHefeiChina
| | - Yijie Hao
- Division of Life Science and Medicine, Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, The First Affiliated Hospital of USTCUniversity of Science and Technology of ChinaHefeiChina
- Division of Life Science and Medicine, The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical SciencesUniversity of Science and Technology of ChinaHefeiChina
| | - Junru Feng
- Division of Life Science and Medicine, Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, The First Affiliated Hospital of USTCUniversity of Science and Technology of ChinaHefeiChina
- Division of Life Science and Medicine, The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical SciencesUniversity of Science and Technology of ChinaHefeiChina
| | - Haiying Liu
- Division of Life Science and Medicine, Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, The First Affiliated Hospital of USTCUniversity of Science and Technology of ChinaHefeiChina
- Division of Life Science and Medicine, The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical SciencesUniversity of Science and Technology of ChinaHefeiChina
| | - Shi‐ting Li
- Division of Life Science and Medicine, Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, The First Affiliated Hospital of USTCUniversity of Science and Technology of ChinaHefeiChina
- Division of Life Science and Medicine, The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical SciencesUniversity of Science and Technology of ChinaHefeiChina
| | - Jiaqian Feng
- Division of Life Science and Medicine, Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, The First Affiliated Hospital of USTCUniversity of Science and Technology of ChinaHefeiChina
- Division of Life Science and Medicine, The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical SciencesUniversity of Science and Technology of ChinaHefeiChina
| | - Zetan Jiang
- Division of Life Science and Medicine, Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, The First Affiliated Hospital of USTCUniversity of Science and Technology of ChinaHefeiChina
- Division of Life Science and Medicine, The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical SciencesUniversity of Science and Technology of ChinaHefeiChina
| | - Ling Ye
- Division of Life Science and Medicine, Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, The First Affiliated Hospital of USTCUniversity of Science and Technology of ChinaHefeiChina
- Division of Life Science and Medicine, The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical SciencesUniversity of Science and Technology of ChinaHefeiChina
| | - Yingli Zhou
- Division of Life Science and Medicine, Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, The First Affiliated Hospital of USTCUniversity of Science and Technology of ChinaHefeiChina
- Division of Life Science and Medicine, The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical SciencesUniversity of Science and Technology of ChinaHefeiChina
| | - Yuchen Sun
- Division of Life Science and Medicine, Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, The First Affiliated Hospital of USTCUniversity of Science and Technology of ChinaHefeiChina
- Division of Life Science and Medicine, The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical SciencesUniversity of Science and Technology of ChinaHefeiChina
| | - Zilong Zhou
- Division of Life Science and Medicine, Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, The First Affiliated Hospital of USTCUniversity of Science and Technology of ChinaHefeiChina
- Division of Life Science and Medicine, The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical SciencesUniversity of Science and Technology of ChinaHefeiChina
| | - Haoran Wei
- Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Ping Gao
- Division of Life Science and Medicine, The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical SciencesUniversity of Science and Technology of ChinaHefeiChina
- Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Huafeng Zhang
- Division of Life Science and Medicine, Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, The First Affiliated Hospital of USTCUniversity of Science and Technology of ChinaHefeiChina
- Division of Life Science and Medicine, The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical SciencesUniversity of Science and Technology of ChinaHefeiChina
- Division of Life Science and Medicine, Anhui Province Key Laboratory of Biomedical Aging ResearchUniversity of Science and Technology of ChinaHefeiChina
| | - Linchong Sun
- Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
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7
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Del Giudice L, Alifano P, Calcagnile M, Di Schiavi E, Bertapelle C, Aletta M, Pontieri P. Mitochondrial ribosomal protein genes connected with Alzheimer's and tellurite toxicity. Mitochondrion 2022; 64:45-58. [PMID: 35218961 DOI: 10.1016/j.mito.2022.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/15/2022] [Accepted: 02/21/2022] [Indexed: 12/19/2022]
Abstract
Mitochondrial diseases are a group of genetic disorders characterized by dysfunctional mitochondria. Within eukaryotic cells, mitochondria contain their own ribosomes, which synthesize small amounts of proteins, all of which are essential for the biogenesis of the oxidative phosphorylation system. The ribosome is an evolutionarily conserved macromolecular machine in nature both from a structural and functional point of view, universally responsible for the synthesis of proteins. Among the diseases afflicting humans, those of ribosomal origin - either cytoplasmic ribosomes (80S) or mitochondrial ribosomes (70S) - are relevant. These are inherited or acquired diseases most commonly caused by either ribosomal protein haploinsufficiency or defects in ribosome biogenesis. Here we review the scientific literature about the recent advances on changes in mitochondrial ribosomal structural and assembly proteins that are implicated in primary mitochondrial diseases and neurodegenerative disorders, and their possible connection with metalloid pollution and toxicity, with a focus on MRPL44, NAM9 (MNA6) and GEP3 (MTG3), whose lack or defect was associated with resistance to tellurite. Finally, we illustrate the suitability of yeast Saccharomyces cerevisiae (S.cerevisiae) and the nematode Caenorhabditis elegans (C.elegans) as model organisms for studying mitochondrial ribosome dysfunctions including those involved in human diseases.
