1
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Cheng Z, Xue K, Xiong C, Zheng Z, Li J, Qiao X. MRPS16 promotes lung adenocarcinoma growth via the PI3K/AKT/Frataxin signalling axis. J Cell Mol Med 2024; 28:e18166. [PMID: 38506080 PMCID: PMC10951875 DOI: 10.1111/jcmm.18166] [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: 06/05/2023] [Revised: 12/26/2023] [Accepted: 01/24/2024] [Indexed: 03/21/2024] Open
Abstract
Although MRPS16 is involved in cancer development, its mechanisms in developing LAUD remain unclear. Herein, qRT-PCR, WB and IHC were utilized for evaluating MRPS16 expression levels, while functional assays besides animal experiments were performed to measure MRPS16 effect on LAUD progression. Using WB, the MRPS16 effect on PI3K/AKT/Frataxin signalling pathway was tested. According to our study, MRPS16 was upregulated in LAUD and was correlated to the advanced TNM stage as well as poor clinical outcomes, which represent an independent prognostic factor. Based on functional assays, MRPS16 is involved in promoting LAUD growth, migration and invasion, which was validated further in subsequent analyses through PI3K/AKT/Frataxin pathway activation. Moreover, MRPS16-knockdown-mediated Frataxin overexpression was shown to restore the reduction in tumour cells proliferation, migration and invasion. Our results revealed that MRPS16 caused an aggressive phenotype to LAUD and was a poor prognosticator; thus, targeting MRPS16 may be effectual in LAUD treatment.
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Affiliation(s)
- Zaixing Cheng
- Department of Thoracic SurgeryUnion Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanHubeiChina
| | - Kaming Xue
- Department of Traditional Chinese MedicineUnion Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanHubeiChina
| | - Cui Xiong
- Department of EndocrinologyUnion Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanHubeiChina
| | - Zhikun Zheng
- Department of Thoracic SurgeryUnion Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanHubeiChina
| | - Jinsong Li
- Department of Thoracic SurgeryUnion Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanHubeiChina
| | - Xinwei Qiao
- Department of Thoracic SurgeryUnion Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanHubeiChina
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2
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Akhunzianov AA, Nesterova AI, Wanrooij S, Filina YV, Rizvanov AA, Miftakhova RR. Unravelling the Therapeutic Potential of Antibiotics in Hypoxia in a Breast Cancer MCF-7 Cell Line Model. Int J Mol Sci 2023; 24:11540. [PMID: 37511298 PMCID: PMC10380719 DOI: 10.3390/ijms241411540] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/04/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Antibiotics inhibit breast cancer stem cells (CSCs) by suppressing mitochondrial biogenesis. However, the effectiveness of antibiotics in clinical settings is inconsistent. This inconsistency raises the question of whether the tumor microenvironment, particularly hypoxia, plays a role in the response to antibiotics. Therefore, the goal of this study was to evaluate the effectiveness of five commonly used antibiotics for inhibiting CSCs under hypoxia using an MCF-7 cell line model. We assessed the number of CSCs through the mammosphere formation assay and aldehyde dehydrogenase (ALDH)-bright cell count. Additionally, we examined the impact of antibiotics on the mitochondrial stress response and membrane potential. Furthermore, we analyzed the levels of proteins associated with therapeutic resistance. There was no significant difference in the number of CSCs between cells cultured under normoxic and hypoxic conditions. However, hypoxia did affect the rate of CSC inhibition by antibiotics. Specifically, azithromycin was unable to inhibit sphere formation in hypoxia. Erythromycin and doxycycline did not reduce the ratio of ALDH-bright cells, despite decreasing the number of mammospheres. Furthermore, treatment with chloramphenicol, doxycycline, and tetracycline led to the overexpression of the breast cancer resistance protein. Our findings suggest that hypoxia may weaken the inhibitory effects of antibiotics on the breast cancer model.
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Affiliation(s)
- Almaz A Akhunzianov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Alfiya I Nesterova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
- Republican Clinical Oncology Dispensary Named after Prof. M.Z. Sigal, 420029 Kazan, Russia
| | - Sjoerd Wanrooij
- Department of Medical Biochemistry and Biophysics, Faculty of Medicine, Umeå University, 907 36 Umeå, Sweden
| | - Yulia V Filina
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Albert A Rizvanov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Regina R Miftakhova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
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3
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Reid K, Daniels EG, Vasam G, Kamble R, Janssens GE, Hu IM, Green AE, Houtkooper RH, Menzies KJ. Reducing mitochondrial ribosomal gene expression does not alter metabolic health or lifespan in mice. Sci Rep 2023; 13:8391. [PMID: 37225705 PMCID: PMC10209074 DOI: 10.1038/s41598-023-35196-3] [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: 11/14/2022] [Accepted: 05/14/2023] [Indexed: 05/26/2023] Open
Abstract
Maintaining mitochondrial function is critical to an improved healthspan and lifespan. Introducing mild stress by inhibiting mitochondrial translation invokes the mitochondrial unfolded protein response (UPRmt) and increases lifespan in several animal models. Notably, lower mitochondrial ribosomal protein (MRP) expression also correlates with increased lifespan in a reference population of mice. In this study, we tested whether partially reducing the gene expression of a critical MRP, Mrpl54, reduced mitochondrial DNA-encoded protein content, induced the UPRmt, and affected lifespan or metabolic health using germline heterozygous Mrpl54 mice. Despite reduced Mrpl54 expression in multiple organs and a reduction in mitochondrial-encoded protein expression in myoblasts, we identified few significant differences between male or female Mrpl54+/- and wild type mice in initial body composition, respiratory parameters, energy intake and expenditure, or ambulatory motion. We also observed no differences in glucose or insulin tolerance, treadmill endurance, cold tolerance, heart rate, or blood pressure. There were no differences in median life expectancy or maximum lifespan. Overall, we demonstrate that genetic manipulation of Mrpl54 expression reduces mitochondrial-encoded protein content but is not sufficient to improve healthspan in otherwise healthy and unstressed mice.
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Affiliation(s)
- Kim Reid
- Department of Biology and Ottawa Institute of Systems Biology, University of Ottawa, 30 Marie Curie Private, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology and the Éric Poulin Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON, Canada
| | - Eileen G Daniels
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology and Metabolism Institute, Amsterdam, The Netherlands
| | - Goutham Vasam
- Interdisciplinary School of Health Sciences, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
| | - Rashmi Kamble
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Georges E Janssens
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology and Metabolism Institute, Amsterdam, The Netherlands
| | - Iman M Hu
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology and Metabolism Institute, Amsterdam, The Netherlands
| | - Alexander E Green
- Interdisciplinary School of Health Sciences, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology and the Éric Poulin Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON, Canada
| | - Riekelt H Houtkooper
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
- Amsterdam Gastroenterology Endocrinology and Metabolism Institute, Amsterdam, The Netherlands.
- Amsterdam Cardiovascular Sciences Institute, Amsterdam, The Netherlands.
| | - Keir J Menzies
- Interdisciplinary School of Health Sciences, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada.
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology and the Éric Poulin Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON, Canada.
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4
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Rodríguez-Almonacid CC, Kellogg MK, Karamyshev AL, Karamysheva ZN. Ribosome Specialization in Protozoa Parasites. Int J Mol Sci 2023; 24:ijms24087484. [PMID: 37108644 PMCID: PMC10138883 DOI: 10.3390/ijms24087484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Ribosomes, in general, are viewed as constitutive macromolecular machines where protein synthesis takes place; however, this view has been recently challenged, supporting the hypothesis of ribosome specialization and opening a completely new field of research. Recent studies have demonstrated that ribosomes are heterogenous in their nature and can provide another layer of gene expression control by regulating translation. Heterogeneities in ribosomal RNA and ribosomal proteins that compose them favor the selective translation of different sub-pools of mRNAs and functional specialization. In recent years, the heterogeneity and specialization of ribosomes have been widely reported in different eukaryotic study models; however, few reports on this topic have been made on protozoa and even less on protozoa parasites of medical importance. This review analyzes heterogeneities of ribosomes in protozoa parasites highlighting the specialization in their functions and their importance in parasitism, in the transition between stages in their life cycle, in the change of host and in response to environmental conditions.
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Affiliation(s)
| | - Morgana K Kellogg
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Andrey L Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
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5
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Koc EC, Hunter CA, Koc H. Phosphorylation of mammalian mitochondrial EF-Tu by Fyn and c-Src kinases. Cell Signal 2023; 101:110524. [PMID: 36379377 DOI: 10.1016/j.cellsig.2022.110524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/31/2022] [Accepted: 11/09/2022] [Indexed: 11/14/2022]
Abstract
Src Family Kinases (SFKs) are tyrosine kinases known to regulate glucose and fatty acid metabolism as well as oxidative phosphorylation (OXPHOS) in mammalian mitochondria. We and others discovered the association of the SFK kinases Fyn and c-Src with mitochondrial translation components. This translational system is responsible for the synthesis of 13 mitochondrial (mt)-encoded subunits of the OXPHOS complexes and is, thus, essential for energy generation. Mitochondrial ribosomal proteins and various translation elongation factors including Tu (EF-Tumt) have been identified as possible Fyn and c-Src kinase targets. However, the phosphorylation of specific residues in EF-Tumt by these kinases and their roles in the regulation of protein synthesis are yet to be explored. In this study, we report the association of EF-Tumt with cSrc kinase and mapping of phosphorylated Tyr (pTyr) residues by these kinases. We determined that a specific Tyr residue in EF-Tumt at position 266 (EF-Tumt-Y266), located in a highly conserved c-Src consensus motif is one of the major phosphorylation sites. The potential role of EF-Tumt-Y266 phosphorylation in regulation of mitochondrial translation investigated by site-directed mutagenesis. Its phosphomimetic to Glu residue (EF-Tumt-E266) inhibited ternary complex (EF-Tumt•GTP•aatRNA) formation and translation in vitro. Our findings along with data mining analysis of the c-Src knock out (KO) mice proteome suggest that the SFKs have possible roles for regulation of mitochondrial protein synthesis and oxidative energy metabolism in animals.
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Affiliation(s)
- Emine C Koc
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25755, United States of America.
| | - Caroline A Hunter
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25755, United States of America
| | - Hasan Koc
- Department of Pharmacological Science, School of Pharmacy, Marshall University, Huntington, WV 25755, United States of America.
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6
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Koc ZC, Sollars VE, Bou Zgheib N, Rankin GO, Koc EC. Evaluation of mitochondrial biogenesis and ROS generation in high-grade serous ovarian cancer. Front Oncol 2023; 13:1129352. [PMID: 36937395 PMCID: PMC10014927 DOI: 10.3389/fonc.2023.1129352] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/08/2023] [Indexed: 03/05/2023] Open
Abstract
Introduction Ovarian cancer is one of the leading causes of death for women with cancer worldwide. Energy requirements for tumor growth in epithelial high-grade serous ovarian cancer (HGSOC) are fulfilled by a combination of aerobic glycolysis and oxidative phosphorylation (OXPHOS). Although reduced OXPHOS activity has emerged as one of the significant contributors to tumor aggressiveness and chemoresistance, up-regulation of mitochondrial antioxidant capacity is required for matrix detachment and colonization into the peritoneal cavity to form malignant ascites in HGSOC patients. However, limited information is available about the mitochondrial biogenesis regulating OXPHOS capacity and generation of mitochondrial reactive oxygen species (mtROS) in HGSOC. Methods To evaluate the modulation of OXPHOS in HGSOC tumor samples and ovarian cancer cell lines, we performed proteomic analyses of proteins involved in mitochondrial energy metabolism and biogenesis and formation of mtROS by immunoblotting and flow cytometry, respectively. Results and discussion We determined that the increased steady-state expression levels of mitochondrial- and nuclear-encoded OXPHOS subunits were associated with increased mitochondrial biogenesis in HGSOC tumors and ovarian cancer cell lines. The more prominent increase in MT-COII expression was in agreement with significant increase in mitochondrial translation factors, TUFM and DARS2. On the other hand, the ovarian cancer cell lines with reduced OXPHOS subunit expression and mitochondrial translation generated the highest levels of mtROS and significantly reduced SOD2 expression. Evaluation of mitochondrial biogenesis suggested that therapies directed against mitochondrial targets, such as those involved in transcription and translation machineries, should be considered in addition to the conventional chemotherapies in HGSOC treatment.
