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Yang X, Han B, Xie Q, Li Y, Li Q, Hu X, Zhao H, Xu X. Low Expression of Mitochondrial Ribosomal Protein S5 is Associated With Poor Prognosis in Patients With Clear Cell Renal Cell Carcinoma. Appl Immunohistochem Mol Morphol 2025; 33:22-28. [PMID: 39636315 PMCID: PMC11614452 DOI: 10.1097/pai.0000000000001236] [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: 04/08/2024] [Accepted: 10/14/2024] [Indexed: 12/07/2024]
Abstract
Mitochondrial ribosomal protein S5 (MRPS5) is abnormally expressed in various tumor tissues and may be a key molecule for the regulation of tumors. Our aim is to investigate the relationship between the expression of MRPS5 in clear cell renal cell carcinoma (ccRCC) and the prognosis of patients. MRPS5 expression in fresh tumoral tissues and peritumoral tissues of patients with ccRCC was examined by quantitative reverse transcription polymerase chain reaction, western blotting, and immunohistochemical staining, respectively. MRPS5 expression level in paraffin-embedded tumoral tissue samples with ccRCC was evaluated by immunohistochemical scoring criteria. The relationship between the expression of MRPS5 and the clinicopathological parameters and prognosis of patients with ccRCC was analyzed statistically. The expression of MRPS5 mRNA and protein in fresh tumoral tissues was lower than that in peritumoral tissues. Among 160 paraffin-embedded tumoral tissue samples, 99 cases (61.9%) showed high expression and 61 cases (38.1%) showed low expression of MRPS5. The expression level of MRPS5 was significantly correlated with T classification, TNM stage, and Fuhrman grade. Kaplan-Meier method and log-rank test indicated that patients with low MRPS5 expression had significantly poorer overall survival and recurrence-free survival than high MRPS5 expression. Multivariate analysis revealed that MRPS5 expression was an independent predictor of overall survival and recurrence-free survival, respectively. MRPS5 low expression was a risk factor for the prognosis of patients. The expression level of MRPS5 is significantly correlated with the postoperative survival status, which has the potential to be used as a novel prognostic biomarker for patients with ccRCC.
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Affiliation(s)
- Xiaoxiao Yang
- Department of Nephrology, First Affiliated Hospital (Southwest Hospital), Army Medical University (Third Military Medical University), Chongqing, China
| | - Bo Han
- Department of Pediatrics, Chongqing Health Center for Women and Children (Women’s and Children’s Hospital of Chongqing Medical University), Chongqing, China
| | - Qian Xie
- Department of General Surgery, 63650 Military Hospital, Xinjiang, China
| | - Yi Li
- Department of Nephrology, First Affiliated Hospital (Southwest Hospital), Army Medical University (Third Military Medical University), Chongqing, China
| | - Qixuan Li
- Department of Nephrology, First Affiliated Hospital (Southwest Hospital), Army Medical University (Third Military Medical University), Chongqing, China
| | - Xuelian Hu
- Department of Nephrology, First Affiliated Hospital (Southwest Hospital), Army Medical University (Third Military Medical University), Chongqing, China
| | - Hongwen Zhao
- Department of Nephrology, First Affiliated Hospital (Southwest Hospital), Army Medical University (Third Military Medical University), Chongqing, China
| | - Xiaosong Xu
- Department of Nephrology, First Affiliated Hospital (Southwest Hospital), Army Medical University (Third Military Medical University), Chongqing, China
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Su Q, Sun H, Mei L, Yan Y, Ji H, Chang L, Wang L. Ribosomal proteins in hepatocellular carcinoma: mysterious but promising. Cell Biosci 2024; 14:133. [PMID: 39487553 PMCID: PMC11529329 DOI: 10.1186/s13578-024-01316-3] [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: 07/09/2024] [Accepted: 10/21/2024] [Indexed: 11/04/2024] Open
Abstract
Ribosomal proteins (RPs) are essential components of ribosomes, playing a role not only in ribosome biosynthesis, but also in various extra-ribosomal functions, some of which are implicated in the development of different types of tumors. As universally acknowledged, hepatocellular carcinoma (HCC) has been garnering global attention due to its complex pathogenesis and challenging treatments. In this review, we analyze the biological characteristics of RPs and emphasize their essential roles in HCC. In addition to regulating related signaling pathways such as the p53 pathway, RPs also act in proliferation and metastasis by influencing cell cycle, apoptosis, angiogenesis, and epithelial-to-mesenchymal transition in HCC. RPs are expected to unfold new possibilities for precise diagnosis and individualized treatment of HCC.
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Affiliation(s)
- Qian Su
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
- National Center for Clinical Laboratories, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Huizhen Sun
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Ling Mei
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
- National Center for Clinical Laboratories, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Ying Yan
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Huimin Ji
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Le Chang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, Beijing, P.R. China.
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China.
- National Center for Clinical Laboratories, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China.
| | - Lunan Wang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, Beijing, P.R. China.
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China.
- National Center for Clinical Laboratories, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China.
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3
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Yoshinaga N, Numata K. Poly(A) Tail Length of Messenger RNA Regulates Translational Efficiency of the Mitochondria-Targeting Delivery System. ACS Biomater Sci Eng 2024; 10:6344-6351. [PMID: 39231264 DOI: 10.1021/acsbiomaterials.4c01169] [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] [Indexed: 09/06/2024]
Abstract
Mitochondria are essential for cellular functions, such as energy production. Human mitochondrial DNA (mtDNA), encoding 13 distinct genes, two rRNA, and 22 tRNA, is crucial for maintaining vital functions, along with nuclear-encoded mitochondrial proteins. However, mtDNA is prone to somatic mutations due to replication errors and reactive oxygen species exposure. These mutations can accumulate, leading to heteroplasmic conditions associated with severe metabolic diseases. Therefore, developing methodologies to improve mitochondrial health is highly demanded. Introducing nucleic acids directly into mitochondria is a promising strategy to control mitochondrial gene expression. Messenger RNA (mRNA) delivery especially offers several advantages such as faster gene expression and reduced risk of genome integration if accidentally delivered to the cell nucleus. In this study, we investigated the effect of the poly(A) tail length of mRNA on the mitochondrial translation to achieve efficient expression. We used a peptide-based mitochondrial targeting system, mitoNEET-(RH)9, comprising a mitochondria-targeting sequence (MTS) and a cationic sequence, to deliver mRNA with various poly(A) tails into the mitochondria. The poly(A) tail length significantly affected translational efficiency, with a medium length of 60 nucleotides maximizing protein expression in various cell lines due to enhanced interaction with mitochondrial RNA-binding proteins. Our findings highlight the importance of optimizing poly(A) tail length for efficient mitochondrial mRNA translation, providing a potential strategy for improving mitochondrial gene therapy. These results pave the way for further exploration of the mechanisms and clinical applications of mitochondrial mRNA delivery systems.
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Affiliation(s)
- Naoto Yoshinaga
- Biomacromolecule Research Team, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama 351-0198, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka-shi, Yamagata 997-0017, Japan
| | - Keiji Numata
- Biomacromolecule Research Team, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama 351-0198, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka-shi, Yamagata 997-0017, Japan
- Department of Material Chemistry, Kyoto University, Kyoto-shi, Kyoto 606-8501, Japan
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4
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Brischigliaro M, Sierra‐Magro A, Ahn A, Barrientos A. Mitochondrial ribosome biogenesis and redox sensing. FEBS Open Bio 2024; 14:1640-1655. [PMID: 38849194 PMCID: PMC11452305 DOI: 10.1002/2211-5463.13844] [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: 03/29/2024] [Revised: 05/06/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024] Open
Abstract
Mitoribosome biogenesis is a complex process involving RNA elements encoded in the mitochondrial genome and mitoribosomal proteins typically encoded in the nuclear genome. This process is orchestrated by extra-ribosomal proteins, nucleus-encoded assembly factors, which play roles across all assembly stages to coordinate ribosomal RNA processing and maturation with the sequential association of ribosomal proteins. Both biochemical studies and recent cryo-EM structures of mammalian mitoribosomes have provided insights into their assembly process. In this article, we will briefly outline the current understanding of mammalian mitoribosome biogenesis pathways and the factors involved. Special attention is devoted to the recent identification of iron-sulfur clusters as structural components of the mitoribosome and a small subunit assembly factor, the existence of redox-sensitive cysteines in mitoribosome proteins and assembly factors, and the role they may play as redox sensor units to regulate mitochondrial translation under stress.
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Affiliation(s)
| | - Ana Sierra‐Magro
- Department of NeurologyUniversity of Miami Miller School of MedicineFLUSA
| | - Ahram Ahn
- Department of Biochemistry and Molecular BiologyUniversity of Miami Miller School of MedicineFLUSA
| | - Antoni Barrientos
- Department of NeurologyUniversity of Miami Miller School of MedicineFLUSA
- Department of Biochemistry and Molecular BiologyUniversity of Miami Miller School of MedicineFLUSA
- Bruce W. Carter Department of Veterans Affairs VA Medical CenterMiamiFLUSA
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5
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Jozwik KM, Held JP, Hecht CA, Patel MR. A viable hypomorphic mutation in the mitochondrial ribosome subunit, MRPS-31, exhibits mitochondrial dysfunction in C. elegans. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001344. [PMID: 39410965 PMCID: PMC11474418 DOI: 10.17912/micropub.biology.001344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Revised: 09/24/2024] [Accepted: 09/27/2024] [Indexed: 10/19/2024]
Abstract
The mitochondrial ribosome (mitoribosome) translates mitochondrial genome encoded proteins essential for cellular energy production. Given this critical role, defects in the mitoribosome can cause mitochondrial stress and manifest as multisystemic diseases. In a screen for unique activators of the mitochondrial unfolded protein response (UPR mt ) in Caenorhabditis elegans , we recovered a strain harboring a missense mutation in the gene encoding mitochondrial ribosome protein S31 ( MRPS-31 )-a component of the mitoribosome small subunit. Herein, we confirm causality of the mrps-31 allele and characterize its induction of UPR mt and impact on organismal development, providing a valuable model for further study of the mitoribosome.
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Affiliation(s)
- Kylie M. Jozwik
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States
| | - James P. Held
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States
| | - Chloe A. Hecht
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States
| | - Maulik R. Patel
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States
- Evolutionary Studies, Vanderbilt University, Nashville, Tennessee, United States
- Diabetes Research and Training Center, Vanderbilt University Medical Center, Nashville, Tennessee, United States
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6
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Box JM, Higgins ME, Stuart RA. Importance of conserved hydrophobic pocket region in yeast mitoribosomal mL44 protein for mitotranslation and transcript preference. J Biol Chem 2024; 300:107519. [PMID: 38950860 PMCID: PMC11345376 DOI: 10.1016/j.jbc.2024.107519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 06/14/2024] [Accepted: 06/19/2024] [Indexed: 07/03/2024] Open
Abstract
The mitochondrial ribosome (mitoribosome) is responsible for the synthesis of key oxidative phosphorylation subunits encoded by the mitochondrial genome. Defects in mitoribosomal function therefore can have serious consequences for the bioenergetic capacity of the cell. Mutation of the conserved mitoribosomal mL44 protein has been directly linked to childhood cardiomyopathy and progressive neurophysiology issues. To further explore the functional significance of the mL44 protein in supporting mitochondrial protein synthesis, we have performed a mutagenesis study of the yeast mL44 homolog, the MrpL3/mL44 protein. We specifically investigated the conserved hydrophobic pocket region of the MrpL3/mL44 protein, where the known disease-related residue in the human mL44 protein (L156R) is located. While our findings identify a number of residues in this region critical for MrpL3/mL44's ability to support the assembly of translationally active mitoribosomes, the introduction of the disease-related mutation into the equivalent position in the yeast protein (residue A186) was found to not have a major impact on function. The human and yeast mL44 proteins share many similarities in sequence and structure; however results presented here indicate that these two proteins have diverged somewhat in evolution. Finally, we observed that mutation of the MrpL3/mL44 does not impact the translation of all mitochondrial encoded proteins equally, suggesting the mitochondrial translation system may exhibit a transcript hierarchy and prioritization.
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Affiliation(s)
- Jodie M Box
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Margo E Higgins
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Rosemary A Stuart
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA.
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Hilander T, Awadhpersad R, Monteuuis G, Broda KL, Pohjanpelto M, Pyman E, Singh SK, Nyman TA, Crevel I, Taylor RW, Saada A, Balboa D, Battersby BJ, Jackson CB, Carroll CJ. Supernumerary proteins of the human mitochondrial ribosomal small subunit are integral for assembly and translation. iScience 2024; 27:110185. [PMID: 39015150 PMCID: PMC11251090 DOI: 10.1016/j.isci.2024.110185] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 03/28/2024] [Accepted: 06/01/2024] [Indexed: 07/18/2024] Open
Abstract
Mitochondrial ribosomes (mitoribosomes) have undergone substantial evolutionary structural remodeling accompanied by loss of ribosomal RNA, while acquiring unique protein subunits located on the periphery. We generated CRISPR-mediated knockouts of all 14 unique (mitochondria-specific/supernumerary) human mitoribosomal proteins (snMRPs) in the small subunit to study the effect on mitoribosome assembly and protein synthesis, each leading to a unique mitoribosome assembly defect with variable impact on mitochondrial protein synthesis. Surprisingly, the stability of mS37 was reduced in all our snMRP knockouts of the small and large ribosomal subunits and patient-derived lines with mitoribosome assembly defects. A redox-regulated CX9C motif in mS37 was essential for protein stability, suggesting a potential mechanism to regulate mitochondrial protein synthesis. Together, our findings support a modular assembly of the human mitochondrial small ribosomal subunit mediated by essential supernumerary subunits and identify a redox regulatory role involving mS37 in mitochondrial protein synthesis in health and disease.
