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Gao Y, Kwan J, Orofino J, Burrone G, Mitra S, Fan TY, English J, Hekman R, Emili A, Lyons SM, Cardamone MD, Perissi V. Inhibition of K63 ubiquitination by G-Protein pathway suppressor 2 (GPS2) regulates mitochondria-associated translation. Pharmacol Res 2024; 207:107336. [PMID: 39094987 DOI: 10.1016/j.phrs.2024.107336] [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: 01/02/2024] [Revised: 07/29/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024]
Abstract
G-Protein Pathway Suppressor 2 (GPS2) is an inhibitor of non-proteolytic K63 ubiquitination mediated by the E2 ubiquitin-conjugating enzyme Ubc13. Previous studies have associated GPS2-mediated restriction of ubiquitination with the regulation of insulin signaling, inflammatory responses and mitochondria-nuclear communication across different tissues and cell types. However, a detailed understanding of the targets of GPS2/Ubc13 activity is lacking. Here, we have dissected the GPS2-regulated K63 ubiquitome in mouse embryonic fibroblasts and human breast cancer cells, unexpectedly finding an enrichment for proteins involved in RNA binding and translation on the outer mitochondrial membrane. Validation of selected targets of GPS2-mediated regulation, including the RNA-binding protein PABPC1 and translation factors RPS1, RACK1 and eIF3M, revealed a mitochondrial-specific strategy for regulating the translation of nuclear-encoded mitochondrial proteins via non-proteolytic ubiquitination. Removal of GPS2-mediated inhibition, either via genetic deletion or stress-induced nuclear translocation, promotes the import-coupled translation of selected mRNAs leading to the increased expression of an adaptive antioxidant program. In light of GPS2 role in nuclear-mitochondria communication, these findings reveal an exquisite regulatory network for modulating mitochondrial gene expression through spatially coordinated transcription and translation.
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Affiliation(s)
- Yuan Gao
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States
| | - Julian Kwan
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States; Center for Network and Systems Biology, Boston University, Boston, MA 02115, United States
| | - Joseph Orofino
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States
| | - Giulia Burrone
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States; Department of Computer Science, University of Torino, Torino, Italy; Department of Clinical and Biological Science, University of Torino, Torino, Italy; Graduate Program in Complex Systems for Quantitative Biomedicine, University of Torino, Torino, Italy
| | - Sahana Mitra
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States
| | - Ting-Yu Fan
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States
| | - Justin English
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States; Graduate Program in Pharmacology and Experimental Therapeutics, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States
| | - Ryan Hekman
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States; Center for Network and Systems Biology, Boston University, Boston, MA 02115, United States
| | - Andrew Emili
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States; Center for Network and Systems Biology, Boston University, Boston, MA 02115, United States; Biology Department, Boston University, Boston, MA 02115, United States
| | - Shawn M Lyons
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States
| | - Maria Dafne Cardamone
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States
| | - Valentina Perissi
- Department of Biochemistry and Cell Biology, Chobanian&Avedisian School of Medicine, Boston University, Boston, MA 02115, United States.
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Wang K, Liu CY, Fang B, Li B, Li YH, Xia QQ, Zhao Y, Cheng XL, Yang SM, Zhang MH, Wang K. The function and therapeutic potential of transfer RNA-derived small RNAs in cardiovascular diseases: A review. Pharmacol Res 2024; 206:107279. [PMID: 38942340 DOI: 10.1016/j.phrs.2024.107279] [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: 03/23/2024] [Revised: 06/20/2024] [Accepted: 06/20/2024] [Indexed: 06/30/2024]
Abstract
Transfer RNA-derived small RNAs (tsRNAs) are a class of small non-coding RNA (sncRNA) molecules derived from tRNA, including tRNA derived fragments (tRFs) and tRNA halfs (tiRNAs). tsRNAs can affect cell functions by participating in gene expression regulation, translation regulation, intercellular signal transduction, and immune response. They have been shown to play an important role in various human diseases, including cardiovascular diseases (CVDs). Targeted regulation of tsRNAs expression can affect the progression of CVDs. The tsRNAs induced by pathological conditions can be detected when released into the extracellular, giving them enormous potential as disease biomarkers. Here, we review the biogenesis, degradation process and related functional mechanisms of tsRNAs, and discuss the research progress and application prospects of tsRNAs in different CVDs, to provide a new perspective on the treatment of CVDs.
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Affiliation(s)
- Kai Wang
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao University, Jinan 250014, China; Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Cui-Yun Liu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Bo Fang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Bo Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Ying-Hui Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Qian-Qian Xia
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Yan Zhao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Xue-Li Cheng
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Su-Min Yang
- Department of Cardiovascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao 266003, China.
| | - Mei-Hua Zhang
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao University, Jinan 250014, China.
| | - Kun Wang
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao University, Jinan 250014, China; Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China.
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3
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Santonoceto G, Jurkiewicz A, Szczesny RJ. RNA degradation in human mitochondria: the journey is not finished. Hum Mol Genet 2024; 33:R26-R33. [PMID: 38779774 DOI: 10.1093/hmg/ddae043] [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: 01/04/2024] [Revised: 03/03/2024] [Accepted: 03/05/2024] [Indexed: 05/25/2024] Open
Abstract
Mitochondria are vital organelles present in almost all eukaryotic cells. Although most of the mitochondrial proteins are nuclear-encoded, mitochondria contain their own genome, whose proper expression is necessary for mitochondrial function. Transcription of the human mitochondrial genome results in the synthesis of long polycistronic transcripts that are subsequently processed by endonucleases to release individual RNA molecules, including precursors of sense protein-encoding mRNA (mt-mRNA) and a vast amount of antisense noncoding RNAs. Because of mitochondrial DNA (mtDNA) organization, the regulation of individual gene expression at the transcriptional level is limited. Although transcription of most protein-coding mitochondrial genes occurs with the same frequency, steady-state levels of mature transcripts are different. Therefore, post-transcriptional processes are important for regulating mt-mRNA levels. The mitochondrial degradosome is a complex composed of the RNA helicase SUV3 (also known as SUPV3L1) and polynucleotide phosphorylase (PNPase, PNPT1). It is the best-characterized RNA-degrading machinery in human mitochondria, which is primarily responsible for the decay of mitochondrial antisense RNA. The mechanism of mitochondrial sense RNA decay is less understood. This review aims to provide a general picture of mitochondrial genome expression, with a particular focus on mitochondrial RNA (mtRNA) degradation.