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Affiliation(s)
- Luigi Del Giudice
- Istituto di Bioscienze e BioRisorse-UOS Napoli-CNR c/o Dipartimento di Biologia, Sezione di Igiene, Napoli 80134, Italy.
| | - Pietro Alifano
- Dipartimento di Scienze e Tecnologie Biologiche e Ambientali, Università del Salento, Lecce 73100, Italy
| | - Matteo Calcagnile
- Dipartimento di Scienze e Tecnologie Biologiche e Ambientali, Università del Salento, Lecce 73100, Italy
| | | | | | | | - Paola Pontieri
- Istituto di Bioscienze e BioRisorse-UOS Napoli-CNR c/o Dipartimento di Biologia, Sezione di Igiene, Napoli 80134, Italy
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8
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Friederich MW, Geddes GC, Wortmann SB, Punnoose A, Wartchow E, Knight KM, Prokisch H, Creadon-Swindell G, Mayr JA, Van Hove JLK. Pathogenic variants in MRPL44 cause infantile cardiomyopathy due to a mitochondrial translation defect. Mol Genet Metab 2021; 133:362-371. [PMID: 34140213 PMCID: PMC8289749 DOI: 10.1016/j.ymgme.2021.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 11/22/2022]
Abstract
Cardiac dysfunction is a common phenotypic manifestation of primary mitochondrial disease with multiple nuclear and mitochondrial DNA pathogenic variants as a cause, including disorders of mitochondrial translation. To date, five patients have been described with pathogenic variants in MRPL44, encoding the ml44 protein which is part of the large subunit of the mitochondrial ribosome (mitoribosome). Three presented as infants with hypertrophic cardiomyopathy, mild lactic acidosis, and easy fatigue and muscle weakness, whereas two presented in adolescence with myopathy and neurological symptoms. We describe two infants who presented with cardiomyopathy from the neonatal period, failure to thrive, hypoglycemia and in one infant lactic acidosis. A decompensation of the cardiac function in the first year resulted in demise. Exome sequencing identified compound heterozygous variants in the MRPL44 gene including the known pathogenic variant c.467 T > G and two novel pathogenic variants. We document a combined respiratory chain enzyme deficiency with emphasis on complex I and IV, affecting heart muscle tissue more than skeletal muscle or fibroblasts. We show this to be caused by reduced mitochondrial DNA encoded protein synthesis affecting all subunits, and resulting in dysfunction of complex I and IV assembly. The degree of oxidative phosphorylation dysfunction correlated with the impairment of mitochondrial protein synthesis due to different pathogenic variants. These functional studies allow for improved understanding of the pathogenesis of MRPL44-associated mitochondrial disorder.