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Affiliation(s)
- Taru Hilander
- Genetics Section, Cardiovascular and Genomics Research Institute, St George’s, University of London, London, UK
| | - Ryan Awadhpersad
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Geoffray Monteuuis
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Krystyna L. Broda
- Genetics Section, Cardiovascular and Genomics Research Institute, St George’s, University of London, London, UK
| | - Max Pohjanpelto
- Genetics Section, Cardiovascular and Genomics Research Institute, St George’s, University of London, London, UK
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Elizabeth Pyman
- Genetics Section, Cardiovascular and Genomics Research Institute, St George’s, University of London, London, UK
| | - Sachin Kumar Singh
- Department of Immunology, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Tuula A. Nyman
- Department of Immunology, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Isabelle Crevel
- Core Facilities, St George’s, University of London, London, UK
| | - Robert W. Taylor
- Mitochondrial Research Group, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 4LP, UK
| | - Ann Saada
- Department of Genetics, Hadassah Medical Center & Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112001 Israel
| | - Diego Balboa
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | | | - Christopher B. Jackson
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Christopher J. Carroll
- Genetics Section, Cardiovascular and Genomics Research Institute, St George’s, University of London, London, UK
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Kremer LS, Rehling P. Coordinating mitochondrial translation with assembly of the OXPHOS complexes. Hum Mol Genet 2024; 33:R47-R52. [PMID: 38779773 PMCID: PMC11112383 DOI: 10.1093/hmg/ddae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/31/2024] [Accepted: 02/09/2024] [Indexed: 05/25/2024] Open
Abstract
The mitochondrial oxidative phosphorylation (OXPHOS) system produces the majority of energy required by cells. Given the mitochondrion's endosymbiotic origin, the OXPHOS machinery is still under dual genetic control where most OXPHOS subunits are encoded by the nuclear DNA and imported into mitochondria, while a small subset is encoded on the mitochondrion's own genome, the mitochondrial DNA (mtDNA). The nuclear and mtDNA encoded subunits must be expressed and assembled in a highly orchestrated fashion to form a functional OXPHOS system and meanwhile prevent the generation of any harmful assembly intermediates. While several mechanisms have evolved in eukaryotes to achieve such a coordinated expression, this review will focus on how the translation of mtDNA encoded OXPHOS subunits is tailored to OXPHOS assembly.
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Affiliation(s)
- Laura S Kremer
- Department of Cellular Biochemistry, University Medical Center Göttingen, Humboldtallee 23, Göttingen 37073, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Humboldtallee 23, Göttingen 37073, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, Robert-Koch-Str. 40, Göttingen 37075, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology, Translational Neuroinflammation and Automated Microscopy, Robert-Koch-Str. 40, Göttingen 37075, Germany
- Max Planck Institute for Multidisciplinary Science, Am Faßberg 11, Göttingen 37077, Germany
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Singh J, Singh S, Emam EAF, Varshney U. Role of Rmd9p in 3'-end processing of mitochondrial 15S rRNA in Saccharomyces cerevisiae. Mitochondrion 2024; 76:101876. [PMID: 38599301 DOI: 10.1016/j.mito.2024.101876] [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: 12/15/2023] [Revised: 02/05/2024] [Accepted: 04/07/2024] [Indexed: 04/12/2024]
Abstract
Ribosome biogenesis, involving processing/assembly of rRNAs and r-proteins is a vital process. In Saccharomyces cerevisiae mitochondria, ribosomal small subunit comprises 15S rRNA (15S). While the 15S 5'-end processing uses Ccm1p and Pet127p, the mechanisms of the 3'-end processing remain unclear. We reveal involvement of Rmd9p in safeguarding/processing 15S 3'-end. Rmd9p deficiency results in a cleavage at a position 183 nucleotides upstream of 15S 3'-end, and in the loss of the 3'-minor domain. Rmd9p binds to the sequences in the 3'-end region of 15S, and a genetic interaction between rmd9 and dss1 indicates that Rmd9p regulates/limits mtEXO activity during the 3'-end spacer processing.
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Affiliation(s)
- Jitendra Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Sudhir Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Elhassan Ali Fathi Emam
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India.
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Papadopoulos T, Gaignard P, Schiff M, Rio M, Karall D, Legendre A, Verloes A, Ruaud L. New description of an MRPS2 homozygous patient: Further features to help expend the phenotype. Eur J Med Genet 2024; 67:104889. [PMID: 38029925 DOI: 10.1016/j.ejmg.2023.104889] [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: 05/26/2023] [Revised: 09/04/2023] [Accepted: 10/29/2023] [Indexed: 12/01/2023]
Abstract
Mutated mito-ribosomal protein S2 (MRPS2) was already described in only three subjects, two with sensorineural hearing impairment, mild developmental delay, hypoglycemia, lactic acidemia and combined oxidative phosphorylation system deficiency and another, recently, presenting with a less severe phenotype. In order to expand the phenotype, we describe a new MRPS2 homozygous subject who shows particular features which have not yet been reported: initial microcephaly, joint hypermobility and autistic features.
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Affiliation(s)
- Thalia Papadopoulos
- APHP.Nord, Robert-Debré University Hospital, Department of Genetics, F-75019, Paris, France
| | - Pauline Gaignard
- Laboratoire de Biochimie Site Bicêtre, Faculté de Pharmacie, Hôpitaux Universitaires Paris-Saclay, Centre de référence des Maladies Mitochondriales, Filière Filnemus, France; Laboratoire de biologie médicale multisites Seqoia - FMG2025, Paris, France
| | - Manuel Schiff
- Necker Hospital, APHP, Reference Center for Inborn Error of Metabolism and Filière G2M, Pediatrics Department, University of Paris, Paris, France; Inserm UMR_S1163, Institut Imagine, Paris, France
| | - Marlène Rio
- Departments of Pediatrics, Neurology and Genetics, Hopital Necker Enfants-Malades, 75015, Paris, France
| | - Daniela Karall
- Clinic for Pediatrics, Inherited Metabolic Disorders, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Adrien Legendre
- Laboratoire de biologie médicale multisites Seqoia - FMG2025, Paris, France
| | - Alain Verloes
- APHP.Nord, Robert-Debré University Hospital, Department of Genetics, F-75019, Paris, France; INSERM UMR 1141, Neurodiderot, University of Paris, F-75019, Paris, France
| | - Lyse Ruaud
- APHP.Nord, Robert-Debré University Hospital, Department of Genetics, F-75019, Paris, France; INSERM UMR 1141, Neurodiderot, University of Paris, F-75019, Paris, France.
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11
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Zhao JW, Zhao WY, Cui XH, Xing L, Shi JC, Yu L. The role of the mitochondrial ribosomal protein family in detecting hepatocellular carcinoma and predicting prognosis, immune features, and drug sensitivity. Clin Transl Oncol 2024; 26:496-514. [PMID: 37407805 DOI: 10.1007/s12094-023-03269-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 06/25/2023] [Indexed: 07/07/2023]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the most common types of malignant tumors, with a slow onset, rapid progression, and frequent recurrence. Previous research has implicated mitochondrial ribosomal genes in the development, metastasis, and prognosis of various cancers. However, further research is necessary to establish a link between mitochondrial ribosomal protein (MRP) family expression and HCC diagnosis, prognosis, ferroptosis-related gene (FRG) expression, m6A modification-related gene expression, tumor immunity, and drug sensitivity. METHODS Bioinformatics resources were used to analyze data from patients with HCC retrieved from the TCGA, ICGC, and GTEx databases (GEPIA, UALCAN, Xiantao tool, cBioPortal, STRING, Cytoscape, TISIDB, and GSCALite). RESULTS Among the 82 MRP family members, 14 MRP genes (MRPS21, MRPS23, MRPL9, DAP3, MRPL13, MRPL17, MRPL24, MRPL55, MRPL16, MRPL14, MRPS17, MRPL47, MRPL21, and MRPL15) were significantly upregulated differentially expressed genes (DEGs) in HCC tumor samples in comparison to normal samples. Receiver-operating characteristic curve analysis indicated that all 14 DEGs show good diagnostic performance. Furthermore, TCGA analysis revealed that the mRNA expression of 39 MRPs was associated with overall survival (OS) in HCC. HCC was divided into two molecular subtypes (C1 and C2) with distinct prognoses using clustering analysis. The clusters showed different FRG expression and m6A methylation profiles and immune features, and prognostic models showed that the model integrating 5 MRP genes (MRPS15, MRPL3, MRPL9, MRPL36, and MRPL37) and 2 FRGs (SLC1A5 and SLC5A11) attained a greater clinical net benefit than three other prognostic models. Finally, analysis of the CTRP and GDSC databases revealed several potential drugs that could target prognostic MRP genes. CONCLUSION We identified 14 MRP genes as HCC diagnostic markers. We investigated FRG and m6A modification-related gene expression profiles and immune features in patients with HCC, and developed and validated a model incorporating MRP and FRG expression that accurately and reliably predicts HCC prognosis and may predict disease progression and treatment response.
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Affiliation(s)
- Jin-Wei Zhao
- Department of Hepatopancreatobiliary Surgery of Second Hospital of Jilin University, State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, No. 218, Ziqiang Street, Nanguan District, Changchun, 130000, Jilin Province, China
| | - Wei-Yi Zhao
- Medical College of YanBian University, YanBian, 133000, China
| | - Xin-Hua Cui
- Department of Hepatopancreatobiliary Surgery of Second Hospital of Jilin University, State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, No. 218, Ziqiang Street, Nanguan District, Changchun, 130000, Jilin Province, China
| | - Lin Xing
- Department of Hepatopancreatobiliary Surgery of Second Hospital of Jilin University, State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, No. 218, Ziqiang Street, Nanguan District, Changchun, 130000, Jilin Province, China
| | - Jia-Cheng Shi
- Department of Hepatopancreatobiliary Surgery of Second Hospital of Jilin University, State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, No. 218, Ziqiang Street, Nanguan District, Changchun, 130000, Jilin Province, China
| | - Lu Yu
- Department of Hepatopancreatobiliary Surgery of Second Hospital of Jilin University, State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, No. 218, Ziqiang Street, Nanguan District, Changchun, 130000, Jilin Province, China.
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12
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Ma T, Huang YB, Chen J, Zhang L, Liu YH, Lu CH. MRPL21 promotes HCC proliferation through TP53 mutation-induced apoptotic resistance. Tissue Cell 2024; 86:102298. [PMID: 38181584 DOI: 10.1016/j.tice.2023.102298] [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: 08/28/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 01/07/2024]
Abstract
BACKGROUND AND AIMS The specific mechanisms underlying the inhibition of hepatocellular carcinoma (HCC) proliferation and metastasis by mitochondrial apoptosis are not yet fully understood. However, it plays a vital role in suppressing HCC's ability to proliferate and spread. The involvement of MRPL21, a member within the family of mitochondrial ribosomal proteins (MRPs), is well-documented in both cellular apoptosis and energy metabolism. This study aims to explore and unravel the underlying mechanisms through which MRPL21 contributes to mitochondrial apoptosis and resistance against apoptosis in HCC. METHODS To evaluate the level of MRPL21 expression at the gene and protein expression levels, analysis was performed on human liver samples and blood using techniques for quantification. A knockdown plasmid targeting MRPL21 was constructed to investigate its impact on the growth and apoptosis of hepatocellular carcinoma (HCC). To evaluate the impact of MRPL21 knockdown on hepatocellular carcinoma (HCC) cell proliferation and apoptosis, various assays were performed including CCK-8 assays, flow cytometry analysis, detection of reactive oxygen species (ROS), and assessment of mitochondrial membrane potential (MMP). Furthermore, the role of MRPL21 in TP53 mutation was examined using Nutlin-3. RESULTS In HCC tissues and blood samples, an upregulation of MRPL21 expression was observed when compared to samples obtained from healthy individuals, and it is correlated with a poor prognosis for HCC. Silencing MRPL21 can effectively suppress Hep3B and HCCLM3 cells proliferation by modulating the mitochondrial membrane potential, it triggers the generation of reactive oxygen species (ROS), thereby leading to G0/G1 cell cycle arrest and initiation of early apoptosis. Furthermore, by inhibiting P53 activity, Nutlin-3 treatment can enhance MRPL21-deficiency-mediated apoptosis in Hep3B and HCCLM3 cells. CONCLUSION Through its influence on TP53 mutation, MRPL21 promotes HCC proliferation and progression while conferring resistance to apoptosis. These findings suggest that MRPL21 holds promise as a valuable biomarker for the treatment of HCC.
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Affiliation(s)
- Tao Ma
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China; Research Center of Clinical Medicine, Nantong University, Affiliated Hospital of Nantong University, Nantong, China
| | - Ya-Bin Huang
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Jing Chen
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China; Research Center of Clinical Medicine, Nantong University, Affiliated Hospital of Nantong University, Nantong, China
| | - Lu Zhang
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China; Research Center of Clinical Medicine, Nantong University, Affiliated Hospital of Nantong University, Nantong, China
| | - Yan-Hua Liu
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China.
| | - Cui-Hua Lu
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China.