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Affiliation(s)
- Zeynep C. Koc
- Department of Obstetrics, Gynecology and Reproductive Sciences, Temple University, Philadelphia, PA, United States
| | - Vincent E. Sollars
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, United States
| | - Nadim Bou Zgheib
- Edwards Comprehensive Cancer Center, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, United States
| | - Gary O. Rankin
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, United States
| | - Emine C. Koc
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, United States
- *Correspondence: Emine C. Koc,
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7
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Srivastava H, Lippincott MJ, Currie J, Canfield R, Lam MPY, Lau E. Protein prediction models support widespread post-transcriptional regulation of protein abundance by interacting partners. PLoS Comput Biol 2022; 18:e1010702. [PMID: 36356032 PMCID: PMC9681107 DOI: 10.1371/journal.pcbi.1010702] [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: 05/11/2022] [Revised: 11/22/2022] [Accepted: 11/01/2022] [Indexed: 11/12/2022] Open
Abstract
Protein and mRNA levels correlate only moderately. The availability of proteogenomics data sets with protein and transcript measurements from matching samples is providing new opportunities to assess the degree to which protein levels in a system can be predicted from mRNA information. Here we examined the contributions of input features in protein abundance prediction models. Using large proteogenomics data from 8 cancer types within the Clinical Proteomic Tumor Analysis Consortium (CPTAC) data set, we trained models to predict the abundance of over 13,000 proteins using matching transcriptome data from up to 958 tumor or normal adjacent tissue samples each, and compared predictive performances across algorithms, data set sizes, and input features. Over one-third of proteins (4,648) showed relatively poor predictability (elastic net r ≤ 0.3) from their cognate transcripts. Moreover, we found widespread occurrences where the abundance of a protein is considerably less well explained by its own cognate transcript level than that of one or more trans locus transcripts. The incorporation of additional trans-locus transcript abundance data as input features increasingly improved the ability to predict sample protein abundance. Transcripts that contribute to non-cognate protein abundance primarily involve those encoding known or predicted interaction partners of the protein of interest, including not only large multi-protein complexes as previously shown, but also small stable complexes in the proteome with only one or few stable interacting partners. Network analysis further shows a complex proteome-wide interdependency of protein abundance on the transcript levels of multiple interacting partners. The predictive model analysis here therefore supports that protein-protein interaction including in small protein complexes exert post-transcriptional influence on proteome compositions more broadly than previously recognized. Moreover, the results suggest mRNA and protein co-expression analysis may have utility for finding gene interactions and predicting expression changes in biological systems.
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Affiliation(s)
- Himangi Srivastava
- Department of Medicine/Cardiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
- Consortium for Fibrosis Research and Translation, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Michael J. Lippincott
- Department of Medicine/Cardiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Jordan Currie
- Department of Medicine/Cardiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Robert Canfield
- Department of Medicine/Cardiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Maggie P. Y. Lam
- Department of Medicine/Cardiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
- Consortium for Fibrosis Research and Translation, University of Colorado School of Medicine, Aurora, Colorado, United States of America
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Edward Lau
- Department of Medicine/Cardiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
- Consortium for Fibrosis Research and Translation, University of Colorado School of Medicine, Aurora, Colorado, United States of America
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8
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Jiang Y, Xiang Y, Lin C, Zhang W, Yang Z, Xiang L, Xiao Y, Chen L, Ran Q, Li Z. Multifunctions of CRIF1 in cancers and mitochondrial dysfunction. Front Oncol 2022; 12:1009948. [PMID: 36263222 PMCID: PMC9574215 DOI: 10.3389/fonc.2022.1009948] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/14/2022] [Indexed: 11/23/2022] Open
Abstract
Sustaining proliferative signaling and enabling replicative immortality are two important hallmarks of cancer. The complex of cyclin-dependent kinase (CDK) and its cyclin plays a decisive role in the transformation of the cell cycle and is also critical in the initiation and progression of cancer. CRIF1, a multifunctional factor, plays a pivotal role in a series of cell biological progresses such as cell cycle, cell proliferation, and energy metabolism. CRIF1 is best known as a negative regulator of the cell cycle, on account of directly binding to Gadd45 family proteins or CDK2. In addition, CRIF1 acts as a regulator of several transcription factors such as Nur77 and STAT3 and partly determines the proliferation of cancer cells. Many studies showed that the expression of CRIF1 is significantly altered in cancers and potentially regarded as a tumor suppressor. This suggests that targeting CRIF1 would enhance the selectivity and sensitivity of cancer treatment. Moreover, CRIF1 might be an indispensable part of mitoribosome and is involved in the regulation of OXPHOS capacity. Further, CRIF1 is thought to be a novel target for the underlying mechanism of diseases with mitochondrial dysfunctions. In summary, this review would conclude the latest aspects of studies about CRIF1 in cancers and mitochondria-related diseases, shed new light on targeted therapy, and provide a more comprehensive holistic view.
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Affiliation(s)
- Yangzhou Jiang
- Laboratory of Radiation Biology, Laboratory Medicine Center, Department of Blood Transfusion, The Second Affiliated Hospital, Army Military Medical University, Chongqing, China
| | - Yang Xiang
- Laboratory of Radiation Biology, Laboratory Medicine Center, Department of Blood Transfusion, The Second Affiliated Hospital, Army Military Medical University, Chongqing, China
| | - Chuanchuan Lin
- Laboratory of Radiation Biology, Laboratory Medicine Center, Department of Blood Transfusion, The Second Affiliated Hospital, Army Military Medical University, Chongqing, China
| | - Weiwei Zhang
- Laboratory of Radiation Biology, Laboratory Medicine Center, Department of Blood Transfusion, The Second Affiliated Hospital, Army Military Medical University, Chongqing, China
| | - Zhenxing Yang
- Laboratory of Radiation Biology, Laboratory Medicine Center, Department of Blood Transfusion, The Second Affiliated Hospital, Army Military Medical University, Chongqing, China
| | - Lixin Xiang
- Laboratory of Radiation Biology, Laboratory Medicine Center, Department of Blood Transfusion, The Second Affiliated Hospital, Army Military Medical University, Chongqing, China
| | - Yanni Xiao
- Laboratory of Radiation Biology, Laboratory Medicine Center, Department of Blood Transfusion, The Second Affiliated Hospital, Army Military Medical University, Chongqing, China
| | - Li Chen
- Laboratory of Radiation Biology, Laboratory Medicine Center, Department of Blood Transfusion, The Second Affiliated Hospital, Army Military Medical University, Chongqing, China
| | - Qian Ran
- Laboratory of Radiation Biology, Laboratory Medicine Center, Department of Blood Transfusion, The Second Affiliated Hospital, Army Military Medical University, Chongqing, China
| | - Zhongjun Li
- Laboratory of Radiation Biology, Laboratory Medicine Center, Department of Blood Transfusion, The Second Affiliated Hospital, Army Military Medical University, Chongqing, China
- State Key Laboratory of Trauma, Burn and Combined Injuries, The Second Affiliated Hospital, Army Medical University, Chongqing, China
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9
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Koc EC, Koc FC, Kartal F, Tirona M, Koc H. Role of mitochondrial translation in remodeling of energy metabolism in ER/PR(+) breast cancer. Front Oncol 2022; 12:897207. [PMID: 36119536 PMCID: PMC9472243 DOI: 10.3389/fonc.2022.897207] [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: 03/15/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Remodeling of mitochondrial energy metabolism is essential for the survival of tumor cells in limited nutrient availability and hypoxic conditions. Defects in oxidative phosphorylation (OXPHOS) and mitochondrial biogenesis also cause a switch in energy metabolism from oxidative to aerobic glycolysis contributing to the tumor heterogeneity in cancer. Specifically, the aberrant expressions of mitochondrial translation components such as ribosomal proteins (MRPs) and translation factors have been increasingly associated with many different cancers including breast cancer. The mitochondrial translation is responsible for the synthesis 13 of mitochondrial-encoded OXPHOS subunits of complexes. In this study, we investigated the contribution of mitochondrial translation in the remodeling of oxidative energy metabolism through altered expression of OXPHOS subunits in 26 ER/PR(+) breast tumors. We observed a significant correlation between the changes in the expression of mitochondrial translation-related proteins and OXPHOS subunits in the majority of the ER/PR(+) breast tumors and breast cancer cell lines. The reduced expression of OXPHOS and mitochondrial translation components also correlated well with the changes in epithelial-mesenchymal transition (EMT) markers, E-cadherin (CHD1), and vimentin (VIM) in the ER/PR(+) tumor biopsies. Data mining analysis of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) breast cancer proteome further supported the correlation between the reduced OXPHOS subunit expression and increased EMT and metastatic marker expression in the majority of the ER/PR(+) tumors. Therefore, understanding the role of MRPs in the remodeling of energy metabolism will be essential in the characterization of heterogeneity at the molecular level and serve as diagnostic and prognostic markers in breast cancer.
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Affiliation(s)
- Emine C. Koc
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, United States
- *Correspondence: Emine C. Koc, ; Hasan Koc,
| | - Fatih C. Koc
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, United States
| | - Funda Kartal
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, United States
| | - Maria Tirona
- Department of Medical Oncology, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, United States
| | - Hasan Koc
- Department of Pharmaceutical Science, School of Pharmacy, Marshall University, Huntington, WV, United States
- *Correspondence: Emine C. Koc, ; Hasan Koc,
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10
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Cascone A, Lalowski M, Lindholm D, Eriksson O. Unveiling the Function of the Mitochondrial Filament-Forming Protein LACTB in Lipid Metabolism and Cancer. Cells 2022; 11:cells11101703. [PMID: 35626737 PMCID: PMC9139886 DOI: 10.3390/cells11101703] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 02/04/2023] Open
Abstract
LACTB is a relatively unknown mitochondrial protein structurally related to the bacterial penicillin-binding and beta-lactamase superfamily of serine proteases. LACTB has recently gained an increased interest due to its potential role in lipid metabolism and tumorigenesis. To date, around ninety studies pertaining to LACTB have been published, but the exact biochemical and cell biological function of LACTB still remain elusive. In this review, we summarise the current knowledge about LACTB with particular attention to the implications of the recently published study on the cryo-electron microscopy structure of the filamentous form of LACTB. From this and other studies, several specific properties of LACTB emerge, suggesting that the protein has distinct functions in different physiological settings. Resolving these issues by further research may ultimately lead to a unified model of LACTB’s function in cell and organismal physiology. LACTB is the only member of its protein family in higher animals and LACTB may, therefore, be of particular interest for future drug targeting initiatives.
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Affiliation(s)
- Annunziata Cascone
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, FIN-00014 Helsinki, Finland; (A.C.); (D.L.)
| | - Maciej Lalowski
- HiLIFE, Meilahti Clinical Proteomics Core Facility, Faculty of Medicine, University of Helsinki, FIN-00014 Helsinki, Finland;
| | - Dan Lindholm
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, FIN-00014 Helsinki, Finland; (A.C.); (D.L.)
- Minerva Foundation Institute for Medical Research, Biomedicum Helsinki 2, Tukholmankatu 8, FIN-00290 Helsinki, Finland
| | - Ove Eriksson
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, FIN-00014 Helsinki, Finland; (A.C.); (D.L.)
- Correspondence:
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11
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Buczyńska A, Sidorkiewicz I, Hameed A, Krętowski AJ, Zbucka-Krętowska M. Future Perspectives in Oxidative Stress in Trisomy 13 and 18 Evaluation. J Clin Med 2022; 11:jcm11071787. [PMID: 35407395 PMCID: PMC8999694 DOI: 10.3390/jcm11071787] [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: 02/07/2022] [Revised: 03/07/2022] [Accepted: 03/22/2022] [Indexed: 02/05/2023] Open
Abstract
Autosomal aneuploidies are the most frequently occurring congenital abnormalities and are related to many metabolic disorders, hormonal dysfunctions, neurotransmitter abnormalities, and intellectual disabilities. Trisomies are generated by an error of chromosomal segregation during cell division. Accumulating evidence has shown that deregulated gene expression resulting from the triplication of chromosomes 13 and 18 is associated with many disturbed cellular processes. Moreover, a disturbed oxidative stress status may be implicated in the occurrence of fetal malformations. Therefore, a literature review was undertaken to provide novel insights into the evaluation of trisomy 13 (T13) and 18 (T18) pathogeneses, with a particular concern on the oxidative stress. Corresponding to the limited literature data focused on factors leading to T13 and T18 phenotype occurrence, the importance of oxidative stress evaluation in T13 and T18 could enable the determination of subsequent disturbed metabolic pathways, highlighting the related role of mitochondrial dysfunction or epigenetics. This review illustrates up-to-date T13 and T18 research and discusses the strengths, limitations, and possible directions for future studies. The progressive unification of trisomy-related research protocols might provide potential medical targets in the future along with the implementation of the foundation of modern prenatal medicine.
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Affiliation(s)
- Angelika Buczyńska
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland; (I.S.); (A.H.); (A.J.K.)
- Correspondence: (A.B.); (M.Z.-K.); Tel.: +48-85-746-85-13 (A.B.); +48-85-746-83-36 (M.Z.-K.)
| | - Iwona Sidorkiewicz
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland; (I.S.); (A.H.); (A.J.K.)
| | - Ahsan Hameed
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland; (I.S.); (A.H.); (A.J.K.)
| | - Adam Jacek Krętowski
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland; (I.S.); (A.H.); (A.J.K.)