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Affiliation(s)
- Giulia Santonoceto
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, Warsaw 02-106, Poland
| | - Aneta Jurkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, Warsaw 02-106, Poland
| | - Roman J Szczesny
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, Warsaw 02-106, Poland
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Cao W, Wang C, Zhang Y, Yang J, Luo X, Zhao Y, Wu M, Cheng S, Wang Y. Identification of the prognostic value of LACTB2 and its correlation with immune infiltrates in ovarian cancer by integrated bioinformatics analyses. Eur J Med Res 2024; 29:166. [PMID: 38475882 DOI: 10.1186/s40001-024-01762-2] [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: 10/26/2023] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
Ovarian cancer (OC) is one of the most common reproductive tumors in women, whereas current treatment options are limited. β-lactamase-like-protein 2 (LACTB2) has been observed to be associated with various cancers, but its function in OC is unknown. Therefore, we evaluate the prognostic value and the underlying function of LACTB2 in OC. In this study, high expression of LACTB2 was observed in OC compared with normal controls. Kaplan-Meier Plotter analysis revealed that overexpressed LACTB2 is strongly correlated with poor prognosis. We conducted GO/KEGG analysis to investigate the potential biological function of LACTB2 in OC. GESA analysis showed that LACTB2 was closely related to immune-related pathways. Subsequently, we explored the relationship between LACTB2 and 24 types of immune cells in OC. The results suggested that LACTB2 was positively associated with multiple tumor-infiltrating immune cells. Importantly, LACTB2 may modulate immune cell infiltration in OC to influence prognosis. In conclusion, LACTB2 can be used as a promising prognostic biomarker and immunotherapy target for OC.
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Affiliation(s)
- Weiwei Cao
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Chao Wang
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Yue Zhang
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Jiani Yang
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Xiaomei Luo
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Yaqian Zhao
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Meixuan Wu
- Department of Obstetrics and Gynecology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201204, China
| | - Shanshan Cheng
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China.
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China.
- Department of Obstetrics and Gynecology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201204, China.
| | - Yu Wang
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China.
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China.
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5
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Yu S, Lin Y, Li Y, Chen S, Zhou L, Song H, Yang C, Zhang H, Zhou J, Sun S, Li Y, Chen J, Feng R, Qiao N, Xie Y, Zhang R, Yin T, Chen S, Li Q, Zhu J, Qu J. Systemic immune profiling of Omicron-infected subjects inoculated with different doses of inactivated virus vaccine. Cell 2023; 186:4615-4631.e16. [PMID: 37769658 DOI: 10.1016/j.cell.2023.08.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 07/03/2023] [Accepted: 08/23/2023] [Indexed: 10/03/2023]
Abstract
SARS-CoV-2 primary strain-based vaccination exerts a protective effect against Omicron variants-initiated infection, symptom occurrence, and disease severity in a booster-dependent manner. Yet, the underlying mechanisms remain unclear. During the 2022 Omicron outbreak in Shanghai, we enrolled 122 infected adults and 50 uninfected controls who had been unvaccinated or vaccinated with two or three doses of COVID-19 inactive vaccines and performed integrative analysis of 41-plex CyTOF, RNA-seq, and Olink on their peripheral blood samples. The frequencies of HLA-DRhi classical monocytes, non-classical monocytes, and Th1-like Tem tended to increase, whereas the frequency of Treg was reduced by booster vaccine, and they influenced symptom occurrence in a vaccine dose-dependent manner. Intercorrelation and mechanistic analysis suggested that the booster vaccination induced monocytic training, which would prime monocytic activation and maturation rather than differentiating into myeloid-derived suppressive cells upon Omicron infections. Overall, our study provides insights into how booster vaccination elaborates protective immunity across SARS-CoV-2 variants.
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Affiliation(s)
- Shanhe Yu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China; Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai 200025, China
| | - Yingni Lin
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Institute of Respiratory Diseases, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China; Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai 200025, China
| | - Yong Li
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Institute of Respiratory Diseases, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China; Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai 200025, China
| | - Shijun Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China
| | - Lina Zhou
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Institute of Respiratory Diseases, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China; Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai 200025, China
| | - Hejie Song
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Institute of Respiratory Diseases, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China; Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai 200025, China
| | - Cuiping Yang
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai 201801, China
| | - Haiqing Zhang
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Institute of Respiratory Diseases, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China; Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai 200025, China
| | - Jianping Zhou
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Institute of Respiratory Diseases, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China; Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai 200025, China
| | - Shunchang Sun
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai 201801, China
| | - Yanan Li
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Institute of Respiratory Diseases, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China; Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai 200025, China
| | - Juan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China
| | - Ruixue Feng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China
| | - Niu Qiao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China
| | - Yinyin Xie
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China
| | - Ruihong Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China
| | - Tong Yin
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China
| | - Saijuan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China.
| | - Qingyun Li
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Institute of Respiratory Diseases, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China; Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai 200025, China.
| | - Jiang Zhu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China; Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai 200025, China.
| | - Jieming Qu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Institute of Respiratory Diseases, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China; Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai 200025, China; National Research Center for Translational Medicine at Shanghai, Shanghai 200025, China.