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13
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Lv M, Zhou W, Hao Y, Li F, Zhang H, Yao X, Shi Y, Zhang L. Structural insights into the specific recognition of mitochondrial ribosome-binding factor hsRBFA and 12 S rRNA by methyltransferase METTL15. Cell Discov 2024; 10:11. [PMID: 38291322 PMCID: PMC10828496 DOI: 10.1038/s41421-023-00634-z] [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: 05/08/2023] [Accepted: 12/02/2023] [Indexed: 02/01/2024] Open
Abstract
Mitochondrial rRNA modifications are essential for mitoribosome assembly and its proper function. The m4C methyltransferase METTL15 maintains mitochondrial homeostasis by catalyzing m4C839 located in 12 S rRNA helix 44 (h44). This modification is essential to fine-tuning the ribosomal decoding center and increasing decoding fidelity according to studies of a conserved site in Escherichia coli. Here, we reported a series of crystal structures of human METTL15-hsRBFA-h44-SAM analog, METTL15-hsRBFA-SAM, METTL15-SAM and apo METTL15. The structures presented specific interactions of METTL15 with different substrates and revealed that hsRBFA recruits METTL15 to mitochondrial small subunit for further modification instead of 12 S rRNA. Finally, we found that METTL15 deficiency caused increased reactive oxygen species, decreased membrane potential and altered cellular metabolic state. Knocking down METTL15 caused an elevated lactate secretion and increased levels of histone H4K12-lactylation and H3K9-lactylation. METTL15 might be a suitable model to study the regulation between mitochondrial metabolism and histone lactylation.
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Affiliation(s)
- Mengqi Lv
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China.
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
| | - Wanwan Zhou
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Yijie Hao
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Fudong Li
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Huafeng Zhang
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Xuebiao Yao
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Yunyu Shi
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Liang Zhang
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China.
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
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14
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Nguyen TG, Ritter C, Kummer E. Structural insights into the role of GTPBP10 in the RNA maturation of the mitoribosome. Nat Commun 2023; 14:7991. [PMID: 38042949 PMCID: PMC10693566 DOI: 10.1038/s41467-023-43599-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/14/2023] [Indexed: 12/04/2023] Open
Abstract
Mitochondria contain their own genetic information and a dedicated translation system to express it. The mitochondrial ribosome is assembled from mitochondrial-encoded RNA and nuclear-encoded ribosomal proteins. Assembly is coordinated in the mitochondrial matrix by biogenesis factors that transiently associate with the maturing particle. Here, we present a structural snapshot of a large mitoribosomal subunit assembly intermediate containing 7 biogenesis factors including the GTPases GTPBP7 and GTPBP10. Our structure illustrates how GTPBP10 aids the folding of the ribosomal RNA during the biogenesis process, how this process is related to bacterial ribosome biogenesis, and why mitochondria require two biogenesis factors in contrast to only one in bacteria.
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Affiliation(s)
- Thu Giang Nguyen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Christina Ritter
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Eva Kummer
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark.
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15
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Wang L, Hilander T, Liu X, Tsang HY, Eriksson O, Jackson CB, Varjosalo M, Zhao H. GTPBP8 is required for mitoribosomal biogenesis and mitochondrial translation. Cell Mol Life Sci 2023; 80:361. [PMID: 37971521 PMCID: PMC10654211 DOI: 10.1007/s00018-023-05014-0] [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: 07/05/2023] [Revised: 09/28/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023]
Abstract
Mitochondrial translation occurs on the mitochondrial ribosome, also known as the mitoribosome. The assembly of mitoribosomes is a highly coordinated process. During mitoribosome biogenesis, various assembly factors transiently associate with the nascent ribosome, facilitating the accurate and efficient construction of the mitoribosome. However, the specific factors involved in the assembly process, the precise mechanisms, and the cellular compartments involved in this vital process are not yet fully understood. In this study, we discovered a crucial role for GTP-binding protein 8 (GTPBP8) in the assembly of the mitoribosomal large subunit (mt-LSU) and mitochondrial translation. GTPBP8 is identified as a novel GTPase located in the matrix and peripherally bound to the inner mitochondrial membrane. Importantly, GTPBP8 is specifically associated with the mt-LSU during its assembly. Depletion of GTPBP8 leads to an abnormal accumulation of mt-LSU, indicating that GTPBP8 is critical for proper mt-LSU assembly. Furthermore, the absence of GTPBP8 results in reduced levels of fully assembled 55S monosomes. This impaired assembly leads to compromised mitochondrial translation and, consequently, impaired mitochondrial function. The identification of GTPBP8 as an important player in these processes provides new insights into the molecular mechanisms underlying mitochondrial protein synthesis and its regulation.
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Affiliation(s)
- Liang Wang
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, West China Medical School, Sichuan University, #1 Keyuan Road, Gaopeng Street, High-Tech Development Zone, West China, Chengdu, 610041, China
| | - Taru Hilander
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
| | - Xiaonan Liu
- Institute of Biotechnology and Helsinki Institute of Life Science, University of Helsinki, 00014, Helsinki, Finland
| | - Hoi Ying Tsang
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
| | - Ove Eriksson
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
| | - Christopher B Jackson
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology and Helsinki Institute of Life Science, University of Helsinki, 00014, Helsinki, Finland
| | - Hongxia Zhao
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland.
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16
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LaPeruta AJ, Micic J, Woolford Jr. JL. Additional principles that govern the release of pre-ribosomes from the nucleolus into the nucleoplasm in yeast. Nucleic Acids Res 2023; 51:10867-10883. [PMID: 35736211 PMCID: PMC10639060 DOI: 10.1093/nar/gkac430] [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: 10/16/2021] [Revised: 05/05/2022] [Accepted: 06/20/2022] [Indexed: 11/14/2022] Open
Abstract
During eukaryotic ribosome biogenesis, pre-ribosomes travel from the nucleolus, where assembly is initiated, to the nucleoplasm and then are exported to the cytoplasm, where assembly concludes. Although nuclear export of pre-ribosomes has been extensively investigated, the release of pre-ribosomes from the nucleolus is an understudied phenomenon. Initial data indicate that unfolded rRNA interacts in trans with nucleolar components and that, when rRNA folds due to ribosomal protein (RP) binding, the number of trans interactions drops below the threshold necessary for nucleolar retention. To validate and expand on this idea, we performed a bioinformatic analysis of the protein components of the Saccharomyces cerevisiae ribosome assembly pathway. We found that ribosome biogenesis factors (RiBi factors) contain significantly more predicted trans interacting regions than RPs. We also analyzed cryo-EM structures of ribosome assembly intermediates to determine how nucleolar pre-ribosomes differ from post-nucleolar pre-ribosomes, specifically the capacity of RPs, RiBi factors, and rRNA components to interact in trans. We observed a significant decrease in the theoretical trans-interacting capability of pre-ribosomes between nucleolar and post-nucleolar stages of assembly due to the release of RiBi factors from particles and the folding of rRNA. Here, we provide a mechanism for the release of pre-ribosomes from the nucleolus.
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Affiliation(s)
- Amber J LaPeruta
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Jelena Micic
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - John L Woolford Jr.
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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17
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Bartal G, Yitzhaky A, Segev A, Hertzberg L. Multiple genes encoding mitochondrial ribosomes are downregulated in brain and blood samples of individuals with schizophrenia. World J Biol Psychiatry 2023; 24:829-837. [PMID: 37158323 DOI: 10.1080/15622975.2023.2211653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/04/2023] [Indexed: 05/10/2023]
Abstract
OBJECTIVES Schizophrenia is a chronic, debilitating mental disorder whose pathophysiology is complex and not fully understood. Numerous studies suggest mitochondrial dysfunction may contribute to the development of schizophrenia. While mitochondrial ribosomes (mitoribosomes) are essential for proper mitochondrial functioning, their gene expression levels have not been studied yet in schizophrenia. METHODS We performed a systematic meta-analysis of the expression of 81 mitoribosomes subunits encoding genes, integrating ten brain samples datasets of patients with schizophrenia compared to healthy controls (overall 422 samples, 211 schizophrenia, and 211 controls). We also performed a meta-analysis of their expression in blood, integrating two blood sample datasets (overall 90 samples, 53 schizophrenia, and 37 controls). RESULTS Multiple mitoribosomes subunits were significantly downregulated in brain samples (18 genes) and in blood samples (11 genes) of individuals with schizophrenia, where two showed significant downregulation in both brain and blood, MRPL4 and MRPS7. CONCLUSIONS Our results support the accumulating evidence of impaired mitochondrial activity in schizophrenia. While further research is needed to validate mitoribosomes' role as biomarkers, this direction has the potential to promote patients' stratification and personalised treatment for schizophrenia.
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Affiliation(s)
- Gideon Bartal
- The Faculty of Health Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Assif Yitzhaky
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Aviv Segev
- The Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Shalvata Mental Health Center, Hod Hasharon, Israel
| | - Libi Hertzberg
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
- The Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Shalvata Mental Health Center, Hod Hasharon, Israel
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18
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Potter A, Cabrera-Orefice A, Spelbrink JN. Let's make it clear: systematic exploration of mitochondrial DNA- and RNA-protein complexes by complexome profiling. Nucleic Acids Res 2023; 51:10619-10641. [PMID: 37615582 PMCID: PMC10602928 DOI: 10.1093/nar/gkad697] [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: 04/15/2023] [Revised: 07/18/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023] Open
Abstract
Complexome profiling (CP) is a powerful tool for systematic investigation of protein interactors that has been primarily applied to study the composition and dynamics of mitochondrial protein complexes. Here, we further optimized this method to extend its application to survey mitochondrial DNA- and RNA-interacting protein complexes. We established that high-resolution clear native gel electrophoresis (hrCNE) is a better alternative to preserve DNA- and RNA-protein interactions that are otherwise disrupted when samples are separated by the widely used blue native gel electrophoresis (BNE). In combination with enzymatic digestion of DNA, our CP approach improved the identification of a wide range of protein interactors of the mitochondrial gene expression system without compromising the detection of other multiprotein complexes. The utility of this approach was particularly demonstrated by analysing the complexome changes in human mitochondria with impaired gene expression after transient, chemically induced mitochondrial DNA depletion. Effects of RNase on mitochondrial protein complexes were also evaluated and discussed. Overall, our adaptations significantly improved the identification of mitochondrial DNA- and RNA-protein interactions by CP, thereby unlocking the comprehensive analysis of a near-complete mitochondrial complexome in a single experiment.
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Affiliation(s)
- Alisa Potter
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alfredo Cabrera-Orefice
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Functional Proteomics, Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main, Germany
| | - Johannes N Spelbrink
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, The Netherlands
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19
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Del Giudice L, Pontieri P, Aletta M, Calcagnile M. Mitochondrial Neurodegenerative Diseases: Three Mitochondrial Ribosomal Proteins as Intermediate Stage in the Pathway That Associates Damaged Genes with Alzheimer's and Parkinson's. BIOLOGY 2023; 12:972. [PMID: 37508402 PMCID: PMC10376763 DOI: 10.3390/biology12070972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023]
Abstract
Currently, numerous research endeavors are dedicated to unraveling the intricate nature of neurodegenerative diseases. These conditions are characterized by the gradual and progressive impairment of specific neuronal systems that exhibit anatomical or physiological connections. In particular, in the last twenty years, remarkable efforts have been made to elucidate neurodegenerative disorders such as Alzheimer's disease and Parkinson's disease. However, despite extensive research endeavors, no cure or effective treatment has been discovered thus far. With the emergence of studies shedding light on the contribution of mitochondria to the onset and advancement of mitochondrial neurodegenerative disorders, researchers are now directing their investigations toward the development of therapies. These therapies include molecules designed to protect mitochondria and neurons from the detrimental effects of aging, as well as mutant proteins. Our objective is to discuss and evaluate the recent discovery of three mitochondrial ribosomal proteins linked to Alzheimer's and Parkinson's diseases. These proteins represent an intermediate stage in the pathway connecting damaged genes to the two mitochondrial neurological pathologies. This discovery potentially could open new avenues for the production of medicinal substances with curative potential for the treatment of these diseases.