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, 15-276 Bialystok, Poland
| | - Monika Zbucka-Krętowska
- Department of Gynecological Endocrinology and Adolescent Gynecology, Medical University of Bialystok, 15-276 Bialystok, Poland
- Correspondence: (A.B.); (M.Z.-K.); Tel.: +48-85-746-85-13 (A.B.); +48-85-746-83-36 (M.Z.-K.)
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12
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Scaltsoyiannes V, Corre N, Waltz F, Giegé P. Types and Functions of Mitoribosome-Specific Ribosomal Proteins across Eukaryotes. Int J Mol Sci 2022; 23:ijms23073474. [PMID: 35408834 PMCID: PMC8998825 DOI: 10.3390/ijms23073474] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 02/04/2023] Open
Abstract
Mitochondria are key organelles that combine features inherited from their bacterial endosymbiotic ancestor with traits that arose during eukaryote evolution. These energy producing organelles have retained a genome and fully functional gene expression machineries including specific ribosomes. Recent advances in cryo-electron microscopy have enabled the characterization of a fast-growing number of the low abundant membrane-bound mitochondrial ribosomes. Surprisingly, mitoribosomes were found to be extremely diverse both in terms of structure and composition. Still, all of them drastically increased their number of ribosomal proteins. Interestingly, among the more than 130 novel ribosomal proteins identified to date in mitochondria, most of them are composed of a-helices. Many of them belong to the nuclear encoded super family of helical repeat proteins. Here we review the diversity of functions and the mode of action held by the novel mitoribosome proteins and discuss why these proteins that share similar helical folds were independently recruited by mitoribosomes during evolution in independent eukaryote clades.
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Affiliation(s)
- Vassilis Scaltsoyiannes
- CNRS, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 67084 Strasbourg, France; (V.S.); (N.C.)
| | - Nicolas Corre
- CNRS, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 67084 Strasbourg, France; (V.S.); (N.C.)
| | - Florent Waltz
- CNRS, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 67084 Strasbourg, France; (V.S.); (N.C.)
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Munich, Germany
- Correspondence: (F.W.); (P.G.); Tel.: +33-3-6715-5363 (P.G.); Fax: +33-3-8861-4442 (P.G.)
| | - Philippe Giegé
- CNRS, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 67084 Strasbourg, France; (V.S.); (N.C.)
- Correspondence: (F.W.); (P.G.); Tel.: +33-3-6715-5363 (P.G.); Fax: +33-3-8861-4442 (P.G.)
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13
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Cheng J, Sha Z, Zhang R, Ge J, Chen P, Kuang X, Chang J, Ren K, Luo X, Chen S, Gou X. L22 ribosomal protein is involved in dynamin-related protein 1-mediated gastric carcinoma progression. Bioengineered 2022; 13:6650-6664. [PMID: 35230214 PMCID: PMC9208493 DOI: 10.1080/21655979.2022.2045842] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Mitochondrial fission depends on dynamin-related protein 1 (Drp1) guanosine triphosphatase activity. Although there is some association between Drp1 and gastric cancer, the detailed mechanism remains largely unknown. In this study, the elevation of Drp1 was observed in human gastric carcinoma specimens including gastric mixed adenocarcinoma tissues, gastric intestinal-type adenocarcinoma tissues, and human gastric cancer cells compared to normal control, but not in diffuse gastric adenocarcinoma tissues. Gastric cancer patients with high Drp1 harbored advanced pathological stages and poor progression-free survival probability compared to those with low Drp1. Mdivi-1-mediated inactivation of Drp1 robustly inhibited cell viability and tumor growth but conversely induced cell apoptotic events in vitro and in vivo. Based on the Encyclopedia of RNA Interactomes Starbase, L22 ribosomal protein (RPL22) was recognized as the potential downstream oncogene of Drp1. Clinically, the significant correlation of Drp1 and RPL22 was also verified. Mechanistically, Drp1 inactivation did not affect the accumulation of RPL22 in gastric carcinoma. However, the intracellular distribution of RPL22 had an endonuclear location in Drp1-inactivated tumors. Of note, Drp1 inactivation notably reduced the expression of cytoplasmic RPL22 and increased its nuclear level in gastric cancer cells. Collectively, Drp1 had high levels in human gastric carcinoma specimens and could serve as a potential diagnostic and prognostic biomarker in gastric carcinoma. The Drp1 inactivation-mediated anti-proliferative and pro-apoptosis effects on gastric cancer were possibly associated with nuclear import of RPL22. This knowledge may provide new therapeutic tools for treating gastric carcinoma via targeting mitochondria-related ribosome pathway.
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Affiliation(s)
- Jianghong Cheng
- Shaanxi Key Laboratory of Brain Disorders and School of Basic Medical Science, Xi'an Medical UniversityChina , Xi'an, China
| | - Zizhuo Sha
- Shaanxi Key Laboratory of Brain Disorders and School of Basic Medical Science, Xi'an Medical UniversityChina , Xi'an, China
| | - Ruisan Zhang
- Shaanxi Key Laboratory of Brain Disorders and School of Basic Medical Science, Xi'an Medical UniversityChina , Xi'an, China
| | - Jinghao Ge
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Peng Chen
- Shaanxi Key Laboratory of Brain Disorders and School of Basic Medical Science, Xi'an Medical UniversityChina , Xi'an, China
| | - Xuefeng Kuang
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Jiazhi Chang
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Kai Ren
- Shaanxi Key Laboratory of Brain Disorders and School of Basic Medical Science, Xi'an Medical UniversityChina , Xi'an, China
| | - Xianyang Luo
- Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, China.,Xiamen Key Laboratory of Otolaryngology Head and Neck Surgery, Xiamen, China
| | - Shuai Chen
- Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, China.,Xiamen Key Laboratory of Otolaryngology Head and Neck Surgery, Xiamen, China
| | - Xingchun Gou
- Shaanxi Key Laboratory of Brain Disorders and School of Basic Medical Science, Xi'an Medical UniversityChina , Xi'an, China.,Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, China.,Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, China
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14
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Schell R, Hale JJ, Mullis MN, Matsui T, Foree R, Ehrenreich IM. Genetic basis of a spontaneous mutation’s expressivity. Genetics 2022; 220:6515283. [PMID: 35078232 PMCID: PMC8893249 DOI: 10.1093/genetics/iyac013] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/19/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Genetic background often influences the phenotypic consequences of mutations, resulting in variable expressivity. How standing genetic variants collectively cause this phenomenon is not fully understood. Here, we comprehensively identify loci in a budding yeast cross that impact the growth of individuals carrying a spontaneous missense mutation in the nuclear-encoded mitochondrial ribosomal gene MRP20. Initial results suggested that a single large effect locus influences the mutation’s expressivity, with one allele causing inviability in mutants. However, further experiments revealed this simplicity was an illusion. In fact, many additional loci shape the mutation’s expressivity, collectively leading to a wide spectrum of mutational responses. These results exemplify how complex combinations of alleles can produce a diversity of qualitative and quantitative responses to the same mutation.
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Affiliation(s)
- Rachel Schell
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Joseph J Hale
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Martin N Mullis
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Takeshi Matsui
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Ryan Foree
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Ian M Ehrenreich
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
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15
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Tirumalai MR, Rivas M, Tran Q, Fox GE. The Peptidyl Transferase Center: a Window to the Past. Microbiol Mol Biol Rev 2021; 85:e0010421. [PMID: 34756086 PMCID: PMC8579967 DOI: 10.1128/mmbr.00104-21] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
In his 2001 article, "Translation: in retrospect and prospect," the late Carl Woese made a prescient observation that there was a need for the then-current view of translation to be "reformulated to become an all-embracing perspective about which 21st century Biology can develop" (RNA 7:1055-1067, 2001, https://doi.org/10.1017/s1355838201010615). The quest to decipher the origins of life and the road to the genetic code are both inextricably linked with the history of the ribosome. After over 60 years of research, significant progress in our understanding of how ribosomes work has been made. Particularly attractive is a model in which the ribosome may facilitate an ∼180° rotation of the CCA end of the tRNA from the A-site to the P-site while the acceptor stem of the tRNA would then undergo a translation from the A-site to the P-site. However, the central question of how the ribosome originated remains unresolved. Along the path from a primitive RNA world or an RNA-peptide world to a proto-ribosome world, the advent of the peptidyl transferase activity would have been a seminal event. This functionality is now housed within a local region of the large-subunit (LSU) rRNA, namely, the peptidyl transferase center (PTC). The PTC is responsible for peptide bond formation during protein synthesis and is usually considered to be the oldest part of the modern ribosome. What is frequently overlooked is that by examining the origins of the PTC itself, one is likely going back even further in time. In this regard, it has been proposed that the modern PTC originated from the association of two smaller RNAs that were once independent and now comprise a pseudosymmetric region in the modern PTC. Could such an association have survived? Recent studies have shown that the extant PTC is largely depleted of ribosomal protein interactions. It is other elements like metallic ion coordination and nonstandard base/base interactions that would have had to stabilize the association of RNAs. Here, we present a detailed review of the literature focused on the nature of the extant PTC and its proposed ancestor, the proto-ribosome.
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Affiliation(s)
- Madhan R. Tirumalai
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - Mario Rivas
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - Quyen Tran
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - George E. Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
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16
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Jakoube P, Cutano V, González-Morena JM, Keckesova Z. Mitochondrial Tumor Suppressors-The Energetic Enemies of Tumor Progression. Cancer Res 2021; 81:4652-4667. [PMID: 34183354 PMCID: PMC9397617 DOI: 10.1158/0008-5472.can-21-0518] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/09/2021] [Accepted: 06/24/2021] [Indexed: 01/07/2023]
Abstract
Tumor suppressors represent a critical line of defense against tumorigenesis. Their mechanisms of action and the pathways they are involved in provide important insights into cancer progression, vulnerabilities, and treatment options. Although nuclear and cytosolic tumor suppressors have been extensively investigated, relatively little is known about tumor suppressors localized within the mitochondria. However, recent research has begun to uncover the roles of these important proteins in suppressing tumorigenesis. Here, we review this newly developing field and summarize available information on mitochondrial tumor suppressors.
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Affiliation(s)
- Pavel Jakoube
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic.,Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Valentina Cutano
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Juan M. González-Morena
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Zuzana Keckesova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic.,Corresponding Author: Zuzana Keckesova, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Namesti 2, Prague 16000, Czech Republic. Phone: 420-2201-83584; E-mail:
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17
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Friedlander JE, Shen N, Zeng A, Korm S, Feng H. Failure to Guard: Mitochondrial Protein Quality Control in Cancer. Int J Mol Sci 2021; 22:ijms22158306. [PMID: 34361072 PMCID: PMC8348654 DOI: 10.3390/ijms22158306] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 07/20/2021] [Accepted: 07/27/2021] [Indexed: 02/07/2023] Open
Abstract
Mitochondria are energetic and dynamic organelles with a crucial role in bioenergetics, metabolism, and signaling. Mitochondrial proteins, encoded by both nuclear and mitochondrial DNA, must be properly regulated to ensure proteostasis. Mitochondrial protein quality control (MPQC) serves as a critical surveillance system, employing different pathways and regulators as cellular guardians to ensure mitochondrial protein quality and quantity. In this review, we describe key pathways and players in MPQC, such as mitochondrial protein translocation-associated degradation, mitochondrial stress responses, chaperones, and proteases, and how they work together to safeguard mitochondrial health and integrity. Deregulated MPQC leads to proteotoxicity and dysfunctional mitochondria, which contributes to numerous human diseases, including cancer. We discuss how alterations in MPQC components are linked to tumorigenesis, whether they act as drivers, suppressors, or both. Finally, we summarize recent advances that seek to target these alterations for the development of anti-cancer drugs.
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Affiliation(s)
- Joseph E. Friedlander
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA; (J.E.F.); (N.S.); (A.Z.); (S.K.)
| | - Ning Shen
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA; (J.E.F.); (N.S.); (A.Z.); (S.K.)
- Department of Medicine, Section of Hematology and Medical Oncology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Aozhuo Zeng
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA; (J.E.F.); (N.S.); (A.Z.); (S.K.)
| | - Sovannarith Korm
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA; (J.E.F.); (N.S.); (A.Z.); (S.K.)
| | - Hui Feng
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA; (J.E.F.); (N.S.); (A.Z.); (S.K.)