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6
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Diene SM, Pontarotti P, Azza S, Armstrong N, Pinault L, Chabrière E, Colson P, Rolain JM, Raoult D. Origin, Diversity, and Multiple Roles of Enzymes with Metallo-β-Lactamase Fold from Different Organisms. Cells 2023; 12:1752. [PMID: 37443786 PMCID: PMC10340364 DOI: 10.3390/cells12131752] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/23/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
β-lactamase enzymes have generated significant interest due to their ability to confer resistance to the most commonly used family of antibiotics in human medicine. Among these enzymes, the class B β-lactamases are members of a superfamily of metallo-β-lactamase (MβL) fold proteins which are characterised by conserved motifs (i.e., HxHxDH) and are not only limited to bacteria. Indeed, as the result of several barriers, including low sequence similarity, default protein annotation, or untested enzymatic activity, MβL fold proteins have long been unexplored in other organisms. However, thanks to search approaches which are more sensitive compared to classical Blast analysis, such as the use of common ancestors to identify distant homologous sequences, we are now able to highlight their presence in different organisms including Bacteria, Archaea, Nanoarchaeota, Asgard, Humans, Giant viruses, and Candidate Phyla Radiation (CPR). These MβL fold proteins are multifunctional enzymes with diverse enzymatic or non-enzymatic activities of which, at least thirteen activities have been reported such as β-lactamase, ribonuclease, nuclease, glyoxalase, lactonase, phytase, ascorbic acid degradation, anti-cancer drug degradation, or membrane transport. In this review, we (i) discuss the existence of MβL fold enzymes in the different domains of life, (ii) present more suitable approaches to better investigating their homologous sequences in unsuspected sources, and (iii) report described MβL fold enzymes with demonstrated enzymatic or non-enzymatic activities.
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Affiliation(s)
- Seydina M. Diene
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
| | - Pierre Pontarotti
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
- CNRS SNC5039, 13005 Marseille, France
| | - Saïd Azza
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
- Assistance Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, 13005 Marseille, France
| | - Nicholas Armstrong
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
- Assistance Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, 13005 Marseille, France
| | - Lucile Pinault
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
- Assistance Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, 13005 Marseille, France
| | - Eric Chabrière
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
| | - Philippe Colson
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
| | - Jean-Marc Rolain
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
| | - Didier Raoult
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
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7
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Xiong W, Ge H, Shen C, Li C, Zhang X, Tang L, Shen Y, Lu S, Zhang H, Wang Z. PRSS37 deficiency leads to impaired energy metabolism in testis and sperm revealed by DIA-based quantitative proteomic analysis. Reprod Sci 2023; 30:145-168. [PMID: 35471551 DOI: 10.1007/s43032-022-00918-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/12/2022] [Indexed: 01/11/2023]
Abstract
Our previous studies have reported that a putative trypsin-like serine protease, PRSS37, is exclusively expressed in testicular germ cells during late spermatogenesis and essential for sperm migration from the uterus into the oviduct and sperm-egg recognition via mediating the interaction between PDILT and ADAM3. In the present study, the global proteome profiles of wild-type (wt) and Prss37-/- mice in testis and sperm were compared employing data independent acquisition (DIA) technology. Overall, 2506 and 459 differentially expressed proteins (DEPs) were identified in Prss37-null testis and sperm, respectively, when compared to control groups. Bioinformatic analyses revealed that most of DEPs were related to energy metabolism. Of note, the DEPs associated with pathways for the catabolism such as glucose via glycolysis, fatty acids via β-oxidation, and amino acids via oxidative deamination were significantly down-regulated. Meanwhile, the DEPs involved in the tricarboxylic acid cycle (TCA cycle) and oxidative phosphorylation (OXPHOS) were remarkably decreased. The DIA data were further confirmed by a markedly reduction of intermediate metabolites (citrate and fumarate) in TCA cycle and terminal metabolite (ATP) in OXPHOS system after disruption of PRSS37. These outcomes not only provide a more comprehensive understanding of the male fertility of energy metabolism modulated by PRSS37 but also furnish a dynamic proteomic resource for further reproductive biology studies.
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Affiliation(s)
- Wenfeng Xiong
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Rui-Jin Hospital Affiliated To Shanghai Jiao Tong University School of Medicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Haoyang Ge
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Rui-Jin Hospital Affiliated To Shanghai Jiao Tong University School of Medicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Chunling Shen
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Rui-Jin Hospital Affiliated To Shanghai Jiao Tong University School of Medicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200025, China.
| | - Chaojie Li
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Rui-Jin Hospital Affiliated To Shanghai Jiao Tong University School of Medicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Xiaohong Zhang
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Rui-Jin Hospital Affiliated To Shanghai Jiao Tong University School of Medicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Lingyun Tang
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Rui-Jin Hospital Affiliated To Shanghai Jiao Tong University School of Medicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Yan Shen
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Rui-Jin Hospital Affiliated To Shanghai Jiao Tong University School of Medicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Shunyuan Lu
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Rui-Jin Hospital Affiliated To Shanghai Jiao Tong University School of Medicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Hongxin Zhang
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Rui-Jin Hospital Affiliated To Shanghai Jiao Tong University School of Medicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Zhugang Wang
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Rui-Jin Hospital Affiliated To Shanghai Jiao Tong University School of Medicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200025, China.