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Affiliation(s)
- Luigi Del Giudice
- Istituto di Bioscienze e BioRisorse-UOS Napoli-CNR c/o Dipartimento di Biologia, Sezione di Igiene, 80134 Napoli, Italy
| | - Paola Pontieri
- Istituto di Bioscienze e BioRisorse-UOS Napoli-CNR c/o Dipartimento di Biologia, Sezione di Igiene, 80134 Napoli, Italy
| | | | - Matteo Calcagnile
- Dipartimento di Scienze e Tecnologie Biologiche e Ambientali, Università del Salento, 73100 Lecce, Italy
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20
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Vila-Sanjurjo A, Mallo N, Elson JL, Smith PM, Blakely EL, Taylor RW. Structural analysis of mitochondrial rRNA gene variants identified in patients with deafness. Front Physiol 2023; 14:1163496. [PMID: 37362424 PMCID: PMC10285412 DOI: 10.3389/fphys.2023.1163496] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/18/2023] [Indexed: 06/28/2023] Open
Abstract
The last few years have witnessed dramatic advances in our understanding of the structure and function of the mammalian mito-ribosome. At the same time, the first attempts to elucidate the effects of mito-ribosomal fidelity (decoding accuracy) in disease have been made. Hence, the time is right to push an important frontier in our understanding of mitochondrial genetics, that is, the elucidation of the phenotypic effects of mtDNA variants affecting the functioning of the mito-ribosome. Here, we have assessed the structural and functional role of 93 mitochondrial (mt-) rRNA variants thought to be associated with deafness, including those located at non-conserved positions. Our analysis has used the structural description of the human mito-ribosome of the highest quality currently available, together with a new understanding of the phenotypic manifestation of mito-ribosomal-associated variants. Basically, any base change capable of inducing a fidelity phenotype may be considered non-silent. Under this light, out of 92 previously reported mt-rRNA variants thought to be associated with deafness, we found that 49 were potentially non-silent. We also dismissed a large number of reportedly pathogenic mtDNA variants, 41, as polymorphisms. These results drastically update our view on the implication of the primary sequence of mt-rRNA in the etiology of deafness and mitochondrial disease in general. Our data sheds much-needed light on the question of how mt-rRNA variants located at non-conserved positions may lead to mitochondrial disease and, most notably, provide evidence of the effect of haplotype context in the manifestation of some mt-rRNA variants.
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Affiliation(s)
- Antón Vila-Sanjurjo
- Grupo GIBE. Departamento de Bioloxía e Centro Interdisciplinar de Química e Bioloxía (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Natalia Mallo
- Grupo GIBE. Departamento de Bioloxía e Centro Interdisciplinar de Química e Bioloxía (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Joanna L. Elson
- The Bioscience Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Paul M. Smith
- Department of Paediatrics, Raigmore Hospital, Inverness, United Kingdom
| | - Emma L. Blakely
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
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21
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Kisty EA, Saart EC, Weerapana E. Identifying Redox-Sensitive Cysteine Residues in Mitochondria. Antioxidants (Basel) 2023; 12:992. [PMID: 37237858 PMCID: PMC10215197 DOI: 10.3390/antiox12050992] [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: 03/02/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
The mitochondrion is the primary energy generator of a cell and is a central player in cellular redox regulation. Mitochondrial reactive oxygen species (mtROS) are the natural byproducts of cellular respiration that are critical for the redox signaling events that regulate a cell's metabolism. These redox signaling pathways primarily rely on the reversible oxidation of the cysteine residues on mitochondrial proteins. Several key sites of this cysteine oxidation on mitochondrial proteins have been identified and shown to modulate downstream signaling pathways. To further our understanding of mitochondrial cysteine oxidation and to identify uncharacterized redox-sensitive cysteines, we coupled mitochondrial enrichment with redox proteomics. Briefly, differential centrifugation methods were used to enrich for mitochondria. These purified mitochondria were subjected to both exogenous and endogenous ROS treatments and analyzed by two redox proteomics methods. A competitive cysteine-reactive profiling strategy, termed isoTOP-ABPP, enabled the ranking of the cysteines by their redox sensitivity, due to a loss of reactivity induced by cysteine oxidation. A modified OxICAT method enabled a quantification of the percentage of reversible cysteine oxidation. Initially, we assessed the cysteine oxidation upon treatment with a range of exogenous hydrogen peroxide concentrations, which allowed us to differentiate the mitochondrial cysteines by their susceptibility to oxidation. We then analyzed the cysteine oxidation upon inducing reactive oxygen species generation via the inhibition of the electron transport chain. Together, these methods identified the mitochondrial cysteines that were sensitive to endogenous and exogenous ROS, including several previously known redox-regulated cysteines and uncharacterized cysteines on diverse mitochondrial proteins.
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22
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Jerome MS, Nanjappa DP, Chakraborty A, Chakrabarty S. Molecular etiology of defective nuclear and mitochondrial ribosome biogenesis: Clinical phenotypes and therapy. Biochimie 2023; 207:122-136. [PMID: 36336106 DOI: 10.1016/j.biochi.2022.11.001] [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: 08/01/2022] [Revised: 10/27/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022]
Abstract
Ribosomopathies are rare congenital disorders associated with defective ribosome biogenesis due to pathogenic variations in genes that encode proteins related to ribosome function and biogenesis. Defects in ribosome biogenesis result in a nucleolar stress response involving the TP53 tumor suppressor protein and impaired protein synthesis leading to a deregulated translational output. Despite the accepted notion that ribosomes are omnipresent and essential for all cells, most ribosomopathies show tissue-specific phenotypes affecting blood cells, hair, spleen, or skin. On the other hand, defects in mitochondrial ribosome biogenesis are associated with a range of clinical manifestations affecting more than one organ. Intriguingly, the deregulated ribosomal function is also a feature in several human malignancies with a selective upregulation or downregulation of specific ribosome components. Here, we highlight the clinical conditions associated with defective ribosome biogenesis in the nucleus and mitochondria with a description of the affected genes and the implicated pathways, along with a note on the treatment strategies currently available for these disorders.
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Affiliation(s)
- Maria Sona Jerome
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Dechamma Pandyanda Nanjappa
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), NITTE (Deemed to Be University), Deralakate, Mangaluru, 575018, India
| | - Anirban Chakraborty
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), NITTE (Deemed to Be University), Deralakate, Mangaluru, 575018, India.
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.
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23
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Echtenkamp FJ, Ishida R, Rivera-Marquez GM, Maisiak M, Johnson OT, Shrimp JH, Sinha A, Ralph SJ, Nisbet I, Cherukuri MK, Gestwicki JE, Neckers LM. Mitoribosome sensitivity to HSP70 inhibition uncovers metabolic liabilities of castration-resistant prostate cancer. PNAS NEXUS 2023; 2:pgad115. [PMID: 37091547 PMCID: PMC10118397 DOI: 10.1093/pnasnexus/pgad115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/07/2023] [Accepted: 03/23/2023] [Indexed: 04/05/2023]
Abstract
The androgen receptor is a key regulator of prostate cancer and the principal target of current prostate cancer therapies collectively termed androgen deprivation therapies. Insensitivity to these drugs is a hallmark of progression to a terminal disease state termed castration-resistant prostate cancer. Therefore, novel therapeutic options that slow progression of castration-resistant prostate cancer and combine effectively with existing agents are in urgent need. We show that JG-98, an allosteric inhibitor of HSP70, re-sensitizes castration-resistant prostate cancer to androgen deprivation drugs by targeting mitochondrial HSP70 (HSPA9) to suppress aerobic respiration. Rather than impacting androgen receptor stability as previously described, JG-98's primary effect is inhibition of mitochondrial translation, leading to disruption of electron transport chain activity. Although functionally distinct from HSPA9 inhibition, direct inhibition of the electron transport chain with a complex I or II inhibitor creates a similar physiological state capable of re-sensitizing castration-resistant prostate cancer to androgen deprivation therapies. These data identify a significant role for HspA9 in mitochondrial ribosome function and highlight an actionable metabolic vulnerability of castration-resistant prostate cancer.
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Affiliation(s)
- Frank J Echtenkamp
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Ryo Ishida
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Genesis M Rivera-Marquez
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Marisa Maisiak
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Oleta T Johnson
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jonathan H Shrimp
- Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Arnav Sinha
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | | | - Ian Nisbet
- Cancure Ltd,Broadbeach, Queensland 4218, Australia
| | - Murali Krishna Cherukuri
- Biophysics Section, Radiation Biology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Leonard M Neckers
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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24
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De Vitis C, Battaglia AM, Pallocca M, Santamaria G, Mimmi MC, Sacco A, De Nicola F, Gaspari M, Salvati V, Ascenzi F, Bruschini S, Esposito A, Ricci G, Sperandio E, Massacci A, Prestagiacomo LE, Vecchione A, Ricci A, Sciacchitano S, Salerno G, French D, Aversa I, Cereda C, Fanciulli M, Chiaradonna F, Solito E, Cuda G, Costanzo F, Ciliberto G, Mancini R, Biamonte F. ALDOC- and ENO2- driven glucose metabolism sustains 3D tumor spheroids growth regardless of nutrient environmental conditions: a multi-omics analysis. J Exp Clin Cancer Res 2023; 42:69. [PMID: 36945054 PMCID: PMC10031988 DOI: 10.1186/s13046-023-02641-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 03/07/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Metastases are the major cause of cancer-related morbidity and mortality. By the time cancer cells detach from their primary site to eventually spread to distant sites, they need to acquire the ability to survive in non-adherent conditions and to proliferate within a new microenvironment in spite of stressing conditions that may severely constrain the metastatic process. In this study, we gained insight into the molecular mechanisms allowing cancer cells to survive and proliferate in an anchorage-independent manner, regardless of both tumor-intrinsic variables and nutrient culture conditions. METHODS 3D spheroids derived from lung adenocarcinoma (LUAD) and breast cancer cells were cultured in either nutrient-rich or -restricted culture conditions. A multi-omics approach, including transcriptomics, proteomics, and metabolomics, was used to explore the molecular changes underlying the transition from 2 to 3D cultures. Small interfering RNA-mediated loss of function assays were used to validate the role of the identified differentially expressed genes and proteins in H460 and HCC827 LUAD as well as in MCF7 and T47D breast cancer cell lines. RESULTS We found that the transition from 2 to 3D cultures of H460 and MCF7 cells is associated with significant changes in the expression of genes and proteins involved in metabolic reprogramming. In particular, we observed that 3D tumor spheroid growth implies the overexpression of ALDOC and ENO2 glycolytic enzymes concomitant with the enhanced consumption of glucose and fructose and the enhanced production of lactate. Transfection with siRNA against both ALDOC and ENO2 determined a significant reduction in lactate production, viability and size of 3D tumor spheroids produced by H460, HCC827, MCF7, and T47D cell lines. CONCLUSIONS Our results show that anchorage-independent survival and growth of cancer cells are supported by changes in genes and proteins that drive glucose metabolism towards an enhanced lactate production. Notably, this finding is valid for all lung and breast cancer cell lines we have analyzed in different nutrient environmental conditions. broader Validation of this mechanism in other cancer cells of different origin will be necessary to broaden the role of ALDOC and ENO2 to other tumor types. Future in vivo studies will be necessary to assess the role of ALDOC and ENO2 in cancer metastasis.
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Affiliation(s)
- Claudia De Vitis
- Department of Clinical and Molecular Medicine, Sant'Andrea Hospital, ''Sapienza'' University of Rome, Rome, Italy
| | - Anna Martina Battaglia
- Department of Experimental and Clinical Medicine, ''Magna Graecia'' University of Catanzaro, Catanzaro, Italy
| | - Matteo Pallocca
- Biostatistics, Bioinformatics and Clinical Trial Center, IRCCS ''Regina Elena'' National Cancer Institute, Rome, Italy
| | - Gianluca Santamaria
- Department of Experimental and Clinical Medicine, ''Magna Graecia'' University of Catanzaro, Catanzaro, Italy
| | | | - Alessandro Sacco
- Department of Experimental and Clinical Medicine, ''Magna Graecia'' University of Catanzaro, Catanzaro, Italy
| | - Francesca De Nicola
- SAFU Laboratory, IRCCS ''Regina Elena'' National Cancer Institute, Rome, Italy
| | - Marco Gaspari
- Department of Experimental and Clinical Medicine, ''Magna Graecia'' University of Catanzaro, Catanzaro, Italy
| | - Valentina Salvati
- Preclinical Models and New Therapeutic Agents Unit, IRCCS ''Regina Elena'' National Cancer Institute, Rome, Italy
| | - Francesca Ascenzi
- Department of Clinical and Molecular Medicine, Sant'Andrea Hospital, ''Sapienza'' University of Rome, Rome, Italy
| | - Sara Bruschini
- Department of Clinical and Molecular Medicine, Sant'Andrea Hospital, ''Sapienza'' University of Rome, Rome, Italy
| | - Antonella Esposito
- Department of Experimental and Clinical Medicine, ''Magna Graecia'' University of Catanzaro, Catanzaro, Italy
| | - Giulia Ricci
- Department of Experimental Medicine, Università Degli Studi Della Campania ''Luigi Vanvitelli'', Naples, Italy
| | - Eleonora Sperandio
- Biostatistics, Bioinformatics and Clinical Trial Center, IRCCS ''Regina Elena'' National Cancer Institute, Rome, Italy
| | - Alice Massacci
- Biostatistics, Bioinformatics and Clinical Trial Center, IRCCS ''Regina Elena'' National Cancer Institute, Rome, Italy
| | - Licia Elvira Prestagiacomo
- Department of Experimental and Clinical Medicine, ''Magna Graecia'' University of Catanzaro, Catanzaro, Italy
| | - Andrea Vecchione
- Department of Clinical and Molecular Medicine, Sant'Andrea Hospital, ''Sapienza'' University of Rome, Rome, Italy
| | - Alberto Ricci
- Respiratory Unit, Sant'Andrea Hospital, Sapienza University of Rome, Rome, Italy
| | - Salvatore Sciacchitano
- Department of Clinical and Molecular Medicine, Sant'Andrea Hospital, ''Sapienza'' University of Rome, Rome, Italy
| | - Gerardo Salerno
- Department of Neurosciences, Mental Health and Sensory Organs (NESMOS), Sapienza University of Rome, Rome, Italy
| | - Deborah French
- Department of Clinical and Molecular Medicine, Sant'Andrea Hospital, ''Sapienza'' University of Rome, Rome, Italy
| | - Ilenia Aversa
- Department of Experimental and Clinical Medicine, ''Magna Graecia'' University of Catanzaro, Catanzaro, Italy
| | - Cristina Cereda
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Maurizio Fanciulli
- SAFU Laboratory, IRCCS ''Regina Elena'' National Cancer Institute, Rome, Italy
| | | | - Egle Solito
- Barts and The London School of Medicine and Dentistry, William Harvey Research Institute, Queen Mary University of London, London, E1 2AT, UK
| | - Giovanni Cuda
- Department of Experimental and Clinical Medicine, ''Magna Graecia'' University of Catanzaro, Catanzaro, Italy
| | - Francesco Costanzo
- Department of Experimental and Clinical Medicine, ''Magna Graecia'' University of Catanzaro, Catanzaro, Italy
- Magna Graecia University of Catanzaro, Interdepartmental Centre of Services, Catanzaro, Italy
| | - Gennaro Ciliberto
- Scientific Director, IRCCS ''Regina Elena'' National Cancer Institute, Rome, Italy
| | - Rita Mancini
- Department of Clinical and Molecular Medicine, Sant'Andrea Hospital, ''Sapienza'' University of Rome, Rome, Italy.