- Department of Medicine, Section of Hematology and Medical Oncology, Boston University School of Medicine, Boston, MA 02118, USA
- Correspondence: ; Tel.: +1-617-358-4688; Fax: +1-617-358-1599
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18
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Policard M, Jain S, Rego S, Dakshanamurthy S. Immune characterization and profiles of SARS-CoV-2 infected patients reveals potential host therapeutic targets and SARS-CoV-2 oncogenesis mechanism. Virus Res 2021; 301:198464. [PMID: 34058265 PMCID: PMC8163696 DOI: 10.1016/j.virusres.2021.198464] [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: 03/19/2021] [Accepted: 05/19/2021] [Indexed: 01/25/2023]
Abstract
The spread of SARS-CoV-2 and the increasing mortality rates of COVID-19 create an urgent need for treatments, which are currently lacking. Although vaccines have been approved by the FDA for emergency use in the U.S., patients will continue to require pharmacologic intervention to reduce morbidity and mortality as vaccine availability remains limited. The rise of new variants makes the development of therapeutic strategies even more crucial to combat the current pandemic and future outbreaks. Evidence from several studies suggests the host immune response to SARS-CoV-2 infection plays a critical role in disease pathogenesis. Consequently, host immune factors are becoming more recognized as potential biomarkers and therapeutic targets for COVID-19. To develop therapeutic strategies to combat current and future coronavirus outbreaks, understanding how the coronavirus hijacks the host immune system during and after the infection is crucial. In this study, we investigated immunological patterns or characteristics of the host immune response to SARS-CoV-2 infection that may contribute to the disease severity of COVID-19 patients. We analyzed large bulk RNASeq and single cell RNAseq data from COVID-19 patient samples to immunoprofile differentially expressed gene sets and analyzed pathways to identify human host protein targets. We observed an immunological profile of severe COVID-19 patients characterized by upregulated cytokines, interferon-induced proteins, and pronounced T cell lymphopenia, supporting findings by previous studies. We identified a number of host immune targets including PERK, PKR, TNF, NF-kB, and other key genes that modulate the significant pathways and genes identified in COVID-19 patients. Finally, we identified genes modulated by COVID-19 infection that are implicated in oncogenesis, including E2F transcription factors and RB1, suggesting a mechanism by which SARS-CoV-2 infection may contribute to oncogenesis. Further clinical investigation of these targets may lead to bonafide therapeutic strategies to treat the current COVID-19 pandemic and protect against future outbreaks and viral escape variants.
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Affiliation(s)
- Martine Policard
- Clinical & Experimental Therapeutics Program, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, New Research Building, 3970 Reservoir Road NW, Washington, DC 20057-1469, United States
| | - Sidharth Jain
- Clinical & Experimental Therapeutics Program, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, New Research Building, 3970 Reservoir Road NW, Washington, DC 20057-1469, United States
| | - Samantha Rego
- Clinical & Experimental Therapeutics Program, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, New Research Building, 3970 Reservoir Road NW, Washington, DC 20057-1469, United States
| | - Sivanesan Dakshanamurthy
- Clinical & Experimental Therapeutics Program, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, New Research Building, 3970 Reservoir Road NW, Washington, DC 20057-1469, United States.
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19
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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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20
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Wang F, Zhang D, Zhang D, Li P, Gao Y. Mitochondrial Protein Translation: Emerging Roles and Clinical Significance in Disease. Front Cell Dev Biol 2021; 9:675465. [PMID: 34277617 PMCID: PMC8280776 DOI: 10.3389/fcell.2021.675465] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/09/2021] [Indexed: 12/28/2022] Open
Abstract
Mitochondria are one of the most important organelles in cells. Mitochondria are semi-autonomous organelles with their own genetic system, and can independently replicate, transcribe, and translate mitochondrial DNA. Translation initiation, elongation, termination, and recycling of the ribosome are four stages in the process of mitochondrial protein translation. In this process, mitochondrial protein translation factors and translation activators, mitochondrial RNA, and other regulatory factors regulate mitochondrial protein translation. Mitochondrial protein translation abnormalities are associated with a variety of diseases, including cancer, cardiovascular diseases, and nervous system diseases. Mutation or deletion of various mitochondrial protein translation factors and translation activators leads to abnormal mitochondrial protein translation. Mitochondrial tRNAs and mitochondrial ribosomal proteins are essential players during translation and mutations in genes encoding them represent a large fraction of mitochondrial diseases. Moreover, there is crosstalk between mitochondrial protein translation and cytoplasmic translation, and the imbalance between mitochondrial protein translation and cytoplasmic translation can affect some physiological and pathological processes. This review summarizes the regulation of mitochondrial protein translation factors, mitochondrial ribosomal proteins, mitochondrial tRNAs, and mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs) in the mitochondrial protein translation process and its relationship with diseases. The regulation of mitochondrial protein translation and cytoplasmic translation in multiple diseases is also summarized.
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Affiliation(s)
- Fei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Deyu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.,Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, China
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21
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Almutairi ZM. Molecular characterization and expression analysis of ribosomal L18/L5e gene in Pennisetum glaucum (L.) R. Br. Saudi J Biol Sci 2021; 28:3585-3593. [PMID: 34121902 PMCID: PMC8176002 DOI: 10.1016/j.sjbs.2021.03.035] [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: 02/23/2020] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 11/21/2022] Open
Abstract
Ribosomal L18/L5e (RL18/L5e) is a member of the ribosomal L18/L5e protein family, which has an essential function in translation of mRNA into protein in the large ribosomal subunit. In this study, RL18/L5e was isolated and sequenced from local Pennisetum glaucum (L.) R. Br. cultivar which is known to adapt to environmental stress. The obtained cDNA for PgRL18/L5e was 699 bp in length, with an open reading frame of 564 bp. The deduced protein sequence contained 187 amino acids and comprised an RL18/L5e domain, which shared high sequence identity with orthologous proteins from Viridiplantae. The obtained PgRL18/L5e cDNA contained two exons of 154 and 545 bp, respectively, and an intron of 1398 bp. Secondary and 3D structures of the deduced PgRL18/L5e protein were predicted using in silico tools. Phylogenetic analysis showed close relationships between the PgRL18/L5e protein and its orthologs from monocot species. Multiple sequence alignment showed high identity in the RL18/L5e domain sequence in all orthologous proteins in Viridiplantae. Moreover, all orthologous RL18/L5e proteins shared the same domain architecture and were nearly equal in length. Quantitative real-time PCR indicated a higher transcript abundance of PgRL18/L5e in shoots than in roots of 3-day-old seedlings. Moreover, the expression of PgRL18/L5e in seedlings under cold and drought stress was substantially lower than that in untreated seedlings, whereas the highest expression was shown under heat stress. This study provides insights into the structure and function of the RL18/L5e gene in tolerant crops, which could facilitate the understanding of the role of the various plant ribosomal proteins in adaptation to extreme environments.
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Affiliation(s)
- Zainab M. Almutairi
- Biology Department, College of Science and Humanities, Prince Sattam bin Abdulaziz University, P.O. Box: 83, Al-kharj 11942, Saudi Arabia
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22
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Alsharhan H, Muraresku C, Ganetzky RD. COXPD9 in an individual from Puerto Rico and literature review. Am J Med Genet A 2021; 185:2519-2525. [PMID: 34008913 DOI: 10.1002/ajmg.a.62344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/28/2021] [Accepted: 05/02/2021] [Indexed: 11/07/2022]
Abstract
Defects of mitoribosome assembly with destabilization of mitochondrial ribosomal proteins and subsequent aberrant mitochondrial translation machinery are one of the emerging categories of human mitochondrial disease. Mitochondrial translation deficiency constitutes a growing cause of combined oxidative phosphorylation deficiency and overall causes a set of clinically heterogeneous multi-systemic diseases. We present here the sixth individual with combined oxidative phosphorylation deficiency-9 (COXPD9) secondary to a likely pathogenic homozygous MRPL3 variant c.571A > C; p.(Thr191Pro). MRPL3 encodes a large mitochondrial ribosome subunit protein, impairing the mitochondrial translation and resulting in multisystem disease. Similar to previously reported individuals, this reported female proband presented with psychomotor retardation, sensorineural hearing loss, hypertrophic cardiomyopathy, failure to thrive, and lactic acidosis. Further, she has additional, previously unreported, features including Leigh syndrome, cataracts, hypotonia, scoliosis, myopathy, exercise intolerance, childhood-onset cardiomyopathy, and microcephaly. This subject is the oldest reported individual with COXPD9. This report also summarizes the clinical and molecular data of the previously reported individuals with COXPD9 to describe the full phenotypic spectrum.
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Affiliation(s)
- Hind Alsharhan
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Section of Biochemical Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Colleen Muraresku
- Division of Human Genetics, Section of Biochemical Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Rebecca D Ganetzky
- Division of Human Genetics, Section of Biochemical Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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23
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Policard M, Jain S, Rego S, Dakshanamurthy S. Immune characterization and profiles of SARS-CoV-2 infected patients reveals potential host therapeutic targets and SARS-CoV-2 oncogenesis mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.17.431721. [PMID: 33619493 PMCID: PMC7899457 DOI: 10.1101/2021.02.17.431721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
The spread of SARS-CoV-2 and the increasing mortality rates of COVID-19 create an urgent need for treatments, which are currently lacking. Although vaccines have been approved by the FDA for emergency use in the U.S., patients will continue to require pharmacologic intervention to reduce morbidity and mortality as vaccine availability remains limited. The rise of new variants makes the development of therapeutic strategies even more crucial to combat the current pandemic and future outbreaks. Evidence from several studies suggests the host immune response to SARS-CoV-2 infection plays a critical role in disease pathogenesis. Consequently, host immune factors are becoming more recognized as potential biomarkers and therapeutic targets for COVID-19. To develop therapeutic strategies to combat current and future coronavirus outbreaks, understanding how the coronavirus hijacks the host immune system during and after the infection is crucial. In this study, we investigated immunological patterns or characteristics of the host immune response to SARS-CoV-2 infection that may contribute to the disease severity of COVID-19 patients. We analyzed large bulk RNASeq and single cell RNAseq data from COVID-19 patient samples to immunoprofile differentially expressed gene sets and analyzed pathways to identify human host protein targets. We observed an immunological profile of severe COVID-19 patients characterized by upregulated cytokines, interferon-induced proteins, and pronounced T cell lymphopenia, supporting findings by previous studies. We identified a number of host immune targets including PERK, PKR, TNF, NF-kB, and other key genes that modulate the significant pathways and genes identified in COVID-19 patients. Finally, we identified genes modulated by COVID-19 infection that are implicated in oncogenesis, including E2F transcription factors and RB1, suggesting a mechanism by which SARS-CoV-2 infection may contribute to oncogenesis. Further clinical investigation of these targets may lead to bonafide therapeutic strategies to treat the current COVID-19 pandemic and protect against future outbreaks and viral escape variants.
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Affiliation(s)
- Martine Policard
- Clinical & Experimental Therapeutics Program, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, New Research Building, 3970 Reservoir Road NW, Washington, DC 20057-1469
| | | | | | - Sivanesan Dakshanamurthy
- Clinical & Experimental Therapeutics Program, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, New Research Building, 3970 Reservoir Road NW, Washington, DC 20057-1469
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24
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Lee M, Matsunaga N, Akabane S, Yasuda I, Ueda T, Takeuchi-Tomita N. Reconstitution of mammalian mitochondrial translation system capable of correct initiation and long polypeptide synthesis from leaderless mRNA. Nucleic Acids Res 2021; 49:371-382. [PMID: 33300043 PMCID: PMC7797035 DOI: 10.1093/nar/gkaa1165] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/12/2020] [Accepted: 11/16/2020] [Indexed: 12/31/2022] Open
Abstract
Mammalian mitochondria have their own dedicated protein synthesis system, which produces 13 essential subunits of the oxidative phosphorylation complexes. We have reconstituted an in vitro translation system from mammalian mitochondria, utilizing purified recombinant mitochondrial translation factors, 55S ribosomes from pig liver mitochondria, and a tRNA mixture from either Escherichia coli or yeast. The system is capable of translating leaderless mRNAs encoding model proteins (DHFR and nanoLuciferase) or some mtDNA-encoded proteins. We show that a leaderless mRNA, encoding nanoLuciferase, is faithfully initiated without the need for any auxiliary factors other than IF-2mt and IF-3mt. We found that the ribosome-dependent GTPase activities of both the translocase EF-G1mt and the recycling factor EF-G2mt are insensitive to fusidic acid (FA), the translation inhibitor that targets bacterial EF-G homologs, and consequently the system is resistant to FA. Moreover, we demonstrate that a polyproline sequence in the protein causes 55S mitochondrial ribosome stalling, yielding ribosome nascent chain complexes. Analyses of the effects of the Mg concentration on the polyproline-mediated ribosome stalling suggested the unique regulation of peptide elongation by the mitoribosome. This system will be useful for analyzing the mechanism of translation initiation, and the interactions between the nascent peptide chain and the mitochondrial ribosome.