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8
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Burgin H, Sharpe AJ, Nie S, Ziemann M, Crameri JJ, Stojanovski D, Pitt J, Ohtake A, Murayama K, McKenzie M. Loss of mitochondrial fatty acid β-oxidation protein short-chain Enoyl-CoA hydratase disrupts oxidative phosphorylation protein complex stability and function. FEBS J 2023; 290:225-246. [PMID: 35962613 PMCID: PMC10087869 DOI: 10.1111/febs.16595] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/24/2022] [Accepted: 08/11/2022] [Indexed: 01/14/2023]
Abstract
Short-chain enoyl-CoA hydratase 1 (ECHS1) is involved in the second step of mitochondrial fatty acid β-oxidation (FAO), catalysing the hydration of short-chain enoyl-CoA esters to short-chain 3-hyroxyl-CoA esters. Genetic deficiency in ECHS1 (ECHS1D) is associated with a specific subset of Leigh Syndrome, a disease typically caused by defects in oxidative phosphorylation (OXPHOS). Here, we examined the molecular pathogenesis of ECHS1D using a CRISPR/Cas9 edited human cell 'knockout' model and fibroblasts from ECHS1D patients. Transcriptome analysis of ECHS1 'knockout' cells showed reductions in key mitochondrial pathways, including the tricarboxylic acid cycle, receptor-mediated mitophagy and nucleotide biosynthesis. Subsequent proteomic analyses confirmed these reductions and revealed additional defects in mitochondrial oxidoreductase activity and fatty acid β-oxidation. Functional analysis of ECHS1 'knockout' cells showed reduced mitochondrial oxygen consumption rates when metabolising glucose or OXPHOS complex I-linked substrates, as well as decreased complex I and complex IV enzyme activities. ECHS1 'knockout' cells also exhibited decreased OXPHOS protein complex steady-state levels (complex I, complex III2 , complex IV, complex V and supercomplexes CIII2 /CIV and CI/CIII2 /CIV), which were associated with a defect in complex I assembly. Patient fibroblasts exhibit varied reduction of mature OXPHOS complex steady-state levels, with defects detected in CIII2 , CIV, CV and the CI/CIII2 /CIV supercomplex. Overall, these findings highlight the contribution of defective OXPHOS function, in particular complex I deficiency, to the molecular pathogenesis of ECHS1D.
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Affiliation(s)
- Harrison Burgin
- School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Geelong, Australia
| | - Alice J Sharpe
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Shuai Nie
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Australia
| | - Mark Ziemann
- School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Geelong, Australia
| | - Jordan J Crameri
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Australia
| | - Diana Stojanovski
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Australia
| | - James Pitt
- Department of Paediatrics, Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, The University of Melbourne, Australia
| | - Akira Ohtake
- Department of Pediatrics & Clinical Genomics, Faculty of Medicine, Saitama Medical University, Japan.,Centre for Intractable Diseases, Saitama Medical University Hospital, Japan
| | - Kei Murayama
- Department of Metabolism, Chiba Children's Hospital, Japan
| | - Matthew McKenzie
- School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Geelong, Australia.,Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, Australia.,Department of Molecular and Translational Science, Monash University, Melbourne, Australia
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9
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Wang S, Luo Z, Yuan L, Lin X, Tang Y, Yin L, Liang P, Jiang B. tRNA-Derived Small RNAs: Novel Insights into the Pathogenesis and Treatment of Cardiovascular Diseases. J Cardiovasc Transl Res 2022; 16:300-309. [PMID: 36190649 DOI: 10.1007/s12265-022-10322-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/12/2022] [Indexed: 12/05/2022]
Abstract
tRNA-derived small RNAs (tsRNAs) are non-coding RNAs with diverse functions in various diseases. Although research on tsRNAs has focused on their roles in cancer, such as gene expression regulation to influence cancer progression and realize clinical effects, a growing number of studies are investigating the association of tsRNAs with cardiovascular diseases (CVDs), including atherosclerosis, myocardial infarction, and pulmonary hypertension. tsRNA expression varies across these diseases and could be regulated by epigenetics, tsRNA structure, and tRNA-binding proteins. tsRNAs play key roles in CVD progression, including the regulation of protein synthesis, and the different mechanisms underlying these functional roles of tsRNAs have been elucidated. Furthermore, tsRNAs are potential diagnostic biomarkers and therapeutic targets in CVDs. In this review, we summarize the biogenesis, classification, and regulation of tsRNAs and their potential application for CVD diagnosis and therapy. We also highlight the current challenges and provide perspectives for further investigation.
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Affiliation(s)
- Shuxin Wang
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, Xiangya School of Medicine, Central South University, Changsha, 410008, Hunan, China
| | - Zhengyang Luo
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, Xiangya School of Medicine, Central South University, Changsha, 410008, Hunan, China
| | - Ludong Yuan
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, Xiangya School of Medicine, Central South University, Changsha, 410008, Hunan, China
| | - Xiaofang Lin
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, Xiangya School of Medicine, Central South University, Changsha, 410008, Hunan, China
| | - Yuting Tang
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, Xiangya School of Medicine, Central South University, Changsha, 410008, Hunan, China
| | - Leijing Yin
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, Xiangya School of Medicine, Central South University, Changsha, 410008, Hunan, China
| | - Pengfei Liang
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Bimei Jiang
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, Xiangya School of Medicine, Central South University, Changsha, 410008, Hunan, China.
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10
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Organization and expression of the mammalian mitochondrial genome. Nat Rev Genet 2022; 23:606-623. [PMID: 35459860 DOI: 10.1038/s41576-022-00480-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2022] [Indexed: 02/07/2023]
Abstract
The mitochondrial genome encodes core subunits of the respiratory chain that drives oxidative phosphorylation and is, therefore, essential for energy conversion. Advances in high-throughput sequencing technologies and cryoelectron microscopy have shed light on the structure and organization of the mitochondrial genome and revealed unique mechanisms of mitochondrial gene regulation. New animal models of impaired mitochondrial protein synthesis have shown how the coordinated regulation of the cytoplasmic and mitochondrial translation machineries ensures the correct assembly of the respiratory chain complexes. These new technologies and disease models are providing a deeper understanding of mitochondrial genome organization and expression and of the diseases caused by impaired energy conversion, including mitochondrial, neurodegenerative, cardiovascular and metabolic diseases. They also provide avenues for the development of treatments for these conditions.