| | - Flavia Biamonte
- Department of Experimental and Clinical Medicine, ''Magna Graecia'' University of Catanzaro, Catanzaro, Italy
- Barts and The London School of Medicine and Dentistry, William Harvey Research Institute, Queen Mary University of London, London, E1 2AT, UK
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25
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Wenger C, Harsman A, Niemann M, Oeljeklaus S, von Känel C, Calderaro S, Warscheid B, Schneider A. The Mba1 homologue of Trypanosoma brucei is involved in the biogenesis of oxidative phosphorylation complexes. Mol Microbiol 2023; 119:537-550. [PMID: 36829306 DOI: 10.1111/mmi.15048] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 02/26/2023]
Abstract
Consistent with other eukaryotes, the Trypanosoma brucei mitochondrial genome encodes mainly hydrophobic core subunits of the oxidative phosphorylation system. These proteins must be co-translationally inserted into the inner mitochondrial membrane and are synthesized by the highly unique trypanosomal mitoribosomes, which have a much higher protein to RNA ratio than any other ribosome. Here, we show that the trypanosomal orthologue of the mitoribosome receptor Mba1 (TbMba1) is essential for normal growth of procyclic trypanosomes but redundant in the bloodstream form, which lacks an oxidative phosphorylation system. Proteomic analyses of TbMba1-depleted mitochondria from procyclic cells revealed reduced levels of many components of the oxidative phosphorylation system, most of which belong to the cytochrome c oxidase (Cox) complex, three subunits of which are mitochondrially encoded. However, the integrity of the mitoribosome and its interaction with the inner membrane were not affected. Pull-down experiments showed that TbMba1 forms a dynamic interaction network that includes the trypanosomal Mdm38/Letm1 orthologue and a trypanosome-specific factor that stabilizes the CoxI and CoxII mRNAs. In summary, our study suggests that the function of Mba1 in the biogenesis of membrane subunits of OXPHOS complexes is conserved among yeast, mammals and trypanosomes, which belong to two eukaryotic supergroups.
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Affiliation(s)
- Christoph Wenger
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Anke Harsman
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Moritz Niemann
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Silke Oeljeklaus
- Faculty of Chemistry and Pharmacy, Biochemistry II, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - Corinne von Känel
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Salvatore Calderaro
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Bettina Warscheid
- Faculty of Chemistry and Pharmacy, Biochemistry II, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany.,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - André Schneider
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.,Institute for Advanced Study (Wissenschaftskolleg) Berlin, Berlin, Germany
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26
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Paredes-Fuentes AJ, Oliva C, Urreizti R, Yubero D, Artuch R. Laboratory testing for mitochondrial diseases: biomarkers for diagnosis and follow-up. Crit Rev Clin Lab Sci 2023; 60:270-289. [PMID: 36694353 DOI: 10.1080/10408363.2023.2166013] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The currently available biomarkers generally lack the specificity and sensitivity needed for the diagnosis and follow-up of patients with mitochondrial diseases (MDs). In this group of rare genetic disorders (mutations in approximately 350 genes associated with MDs), all clinical presentations, ages of disease onset and inheritance types are possible. Blood, urine, and cerebrospinal fluid surrogates are well-established biomarkers that are used in clinical practice to assess MD. One of the main challenges is validating specific and sensitive biomarkers for the diagnosis of disease and prediction of disease progression. Profiling of lactate, amino acids, organic acids, and acylcarnitine species is routinely conducted to assess MD patients. New biomarkers, including some proteins and circulating cell-free mitochondrial DNA, with increased diagnostic specificity have been identified in the last decade and have been proposed as potentially useful in the assessment of clinical outcomes. Despite these advances, even these new biomarkers are not sufficiently specific and sensitive to assess MD progression, and new biomarkers that indicate MD progression are urgently needed to monitor the success of novel therapeutic strategies. In this report, we review the mitochondrial biomarkers that are currently analyzed in clinical laboratories, new biomarkers, an overview of the most common laboratory diagnostic techniques, and future directions regarding targeted versus untargeted metabolomic and genomic approaches in the clinical laboratory setting. Brief descriptions of the current methodologies are also provided.
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Affiliation(s)
- Abraham J Paredes-Fuentes
- Division of Inborn Errors of Metabolism-IBC, Biochemistry and Molecular Genetics Department, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Clara Oliva
- Clinical Biochemistry Department, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Roser Urreizti
- Clinical Biochemistry Department, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Delia Yubero
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Department of Genetic and Molecular Medicine-IPER, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Rafael Artuch
- Clinical Biochemistry Department, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
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27
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Modopathies Caused by Mutations in Genes Encoding for Mitochondrial RNA Modifying Enzymes: Molecular Mechanisms and Yeast Disease Models. Int J Mol Sci 2023; 24:ijms24032178. [PMID: 36768505 PMCID: PMC9917222 DOI: 10.3390/ijms24032178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 01/25/2023] Open
Abstract
In eukaryotes, mitochondrial RNAs (mt-tRNAs and mt-rRNAs) are subject to specific nucleotide modifications, which are critical for distinct functions linked to the synthesis of mitochondrial proteins encoded by mitochondrial genes, and thus for oxidative phosphorylation. In recent years, mutations in genes encoding for mt-RNAs modifying enzymes have been identified as being causative of primary mitochondrial diseases, which have been called modopathies. These latter pathologies can be caused by mutations in genes involved in the modification either of tRNAs or of rRNAs, resulting in the absence of/decrease in a specific nucleotide modification and thus on the impairment of the efficiency or the accuracy of the mitochondrial protein synthesis. Most of these mutations are sporadic or private, thus it is fundamental that their pathogenicity is confirmed through the use of a model system. This review will focus on the activity of genes that, when mutated, are associated with modopathies, on the molecular mechanisms through which the enzymes introduce the nucleotide modifications, on the pathological phenotypes associated with mutations in these genes and on the contribution of the yeast Saccharomyces cerevisiae to confirming the pathogenicity of novel mutations and, in some cases, for defining the molecular defects.
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28
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Conor Moran J, Del'Olio S, Choi A, Zhong H, Barrientos A. Mitoribosome Biogenesis. Methods Mol Biol 2023; 2661:23-51. [PMID: 37166630 PMCID: PMC10639111 DOI: 10.1007/978-1-0716-3171-3_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] [Indexed: 05/12/2023]
Abstract
Mitoribosome biogenesis is a complex and energetically costly process that involves RNA elements encoded in the mitochondrial genome and mitoribosomal proteins most frequently encoded in the nuclear genome. The process is catalyzed by extra-ribosomal proteins, nucleus-encoded assembly factors that act in all stages of the assembly process to coordinate the processing and maturation of ribosomal RNAs with the hierarchical association of ribosomal proteins. Biochemical studies and recent cryo-EM structures of mammalian mitoribosomes have provided hints regarding their assembly. In this general concept chapter, we will briefly describe the current knowledge, mainly regarding the mammalian mitoribosome biogenesis pathway and factors involved, and will emphasize the biological sources and approaches that have been applied to advance the field.
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Affiliation(s)
- J Conor Moran
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Samuel Del'Olio
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Austin Choi
- Department of Neurology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Hui Zhong
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Antoni Barrientos
- Department of Neurology and Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL, USA.
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29
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Bertgen L, Flohr T, Herrmann JM. Methods to Study the Biogenesis of Mitoribosomal Proteins in Yeast. Methods Mol Biol 2023; 2661:143-161. [PMID: 37166637 DOI: 10.1007/978-1-0716-3171-3_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The biogenesis of mitoribosomes is an intricate process that relies on the coordinated synthesis of nuclear-encoded mitoribosomal proteins (MRPs) in the cytosol, their translocation across mitochondrial membranes, the transcription of rRNA molecules in the matrix as well as the assembly of the roughly 80 different constituents of the mitoribosome. Numerous chaperones, translocases, processing peptidases, and assembly factors of the cytosol and in mitochondria support this complex reaction. The budding yeast Saccharomyces cerevisiae served as a powerful model organism to unravel the different steps by which MRPs are imported into mitochondria, fold into their native structures, and assemble into functional ribosomes.In this chapter, we provide established protocols to study these different processes experimentally. In particular, we describe methods to purify mitochondria from yeast cells, to import radiolabeled MRPs into isolated mitochondria, and to elucidate the assembly reaction of MRPs by immunoprecipitation. These protocols and the list of dos and don'ts will enable beginners and experienced scientists to study the import and assembly of MRPs.
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Affiliation(s)
- Lea Bertgen
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Tamara Flohr
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
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30
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Mechanisms and players of mitoribosomal biogenesis revealed in trypanosomatids. Trends Parasitol 2022; 38:1053-1067. [PMID: 36075844 DOI: 10.1016/j.pt.2022.08.010] [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: 06/21/2022] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 01/13/2023]
Abstract
Translation in mitochondria is mediated by mitochondrial ribosomes, or mitoribosomes, complex ribonucleoprotein machines with dual genetic origin. Mitoribosomes in trypanosomatid parasites diverged markedly from their bacterial ancestors and other eukaryotic lineages in terms of protein composition, rRNA content, and overall architecture, yet their core functional elements remained conserved. Recent cryo-electron microscopy studies provided atomic models of trypanosomatid large and small mitoribosomal subunits and their precursors, making these parasites the organisms with the best-understood biogenesis of mitoribosomes. The structures revealed molecular mechanisms and players involved in the assembly of mitoribosomes not only in the parasites, but also in eukaryotes in general.
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31
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Bao S, Zhang C, Luo S, Jiang L, Li Q, Kong Y, Cao J. HMGA2 mediates Cr (VI)-induced metabolic reprogramming through binding to mitochondrial D-Loop region. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 244:114085. [PMID: 36116352 DOI: 10.1016/j.ecoenv.2022.114085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 09/07/2022] [Accepted: 09/13/2022] [Indexed: 06/15/2023]
Abstract
Hexavalent chromium [Cr (VI)] exists environmentally and occupationally. It has been shown to pose a carcinogenic hazard in certain occupations. This study was to investigate the role of high mobility group A2 (HMGA2) in Cr (VI)-induced metabolism reprogramming from oxidative phosphorylation (OXPHOS) to glycolysis in A549 and HELF cells. First, knockdown of HMGA2 by siHMGA2 significantly attenuated Cr (VI)-reduced expression of OXPHOS-related proteins (COX IV and ND1) and mitochondrial mass, indicating that HMGA2 was involved in Cr (VI)-reduced OXPHOS. Overexpression of HMGA2 by transfection of HMGA2-DNA plasmids reduced the expression of COX IV, ND1 and mitochondrial mass, suggesting the negative role of HMGA2 in OXPHOS. Secondly, both CCCP, the inhibitor of mitochondrial function, and the ER stress inhibitor, 4-phenylbutyric acid (4-PBA), decreased the level of HMGA2, indicating that the interaction of mitochondrial dysfunction and ER stress resulted in Cr (VI)-induced HMGA2 expression. Further study demonstrated that ER stress/HMGA2 axis mediated the metabolism rewiring from OXPHOS to aerobic glycolysis. Notably, Cr (VI) induced the accumulation of HMGA2 proteins in mitochondria and ChIP assay demonstrated that HMGA2 proteins could bind to D-loop region of mitochondrial DNA (mtDNA), which provided the proof for HMGA2-modulating OXPHOS. Taken together, our results suggested that the interaction of mitochondria and ER stress-enhanced HMGA2 played an important role in Cr (VI)-induced metabolic reprogramming from OXPHOS to glycolysis by binding directly to D-loop region of mtDNA. This work informs on the potential mode of action for Cr (VI)-induced tumors and builds on growing evidence regarding the contribution of cellular metabolic disruption contributing to carcinogenicity.