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Affiliation(s)
- Muhoon Lee
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Noriko Matsunaga
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Shiori Akabane
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan.,Department of Life Science, Rikkyo University, Tokyo, 171-8501, Japan
| | - Ippei Yasuda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Takuya Ueda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan.,Department of Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, Tokyo, Shinjuku 162-8480, Japan
| | - Nono Takeuchi-Tomita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
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25
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Hennig O, Philipp S, Bonin S, Rollet K, Kolberg T, Jühling T, Betat H, Sauter C, Mörl M. Adaptation of the Romanomermis culicivorax CCA-Adding Enzyme to Miniaturized Armless tRNA Substrates. Int J Mol Sci 2020; 21:E9047. [PMID: 33260740 PMCID: PMC7730189 DOI: 10.3390/ijms21239047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 11/25/2020] [Indexed: 11/17/2022] Open
Abstract
The mitochondrial genome of the nematode Romanomermis culicivorax encodes for miniaturized hairpin-like tRNA molecules that lack D- as well as T-arms, strongly deviating from the consensus cloverleaf. The single tRNA nucleotidyltransferase of this organism is fully active on armless tRNAs, while the human counterpart is not able to add a complete CCA-end. Transplanting single regions of the Romanomermis enzyme into the human counterpart, we identified a beta-turn element of the catalytic core that-when inserted into the human enzyme-confers full CCA-adding activity on armless tRNAs. This region, originally identified to position the 3'-end of the tRNA primer in the catalytic core, dramatically increases the enzyme's substrate affinity. While conventional tRNA substrates bind to the enzyme by interactions with the T-arm, this is not possible in the case of armless tRNAs, and the strong contribution of the beta-turn compensates for an otherwise too weak interaction required for the addition of a complete CCA-terminus. This compensation demonstrates the remarkable evolutionary plasticity of the catalytic core elements of this enzyme to adapt to unconventional tRNA substrates.
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Affiliation(s)
- Oliver Hennig
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany; (O.H.); (S.P.); (S.B.); (K.R.); (T.K.); (T.J.); (H.B.)
| | - Susanne Philipp
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany; (O.H.); (S.P.); (S.B.); (K.R.); (T.K.); (T.J.); (H.B.)
| | - Sonja Bonin
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany; (O.H.); (S.P.); (S.B.); (K.R.); (T.K.); (T.J.); (H.B.)
| | - Kévin Rollet
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany; (O.H.); (S.P.); (S.B.); (K.R.); (T.K.); (T.J.); (H.B.)
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France;
| | - Tim Kolberg
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany; (O.H.); (S.P.); (S.B.); (K.R.); (T.K.); (T.J.); (H.B.)
| | - Tina Jühling
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany; (O.H.); (S.P.); (S.B.); (K.R.); (T.K.); (T.J.); (H.B.)
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France;
| | - Heike Betat
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany; (O.H.); (S.P.); (S.B.); (K.R.); (T.K.); (T.J.); (H.B.)
| | - Claude Sauter
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France;
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany; (O.H.); (S.P.); (S.B.); (K.R.); (T.K.); (T.J.); (H.B.)
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26
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Laptev I, Dontsova O, Sergiev P. Epitranscriptomics of Mammalian Mitochondrial Ribosomal RNA. Cells 2020; 9:E2181. [PMID: 32992603 PMCID: PMC7600485 DOI: 10.3390/cells9102181] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/20/2020] [Accepted: 09/23/2020] [Indexed: 12/16/2022] Open
Abstract
Modified nucleotides are present in all ribosomal RNA molecules. Mitochondrial ribosomes are unique to have a set of methylated residues that includes universally conserved ones, those that could be found either in bacterial or in archaeal/eukaryotic cytosolic ribosomes and those that are present exclusively in mitochondria. A single pseudouridine within the mt-rRNA is located in the peptidyltransferase center at a position similar to that in bacteria. After recent completion of the list of enzymes responsible for the modification of mammalian mitochondrial rRNA it became possible to summarize an evolutionary history, functional role of mt-rRNA modification enzymes and an interplay of the mt-rRNA modification and mitoribosome assembly process, which is a goal of this review.
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Affiliation(s)
- Ivan Laptev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; (I.L.); (O.D.)
| | - Olga Dontsova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; (I.L.); (O.D.)
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143028 Moscow Region, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119992 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Petr Sergiev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; (I.L.); (O.D.)
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143028 Moscow Region, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119992 Moscow, Russia
- Institute of Functional Genomics, Lomonosov Moscow State University, 119992 Moscow, Russia
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27
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Karakaidos P, Rampias T. Mitonuclear Interactions in the Maintenance of Mitochondrial Integrity. Life (Basel) 2020; 10:life10090173. [PMID: 32878185 PMCID: PMC7555762 DOI: 10.3390/life10090173] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 08/28/2020] [Indexed: 12/27/2022] Open
Abstract
In eukaryotic cells, mitochondria originated in an α-proteobacterial endosymbiont. Although these organelles harbor their own genome, the large majority of genes, originally encoded in the endosymbiont, were either lost or transferred to the nucleus. As a consequence, mitochondria have become semi-autonomous and most of their processes require the import of nuclear-encoded components to be functional. Therefore, the mitochondrial-specific translation has evolved to be coordinated by mitonuclear interactions to respond to the energetic demands of the cell, acquiring unique and mosaic features. However, mitochondrial-DNA-encoded genes are essential for the assembly of the respiratory chain complexes. Impaired mitochondrial function due to oxidative damage and mutations has been associated with numerous human pathologies, the aging process, and cancer. In this review, we highlight the unique features of mitochondrial protein synthesis and provide a comprehensive insight into the mitonuclear crosstalk and its co-evolution, as well as the vulnerabilities of the animal mitochondrial genome.
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28
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Koripella RK, Sharma MR, Bhargava K, Datta PP, Kaushal PS, Keshavan P, Spremulli LL, Banavali NK, Agrawal RK. Structures of the human mitochondrial ribosome bound to EF-G1 reveal distinct features of mitochondrial translation elongation. Nat Commun 2020; 11:3830. [PMID: 32737313 PMCID: PMC7395135 DOI: 10.1038/s41467-020-17715-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023] Open
Abstract
The mammalian mitochondrial ribosome (mitoribosome) and its associated translational factors have evolved to accommodate greater participation of proteins in mitochondrial translation. Here we present the 2.68-3.96 Å cryo-EM structures of the human 55S mitoribosome in complex with the human mitochondrial elongation factor G1 (EF-G1mt) in three distinct conformational states, including an intermediate state and a post-translocational state. These structures reveal the role of several mitochondria-specific (mito-specific) mitoribosomal proteins (MRPs) and a mito-specific segment of EF-G1mt in mitochondrial tRNA (tRNAmt) translocation. In particular, the mito-specific C-terminal extension in EF-G1mt is directly involved in translocation of the acceptor arm of the A-site tRNAmt. In addition to the ratchet-like and independent head-swiveling motions exhibited by the small mitoribosomal subunit, we discover significant conformational changes in MRP mL45 at the nascent polypeptide-exit site within the large mitoribosomal subunit that could be critical for tethering of the elongating mitoribosome onto the inner-mitochondrial membrane.
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MESH Headings
- Amino Acid Sequence
- Binding Sites
- Cryoelectron Microscopy
- HEK293 Cells
- Humans
- Mitochondria/metabolism
- Mitochondria/ultrastructure
- Mitochondrial Membranes/metabolism
- Mitochondrial Membranes/ultrastructure
- Mitochondrial Proteins/chemistry
- Mitochondrial Proteins/genetics
- Mitochondrial Proteins/metabolism
- Models, Molecular
- Nucleic Acid Conformation
- Peptide Chain Elongation, Translational
- Peptide Elongation Factor G/chemistry
- Peptide Elongation Factor G/genetics
- Peptide Elongation Factor G/metabolism
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- RNA, Mitochondrial/chemistry
- RNA, Mitochondrial/genetics
- RNA, Mitochondrial/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosomes/metabolism
- Ribosomes/ultrastructure
- Sequence Alignment
- Sequence Homology, Amino Acid
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Affiliation(s)
- Ravi Kiran Koripella
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY, 12201, USA
| | - Manjuli R Sharma
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY, 12201, USA
| | - Kalpana Bhargava
- Department of Chemistry, Campus Box 3290, University of North Carolina, Chapel Hill, NC, USA
- High Energy Material Research Lab, Defense Research and Development Organization, Sutarwadi, Pashan, Pune, Maharashtra, 411021, India
| | - Partha P Datta
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY, 12201, USA
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, 741246, India
| | - Prem S Kaushal
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY, 12201, USA
- Regional Centre for Biotechnology, 3rd Milestone, Faridabad-Gurgaon Expressway, PO Box # 3, Faridabad, Haryana, 121001, India
| | - Pooja Keshavan
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY, 12201, USA
| | - Linda L Spremulli
- Department of Chemistry, Campus Box 3290, University of North Carolina, Chapel Hill, NC, USA
| | - Nilesh K Banavali
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY, 12201, USA
- Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY, 12201-0509, USA
| | - Rajendra K Agrawal
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY, 12201, USA.
- Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY, 12201-0509, USA.
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29
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Seal RL, Chen LL, Griffiths-Jones S, Lowe TM, Mathews MB, O'Reilly D, Pierce AJ, Stadler PF, Ulitsky I, Wolin SL, Bruford EA. A guide to naming human non-coding RNA genes. EMBO J 2020; 39:e103777. [PMID: 32090359 PMCID: PMC7073466 DOI: 10.15252/embj.2019103777] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/23/2020] [Accepted: 01/30/2020] [Indexed: 12/15/2022] Open
Abstract
Research on non-coding RNA (ncRNA) is a rapidly expanding field. Providing an official gene symbol and name to ncRNA genes brings order to otherwise potential chaos as it allows unambiguous communication about each gene. The HUGO Gene Nomenclature Committee (HGNC, www.genenames.org) is the only group with the authority to approve symbols for human genes. The HGNC works with specialist advisors for different classes of ncRNA to ensure that ncRNA nomenclature is accurate and informative, where possible. Here, we review each major class of ncRNA that is currently annotated in the human genome and describe how each class is assigned a standardised nomenclature.
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Affiliation(s)
- Ruth L Seal
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Science, Shanghai, China
| | - Sam Griffiths-Jones
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Todd M Lowe
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Michael B Mathews
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Dawn O'Reilly
- Computational Biology and Integrative Genomics Lab, MRC/CRUK Oxford Institute and Department of Oncology, University of Oxford, Oxford, UK
| | - Andrew J Pierce
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria.,Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Colombia.,Santa Fe Institute, Santa Fe, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Sandra L Wolin
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Elspeth A Bruford
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
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30
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Wang Z, Li J, Long X, Jiao L, Zhou M, Wu K. MRPS16 facilitates tumor progression via the PI3K/AKT/Snail signaling axis. J Cancer 2020; 11:2032-2043. [PMID: 32127931 PMCID: PMC7052926 DOI: 10.7150/jca.39671] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 01/04/2020] [Indexed: 02/07/2023] Open
Abstract
Background: Although aberrant expression of MRPS16 (mitochondrial ribosomal protein S16) contributes to biological dysfunction, especially mitochondrial translation defects, the status of MRPS16 and its correlation with prognosis in tumors, especially glioma, which is a common, morbid and frequently lethal malignancy, are still controversial. Methods: Herein, we used high-throughput sequencing to identify the target molecule MRPS16. Subsequently, we detected MRPS16 protein and mRNA expression levels in normal brain tissue (NBT) and different grades of glioma tissue. The molecular effects of MRPS16 in glioma cells were tested by Western blotting, quantitative polymerase chain reaction (qRT-PCR), EdU, CCK-8, colony formation, Transwell migration and invasion assays. Results: Intriguingly, we found that MRPS16 knockdown suppressed tumor cell growth, migration and invasion. Conversely, MRPS16 over-expression increased tumor cell growth, migration and invasion. In addition, subsequent mechanistic studies indicated that MRPS16 promoted glioma cell growth, migration and invasion by the activating PI3K/AKT/Snail axis. Furthermore, we observed that the decrease in tumor cell growth, migration, invasion and Snail expression mediated by MRPS16 knockdown could be rescued by Snail over-expression. Conclusion: In short, our data demonstrate that MRPS16 over-expression remarkably promotes tumor cell growth, migration and invasion via the PI3K/AKT/Snail axis, which may be a promising prognostic marker for glioma.
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Affiliation(s)
- Zhen Wang
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Street, Wuhan 430030, P.R. China
| | - Junjun Li
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Street, Wuhan 430022, P.R. China
| | - Xiaobing Long
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Street, Wuhan 430030, P.R. China
| | - Liwu Jiao
- Department of Neurosurgery, The First People Hospital of Qujing, Qujing 655000, P.R. China
| | - Minghui Zhou
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Street, Wuhan 430030, P.R. China
| | - Kang Wu
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Street, Wuhan 430030, P.R. China
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31
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Waltz F, Giegé P. Striking Diversity of Mitochondria-Specific Translation Processes across Eukaryotes. Trends Biochem Sci 2019; 45:149-162. [PMID: 31780199 DOI: 10.1016/j.tibs.2019.10.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/03/2019] [Accepted: 10/08/2019] [Indexed: 12/13/2022]
Abstract
Mitochondria are essential organelles that act as energy conversion powerhouses and metabolic hubs. Their gene expression machineries combine traits inherited from prokaryote ancestors and specific features acquired during eukaryote evolution. Mitochondrial research has wide implications ranging from human health to agronomy. We highlight recent advances in mitochondrial translation. Functional, biochemical, and structural data have revealed an unexpected diversity of mitochondrial translation systems, particularly of their key players, the mitochondrial ribosomes (mitoribosomes). Ribosome assembly and translation mechanisms, such as initiation, are discussed and put in perspective with the prevalence of eukaryote-specific families of mitochondrial translation factors such as pentatricopeptide repeat (PPR) proteins.