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Affiliation(s)
- Marisa W Friederich
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO, USA; Department of Pathology and Laboratory Services, Children's Hospital Colorado, Aurora, CO, USA
| | - Gabrielle C Geddes
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA; Department of Molecular and Medical Genetics, Indiana University, Indianapolis, IN, USA
| | - Saskia B Wortmann
- University Children's Hospital, Paracelsus Medical University (PMU), Salzburg, Austria; Amalia Children's Hospital, RadboudUMC, Nijmegen, the Netherlands
| | - Ann Punnoose
- Herma Heart Institute, Children's Hospital of Wisconsin, Milwaukee, WI, USA
| | - Eric Wartchow
- Department of Pathology and Laboratory Services, Children's Hospital Colorado, Aurora, CO, USA
| | - Kaz M Knight
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO, USA
| | - Holger Prokisch
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany; Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | | | - Johannes A Mayr
- University Children's Hospital, Paracelsus Medical University (PMU), Salzburg, Austria
| | - Johan L K Van Hove
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO, USA; Department of Pathology and Laboratory Services, Children's Hospital Colorado, Aurora, CO, USA.
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9
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Abnormal Expression of Mitochondrial Ribosomal Proteins and Their Encoding Genes with Cell Apoptosis and Diseases. Int J Mol Sci 2020; 21:ijms21228879. [PMID: 33238645 PMCID: PMC7700125 DOI: 10.3390/ijms21228879] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/15/2020] [Accepted: 11/17/2020] [Indexed: 12/11/2022] Open
Abstract
Mammalian mitochondrial ribosomes translate 13 proteins encoded by mitochondrial genes, all of which play roles in the mitochondrial respiratory chain. After a long period of reconstruction, mitochondrial ribosomes are the most protein-rich ribosomes. Mitochondrial ribosomal proteins (MRPs) are encoded by nuclear genes, synthesized in the cytoplasm and then, transported to the mitochondria to be assembled into mitochondrial ribosomes. MRPs not only play a role in mitochondrial oxidative phosphorylation (OXPHOS). Moreover, they participate in the regulation of cell state as apoptosis inducing factors. Abnormal expressions of MRPs will lead to mitochondrial metabolism disorder, cell dysfunction, etc. Many researches have demonstrated the abnormal expression of MRPs in various tumors. This paper reviews the basic structure of mitochondrial ribosome, focuses on the structure and function of MRPs, and their relationships with cell apoptosis and diseases. It provides a reference for the study of the function of MRPs and the disease diagnosis and treatment.
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10
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Bruni F, Proctor-Kent Y, Lightowlers RN, Chrzanowska-Lightowlers ZM. Messenger RNA delivery to mitoribosomes - hints from a bacterial toxin. FEBS J 2020; 288:437-451. [PMID: 32329962 PMCID: PMC7891357 DOI: 10.1111/febs.15342] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 04/06/2020] [Accepted: 04/21/2020] [Indexed: 11/28/2022]
Abstract
In mammalian mitochondria, messenger RNA is processed and matured from large primary transcripts in structures known as RNA granules. The identity of the factors and process transferring the matured mRNA to the mitoribosome for translation is unclear. Nascent mature transcripts are believed to associate initially with the small mitoribosomal subunit prior to recruitment of the large subunit to form the translationally active monosome. When the small subunit fails to assemble, however, the stability of mt‐mRNA is only marginally affected, and under these conditions, the LRPPRC/SLIRP RNA‐binding complex has been implicated in maintaining mt‐mRNA stability. Here, we exploit the activity of a bacterial ribotoxin, VapC20, to show that in the absence of the large mitoribosomal subunit, mt‐mRNA species are selectively lost. Further, if the small subunit is also depleted, the mt‐mRNA levels are recovered. As a consequence of these data, we suggest a natural pathway for loading processed mt‐mRNA onto the mitoribosome.