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Affiliation(s)
- Shibo Bao
- Department of Occupational and Environmental Health, Dalian Medical University, No. 9 W. Lvshun South Road, Dalian 116044, China
| | - Cong Zhang
- Department of Food Nutrition and Safety, Dalian Medical University, Dalian 116044, China
| | - Shengxiang Luo
- Department of Occupational and Environmental Health, Dalian Medical University, No. 9 W. Lvshun South Road, Dalian 116044, China
| | - Liping Jiang
- Department of Occupational and Environmental Health, Dalian Medical University, No. 9 W. Lvshun South Road, Dalian 116044, China
| | - Qiujuan Li
- Department of Occupational and Environmental Health, Dalian Medical University, No. 9 W. Lvshun South Road, Dalian 116044, China
| | - Ying Kong
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China
| | - Jun Cao
- Department of Occupational and Environmental Health, Dalian Medical University, No. 9 W. Lvshun South Road, Dalian 116044, China.
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32
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Wang Y, Luo Y, Huang Y. Schizosaccharomyces pombe
Sls1 is primarily required for
cox1
mRNA translation. Yeast 2022; 39:521-534. [DOI: 10.1002/yea.3813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/26/2022] [Accepted: 09/08/2022] [Indexed: 11/10/2022] Open
Affiliation(s)
- Yirong Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, School of Life SciencesNanjing Normal University1 Wenyuan RoadNanjing210023China
| | - Ying Luo
- Jiangsu Key Laboratory for Microbes and Functional Genomics, School of Life SciencesNanjing Normal University1 Wenyuan RoadNanjing210023China
| | - Ying Huang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, School of Life SciencesNanjing Normal University1 Wenyuan RoadNanjing210023China
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33
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Liu C, Wei Q, Li X, Han D, Liu J, Huang F, Zhang C. Proteomic analyses of mitochondrial damage in postmortem beef muscles. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:4182-4191. [PMID: 35000191 DOI: 10.1002/jsfa.11767] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/03/2022] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The objective of the study was to examine the expression profiles of mitochondrial proteins in at-death and 24 h postmortem (PM) using tandem mass tag (TMT) approach to characterize the mitochondria possible mechanisms that are affiliated with tenderization. RESULTS Results showed that the tender meat at 24 h PM emerged with more serious mitochondrial damage. Altogether 456 mitochondrial proteins were identified, including 442 down-regulated and 14 up-regulated proteins. These differentially-expressed proteins were primarily involved in the progress of PM energy metabolism, apoptosis, and the morphological alterations of mitochondrial. Among them, 47 subunits (such as NDUFA2, COX4I1, and ATP5PB) were annotated into the oxidative phosphorylation pathway. VDAC1, VDAC2, and VDAC3 involving in the damage of MPTP, and IMMT, CHCHD3, APOL and APOO modulating the morphology of mitochondria, and DIABLO and AIFM1 released from mitochondria affect caspase's activation. HSPD1 and HSPE1 involved in apoptosis, mitochondrial physiological and morphological alterations. CONCLUSION The earlier-mentioned proteins were validated as potential indicators of tenderness regulated by mitochondrial damage. These results highlighted that mitochondrial damage possibly participate in PM tenderization of beef muscles by energy metabolism and cell apoptosis status. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Chunmei Liu
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Products Processing, Ministry of Agriculture, Beijing, China
| | - Qichao Wei
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Products Processing, Ministry of Agriculture, Beijing, China
| | - Xia Li
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Products Processing, Ministry of Agriculture, Beijing, China
| | - Dong Han
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Products Processing, Ministry of Agriculture, Beijing, China
| | - Jiqian Liu
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Products Processing, Ministry of Agriculture, Beijing, China
| | - Feng Huang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Products Processing, Ministry of Agriculture, Beijing, China
| | - Chunhui Zhang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Products Processing, Ministry of Agriculture, Beijing, China
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Di Mauro S, Scamporrino A, Filippello A, Di Marco M, Di Martino MT, Scionti F, Di Pino A, Scicali R, Malaguarnera R, Purrello F, Piro S. Mitochondrial RNAs as Potential Biomarkers of Functional Impairment in Diabetic Kidney Disease. Int J Mol Sci 2022; 23:ijms23158198. [PMID: 35897772 PMCID: PMC9331991 DOI: 10.3390/ijms23158198] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/21/2022] [Accepted: 07/23/2022] [Indexed: 11/16/2022] Open
Abstract
Type 2 diabetes and renal damage are strictly linked. The progressive increase in T2D incidence has stimulated the interest in novel biomarkers to improve the diagnostic performance of the commonly utilized markers such as albuminuria and eGFR. Through microarray method, we analyzed the entire transcriptome expressed in 12 serum samples of diabetic patients, six without DKD and six with DKD; the downregulation of the most dysregulated transcripts was validated in a wider cohort of 69 patients by qPCRs. We identified a total of 33 downregulated transcripts. The downregulation of four mitochondrial messenger RNAs (MT-ATP6, MT-ATP8, MT-COX3, MT-ND1) and other two transcripts (seysnoy, skerdo) was validated in patients with eGFR stage G3 versus G2 and G1. The four messenger RNAs correlated with creatinine and eGFR stages, while seysnoy and skerdo were associated with white blood cell values. All transcripts correlated also with Blood Urea Nitrogen. The four mitochondrial messenger RNAs had a high diagnostic performance in G3 versus G2 discrimination, with AUC values above 0.8. The most performant transcript was MT-ATP6, with an AUC of 0.846; sensitivity = 90%, specificity = 76%, p-value = 7.8 × 10−5. This study led to the identification of a specific molecular signature of DKD, proposing the dosage of RNAs, especially mitochondrial RNAs, as noninvasive biomarkers of diabetes complication.
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Affiliation(s)
- Stefania Di Mauro
- Department of Clinical and Experimental Medicine, Internal Medicine, Garibaldi-Nesima Hospital, University of Catania, 95122 Catania, Italy; (S.D.M.); (A.S.); (A.F.); (M.D.M.); (A.D.P.); (R.S.); (S.P.)
| | - Alessandra Scamporrino
- Department of Clinical and Experimental Medicine, Internal Medicine, Garibaldi-Nesima Hospital, University of Catania, 95122 Catania, Italy; (S.D.M.); (A.S.); (A.F.); (M.D.M.); (A.D.P.); (R.S.); (S.P.)
| | - Agnese Filippello
- Department of Clinical and Experimental Medicine, Internal Medicine, Garibaldi-Nesima Hospital, University of Catania, 95122 Catania, Italy; (S.D.M.); (A.S.); (A.F.); (M.D.M.); (A.D.P.); (R.S.); (S.P.)
| | - Maurizio Di Marco
- Department of Clinical and Experimental Medicine, Internal Medicine, Garibaldi-Nesima Hospital, University of Catania, 95122 Catania, Italy; (S.D.M.); (A.S.); (A.F.); (M.D.M.); (A.D.P.); (R.S.); (S.P.)
| | - Maria Teresa Di Martino
- Department of Experimental and Clinical Medicine, Magna Graecia University, 88100 Catanzaro, Italy;
| | - Francesca Scionti
- Institute for Biomedical Research and Innovation (IRIB), National Research Council of Italy (CNR), 98164 Messina, Italy;
| | - Antonino Di Pino
- Department of Clinical and Experimental Medicine, Internal Medicine, Garibaldi-Nesima Hospital, University of Catania, 95122 Catania, Italy; (S.D.M.); (A.S.); (A.F.); (M.D.M.); (A.D.P.); (R.S.); (S.P.)
| | - Roberto Scicali
- Department of Clinical and Experimental Medicine, Internal Medicine, Garibaldi-Nesima Hospital, University of Catania, 95122 Catania, Italy; (S.D.M.); (A.S.); (A.F.); (M.D.M.); (A.D.P.); (R.S.); (S.P.)
| | | | - Francesco Purrello
- Department of Clinical and Experimental Medicine, Internal Medicine, Garibaldi-Nesima Hospital, University of Catania, 95122 Catania, Italy; (S.D.M.); (A.S.); (A.F.); (M.D.M.); (A.D.P.); (R.S.); (S.P.)
- Correspondence: ; Tel.: +39-095-759-8401
| | - Salvatore Piro
- Department of Clinical and Experimental Medicine, Internal Medicine, Garibaldi-Nesima Hospital, University of Catania, 95122 Catania, Italy; (S.D.M.); (A.S.); (A.F.); (M.D.M.); (A.D.P.); (R.S.); (S.P.)
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35
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Maurya SK, Gupta S, Bakshi A, Kaur H, Jain A, Senapati S, Baghel MS. Targeting mitochondria in the regulation of neurodegenerative diseases: A comprehensive review. J Neurosci Res 2022; 100:1845-1861. [PMID: 35856508 DOI: 10.1002/jnr.25110] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/21/2022] [Accepted: 07/09/2022] [Indexed: 11/09/2022]
Abstract
Mitochondria are one of the essential cellular organelles. Apart from being considered as the powerhouse of the cell, mitochondria have been widely known to regulate redox reaction, inflammation, cell survival, cell death, metabolism, etc., and are implicated in the progression of numerous disease conditions including neurodegenerative diseases. Since brain is an energy-demanding organ, mitochondria and their functions are important for maintaining normal brain homeostasis. Alterations in mitochondrial gene expression, mutations, and epigenetic modification contribute to inflammation and neurodegeneration. Dysregulation of reactive oxygen species production by mitochondria and aggregation of proteins in neurons leads to alteration in mitochondria functions which further causes neuronal death and progression of neurodegeneration. Pharmacological studies have prioritized mitochondria as a possible drug target in the regulation of neurodegenerative diseases. Therefore, the present review article has been intended to provide a comprehensive understanding of mitochondrial role in the development and progression of neurodegenerative diseases mainly Alzheimer's, Parkinson's, multiple sclerosis, and amyotrophic lateral sclerosis followed by possible intervention and future treatment strategies to combat mitochondrial-mediated neurodegeneration.
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Affiliation(s)
| | - Suchi Gupta
- Stem Cell Facility, All India Institute of Medical Sciences, Delhi, India
| | - Amrita Bakshi
- Department of Zoology, University of Delhi, Delhi, India
| | - Harpreet Kaur
- Department of Zoology, University of Delhi, Delhi, India.,Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Arushi Jain
- Immunogenomics Laboratory, Department of Human Genetics & Molecular Medicine, Central University of Punjab, Bathinda, India
| | - Sabyasachi Senapati
- Immunogenomics Laboratory, Department of Human Genetics & Molecular Medicine, Central University of Punjab, Bathinda, India
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36
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Hong HJ, Joung KH, Kim YK, Choi MJ, Kang SG, Kim JT, Kang YE, Chang JY, Moon JH, Jun S, Ro HJ, Lee Y, Kim H, Park JH, Kang BE, Jo Y, Choi H, Ryu D, Lee CH, Kim H, Park KS, Kim HJ, Shong M. Mitoribosome insufficiency in β cells is associated with type 2 diabetes-like islet failure. EXPERIMENTAL & MOLECULAR MEDICINE 2022; 54:932-945. [PMID: 35804190 PMCID: PMC9355985 DOI: 10.1038/s12276-022-00797-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/22/2022] [Accepted: 03/14/2022] [Indexed: 12/04/2022]
Abstract
Genetic variations in mitoribosomal subunits and mitochondrial transcription factors are related to type 2 diabetes. However, the role of islet mitoribosomes in the development of type 2 diabetes has not been determined. We investigated the effects of the mitoribosomal gene on β-cell function and glucose homeostasis. Mitoribosomal gene expression was analyzed in datasets from the NCBI GEO website (GSE25724, GSE76894, and GSE76895) and the European Nucleotide Archive (ERP017126), which contain the transcriptomes of type 2 diabetic and nondiabetic organ donors. We found deregulation of most mitoribosomal genes in islets from individuals with type 2 diabetes, including partial downregulation of CRIF1. The phenotypes of haploinsufficiency in a single mitoribosomal gene were examined using β-cell-specific Crif1 (Mrpl59) heterozygous-deficient mice. Crif1beta+/− mice had normal glucose tolerance, but their islets showed a loss of first-phase glucose-stimulated insulin secretion. They also showed increased β-cell mass associated with higher expression of Reg family genes. However, Crif1beta+/− mice showed earlier islet failure in response to high-fat feeding, which was exacerbated by aging. Haploinsufficiency of a single mitoribosomal gene predisposes rodents to glucose intolerance, which resembles the early stages of type 2 diabetes in humans. Disruptions in the mitochondrial protein synthesis machinery give rise to metabolic disturbances that lay the foundation for type 2 diabetes. As physiological glucose levels rise, the energy-generating machinery of the mitochondria responds with increased activity, which stimulates insulin secretion. Many proteins responsible for mitochondrial metabolism are produced by ribosomes within this cellular organelle. Researchers led by Hyun Jin Kim and Minho Shong at Chungnam National University, Daejon, South Korea, have determined that mutations affecting a mitochondrial ribosomal protein called CRIF1 can lead to impaired insulin release. Mice with reduced CRIF1 were initially healthy, but as they aged, exhibited signs of impaired pancreatic function similar to those seen in patients with early-stage diabetes. This process was accelerated by consumption of a high-fat diet, and the researchers propose that this mechanism may be directly relevant to human disease.