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11
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Kamoshita M, Kumar R, Anteghini M, Kunze M, Islinger M, Martins dos Santos V, Schrader M. Insights Into the Peroxisomal Protein Inventory of Zebrafish. Front Physiol 2022; 13:822509. [PMID: 35295584 PMCID: PMC8919083 DOI: 10.3389/fphys.2022.822509] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/07/2022] [Indexed: 12/19/2022] Open
Abstract
Peroxisomes are ubiquitous, oxidative subcellular organelles with important functions in cellular lipid metabolism and redox homeostasis. Loss of peroxisomal functions causes severe disorders with developmental and neurological abnormalities. Zebrafish are emerging as an attractive vertebrate model to study peroxisomal disorders as well as cellular lipid metabolism. Here, we combined bioinformatics analyses with molecular cell biology and reveal the first comprehensive inventory of Danio rerio peroxisomal proteins, which we systematically compared with those of human peroxisomes. Through bioinformatics analysis of all PTS1-carrying proteins, we demonstrate that D. rerio lacks two well-known mammalian peroxisomal proteins (BAAT and ZADH2/PTGR3), but possesses a putative peroxisomal malate synthase (Mlsl) and verified differences in the presence of purine degrading enzymes. Furthermore, we revealed novel candidate peroxisomal proteins in D. rerio, whose function and localisation is discussed. Our findings confirm the suitability of zebrafish as a vertebrate model for peroxisome research and open possibilities for the study of novel peroxisomal candidate proteins in zebrafish and humans.
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Affiliation(s)
- Maki Kamoshita
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Rechal Kumar
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Marco Anteghini
- LifeGlimmer GmbH, Berlin, Germany
- Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Markus Kunze
- Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Markus Islinger
- Institute of Neuroanatomy, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Vítor Martins dos Santos
- LifeGlimmer GmbH, Berlin, Germany
- Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Michael Schrader
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, United Kingdom
- *Correspondence: Michael Schrader,
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12
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Shaukat AN, Kaliatsi EG, Stamatopoulou V, Stathopoulos C. Mitochondrial tRNA-Derived Fragments and Their Contribution to Gene Expression Regulation. Front Physiol 2021; 12:729452. [PMID: 34539450 PMCID: PMC8446549 DOI: 10.3389/fphys.2021.729452] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/09/2021] [Indexed: 01/14/2023] Open
Abstract
Mutations in human mitochondrial tRNAs (mt-tRNAs) are responsible for several and sometimes severe clinical phenotypes, classified among mitochondrial diseases. In addition, post-transcriptional modifications of mt-tRNAs in correlation with several stress signals can affect their stability similarly to what has been described for their nuclear-encoded counterparts. Many of the perturbations related to either point mutations or aberrant modifications of mt-tRNAs can lead to specific cleavage and the production of mitochondrial tRNA-derived fragments (mt-tRFs). Although mt-tRFs have been detected in several studies, the exact biogenesis steps and biological role remain, to a great extent, unexplored. Several mt-tRFs are produced because of the excessive oxidative stress which predominantly affects mitochondrial DNA integrity. In addition, mt-tRFs have been detected in various diseases with possible detrimental consequences, but also their production may represent a response mechanism to external stimuli, including infections from pathogens. Finally, specific point mutations on mt-tRNAs have been reported to impact the pool of the produced mt-tRFs and there is growing evidence suggesting that mt-tRFs can be exported and act in the cytoplasm. In this review, we summarize current knowledge on mitochondrial tRNA-deriving fragments and their possible contribution to gene expression regulation.
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Affiliation(s)
| | - Eleni G Kaliatsi
- Department of Biochemistry, School of Medicine, University of Patras, Patras, Greece
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13
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Proteomic analysis demonstrates the role of the quality control protease LONP1 in mitochondrial protein aggregation. J Biol Chem 2021; 297:101134. [PMID: 34461102 PMCID: PMC8503632 DOI: 10.1016/j.jbc.2021.101134] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 11/20/2022] Open
Abstract
The mitochondrial matrix protease LONP1 is an essential part of the organellar protein quality control system. LONP1 has been shown to be involved in respiration control and apoptosis. Furthermore, a reduction in LONP1 level correlates with aging. Up to now, the effects of a LONP1 defect were mostly studied by utilizing transient, siRNA-mediated knockdown approaches. We generated a new cellular model system for studying the impact of LONP1 on mitochondrial protein homeostasis by a CRISPR/Cas-mediated genetic knockdown (gKD). These cells showed a stable reduction of LONP1 along with a mild phenotype characterized by absent morphological differences and only small negative effects on mitochondrial functions under normal culture conditions. To assess the consequences of a permanent LONP1 depletion on the mitochondrial proteome, we analyzed the alterations of protein levels by quantitative mass spectrometry, demonstrating small adaptive changes, in particular with respect to mitochondrial protein biogenesis. In an additional proteomic analysis, we determined the temperature-dependent aggregation behavior of mitochondrial proteins and its dependence on a reduction of LONP1 activity, demonstrating the important role of the protease for mitochondrial protein homeostasis in mammalian cells. We identified a significant number of mitochondrial proteins that are affected by a reduced LONP1 activity especially with respect to their stress-induced solubility. Taken together, our results suggest a very good applicability of the LONP1 gKD cell line as a model system for human aging processes.
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14
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Inverse association between use of broad spectrum penicllin with beta-lactamase inhibitors and prevalence of type 1 diabetes mellitus in Europe. Sci Rep 2021; 11:16768. [PMID: 34408224 PMCID: PMC8373876 DOI: 10.1038/s41598-021-96301-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 08/05/2021] [Indexed: 12/16/2022] Open
Abstract
Increasing incidence of type 1 diabetes is supposed to be induced by environmental factors. Microbiome modulated by antibiotics seems to serve as one of the environmental factors which could influence the development of T1DM. Mitochondria, as autochthonous environmental bacteria living in our cells, and other bacteria share many common enzymes including beta-lactamases and it is supported by evidence that some beta-lactamase inhibitors are able to interact with counterpart enzymes. Thus, antibiotics may utilize two different pathways influencing the development of T1DM; one through modulation of microbiome and a second one via the interaction of mitochondrial enzymes. Data of consumption of penicillin (both narrow and broad spectrum) and beta-lactamase inhibitors in 30 European countries were collected from the database of the European Centre for Disease Prevention and Control. These data were correlated with the prevalence reported by the International Diabetes Federation (2019) referring to type 1 diabetes in Europe. No correlation was found between total penicillin consumption or use of broad spectrum penicillin and the prevalence of type 1 diabetes. Nevertheless, broad spectrum penicillin, in combination with beta-lactamase inhibitor, was in inverse correlation with the prevalence of type 1 diabetes (r = − 0.573, p = 0.001). On the other hand, narrow spectrum penicillin was in positive correlation with type 1 diabetes (r = 0.523, p = 0.003). Prevalence of type 1 diabetes showed an inverse correlation with the use of beta-lactamase inhibitors and a positive one with that of narrow spectrum penicillin. Such a detailed analysis has not so far been provided referring to the penicillin group. In the background of this association either microbiomal or direct mitochondrial effects can be supposed.