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Affiliation(s)
- Florent Waltz
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France; Institut Européen de Chimie et de Biologie, l'Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Bordeaux, 2 rue Robert Escarpit, 33607 Pessac, France.
| | - Philippe Giegé
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
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32
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Ayyub SA, Varshney U. Translation initiation in mammalian mitochondria- a prokaryotic perspective. RNA Biol 2019; 17:165-175. [PMID: 31696767 DOI: 10.1080/15476286.2019.1690099] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
ATP is generated in mitochondria of eukaryotic cells by oxidative phosphorylation (OXPHOS). The OXPHOS complex, which is crucial for cellular metabolism, comprises of both nuclear and mitochondrially encoded subunits. Also, the occurrence of several pathologies because of mutations in the mitochondrial translation apparatus indicates the importance of mitochondrial translation and its regulation. The mitochondrial translation apparatus is similar to its prokaryotic counterpart due to a common origin of evolution. However, mitochondrial translation has diverged from prokaryotic translation in many ways by reductive evolution. In this review, we focus on mammalian mitochondrial translation initiation, a highly regulated step of translation, and present a comparison with prokaryotic translation.
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Affiliation(s)
- Shreya Ahana Ayyub
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.,Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
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Dong Z, Abbas MN, Kausar S, Yang J, Li L, Tan L, Cui H. Biological Functions and Molecular Mechanisms of Antibiotic Tigecycline in the Treatment of Cancers. Int J Mol Sci 2019; 20:ijms20143577. [PMID: 31336613 PMCID: PMC6678986 DOI: 10.3390/ijms20143577] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/17/2019] [Accepted: 07/19/2019] [Indexed: 12/14/2022] Open
Abstract
As an FDA-approved drug, glycylcycline tigecycline has been used to treat complicated microbial infections. However, recent studies in multiple hematologic and malignant solid tumors reveal that tigecycline treatment induces cell cycle arrest, apoptosis, autophagy and oxidative stress. In addition, tigecycline also inhibits mitochondrial oxidative phosphorylation, cell proliferation, migration, invasion and angiogenesis. Importantly, combinations of tigecycline with chemotherapeutic or targeted drugs such as venetoclax, doxorubicin, vincristine, paclitaxel, cisplatin, and imatinib, have shown to be promising strategies for cancer treatment. Mechanism of action studies reveal that tigecycline leads to the inhibition of mitochondrial translation possibly through interacting with mitochondrial ribosome. Meanwhile, this drug also interferes with several other cell pathways/targets including MYC, HIFs, PI3K/AKT or AMPK-mediated mTOR, cytoplasmic p21 CIP1/Waf1, and Wnt/β-catenin signaling. These evidences indicate that antibiotic tigecycline is a promising drug for cancer treatment alone or in combination with other anticancer drugs. This review summarizes the biological function of tigecycline in the treatment of tumors and comprehensively discusses its mode of action.
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Affiliation(s)
- Zhen Dong
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Beibei, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Beibei, Chongqing 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Beibei, Chongqing 400716, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Beibei, Chongqing 400716, China
| | - Muhammad Nadeem Abbas
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Beibei, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Beibei, Chongqing 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Beibei, Chongqing 400716, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Beibei, Chongqing 400716, China
| | - Saima Kausar
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Beibei, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Beibei, Chongqing 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Beibei, Chongqing 400716, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Beibei, Chongqing 400716, China
| | - Jie Yang
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Beibei, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Beibei, Chongqing 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Beibei, Chongqing 400716, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Beibei, Chongqing 400716, China
| | - Lin Li
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Beibei, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Beibei, Chongqing 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Beibei, Chongqing 400716, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Beibei, Chongqing 400716, China
| | - Li Tan
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Beibei, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Beibei, Chongqing 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Beibei, Chongqing 400716, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Beibei, Chongqing 400716, China
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Beibei, Chongqing 400716, China.
- Cancer Center, Medical Research Institute, Southwest University, Beibei, Chongqing 400716, China.
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Beibei, Chongqing 400716, China.
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Beibei, Chongqing 400716, China.
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Prajapati P, Dalwadi P, Gohel D, Singh K, Sripada L, Bhatelia K, Joshi B, Roy M, Wang WX, Springer JE, Singh R, Singh R. Enforced lysosomal biogenesis rescues erythromycin- and clindamycin-induced mitochondria-mediated cell death in human cells. Mol Cell Biochem 2019; 461:23-36. [PMID: 31309409 DOI: 10.1007/s11010-019-03585-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 07/04/2019] [Indexed: 12/23/2022]
Abstract
Antibiotics are the front-line treatment against many bacterial infectious diseases in human. The excessive and long-term use of antibiotics in human cause several side effects. It is important to understand the underlying molecular mechanisms of action of antibiotics in the host cell to avoid the side effects due to the prevalent uses. In the current study, we investigated the crosstalk between mitochondria and lysosomes in the presence of widely used antibiotics: erythromycin (ERM) and clindamycin (CLDM), which target the 50S subunit of bacterial ribosomes. We report here that both ERM and CLDM induced caspase activation and cell death in several different human cell lines. The activity of the mitochondrial respiratory chain was compromised in the presence of ERM and CLDM leading to bioenergetic crisis and generation of reactive oxygen species. Antibiotics treatment impaired autophagy flux and lysosome numbers, resulting in decreased removal of damaged mitochondria through mitophagy, hence accumulation of defective mitochondria. We further show that over-expression of transcription factor EB (TFEB) increased the lysosome number, restored mitochondrial function and rescued ERM- and CLDM-induced cell death. These studies indicate that antibiotics alter mitochondria and lysosome interactions leading to apoptotsis and may develop a novel approach for targeting inter-organelle crosstalk to limit deleterious antibiotic-induced side effects.
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Affiliation(s)
- Paresh Prajapati
- Department of Bio-Chemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Sayajigunj, Vadodara, Gujarat, 390002, India.,Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, 40536, USA.,Neuroscience, University of Kentucky, Lexington, KY, 40536, USA
| | - Pooja Dalwadi
- Department of Bio-Chemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Sayajigunj, Vadodara, Gujarat, 390002, India
| | - Dhruv Gohel
- Department of Bio-Chemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Sayajigunj, Vadodara, Gujarat, 390002, India
| | - Kritarth Singh
- Department of Bio-Chemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Sayajigunj, Vadodara, Gujarat, 390002, India
| | - Lakshmi Sripada
- Department of Bio-Chemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Sayajigunj, Vadodara, Gujarat, 390002, India
| | - Khyati Bhatelia
- Department of Bio-Chemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Sayajigunj, Vadodara, Gujarat, 390002, India
| | - Bhavana Joshi
- Department of Bio-Chemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Sayajigunj, Vadodara, Gujarat, 390002, India
| | - Milton Roy
- Department of Bio-Chemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Sayajigunj, Vadodara, Gujarat, 390002, India
| | - Wang-Xia Wang
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, 40536, USA.,Sanders Brown Center on Aging Center, University of Kentucky, Lexington, KY, 40536, USA.,Pathology & Laboratory Medicine, University of Kentucky, Lexington, KY, 40536, USA
| | - Joe E Springer
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, 40536, USA.,Neuroscience, University of Kentucky, Lexington, KY, 40536, USA
| | - Rochika Singh
- Department of Cell Biology, School of Biological Sciences and Biotechnology, Indian Institute of Advanced Research, Koba Institutional Area, Gandhinagar, Gujarat, 382007, India.
| | - Rajesh Singh
- Department of Bio-Chemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Sayajigunj, Vadodara, Gujarat, 390002, India.
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Waltz F, Nguyen TT, Arrivé M, Bochler A, Chicher J, Hammann P, Kuhn L, Quadrado M, Mireau H, Hashem Y, Giegé P. Small is big in Arabidopsis mitochondrial ribosome. NATURE PLANTS 2019; 5:106-117. [PMID: 30626926 DOI: 10.1038/s41477-018-0339-y] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/27/2018] [Indexed: 05/24/2023]
Abstract
Mitochondria are responsible for energy production through aerobic respiration, and represent the powerhouse of eukaryotic cells. Their metabolism and gene expression processes combine bacterial-like features and traits that evolved in eukaryotes. Among mitochondrial gene expression processes, translation remains the most elusive. In plants, while numerous pentatricopeptide repeat (PPR) proteins are involved in all steps of gene expression, their function in mitochondrial translation remains unclear. Here we present the biochemical characterization of Arabidopsis mitochondrial ribosomes and identify their protein subunit composition. Complementary biochemical approaches identified 19 plant-specific mitoribosome proteins, of which ten are PPR proteins. The knockout mutations of ribosomal PPR (rPPR) genes result in distinct macroscopic phenotypes, including lethality and severe growth delay. The molecular analysis of rppr1 mutants using ribosome profiling, as well as the analysis of mitochondrial protein levels, demonstrate rPPR1 to be a generic translation factor that is a novel function for PPR proteins. Finally, single-particle cryo-electron microscopy (cryo-EM) reveals the unique structural architecture of Arabidopsis mitoribosomes, characterized by a very large small ribosomal subunit, larger than the large subunit, bearing an additional RNA domain grafted onto the head. Overall, our results show that Arabidopsis mitoribosomes are substantially divergent from bacterial and other eukaryote mitoribosomes, in terms of both structure and protein content.
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Affiliation(s)
- Florent Waltz
- Institut de biologie de moléculaire des plantes UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Tan-Trung Nguyen
- Institut Jean-Pierre Bourgin INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Mathilde Arrivé
- Institut de biologie de moléculaire des plantes UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Anthony Bochler
- Institut Européen de Chimie et Biologie U1212 Inserm, Université de Bordeaux, Pessac, France
| | - Johana Chicher
- Plateforme protéomique Strasbourg Esplanade FRC1589 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Philippe Hammann
- Plateforme protéomique Strasbourg Esplanade FRC1589 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Lauriane Kuhn
- Plateforme protéomique Strasbourg Esplanade FRC1589 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Martine Quadrado
- Institut Jean-Pierre Bourgin INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Hakim Mireau
- Institut Jean-Pierre Bourgin INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France.
| | - Yaser Hashem
- Institut Européen de Chimie et Biologie U1212 Inserm, Université de Bordeaux, Pessac, France.
| | - Philippe Giegé
- Institut de biologie de moléculaire des plantes UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France.
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Aslam ML, Carraro R, Bestin A, Cariou S, Sonesson AK, Bruant JS, Haffray P, Bargelloni L, Meuwissen THE. Genetics of resistance to photobacteriosis in gilthead sea bream (Sparus aurata) using 2b-RAD sequencing. BMC Genet 2018; 19:43. [PMID: 29996763 PMCID: PMC6042378 DOI: 10.1186/s12863-018-0631-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 06/25/2018] [Indexed: 12/11/2022] Open
Abstract
Background Photobacteriosis is an infectious disease developed by a Gram-negative bacterium Photobacterium damselae subsp. piscicida (Phdp), which may cause high mortalities (90–100%) in sea bream. Selection and breeding for resistance against infectious diseases is a highly valuable tool to help prevent or diminish disease outbreaks, and currently available advanced selection methods with the application of genomic information could improve the response to selection. An experimental group of sea bream juveniles was derived from a Ferme Marine de Douhet (FMD, Oléron Island, France) selected line using ~ 109 parents (~ 25 females and 84 males). This group of 1187 individuals represented 177 full-sib families with 1–49 sibs per family, which were challenged with virulent Phdp for a duration of 18 days, and mortalities were recorded within this duration. Tissue samples were collected from the parents and the recorded offspring for DNA extraction, library preparation using 2b-RAD and genotyping by sequencing. Genotypic data was used to develop a linkage map, genome wide association analysis and for the estimation of breeding values. Results The analysis of genetic variation for resistance against Phdp revealed moderate genomic heritability with estimates of ~ 0.32. A genome-wide association analysis revealed a quantitative trait locus (QTL) including 11 SNPs at linkage group 17 presenting significant association to the trait with p-value crossing genome-wide Bonferroni corrected threshold P ≤ 2.22e-06. The proportion total genetic variance explained by the single top most significant SNP was ranging from 13.28–16.14% depending on the method used to compute the variance. The accuracies of predicting breeding values obtained using genomic vs. pedigree information displayed 19–24% increase when using genomic information. Conclusion The current study demonstrates that SNPs-based genotyping of a sea bream population with 2b-RAD approach is effective at capturing the genetic variation for resistance against Phdp. Prediction accuracies obtained using genomic information were significantly higher than the accuracies obtained using pedigree information which highlights the importance and potential of genomic selection in commercial breeding programs. Electronic supplementary material The online version of this article (10.1186/s12863-018-0631-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Anastasia Bestin
- SYSAAF, French poultry and aquaculture breeders, 35042, Rennes Cedex, France
| | | | | | | | - Pierrick Haffray
- SYSAAF, French poultry and aquaculture breeders, 35042, Rennes Cedex, France
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Korovesi AG, Ntertilis M, Kouvelis VN. Mt-rps3 is an ancient gene which provides insight into the evolution of fungal mitochondrial genomes. Mol Phylogenet Evol 2018; 127:74-86. [PMID: 29763662 DOI: 10.1016/j.ympev.2018.04.037] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Revised: 02/24/2018] [Accepted: 04/23/2018] [Indexed: 12/30/2022]
Abstract
The nuclear ribosomal protein S3 (Rps3) is implicated in the assembly of the ribosomal small subunit. Fungi and plants present a gene copy in their mitochondrial (mt) genomes. An analysis of 303 complete fungal mt genomes showed that, when rps3 is found, it is either a free-standing gene or an anchored gene within the omega intron of the rnl gene. Early divergent fungi, Basidiomycota and all yeasts but the CTG group belong to the first case, and Pezizomycotina to the second. Its position, size and genetic code employed are conserved within species of the same Order. Size variability is attributed to different number of repeats. These repeats consist of AT-rich sequences. MtRps3 proteins lack the KH domain, necessary for binding to rRNA, in their N-terminal region. Their C-terminal region is conserved in all Domains of life. Phylogenetic analysis showed that nuclear and mtRps3 proteins are descendants of archaeal and a-proteobacterial homologues, respectively. Thus, fungal mt-rps3 gene is an ancient gene which evolved within the endosymbiotic model and presents different evolutionary routes: (a) coming from a-proteobacteria, it was relocated to another region of the mt genome, (b) via its insertion to the omega intron, it was transferred to the nucleus and/or got lost, and (c) it was re-routed to the mt genome again. Today, Basidiomycota and Saccharomycetales seem to follow the first evolutionary route and almost all Pezizomycotina support the second scenario with their exceptions being the result of the third scenario, i.e., the gene's re-entry to the mt genome.