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Affiliation(s)
- Hyun Jung Hong
- Research Center for Endocrine and Metabolic Diseases, Chungnam National University School of Medicine, Daejeon, 35015, Korea.,Department of Medical Science, Chungnam National University School of Medicine, Daejeon, 35015, Korea
| | - Kyong Hye Joung
- Research Center for Endocrine and Metabolic Diseases, Chungnam National University School of Medicine, Daejeon, 35015, Korea.,Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, 35015, Korea
| | - Yong Kyung Kim
- Research Center for Endocrine and Metabolic Diseases, Chungnam National University School of Medicine, Daejeon, 35015, Korea
| | - Min Jeong Choi
- Research Center for Endocrine and Metabolic Diseases, Chungnam National University School of Medicine, Daejeon, 35015, Korea
| | - Seul Gi Kang
- Research Center for Endocrine and Metabolic Diseases, Chungnam National University School of Medicine, Daejeon, 35015, Korea
| | - Jung Tae Kim
- Research Center for Endocrine and Metabolic Diseases, Chungnam National University School of Medicine, Daejeon, 35015, Korea.,Department of Medical Science, Chungnam National University School of Medicine, Daejeon, 35015, Korea
| | - Yea Eun Kang
- Research Center for Endocrine and Metabolic Diseases, Chungnam National University School of Medicine, Daejeon, 35015, Korea.,Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, 35015, Korea
| | - Joon Young Chang
- Research Center for Endocrine and Metabolic Diseases, Chungnam National University School of Medicine, Daejeon, 35015, Korea.,Department of Medical Science, Chungnam National University School of Medicine, Daejeon, 35015, Korea
| | - Joon Ho Moon
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea
| | - Sangmi Jun
- Center for Research Equipment, Korea Basic Science Institute, Cheongju, 28119, Korea.,Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, Korea
| | - Hyun-Joo Ro
- Center for Research Equipment, Korea Basic Science Institute, Cheongju, 28119, Korea.,Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, Korea
| | - Yujeong Lee
- Center for Research Equipment, Korea Basic Science Institute, Cheongju, 28119, Korea.,Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, Korea
| | - Hyeongseok Kim
- Department of Biochemistry, Chungnam National University School of Medicine, Daejeon, 35015, Korea
| | - Jae-Hyung Park
- Department of Physiology, Keimyung University School of Medicine, Daegu, 704-200, Korea
| | - Baeki E Kang
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Korea
| | - Yunju Jo
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Korea
| | - Heejung Choi
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Korea
| | - Dongryeol Ryu
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Korea.,Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, Suwon, 16419, Korea.,Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, 06351, Korea
| | - Chul-Ho Lee
- Animal Model Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea
| | - Hail Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea
| | - Kyu-Sang Park
- Department of Physiology, Yonsei University Wonju College of Medicine, Wonju, 26426, Korea
| | - Hyun Jin Kim
- Research Center for Endocrine and Metabolic Diseases, Chungnam National University School of Medicine, Daejeon, 35015, Korea. .,Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, 35015, Korea.
| | - Minho Shong
- Research Center for Endocrine and Metabolic Diseases, Chungnam National University School of Medicine, Daejeon, 35015, Korea. .,Department of Medical Science, Chungnam National University School of Medicine, Daejeon, 35015, Korea. .,Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, 35015, Korea.
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37
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Mitoribosomal Deregulation Drives Senescence via TPP1-Mediated Telomere Deprotection. Cells 2022; 11:cells11132079. [PMID: 35805162 PMCID: PMC9265344 DOI: 10.3390/cells11132079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/13/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022] Open
Abstract
While mitochondrial bioenergetic deregulation has long been implicated in cellular senescence, its mechanistic involvement remains unclear. By leveraging diverse mitochondria-related gene expression profiles derived from two different cellular senescence models of human diploid fibroblasts, we found that the expression of mitoribosomal proteins (MRPs) was generally decreased during the early-to-middle transition prior to the exhibition of noticeable SA-β-gal activity. Suppressed expression patterns of the identified senescence-associated MRP signatures (SA-MRPs) were validated in aged human cells and rat and mouse skin tissues and in aging mouse fibroblasts at single-cell resolution. TIN2- and POT1-interaction protein (TPP1) was concurrently suppressed, which induced senescence, accompanied by telomere DNA damage. Lastly, we show that SA-MRP deregulation could be a potential upstream regulator of TPP1 suppression. Our results indicate that mitoribosomal deregulation could represent an early event initiating mitochondrial dysfunction and serve as a primary driver of cellular senescence and an upstream regulator of shelterin-mediated telomere deprotection.
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38
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Ziemann M, Wu W, Deng XL, Du XJ. Transcriptomic Analysis of Dysregulated Genes of the nDNA-mtDNA Axis in a Mouse Model of Dilated Cardiomyopathy. Front Genet 2022; 13:921610. [PMID: 35754828 PMCID: PMC9214240 DOI: 10.3389/fgene.2022.921610] [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: 04/22/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022] Open
Abstract
Background: Mitochondrial dysfunction is implicated in the development of cardiomyopathy and heart failure. Transcription of mitochondrial DNA (mtDNA) encoded genes and subsequent protein synthesis are tightly regulated by nuclear DNA (nDNA) encoded proteins forming the nDNA-mtDNA axis. The scale of abnormalities in this axis in dilated cardiomyopathy (DCM) is unclear. We previously demonstrated, in a mouse DCM model with cardiac Mst1 overexpression, extensive downregulation of mitochondrial genes and mitochondrial dysfunction. Using the pre-acquired transcriptome sequencing database, we studied expression of gene sets of the nDNA-mtDNA axis. Methods: Using RNA-sequencing data from DCM hearts of mice at early and severe disease stages, transcriptome was performed for dysregulated nDNA-encoded gene sets that govern mtDNA transcription and in situ protein synthesis. To validate gene data, expression of a panel of proteins was determined by immunoblotting. Results: Relative to littermate controls, DCM hearts showed significant downregulation of all mtDNA encoded mRNAs, as well as mtDNA transcriptional activators. Downregulation was also evident for gene sets of mt-rRNA processing, aminoacyl-tRNA synthases, and mitoribosome subunits for in situ protein synthesis. Multiple downregulated genes belong to mitochondrial protein-importing machinery indicating compromised importing of proteins for mtDNA transcription and translation. Diverse changes were genes of mtRNA-binding proteins that govern maturation and stability of mtDNA-derived RNAs. Expression of mtDNA replicome genes was largely unchanged. These changes were similarly observed in mouse hearts at early and severe stages of DCM. Conclusion: Transcriptome revealed in our DCM model dysregulation of multiple gene sets of the nDNA-mtDNA axis, that is, expected to interfere with mtDNA transcription and in situ protein synthesis. Dysfunction of the nDNA-mtDNA axis might contribute to mitochondrial dysfunction and ultimately development of DCM.
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Affiliation(s)
- Mark Ziemann
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Wei Wu
- Key Laboratory of Environment and Genes Related to Diseases, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Ministry of Education, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Xiu-Ling Deng
- Key Laboratory of Environment and Genes Related to Diseases, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Ministry of Education, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Xiao-Jun Du
- Key Laboratory of Environment and Genes Related to Diseases, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Ministry of Education, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
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Mitochondrial Ribosome Dysfunction in Human Alveolar Type II Cells in Emphysema. Biomedicines 2022; 10:biomedicines10071497. [PMID: 35884802 PMCID: PMC9313339 DOI: 10.3390/biomedicines10071497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 04/17/2022] [Accepted: 04/26/2022] [Indexed: 11/16/2022] Open
Abstract
Pulmonary emphysema is characterized by airspace enlargement and the destruction of alveoli. Alveolar type II (ATII) cells are very abundant in mitochondria. OXPHOS complexes are composed of proteins encoded by the mitochondrial and nuclear genomes. Mitochondrial 12S and 16S rRNAs are required to assemble the small and large subunits of the mitoribosome, respectively. We aimed to determine the mechanism of mitoribosome dysfunction in ATII cells in emphysema. ATII cells were isolated from control nonsmokers and smokers, and emphysema patients. Mitochondrial transcription and translation were analyzed. We also determined the miRNA expression. Decreases in ND1 and UQCRC2 expression levels were found in ATII cells in emphysema. Moreover, nuclear NDUFS1 and SDHB levels increased, and mitochondrial transcribed ND1 protein expression decreased. These results suggest an impairment of the nuclear and mitochondrial stoichiometry in this disease. We also detected low levels of the mitoribosome structural protein MRPL48 in ATII cells in emphysema. Decreased 16S rRNA expression and increased 12S rRNA levels were observed. Moreover, we analyzed miR4485-3p levels in this disease. Our results suggest a negative feedback loop between miR-4485-3p and 16S rRNA. The obtained results provide molecular mechanisms of mitoribosome dysfunction in ATII cells in emphysema.
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40
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Bao S, Wang X, Li M, Gao Z, Zheng D, Shen D, Liu L. Potential of Mitochondrial Ribosomal Genes as Cancer Biomarkers Demonstrated by Bioinformatics Results. Front Oncol 2022; 12:835549. [PMID: 35719986 PMCID: PMC9204274 DOI: 10.3389/fonc.2022.835549] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 04/27/2022] [Indexed: 12/15/2022] Open
Abstract
Next-generation sequencing and bioinformatics analyses have clearly revealed the roles of mitochondrial ribosomal genes in cancer development. Mitochondrial ribosomes are composed of three RNA components encoded by mitochondrial DNA and 82 specific protein components encoded by nuclear DNA. They synthesize mitochondrial inner membrane oxidative phosphorylation (OXPHOS)-related proteins and participate in various biological activities via the regulation of energy metabolism and apoptosis. Mitochondrial ribosomal genes are strongly associated with clinical features such as prognosis and foci metastasis in patients with cancer. Accordingly, mitochondrial ribosomes have become an important focus of cancer research. We review recent advances in bioinformatics research that have explored the link between mitochondrial ribosomes and cancer, with a focus on the potential of mitochondrial ribosomal genes as biomarkers in cancer.
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Affiliation(s)
- Shunchao Bao
- Department of Radiotherapy, Second Hospital of Jilin University, Changchun, China
| | - Xinyu Wang
- Department of Breast Surgery, Second Hospital of Jilin University, Changchun, China
| | - Mo Li
- Department of Radiotherapy, Second Hospital of Jilin University, Changchun, China
| | - Zhao Gao
- Nuclear Medicine Department, Second Hospital of Jilin University, Changchun, China
| | - Dongdong Zheng
- Department of Cardiovascular Surgery, Second Hospital of Jilin University, Changchun, China
| | - Dihan Shen
- Medical Research Center, Second Hospital of Jilin University, Changchun, China
| | - Linlin Liu
- Department of Radiotherapy, Second Hospital of Jilin University, Changchun, China
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41
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Kimura Y, Saito H, Osaki T, Ikegami Y, Wakigawa T, Ikeuchi Y, Iwasaki S. Mito-FUNCAT-FACS reveals cellular heterogeneity in mitochondrial translation. RNA (NEW YORK, N.Y.) 2022; 28:895-904. [PMID: 35256452 PMCID: PMC9074903 DOI: 10.1261/rna.079097.122] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 02/12/2022] [Indexed: 06/03/2023]
Abstract
Mitochondria possess their own genome that encodes components of oxidative phosphorylation (OXPHOS) complexes, and mitochondrial ribosomes within the organelle translate the mRNAs expressed from the mitochondrial genome. Given the differential OXPHOS activity observed in diverse cell types, cell growth conditions, and other circumstances, cellular heterogeneity in mitochondrial translation can be expected. Although individual protein products translated in mitochondria have been monitored, the lack of techniques that address the variation in overall mitochondrial protein synthesis in cell populations poses analytic challenges. Here, we adapted mitochondrial-specific fluorescent noncanonical amino acid tagging (FUNCAT) for use with fluorescence-activated cell sorting (FACS) and developed mito-FUNCAT-FACS. The click chemistry-compatible methionine analog L-homopropargylglycine (HPG) enabled the metabolic labeling of newly synthesized proteins. In the presence of cytosolic translation inhibitors, HPG was selectively incorporated into mitochondrial nascent proteins and conjugated to fluorophores via the click reaction (mito-FUNCAT). The application of in situ mito-FUNCAT to flow cytometry allowed us to separate changes in net mitochondrial translation activity from those of the organelle mass and detect variations in mitochondrial translation in cancer cells. Our approach provides a useful methodology for examining mitochondrial protein synthesis in individual cells.
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Affiliation(s)
- Yusuke Kimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Hironori Saito
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Tatsuya Osaki
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo 153-8505, Japan
| | - Yasuhiro Ikegami
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo 153-8505, Japan
| | - Taisei Wakigawa
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Yoshiho Ikeuchi
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo 153-8505, Japan
- Institute for AI and Beyond, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shintaro Iwasaki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
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42
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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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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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44
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Del Giudice L, Alifano P, Calcagnile M, Di Schiavi E, Bertapelle C, Aletta M, Pontieri P. Mitochondrial ribosomal protein genes connected with Alzheimer's and tellurite toxicity. Mitochondrion 2022; 64:45-58. [PMID: 35218961 DOI: 10.1016/j.mito.2022.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/15/2022] [Accepted: 02/21/2022] [Indexed: 12/19/2022]
Abstract
Mitochondrial diseases are a group of genetic disorders characterized by dysfunctional mitochondria. Within eukaryotic cells, mitochondria contain their own ribosomes, which synthesize small amounts of proteins, all of which are essential for the biogenesis of the oxidative phosphorylation system. The ribosome is an evolutionarily conserved macromolecular machine in nature both from a structural and functional point of view, universally responsible for the synthesis of proteins. Among the diseases afflicting humans, those of ribosomal origin - either cytoplasmic ribosomes (80S) or mitochondrial ribosomes (70S) - are relevant. These are inherited or acquired diseases most commonly caused by either ribosomal protein haploinsufficiency or defects in ribosome biogenesis. Here we review the scientific literature about the recent advances on changes in mitochondrial ribosomal structural and assembly proteins that are implicated in primary mitochondrial diseases and neurodegenerative disorders, and their possible connection with metalloid pollution and toxicity, with a focus on MRPL44, NAM9 (MNA6) and GEP3 (MTG3), whose lack or defect was associated with resistance to tellurite. Finally, we illustrate the suitability of yeast Saccharomyces cerevisiae (S.cerevisiae) and the nematode Caenorhabditis elegans (C.elegans) as model organisms for studying mitochondrial ribosome dysfunctions including those involved in human diseases.