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Affiliation(s)
- Francesco Bruni
- The Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, UK.,Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, Italy
| | - Yasmin Proctor-Kent
- The Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, UK
| | - Robert N Lightowlers
- The Wellcome Centre for Mitochondrial Research, Institute for Cell and Molecular Biosciences, Newcastle University, UK
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11
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Boucherat O, Peterlini T, Bourgeois A, Nadeau V, Breuils-Bonnet S, Boilet-Molez S, Potus F, Meloche J, Chabot S, Lambert C, Tremblay E, Chae YC, Altieri DC, Sutendra G, Michelakis ED, Paulin R, Provencher S, Bonnet S. Mitochondrial HSP90 Accumulation Promotes Vascular Remodeling in Pulmonary Arterial Hypertension. Am J Respir Crit Care Med 2019; 198:90-103. [PMID: 29394093 DOI: 10.1164/rccm.201708-1751oc] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
RATIONALE Pulmonary arterial hypertension (PAH) is a vascular remodeling disease with a poor prognosis and limited therapeutic options. Although the mechanisms contributing to vascular remodeling in PAH are still unclear, several features, including hyperproliferation and resistance to apoptosis of pulmonary artery smooth muscle cells (PASMCs), have led to the emergence of the cancer-like concept. The molecular chaperone HSP90 (heat shock protein 90) is directly associated with malignant growth and proliferation under stress conditions. In addition to being highly expressed in the cytosol, HSP90 exists in a subcellular pool compartmentalized in the mitochondria (mtHSP90) of tumor cells, but not in normal cells, where it promotes cell survival. OBJECTIVES We hypothesized that mtHSP90 in PAH-PASMCs represents a protective mechanism against stress, promoting their proliferation and resistance to apoptosis. METHODS Expression and localization of HSP90 were analyzed by Western blot, immunofluorescence, and immunogold electron microscopy. In vitro, effects of mtHSP90 inhibition on mitochondrial DNA integrity, bioenergetics, cell proliferation and resistance to apoptosis were assessed. In vivo, the therapeutic potential of Gamitrinib, a mitochondria-targeted HSP90 inhibitor, was tested in fawn-hooded and monocrotaline rats. MEASUREMENTS AND MAIN RESULTS We demonstrated that, in response to stress, HSP90 preferentially accumulates in PAH-PASMC mitochondria (dual immunostaining, immunoblot, and immunogold electron microscopy) to ensure cell survival by preserving mitochondrial DNA integrity and bioenergetic functions. Whereas cytosolic HSP90 inhibition displays a lack of absolute specificity for PAH-PASMCs, Gamitrinib decreased mitochondrial DNA content and repair capacity and bioenergetic functions, thus repressing PAH-PASMC proliferation (Ki67 labeling) and resistance to apoptosis (Annexin V assay) without affecting control cells. In vivo, Gamitrinib improves PAH in two experimental rat models (monocrotaline and fawn-hooded rat). CONCLUSIONS Our data show for the first time that accumulation of mtHSP90 is a feature of PAH-PASMCs and a key regulator of mitochondrial homeostasis contributing to vascular remodeling in PAH.
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Affiliation(s)
- Olivier Boucherat
- 1 Pulmonary Hypertension Research Group, Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec City, Québec, Canada
| | - Thibaut Peterlini
- 1 Pulmonary Hypertension Research Group, Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec City, Québec, Canada
| | - Alice Bourgeois
- 1 Pulmonary Hypertension Research Group, Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec City, Québec, Canada
| | - Valérie Nadeau
- 1 Pulmonary Hypertension Research Group, Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec City, Québec, Canada
| | - Sandra Breuils-Bonnet
- 1 Pulmonary Hypertension Research Group, Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec City, Québec, Canada
| | - Stéphanie Boilet-Molez
- 1 Pulmonary Hypertension Research Group, Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec City, Québec, Canada
| | - François Potus
- 1 Pulmonary Hypertension Research Group, Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec City, Québec, Canada
| | - Jolyane Meloche
- 1 Pulmonary Hypertension Research Group, Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec City, Québec, Canada
| | - Sophie Chabot
- 1 Pulmonary Hypertension Research Group, Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec City, Québec, Canada
| | - Caroline Lambert
- 1 Pulmonary Hypertension Research Group, Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec City, Québec, Canada