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15
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Bahr G, González LJ, Vila AJ. Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design. Chem Rev 2021; 121:7957-8094. [PMID: 34129337 PMCID: PMC9062786 DOI: 10.1021/acs.chemrev.1c00138] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antimicrobial resistance is one of the major problems in current practical medicine. The spread of genes coding for resistance determinants among bacteria challenges the use of approved antibiotics, narrowing the options for treatment. Resistance to carbapenems, last resort antibiotics, is a major concern. Metallo-β-lactamases (MBLs) hydrolyze carbapenems, penicillins, and cephalosporins, becoming central to this problem. These enzymes diverge with respect to serine-β-lactamases by exhibiting a different fold, active site, and catalytic features. Elucidating their catalytic mechanism has been a big challenge in the field that has limited the development of useful inhibitors. This review covers exhaustively the details of the active-site chemistries, the diversity of MBL alleles, the catalytic mechanism against different substrates, and how this information has helped developing inhibitors. We also discuss here different aspects critical to understand the success of MBLs in conferring resistance: the molecular determinants of their dissemination, their cell physiology, from the biogenesis to the processing involved in the transit to the periplasm, and the uptake of the Zn(II) ions upon metal starvation conditions, such as those encountered during an infection. In this regard, the chemical, biochemical and microbiological aspects provide an integrative view of the current knowledge of MBLs.
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Affiliation(s)
- Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Lisandro J. González
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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16
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Chen Q, Zheng W, Zhu L, Liu H, Song Y, Hu S, Bai Y, Pan Y, Zhang J, Guan J, Shao C. LACTB2 renders radioresistance by activating PINK1/Parkin-dependent mitophagy in nasopharyngeal carcinoma. Cancer Lett 2021; 518:127-139. [PMID: 34271102 DOI: 10.1016/j.canlet.2021.07.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 01/04/2023]
Abstract
Radiotherapy is a standard and conventional treatment strategy for nasopharyngeal carcinoma (NPC); however, radioresistance remains refractory to clinical outcomes. Understanding the molecular mechanism of radioresistance is crucial for advancing the efficacy of radiotherapy and improving the prognosis of NPC. In this study, β-lactamase-like-protein 2 (LACTB2) was identified as a potential biomarker for radioresistance using tandem mass tag proteomic analysis of NPC cells, gene chip analysis of NPC tissues, and differential gene analysis between NPC and normal nasopharyngeal tissues from the Gene Expression Omnibus database GSE68799. Meanwhile, LACTB2 levels were elevated in the serum of patients with NPC after radiotherapy. Inhibiting LACTB2 levels and mitophagy can sensitize NPC cells to ionizing radiation. In NPC cells, LACTB2 was augmented at the transcription and protein levels after radiation rather than nucleus-cytoplasm-mitochondria transposition to activate PTEN-induced kinase 1 (PINK1) and mitophagy. In addition, LACTB2 was first authenticated to co-locate with PINK1 by interacting with its N-terminal domain. Together, our findings indicate that overexpressed LACTB2 provoked PINK1-dependent mitophagy to promote radioresistance and thus might serve as a prognostic biomarker for NPC radiotherapy.
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Affiliation(s)
- Qianping Chen
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Wang Zheng
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Lin Zhu
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Hongxia Liu
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yimeng Song
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Songling Hu
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yang Bai
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yan Pan
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Jianghong Zhang
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Jian Guan
- Department of Radiation Oncology, Nanfang Hospital of Southern Medical University, Guangzhou, Guangdong, 510515, China.
| | - Chunlin Shao
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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17
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Barchiesi A, Bazzani V, Jabczynska A, Borowski LS, Oeljeklaus S, Warscheid B, Chacinska A, Szczesny RJ, Vascotto C. DNA Repair Protein APE1 Degrades Dysfunctional Abasic mRNA in Mitochondria Affecting Oxidative Phosphorylation. J Mol Biol 2021; 433:167125. [PMID: 34224750 DOI: 10.1016/j.jmb.2021.167125] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/25/2021] [Accepted: 06/26/2021] [Indexed: 11/19/2022]
Abstract
APE1 is a multifunctional protein which plays a central role in the maintenance of nuclear and mitochondrial genomes repairing DNA lesions caused by oxidative and alkylating agents. In addition, it works as a redox signaling protein regulating gene expression by interacting with many transcriptional factors. Apart from these canonical activities, recent studies have shown that APE1 is also enzymatically active on RNA molecules. The present study unveils for the first time a new role of the mitochondrial form of APE1 protein in the metabolism of RNA in mitochondria. Our data demonstrate that APE1 is associated with mitochondrial messenger RNA and exerts endoribonuclease activity on abasic sites. Loss of APE1 results in the accumulation of damaged mitochondrial mRNA species, determining impairment in protein translation and reduced expression of mitochondrial-encoded proteins, finally leading to less efficient mitochondrial respiration. Altogether, our data demonstrate that APE1 plays an active role in the degradation of the mitochondrial mRNA and has a profound impact on mitochondrial well-being.