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Affiliation(s)
- Artemis G Korovesi
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Ntertilis
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Vassili N Kouvelis
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece.
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39
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Ratnu VS, Emami MR, Bredy TW. Genetic and epigenetic factors underlying sex differences in the regulation of gene expression in the brain. J Neurosci Res 2017; 95:301-310. [PMID: 27870402 DOI: 10.1002/jnr.23886] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/13/2016] [Accepted: 07/25/2016] [Indexed: 12/14/2022]
Abstract
There are inherent biological differences between males and females that contribute to sex differences in brain function and to many sex-specific illnesses and disorders. Traditionally, it has been thought that such differences are due largely to hormonal regulation; however, there are also genetic and epigenetic effects caused by the inheritance and unequal dosage of genes located on the X and Y chromosomes. Here we discuss the evidence in favor of a genetic and epigenetic basis for sexually dimorphic behavior, as a consequence of underlying differences in the regulation of genes that drive brain function. A better understanding of sex-specific molecular processes in the brain will provide further insight for the development of novel therapeutic approaches for the treatment of neuropsychiatric disorders characterized by sex differences. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Vikram S Ratnu
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Michael R Emami
- Department of Neurobiology and Behavior, University of California, Irvine, California
| | - Timothy W Bredy
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia.,Department of Neurobiology and Behavior, University of California, Irvine, California
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40
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Tian X, Zhu X, Yan T, Yu C, Shen C, Hu Y, Hong J, Chen H, Fang JY. Recurrence-associated gene signature optimizes recurrence-free survival prediction of colorectal cancer. Mol Oncol 2017; 11:1544-1560. [PMID: 28796930 PMCID: PMC5664005 DOI: 10.1002/1878-0261.12117] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/27/2017] [Accepted: 07/29/2017] [Indexed: 12/28/2022] Open
Abstract
High throughput gene expression profiling has showed great promise in providing insight into molecular mechanisms. Metastasis‐related mRNAs may potentially enrich genes with the ability to predict cancer recurrence, therefore we attempted to build a recurrence‐associated gene signature to improve prognostic prediction of colorectal cancer (CRC). We identified 2848 differentially expressed mRNAs by analyzing CRC tissues with or without metastasis. For the selection of prognostic genes, a LASSO Cox regression model (least absolute shrinkage and selection operator method) was employed. Using this method, a 13‐mRNA signature was identified and then validated in two independent Gene Expression Omnibus cohorts. This classifier could successfully discriminate the high‐risk patients in discovery cohort [hazard ratio (HR) = 5.27, 95% confidence interval (CI) 2.30–12.08, P < 0.0001). Analysis in two independent cohorts yielded consistent results (GSE14333: HR = 4.55, 95% CI 2.18–9.508, P < 0.0001; GSE33113: HR = 3.26, 95% CI 2.16–9.16, P = 0.0176). Further analysis revealed that the prognostic value of this signature was independent of tumor stage, postoperative chemotherapy and somatic mutation. Receiver operating characteristic (ROC) analysis showed that the area under ROC curve of this signature was 0.8861 and 0.8157 in the discovery and validation cohort, respectively. A nomogram was constructed for clinicians, and did well in the calibration plots. Furthermore, this 13‐mRNA signature outperformed other known gene signatures, including oncotypeDX colon cancer assay. Single‐sample gene‐set enrichment analysis revealed that a group of pathways related to drug resistance, cancer metastasis and stemness were significantly enriched in the high‐risk patients. In conclusion, this 13‐mRNA signature may be a useful tool for prognostic evaluation and will facilitate personalized management of CRC patients.
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Affiliation(s)
- Xianglong Tian
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai JiaoTong University, China
| | - Xiaoqiang Zhu
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai JiaoTong University, China
| | - Tingting Yan
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai JiaoTong University, China
| | - Chenyang Yu
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai JiaoTong University, China
| | - Chaoqin Shen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai JiaoTong University, China
| | - Ye Hu
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai JiaoTong University, China
| | - Jie Hong
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai JiaoTong University, China
| | - Haoyan Chen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai JiaoTong University, China
| | - Jing-Yuan Fang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai JiaoTong University, China
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Ozsvari B, Fiorillo M, Bonuccelli G, Cappello AR, Frattaruolo L, Sotgia F, Trowbridge R, Foster R, Lisanti MP. Mitoriboscins: Mitochondrial-based therapeutics targeting cancer stem cells (CSCs), bacteria and pathogenic yeast. Oncotarget 2017; 8:67457-67472. [PMID: 28978045 PMCID: PMC5620185 DOI: 10.18632/oncotarget.19084] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 05/17/2017] [Indexed: 12/26/2022] Open
Abstract
The "endo-symbiotic theory of mitochondrial evolution" states that mitochondrial organelles evolved from engulfed aerobic bacteria, after millions of years of symbiosis and adaptation. Here, we have exploited this premise to design new antibiotics and novel anti-cancer therapies, using a convergent approach. First, virtual high-throughput screening (vHTS) and computational chemistry were used to identify novel compounds binding to the 3D structure of the mammalian mitochondrial ribosome. The resulting library of ∼880 compounds was then subjected to phenotypic drug screening on human cancer cells, to identify which compounds functionally induce ATP-depletion, which is characteristic of mitochondrial inhibition. Notably, the top ten "hit" compounds define four new classes of mitochondrial inhibitors. Next, we further validated that these novel mitochondrial inhibitors metabolically target mitochondrial respiration in cancer cells and effectively inhibit the propagation of cancer stem-like cells in vitro. Finally, we show that these mitochondrial inhibitors possess broad-spectrum antibiotic activity, preventing the growth of both gram-positive and gram-negative bacteria, as well as C. albicans - a pathogenic yeast. Remarkably, these novel antibiotics also were effective against methicillin-resistant Staphylococcus aureus (MRSA). Thus, this simple, yet systematic, approach to the discovery of mitochondrial ribosome inhibitors could provide a plethora of anti-microbials and anti-cancer therapies, to target drug-resistance that is characteristic of both i) tumor recurrence and ii) infectious disease. In summary, we have successfully used vHTS combined with phenotypic drug screening of human cancer cells to identify several new classes of broad-spectrum antibiotics that target both bacteria and pathogenic yeast. We propose the new term "mitoriboscins" to describe these novel mitochondrial-related antibiotics. Thus far, we have identified four different classes of mitoriboscins, such as: 1) mitoribocyclines, 2) mitoribomycins, 3) mitoribosporins and 4) mitoribofloxins. However, we broadly define mitoriboscins as any small molecule(s) or peptide(s) that bind to the mitoribosome (large or small subunits) and, as a consequence, inhibit mitochondrial function, i.e., mitoribosome inhibitors.
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Affiliation(s)
- Bela Ozsvari
- Translational Medicine, School of Environment & Life Sciences, University of Salford, Greater Manchester, UK.,The Paterson Institute, University of Manchester, Withington, UK
| | - Marco Fiorillo
- Translational Medicine, School of Environment & Life Sciences, University of Salford, Greater Manchester, UK.,The Paterson Institute, University of Manchester, Withington, UK.,The Department of Pharmacy, Health and Nutritional Sciences, The University of Calabria, Cosenza, Italy
| | - Gloria Bonuccelli
- Translational Medicine, School of Environment & Life Sciences, University of Salford, Greater Manchester, UK.,The Paterson Institute, University of Manchester, Withington, UK
| | - Anna Rita Cappello
- The Department of Pharmacy, Health and Nutritional Sciences, The University of Calabria, Cosenza, Italy
| | - Luca Frattaruolo
- The Department of Pharmacy, Health and Nutritional Sciences, The University of Calabria, Cosenza, Italy
| | - Federica Sotgia
- Translational Medicine, School of Environment & Life Sciences, University of Salford, Greater Manchester, UK.,The Paterson Institute, University of Manchester, Withington, UK
| | - Rachel Trowbridge
- School of Chemistry, Faculty of Mathematics and Physical Sciences, University of Leeds, West Yorkshire, UK
| | - Richard Foster
- Astbury Centre for Structural Molecular Biology, University of Leeds, West Yorkshire, UK.,School of Chemistry, Faculty of Mathematics and Physical Sciences, University of Leeds, West Yorkshire, UK
| | - Michael P Lisanti
- Translational Medicine, School of Environment & Life Sciences, University of Salford, Greater Manchester, UK.,The Paterson Institute, University of Manchester, Withington, UK
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RSM22, mtYsxC and PNKD-like proteins are required for mitochondrial translation in Trypanosoma brucei. Mitochondrion 2017; 34:67-74. [DOI: 10.1016/j.mito.2017.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 12/07/2016] [Accepted: 01/10/2017] [Indexed: 11/20/2022]
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Lin X, Zheng HX, Davie A, Zhou S, Wen L, Meng J, Zhang Y, Aladaer Q, Liu B, Liu WJ, Yao XK. Association of low race performance with mtDNA haplogroup L3b of Australian thoroughbred horses. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:323-330. [PMID: 28129729 DOI: 10.1080/24701394.2016.1278535] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Mitochondrial DNA (mtDNA) encodes the genes for respiratory chain sub-units that determine the efficiency of oxidative phosphorylation in mitochondria. The aim of this study was to determine if there were any haplogroups and variants in mtDNA that could be associated with athletic performance of Thoroughbred horses. The whole mitochondrial genomes of 53 maternally unrelated Australian Thoroughbred horses were sequenced and an association study was performed with the competition histories of 1123 horses within their maternal lineages. A horse mtDNA phylogenetic tree was constructed based on a total of 195 sequences (including 142 from previous reports). The association analysis showed that the sample groups with poor racing performance history were enriched in haplogroup L3b (p = .0003) and its sub-haplogroup L3b1a (p = .0007), while those that had elite performance appeared to be not significantly associated with haplogroups G2 and L3a1a1a (p > .05). Haplogroup L3b and L3b1a bear two and five specific variants of which variant T1458C (site 345 in 16s rRNA) is the only potential functional variant. Furthermore, secondary reconstruction of 16s RNA showed considerable differences between two types of 16s RNA molecules (with and without T1458C), indicating a potential functional effect. The results suggested that haplogroup L3b, could have a negative association with elite performance. The T1458C mutation harboured in haplogroup L3b could have a functional effect that is related to poor athletic performance.