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Affiliation(s)
- Luigi Del Giudice
- Istituto di Bioscienze e BioRisorse-UOS Napoli-CNR c/o Dipartimento di Biologia, Sezione di Igiene, Napoli 80134, Italy.
| | - Pietro Alifano
- Dipartimento di Scienze e Tecnologie Biologiche e Ambientali, Università del Salento, Lecce 73100, Italy
| | - Matteo Calcagnile
- Dipartimento di Scienze e Tecnologie Biologiche e Ambientali, Università del Salento, Lecce 73100, Italy
| | | | | | | | - Paola Pontieri
- Istituto di Bioscienze e BioRisorse-UOS Napoli-CNR c/o Dipartimento di Biologia, Sezione di Igiene, Napoli 80134, Italy
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45
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Apostolopoulos A, Iwasaki S. Into the matrix: current methods for mitochondrial translation studies. J Biochem 2022; 171:379-387. [PMID: 35080613 DOI: 10.1093/jb/mvac005] [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: 12/27/2021] [Accepted: 01/18/2022] [Indexed: 11/12/2022] Open
Abstract
In addition to the cytoplasmic translation system, eukaryotic cells house additional protein synthesis machinery in mitochondria. The importance of this in organello translation is exemplified by clinical pathologies associated with mutations in mitochondrial translation factors. Although a detailed understanding of mitochondrial translation has long been awaited, quantitative, comprehensive, and spatiotemporal measurements have posed analytic challenges. The recent development of novel approaches for studying mitochondrial protein synthesis has overcome these issues and expands our understanding of the unique translation system. Here, we review the current technologies for the investigation of mitochondrial translation and the insights provided by their application.
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Affiliation(s)
- Antonios Apostolopoulos
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan.,RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Shintaro Iwasaki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan.,RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
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46
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Lenarčič T, Niemann M, Ramrath DJF, Calderaro S, Flügel T, Saurer M, Leibundgut M, Boehringer D, Prange C, Horn EK, Schneider A, Ban N. Mitoribosomal small subunit maturation involves formation of initiation-like complexes. Proc Natl Acad Sci U S A 2022; 119:e2114710118. [PMID: 35042777 PMCID: PMC8784144 DOI: 10.1073/pnas.2114710118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/29/2021] [Indexed: 01/02/2023] Open
Abstract
Mitochondrial ribosomes (mitoribosomes) play a central role in synthesizing mitochondrial inner membrane proteins responsible for oxidative phosphorylation. Although mitoribosomes from different organisms exhibit considerable structural variations, recent insights into mitoribosome assembly suggest that mitoribosome maturation follows common principles and involves a number of conserved assembly factors. To investigate the steps involved in the assembly of the mitoribosomal small subunit (mt-SSU) we determined the cryoelectron microscopy structures of middle and late assembly intermediates of the Trypanosoma brucei mitochondrial small subunit (mt-SSU) at 3.6- and 3.7-Å resolution, respectively. We identified five additional assembly factors that together with the mitochondrial initiation factor 2 (mt-IF-2) specifically interact with functionally important regions of the rRNA, including the decoding center, thereby preventing premature mRNA or large subunit binding. Structural comparison of assembly intermediates with mature mt-SSU combined with RNAi experiments suggests a noncanonical role of mt-IF-2 and a stepwise assembly process, where modular exchange of ribosomal proteins and assembly factors together with mt-IF-2 ensure proper 9S rRNA folding and protein maturation during the final steps of assembly.
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Affiliation(s)
- Tea Lenarčič
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Moritz Niemann
- Department of Chemistry, Biochemistry, and Pharmaceutical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - David J F Ramrath
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Salvatore Calderaro
- Department of Chemistry, Biochemistry, and Pharmaceutical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - Timo Flügel
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Martin Saurer
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Marc Leibundgut
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Daniel Boehringer
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Céline Prange
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Elke K Horn
- Department of Chemistry, Biochemistry, and Pharmaceutical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - André Schneider
- Department of Chemistry, Biochemistry, and Pharmaceutical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland;
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47
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Zhao L, Han L, Wei X, Zhou Y, Zhang Y, Si N, Wang H, Yang J, Bian B, Zhao H. Toxicokinetics of Arenobufagin and its Cardiotoxicity Mechanism Exploration Based on Lipidomics and Proteomics Approaches in Rats. Front Pharmacol 2022; 12:780016. [PMID: 35002716 PMCID: PMC8727535 DOI: 10.3389/fphar.2021.780016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/22/2021] [Indexed: 12/17/2022] Open
Abstract
Arenobufagin (ArBu), one of the main active bufadienolides of toad venom with cardiotonic effect, analgesic effect, and outstanding anti-tumor potentiality, is also a potential cardiotoxic component. In the present study, the cardiac effect of ArBu and its underlying mechanism were explored by integrating data such as heart rates, toxicokinetics, myocardial enzyme and brain natriuretic peptide (BNP) activity, pathological sections, lipidomics and proteomics. Under different doses, the cardiac effects turned out to be different. The oral dose of 60 mg/kg of ArBu sped up the heart rate. However, 120 mg/kg ArBu mainly reduced the heart rate. Over time, they all returned to normal, consisting of the trend of ArBu concentration-time curve. High concentrations of myocardial enzymes and BNP indicated that ArBu inhibited or impaired the cardiac function of rats. Pathological sections of hearts also showed that ArBu caused myocardial fiber disorder and rupture, in which the high-dose group was more serious. At the same time, serum and heart tissue lipidomics were used to explore the changes in body lipid metabolism under different doses. The data indicated a larger difference in the high-dose ArBu group. There were likewise many significant differences in the proteomics of the heart. Furthermore, a multi-layered network was used to integrate the above information to explore the potential mechanism. Finally, 4 proteins that were shown to be significantly and differentially expressed were validated by targeted proteomics using parallel reaction monitoring (PRM) analysis. Our findings indicated that ArBu behaved as a bidirectional regulation of the heart. The potential mechanism of cardiac action was revealed with the increased dose, which provided a useful reference for the safety of clinical application of ArBu.
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Affiliation(s)
- Lijuan Zhao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.,Shaanxi Chinese Medicine Institute (Shaanxi Pharmaceutical Information Center), Xianyang, China
| | - Lingyu Han
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.,School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Xiaolu Wei
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yanyan Zhou
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yanqiong Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Nan Si
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Hongjie Wang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jian Yang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Baolin Bian
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Haiyu Zhao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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48
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Jüttner M, Ferreira-Cerca S. A Comparative Perspective on Ribosome Biogenesis: Unity and Diversity Across the Tree of Life. Methods Mol Biol 2022; 2533:3-22. [PMID: 35796979 PMCID: PMC9761495 DOI: 10.1007/978-1-0716-2501-9_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Ribosomes are universally conserved ribonucleoprotein complexes involved in the decoding of the genetic information contained in messenger RNAs into proteins. Accordingly, ribosome biogenesis is a fundamental cellular process required for functional ribosome homeostasis and to preserve satisfactory gene expression capability.Although the ribosome is universally conserved, its biogenesis shows an intriguing degree of variability across the tree of life . These differences also raise yet unresolved questions. Among them are (a) what are, if existing, the remaining ancestral common principles of ribosome biogenesis ; (b) what are the molecular impacts of the evolution history and how did they contribute to (re)shape the ribosome biogenesis pathway across the tree of life ; (c) what is the extent of functional divergence and/or convergence (functional mimicry), and in the latter case (if existing) what is the molecular basis; (d) considering the universal ribosome conservation, what is the capability of functional plasticity and cellular adaptation of the ribosome biogenesis pathway?In this review, we provide a brief overview of ribosome biogenesis across the tree of life and try to illustrate some potential and/or emerging answers to these unresolved questions.
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Affiliation(s)
- Michael Jüttner
- Biochemistry III-Regensburg Center for Biochemistry-Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
| | - Sébastien Ferreira-Cerca
- Biochemistry III-Regensburg Center for Biochemistry-Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany.
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49
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Karim L, Kosmider B, Bahmed K. Mitochondrial ribosomal stress in lung diseases. Am J Physiol Lung Cell Mol Physiol 2021; 322:L507-L517. [PMID: 34873929 DOI: 10.1152/ajplung.00078.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Mitochondria are involved in a variety of critical cellular functions, and their impairment drives cell injury. The mitochondrial ribosome (mitoribosome) is responsible for the protein synthesis of mitochondrial DNA encoded genes. These proteins are involved in oxidative phosphorylation, respiration, and ATP production required in the cell. Mitoribosome components originate from both mitochondrial and nuclear genomes. Their dysfunction can be caused by impaired mitochondrial protein synthesis or mitoribosome misassembly, leading to a decline in mitochondrial translation. This decrease can trigger mitochondrial ribosomal stress and contribute to pulmonary cell injury, death, and diseases. This review focuses on the contribution of the impaired mitoribosome structural components and function to respiratory disease pathophysiology. We present recent findings in the fields of lung cancer, chronic obstructive pulmonary disease, interstitial lung disease, and asthma. We also include reports on the mitoribosome dysfunction in pulmonary hypertension, high altitude pulmonary edema, bacterial and viral infections. Studies of the mitoribosome alterations in respiratory diseases can lead to novel therapeutic targets.
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Affiliation(s)
- Loukmane Karim
- Department of Microbiology, Immunology, and Inflammation, Temple University, Philadelphia, PA, United States.,Center for Inflammation and Lung Research, Temple University, Philadelphia, PA, United States
| | - Beata Kosmider
- Department of Microbiology, Immunology, and Inflammation, Temple University, Philadelphia, PA, United States.,Center for Inflammation and Lung Research, Temple University, Philadelphia, PA, United States.,Department of Biomedical Education and Data Science, Temple University, Philadelphia, PA, United States
| | - Karim Bahmed
- Center for Inflammation and Lung Research, Temple University, Philadelphia, PA, United States.,Department of Thoracic Medicine and Surgery, Temple University, Philadelphia, PA, United States
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50
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Qin Y, Huttlin EL, Winsnes CF, Gosztyla ML, Wacheul L, Kelly MR, Blue SM, Zheng F, Chen M, Schaffer LV, Licon K, Bäckström A, Vaites LP, Lee JJ, Ouyang W, Liu SN, Zhang T, Silva E, Park J, Pitea A, Kreisberg JF, Gygi SP, Ma J, Harper JW, Yeo GW, Lafontaine DLJ, Lundberg E, Ideker T. A multi-scale map of cell structure fusing protein images and interactions. Nature 2021; 600:536-542. [PMID: 34819669 PMCID: PMC9053732 DOI: 10.1038/s41586-021-04115-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/08/2021] [Indexed: 02/07/2023]
Abstract
The cell is a multi-scale structure with modular organization across at least four orders of magnitude1. Two central approaches for mapping this structure-protein fluorescent imaging and protein biophysical association-each generate extensive datasets, but of distinct qualities and resolutions that are typically treated separately2,3. Here we integrate immunofluorescence images in the Human Protein Atlas4 with affinity purifications in BioPlex5 to create a unified hierarchical map of human cell architecture. Integration is achieved by configuring each approach as a general measure of protein distance, then calibrating the two measures using machine learning. The map, known as the multi-scale integrated cell (MuSIC 1.0), resolves 69 subcellular systems, of which approximately half are to our knowledge undocumented. Accordingly, we perform 134 additional affinity purifications and validate subunit associations for the majority of systems. The map reveals a pre-ribosomal RNA processing assembly and accessory factors, which we show govern rRNA maturation, and functional roles for SRRM1 and FAM120C in chromatin and RPS3A in splicing. By integration across scales, MuSIC increases the resolution of imaging while giving protein interactions a spatial dimension, paving the way to incorporate diverse types of data in proteome-wide cell maps.
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Affiliation(s)
- Yue Qin
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Edward L Huttlin
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Casper F Winsnes
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Maya L Gosztyla
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ludivine Wacheul
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université Libre de Bruxelles (ULB), Charleroi-Gosselies, Belgium
| | - Marcus R Kelly
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Steven M Blue
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Fan Zheng
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Michael Chen
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Leah V Schaffer
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Katherine Licon
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Anna Bäckström
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - John J Lee
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Wei Ouyang
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Sophie N Liu
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tian Zhang
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Erica Silva
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jisoo Park
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Adriana Pitea
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jason F Kreisberg
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Jianzhu Ma
- Institute for Artificial Intelligence, Peking University, Beijing, China
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Gene W Yeo
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Denis L J Lafontaine
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université Libre de Bruxelles (ULB), Charleroi-Gosselies, Belgium
| | - Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA.
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
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