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Affiliation(s)
| | | | - Agata Jabczynska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Lukasz S Borowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Silke Oeljeklaus
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Bettina Warscheid
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Germany
| | - Agnieszka Chacinska
- Laboratory of Mitochondrial Biogenesis, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland; ReMedy International Research Agenda Unit, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Roman J Szczesny
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Carlo Vascotto
- Department of Medicine, University of Udine, 33100 Udine, Italy; Laboratory of Mitochondrial Biogenesis, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland.
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18
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Yammine T, Reynaud N, Lejeune H, Diguet F, Rollat-Farnier PA, Labalme A, Plotton I, Farra C, Sanlaville D, Chouery E, Schluth-Bolard C. Deciphering balanced translocations in infertile males by next-generation sequencing to identify candidate genes for spermatogenesis disorders. Mol Hum Reprod 2021; 27:6261938. [PMID: 34009290 DOI: 10.1093/molehr/gaab034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 04/14/2021] [Indexed: 12/29/2022] Open
Abstract
Male infertility affects about 7% of the general male population. Balanced structural chromosomal rearrangements are observed in 0.4-1.4% of infertile males and are considered as a well-established cause of infertility. However, underlying pathophysiological mechanisms still need to be clarified. A strategy combining standard and high throughput cytogenetic and molecular technologies was applied in order to identify the candidate genes that might be implicated in the spermatogenesis defect in three male carriers of different balanced translocations. Fluorescence in situ hybridization (FISH) and whole-genome paired-end sequencing were used to characterize translocation breakpoints at the molecular level while exome sequencing was performed in order to exclude the presence of any molecular event independent from the chromosomal rearrangement in the patients. All translocation breakpoints were characterized in the three patients. We identified four variants: a position effect on LACTB2 gene in Patient 1, a heterozygous CTDP1 gene disruption in Patient 2, two single-nucleotide variations (SNVs) in DNAH5 gene and a heterozygous 17q12 deletion in Patient 3. The variants identified in this study need further validation to assess their roles in male infertility. This study shows that beside the mechanical effect of structural rearrangement on meiosis, breakpoints could result in additional alterations such as gene disruption or position effect. Moreover, additional SNVs or copy number variations may be fortuitously present and could explain the variable impact of chromosomal rearrangements on spermatogenesis. In conclusion, this study confirms the relevance of combining different cytogenetic and molecular techniques to investigate patients with spermatogenesis disorders and structural rearrangements on genomic scale.
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Affiliation(s)
- T Yammine
- Medical Genetics Unit (UGM), Faculty of Medicine, Saint Joseph University, Beirut, Lebanon.,Institut Neuromyogène, Equipe Métabolisme énergétique et développement neuronal, CNRS UMR 5310, INSERM U1217, Université Lyon 1, Lyon, France
| | - N Reynaud
- Hospices Civils de Lyon, Service de Génétique, Bron, France.,Service de Médecine de la Reproduction, Hôpital Femme Mère Enfant, Hospices Civils de Lyon, Bron, France
| | - H Lejeune
- Service de Médecine de la Reproduction, Hôpital Femme Mère Enfant, Hospices Civils de Lyon, Bron, France.,Laboratoire d'hormonologie et endocrinologie Moléculaire, Hospices Civils de Lyon, Bron, France
| | - F Diguet
- Hospices Civils de Lyon, Service de Génétique, Bron, France
| | - P A Rollat-Farnier
- Hospices Civils de Lyon, Service de Génétique, Bron, France.,Cellule Bioinformatique, Hospices Civils de Lyon, Bron, France
| | - A Labalme
- Hospices Civils de Lyon, Service de Génétique, Bron, France
| | - I Plotton
- Service de Médecine de la Reproduction, Hôpital Femme Mère Enfant, Hospices Civils de Lyon, Bron, France.,Laboratoire d'hormonologie et endocrinologie Moléculaire, Hospices Civils de Lyon, Bron, France.,Unite INSERM 1208, Université Lyon 1, Lyon, France
| | - C Farra
- Medical Genetics Unit (UGM), Faculty of Medicine, Saint Joseph University, Beirut, Lebanon.,Department of Genetics, Hotel Dieu de France Medical Center, Beirut, Lebanon
| | - D Sanlaville
- Institut Neuromyogène, Equipe Métabolisme énergétique et développement neuronal, CNRS UMR 5310, INSERM U1217, Université Lyon 1, Lyon, France.,Hospices Civils de Lyon, Service de Génétique, Bron, France
| | - E Chouery
- Medical Genetics Unit (UGM), Faculty of Medicine, Saint Joseph University, Beirut, Lebanon.,Department of Human Genetics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
| | - C Schluth-Bolard
- Institut Neuromyogène, Equipe Métabolisme énergétique et développement neuronal, CNRS UMR 5310, INSERM U1217, Université Lyon 1, Lyon, France.,Hospices Civils de Lyon, Service de Génétique, Bron, France
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19
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Harwood JC, Leonenko G, Sims R, Escott-Price V, Williams J, Holmans P. Defining functional variants associated with Alzheimer's disease in the induced immune response. Brain Commun 2021; 3:fcab083. [PMID: 33959712 PMCID: PMC8087896 DOI: 10.1093/braincomms/fcab083] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 03/17/2021] [Accepted: 03/22/2021] [Indexed: 12/14/2022] Open
Abstract
Defining the mechanisms involved in the aetiology of Alzheimer’s disease from genome-wide association studies alone is challenging since Alzheimer’s disease is polygenic and most genetic variants are non-coding. Non-coding Alzheimer’s disease risk variants can influence gene expression by affecting miRNA binding and those located within enhancers and within CTCF sites may influence gene expression through alterations in chromatin states. In addition, their function can be cell-type specific. They can function specifically in microglial enhancers thus affecting gene expression in the brain. Hence, transcriptome-wide association studies have been applied to test the genetic association between disease risk and cell-/tissue-specific gene expression. Many Alzheimer’s disease-associated loci are involved in the pathways of the innate immune system. Both microglia, the primary immune cells of the brain, and monocytes which can infiltrate the brain and differentiate into activated macrophages, have roles in neuroinflammation and β‐amyloid clearance through phagocytosis. In monocytes the function of regulatory variants can be context-specific after immune stimulation. To dissect the variants associated with Alzheimer’s disease in the context of monocytes, we utilized data from naïve monocytes and following immune stimulation in vitro, in combination with genome-wide association studies of Alzheimer’s disease in transcriptome-wide association studies. Of the nine genes with statistically independent transcriptome-wide association signals, seven are located in known Alzheimer’s disease risk loci: BIN1, PTK2B, SPI1, MS4A4A, MS4A6E, APOE and PVR. The transcriptome-wide association signal for MS4A6E, PTK2B and PVR and the direction of effect replicated in an independent genome-wide association studies. Our analysis identified two novel candidate genes for Alzheimer’s disease risk, LACTB2 and PLIN2/ADRP. LACTB2 replicated in a transcriptome-wide association study using independent expression weights. LACTB2 and PLIN2/ADRP are involved in mitochondrial function and lipid metabolism, respectively. Comparison of transcriptome-wide association study results from monocytes, whole blood and brain showed that the signal for PTK2B is specific to blood and MS4A6E is specific to LPS stimulated monocytes.