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Affiliation(s)
- Xiang Lin
- a Tianjin Key Laboratory of Exercise Physiology and Sports Medicine , Tianjin University of Sports , Tianjin , P.R. China
| | - Hong-Xiang Zheng
- b State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences , Fudan University , Shanghai , P.R.China
| | - Allan Davie
- c School of Health and Human Sciences , Southern Cross University , Lismore , New South Wales , Australia
| | - Shi Zhou
- c School of Health and Human Sciences , Southern Cross University , Lismore , New South Wales , Australia
| | - Li Wen
- a Tianjin Key Laboratory of Exercise Physiology and Sports Medicine , Tianjin University of Sports , Tianjin , P.R. China
| | - Jun Meng
- d College of Animal Sciences , Xinjiang Agricultural University , Urumuqi , China
| | - Yong Zhang
- a Tianjin Key Laboratory of Exercise Physiology and Sports Medicine , Tianjin University of Sports , Tianjin , P.R. China
| | - Qimude Aladaer
- e Center of Systematic Genomics, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences , Urumqi , China
| | - Bin Liu
- e Center of Systematic Genomics, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences , Urumqi , China
| | - Wu-Jun Liu
- d College of Animal Sciences , Xinjiang Agricultural University , Urumuqi , China
| | - Xin-Kui Yao
- d College of Animal Sciences , Xinjiang Agricultural University , Urumuqi , China
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44
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Fyn kinase regulates translation in mammalian mitochondria. Biochim Biophys Acta Gen Subj 2016; 1861:533-540. [PMID: 27940153 DOI: 10.1016/j.bbagen.2016.12.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 11/22/2016] [Accepted: 12/05/2016] [Indexed: 11/24/2022]
Abstract
BACKGROUND Mitochondrial translation machinery solely exists for the synthesis of 13 mitochondrially-encoded subunits of the oxidative phosphorylation (OXPHOS) complexes in mammals. Therefore, it plays a critical role in mitochondrial energy production. However, regulation of the mitochondrial translation machinery is still poorly understood. In comprehensive proteomics studies with normal and diseased tissues and cell lines, we and others have found the majority of mitochondrial ribosomal proteins (MRPs) to be phosphorylated. Neither the kinases for these phosphorylation events nor their specific roles in mitochondrial translation are known. METHODS Mitochondrial kinases are responsible for phosphorylation of MRPs enriched from bovine mitoplasts by strong cation-exchange chromatography and identified by mass spectrometry-based proteomics analyses of kinase rich fractions. Phosphorylation of recombinant MRPs and 55S ribosomes was assessed by in vitro phosphorylation assays using the kinase-rich fractions. The effect of identified kinase on OXPHOS and mitochondrial translation was assessed by various cell biological and immunoblotting approaches. RESULTS Here, we provide the first evidence for the association of Fyn kinase, a Src family kinase, with mitochondrial translation components and its involvement in phosphorylation of 55S ribosomal proteins in vitro. Modulation of Fyn expression in human cell lines has provided a link between mitochondrial translation and energy metabolism, which was evident by the changes in 13 mitochondrially encoded subunits of OXPHOS complexes. CONCLUSIONS AND GENERAL SIGNIFICANCE Our findings suggest that Fyn kinase is part of a complex mechanism that regulates protein synthesis and OXPHOS possibly by tyrosine phosphorylation of translation components in mammalian mitochondria.
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Cryo-EM structure of the large subunit of the spinach chloroplast ribosome. Sci Rep 2016; 6:35793. [PMID: 27762343 PMCID: PMC5071890 DOI: 10.1038/srep35793] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 10/04/2016] [Indexed: 12/16/2022] Open
Abstract
Protein synthesis in the chloroplast is mediated by the chloroplast ribosome (chloro-ribosome). Overall architecture of the chloro-ribosome is considerably similar to the Escherichia coli (E. coli) ribosome but certain differences are evident. The chloro-ribosome proteins are generally larger because of the presence of chloroplast-specific extensions in their N- and C-termini. The chloro-ribosome harbours six plastid-specific ribosomal proteins (PSRPs); four in the small subunit and two in the large subunit. Deletions and insertions occur throughout the rRNA sequence of the chloro-ribosome (except for the conserved peptidyl transferase center region) but the overall length of the rRNAs do not change significantly, compared to the E. coli. Although, recent advancements in cryo-electron microscopy (cryo-EM) have provided detailed high-resolution structures of ribosomes from many different sources, a high-resolution structure of the chloro-ribosome is still lacking. Here, we present a cryo-EM structure of the large subunit of the chloro-ribosome from spinach (Spinacia oleracea) at an average resolution of 3.5 Å. High-resolution map enabled us to localize and model chloro-ribosome proteins, chloroplast-specific protein extensions, two PSRPs (PSRP5 and 6) and three rRNA molecules present in the chloro-ribosome. Although comparable to E. coli, the polypeptide tunnel and the tunnel exit site show chloroplast-specific features.
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46
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Woellhaf MW, Sommer F, Schroda M, Herrmann JM. Proteomic profiling of the mitochondrial ribosome identifies Atp25 as a composite mitochondrial precursor protein. Mol Biol Cell 2016; 27:3031-3039. [PMID: 27582385 PMCID: PMC5063612 DOI: 10.1091/mbc.e16-07-0513] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 08/18/2016] [Accepted: 08/23/2016] [Indexed: 11/15/2022] Open
Abstract
Whereas the structure and function of cytosolic ribosomes are well characterized, we only have a limited understanding of the mitochondrial translation apparatus. Using SILAC-based proteomic profiling, we identified 13 proteins that cofractionated with the mitochondrial ribosome, most of which play a role in translation or ribosomal biogenesis. One of these proteins is a homologue of the bacterial ribosome-silencing factor (Rsf). This protein is generated from the composite precursor protein Atp25 upon internal cleavage by the matrix processing peptidase MPP, and in this respect, it differs from all other characterized mitochondrial proteins of baker's yeast. We observed that cytosolic expression of Rsf, but not of noncleaved Atp25 protein, is toxic. Our results suggest that eukaryotic cells face the challenge of avoiding negative interference from the biogenesis of their two distinct translation machineries.
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Affiliation(s)
- Michael W Woellhaf
- Cell Biology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Frederik Sommer
- Molecular Biotechnology and Systems Biology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Michael Schroda
- Molecular Biotechnology and Systems Biology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
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Li HB, Wang RX, Jiang HB, Zhang ED, Tan JQ, Xu HZ, Zhou RR, Xia XB. Mitochondrial Ribosomal Protein L10 Associates with Cyclin B1/Cdk1 Activity and Mitochondrial Function. DNA Cell Biol 2016; 35:680-690. [PMID: 27726420 PMCID: PMC5105351 DOI: 10.1089/dna.2016.3271] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Mitochondrial ribosomal proteins are important for mitochondrial-encoded protein synthesis and mitochondrial function. In addition to their roles in mitoribosome assembly, several mitochondrial ribosome proteins are also implicated in cellular processes like cell cycle regulation, apoptosis, and mitochondrial homeostasis regulation. Here, we demonstrate that MRPL10 regulates cyclin B1/Cdk1 (cyclin-dependent kinase 1) activity and mitochondrial protein synthesis in mammalian cells. In Drosophila, inactivation of mRpL10 (the Drosophila ortholog of mammalian MRPL10) in eyes results in abnormal eye development. Furthermore, expression of human cyclin B1 suppresses eye phenotypes and mitochondrial abnormality of mRpL10 knockdown Drosophila. This study identified that the physiological regulatory pathway of MRPL10 and providing new insights into the role of MRPL10 in growth control and mitochondrial function.
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Affiliation(s)
- Hai-Bo Li
- 1 Department of Ophthalmology, Xiangya Hospital, Central South University , Changsha, China .,2 The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University , Changsha, China
| | - Ruo-Xi Wang
- 2 The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University , Changsha, China
| | - Hai-Bo Jiang
- 1 Department of Ophthalmology, Xiangya Hospital, Central South University , Changsha, China
| | - En-Dong Zhang
- 1 Department of Ophthalmology, Xiangya Hospital, Central South University , Changsha, China
| | - Jie-Qiong Tan
- 2 The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University , Changsha, China
| | - Hui-Zhuo Xu
- 1 Department of Ophthalmology, Xiangya Hospital, Central South University , Changsha, China
| | - Rong-Rong Zhou
- 3 Department of Oncology, Xiangya Hospital, Central South University , Changsha, China
| | - Xiao-Bo Xia
- 1 Department of Ophthalmology, Xiangya Hospital, Central South University , Changsha, China
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Abstract
Oxidative phosphorylation (OXPHOS) is the mechanism whereby ATP, the major energy source for the cell, is produced by harnessing cellular respiration in the mitochondrion. This is facilitated by five multi-subunit complexes housed within the inner mitochondrial membrane. These complexes, with the exception of complex II, are of a dual genetic origin, requiring expression from nuclear and mitochondrial genes. Mitochondrially encoded mRNA is translated on the mitochondrial ribosome (mitoribosome) and the recent release of the near atomic resolution structure of the mammalian mitoribosome has highlighted its peculiar features. However, whereas some aspects of mitochondrial translation are understood, much is to be learnt about the presentation of mitochondrial mRNA to the mitoribosome, the biogenesis of the machinery, the exact role of the membrane, the constitution of the translocon/insertion machinery and the regulation of translation in the mitochondrion. This review addresses our current knowledge of mammalian mitochondrial gene expression, highlights key questions and indicates how defects in this process can result in profound mitochondrial disease.
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49
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Karniely S, Weekes MP, Antrobus R, Rorbach J, van Haute L, Umrania Y, Smith DL, Stanton RJ, Minczuk M, Lehner PJ, Sinclair JH. Human Cytomegalovirus Infection Upregulates the Mitochondrial Transcription and Translation Machineries. mBio 2016; 7:e00029. [PMID: 27025248 PMCID: PMC4807356 DOI: 10.1128/mbio.00029-16] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 02/25/2016] [Indexed: 12/14/2022] Open
Abstract
UNLABELLED Infection with human cytomegalovirus (HCMV) profoundly affects cellular metabolism. Like in tumor cells, HCMV infection increases glycolysis, and glucose carbon is shifted from the mitochondrial tricarboxylic acid cycle to the biosynthesis of fatty acids. However, unlike in many tumor cells, where aerobic glycolysis is accompanied by suppression of mitochondrial oxidative phosphorylation, HCMV induces mitochondrial biogenesis and respiration. Here, we affinity purified mitochondria and used quantitative mass spectrometry to determine how the mitochondrial proteome changes upon HCMV infection. We found that the mitochondrial transcription and translation systems are induced early during the viral replication cycle. Specifically, proteins involved in biogenesis of the mitochondrial ribosome were highly upregulated by HCMV infection. Inhibition of mitochondrial translation with chloramphenicol or knockdown of HCMV-induced ribosome biogenesis factor MRM3 abolished the HCMV-mediated increase in mitochondrially encoded proteins and significantly impaired viral growth under bioenergetically restricting conditions. Our findings demonstrate how HCMV manipulates mitochondrial biogenesis to support its replication. IMPORTANCE Human cytomegalovirus (HCMV), a betaherpesvirus, is a leading cause of morbidity and mortality during congenital infection and among immunosuppressed individuals. HCMV infection significantly changes cellular metabolism. Akin to tumor cells, in HCMV-infected cells, glycolysis is increased and glucose carbon is shifted from the tricarboxylic acid cycle to fatty acid biosynthesis. However, unlike in tumor cells, HCMV induces mitochondrial biogenesis even under aerobic glycolysis. Here, we have affinity purified mitochondria and used quantitative mass spectrometry to determine how the mitochondrial proteome changes upon HCMV infection. We find that the mitochondrial transcription and translation systems are induced early during the viral replication cycle. Specifically, proteins involved in biogenesis of the mitochondrial ribosome were highly upregulated by HCMV infection. Inhibition of mitochondrial translation with chloramphenicol or knockdown of HCMV-induced ribosome biogenesis factor MRM3 abolished the HCMV-mediated increase in mitochondrially encoded proteins and significantly impaired viral growth. Our findings demonstrate how HCMV manipulates mitochondrial biogenesis to support its replication.
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Affiliation(s)
- S Karniely
- Department of Medicine, University of Cambridge Clinical School, Addenbrookes Hospital, Cambridge, United Kingdom
| | - M P Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - R Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - J Rorbach
- MRC, Mitochondrial Biology Unit, Cambridge, United Kingdom
| | - L van Haute
- MRC, Mitochondrial Biology Unit, Cambridge, United Kingdom
| | - Y Umrania
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - D L Smith
- Paterson Institute for Cancer Research, University of Manchester, Withington, Manchester, United Kingdom
| | - R J Stanton
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - M Minczuk
- MRC, Mitochondrial Biology Unit, Cambridge, United Kingdom
| | - P J Lehner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - J H Sinclair
- Department of Medicine, University of Cambridge Clinical School, Addenbrookes Hospital, Cambridge, United Kingdom
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50
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Abstract
Mitochondrial ribosomes (mitoribosomes) perform protein synthesis inside mitochondria, the organelles responsible for energy conversion and adenosine triphosphate production in eukaryotic cells. Throughout evolution, mitoribosomes have become functionally specialized for synthesizing mitochondrial membrane proteins, and this has been accompanied by large changes to their structure and composition. We review recent high-resolution structural data that have provided unprecedented insight into the structure and function of mitoribosomes in mammals and fungi.
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Affiliation(s)
- Basil J Greber
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland; .,*Present address: California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720-3220
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland;
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