| | - Eve Tremblay
- 1 Pulmonary Hypertension Research Group, Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec City, Québec, Canada
| | - Young Chan Chae
- 2 Prostate Cancer Discovery and Development Program, Tumor Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, Pennsylvania; and
| | - Dario C Altieri
- 2 Prostate Cancer Discovery and Development Program, Tumor Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, Pennsylvania; and
| | - Gopinath Sutendra
- 3 Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | | | - Roxane Paulin
- 1 Pulmonary Hypertension Research Group, Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec City, Québec, Canada
| | - Steeve Provencher
- 1 Pulmonary Hypertension Research Group, Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec City, Québec, Canada
| | - Sébastien Bonnet
- 1 Pulmonary Hypertension Research Group, Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec City, Québec, Canada
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Pontieri P, Hartings H, Di Salvo M, Massardo DR, De Stefano M, Pizzolante G, Romano R, Troisi J, Del Giudice A, Alifano P, Del Giudice L. Mitochondrial ribosomal proteins involved in tellurite resistance in yeast Saccharomyces cerevisiae. Sci Rep 2018; 8:12022. [PMID: 30104660 PMCID: PMC6089990 DOI: 10.1038/s41598-018-30479-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 07/23/2018] [Indexed: 11/22/2022] Open
Abstract
A considerable body of evidence links together mitochondrial dysfunctions, toxic action of metalloid oxyanions, and system and neurodegenerative disorders. In this study we have used the model yeast Saccharomyces cerevisiae to investigate the genetic determinants associated with tellurite resistance/sensitivity. Nitrosoguanidine-induced K2TeO3-resistant mutants were isolated, and one of these mutants, named Sc57-Te5R, was characterized. Both random spore analysis and tetrad analysis and growth of heterozygous (TeS/Te5R) diploid from Sc57-Te5R mutant revealed that nuclear and recessive mutation(s) was responsible for the resistance. To get insight into the mechanisms responsible for K2TeO3-resistance, RNA microarray analyses were performed with K2TeO3-treated and untreated Sc57-Te5R cells. A total of 372 differentially expressed loci were identified corresponding to 6.37% of the S. cerevisiae transcriptome. Of these, 288 transcripts were up-regulated upon K2TeO3 treatment. About half of up-regulated transcripts were associated with the following molecular functions: oxidoreductase activity, structural constituent of cell wall, transporter activity. Comparative whole-genome sequencing allowed us to identify nucleotide variants distinguishing Sc57-Te5R from parental strain Sc57. We detected 15 CDS-inactivating mutations, and found that 3 of them affected genes coding mitochondrial ribosomal proteins (MRPL44 and NAM9) and mitochondrial ribosomal biogenesis (GEP3) pointing out to alteration of mitochondrial ribosome as main determinant of tellurite resistance.
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Affiliation(s)
- Paola Pontieri
- Istituto di Bioscienze e BioRisorse-UOS Portici-CNR c/o Dipartimento di Biologia, Sezione di Igiene, Via Mezzocannone 16, Napoli, 80134, Italy
| | - Hans Hartings
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Via Stezzano 24, Bergamo, 24126, Italy
| | - Marco Di Salvo
- Dipartimento di Scienze e Tecnologie Biologiche e Ambientali, Università del Salento, Lecce, 73100, Italy
| | - Domenica R Massardo
- Istituto di Bioscienze e BioRisorse-UOS Portici-CNR c/o Dipartimento di Biologia, Sezione di Igiene, Via Mezzocannone 16, Napoli, 80134, Italy
| | - Mario De Stefano
- Dipartimento di Scienze Ambientali, Seconda Università degli Studi di Napoli, Via A. Vivaldi 43, Caserta, 81100, Italy
| | - Graziano Pizzolante
- ZooPlantLab, Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, Milano, 20126, Italy
| | - Roberta Romano
- Dipartimento di Ingegneria Civile, Chimica, Ambientale e dei Materiali (DICAM), Università di Bologna, Via Terracini 28, Bologna, 40131, Italy
| | - Jacopo Troisi
- Theoreo srl - Spin off dell' Università di Salerno, Via Salvatore Derenzi 50, Montecorvino Pugliano, 84125, (SA), Italy
| | - Angelica Del Giudice
- Amb di allergologia Osp Martini asl città di Torino, via Tofane 71, Torino, 10171, Italy
| | - Pietro Alifano
- Dipartimento di Scienze e Tecnologie Biologiche e Ambientali, Università del Salento, Lecce, 73100, Italy
| | - Luigi Del Giudice
- Istituto di Bioscienze e BioRisorse-UOS Portici-CNR c/o Dipartimento di Biologia, Sezione di Igiene, Via Mezzocannone 16, Napoli, 80134, Italy.
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