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Affiliation(s)
- Janet C Harwood
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Ganna Leonenko
- UK Dementia Research Institute at Cardiff University, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Rebecca Sims
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Valentina Escott-Price
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK.,UK Dementia Research Institute at Cardiff University, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Julie Williams
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK.,UK Dementia Research Institute at Cardiff University, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Peter Holmans
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
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20
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González JM. Visualizing the superfamily of metallo-β-lactamases through sequence similarity network neighborhood connectivity analysis. Heliyon 2021; 7:e05867. [PMID: 33426353 PMCID: PMC7785958 DOI: 10.1016/j.heliyon.2020.e05867] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/19/2020] [Accepted: 12/23/2020] [Indexed: 12/13/2022] Open
Abstract
Protein sequence similarity networks (SSNs) constitute a convenient approach to analyze large polypeptide sequence datasets, and have been successfully applied to study a number of protein families over the past decade. SSN analysis is herein combined with traditional cladistic and phenetic phylogenetic analysis (respectively based on multiple sequence alignments and all-against-all three-dimensional protein structure comparisons) in order to assist the ancestral reconstruction and integrative revision of the superfamily of metallo-β-lactamases (MBLs). It is shown that only 198 out of 15,292 representative nodes contain at least one experimentally obtained protein structure in the Protein Data Bank or a manually annotated SwissProt entry, that is to say, only 1.3 % of the superfamily has been functionally and/or structurally characterized. Besides, neighborhood connectivity coloring, which measures local network interconnectivity, is introduced for detection of protein families within SSN clusters. This approach provides a clear picture of how many families remain unexplored in the superfamily, while most MBL research is heavily biased towards a few families. Further research is suggested in order to determine the SSN topological properties, which will be instrumental for the improvement of automated sequence annotation methods.
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21
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Malgapo MIP, Safadi JM, Linder ME. Metallo-β-lactamase domain-containing protein 2 is S-palmitoylated and exhibits acyl-CoA hydrolase activity. J Biol Chem 2021; 296:100106. [PMID: 33219126 PMCID: PMC7949124 DOI: 10.1074/jbc.ra120.015701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/12/2020] [Accepted: 11/20/2020] [Indexed: 11/24/2022] Open
Abstract
Members of the metallo-β-lactamase (MBL) superfamily of enzymes harbor a highly conserved αββα MBL-fold domain and were first described as inactivators of common β-lactam antibiotics. In humans, these enzymes have been shown to exhibit diverse functions, including hydrolase activity toward amides, esters, and thioesters. An uncharacterized member of the human MBL family, MBLAC2, was detected in multiple palmitoylproteomes, identified as a zDHHC20 S-acyltransferase interactor, and annotated as a potential thioesterase. In this study, we confirmed that MBLAC2 is palmitoylated and identified the likely S-palmitoylation site as Cys254. S-palmitoylation of MBLAC2 is increased in cells when expressed with zDHHC20, and MBLAC2 is a substrate for purified zDHHC20 in vitro. To determine its biochemical function, we tested the ability of MBLAC2 to hydrolyze a variety of small molecules and acylprotein substrates. MBLAC2 has acyl-CoA thioesterase activity with kinetic parameters and acyl-CoA selectivity comparable with acyl-CoA thioesterase 1 (ACOT1). Two predicted zinc-binding residues, Asp87 and His88, are required for MBLAC2 hydrolase activity. Consistent with a role in fatty acid metabolism in cells, MBLAC2 was cross-linked to a photoactivatable fatty acid in a manner that was independent of its S-fatty acylation at Cys254. Our study adds to previous investigations demonstrating the versatility of the MBL-fold domain in supporting a variety of enzymatic reactions.
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Affiliation(s)
- Martin Ian P Malgapo
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Jenelle M Safadi
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Maurine E Linder
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA.
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22
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Expression analysis of mammalian mitochondrial ribosomal protein genes. Gene Expr Patterns 2020; 38:119147. [PMID: 32987154 DOI: 10.1016/j.gep.2020.119147] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/14/2020] [Accepted: 09/20/2020] [Indexed: 02/07/2023]
Abstract
Mitochondrial ribosomal proteins (MRPs) are essential components for the structural and functional integrity of the mitoribosome complex. Throughout evolution, the mammalian mitoribosome has acquired new Mrp genes to compensate for loss of ribosomal RNA. More than 80 MRPs have been identified in mammals. Here we document expression pattern of 79 Mrp genes during mouse development and adult tissues and find that these genes are consistently expressed throughout early embryogenesis with little stage or tissue specificity. Further investigation of the amino acid sequence reveals that this group of proteins has little to no protein similarity. Recent work has shown that the majority of Mrp genes are essential resulting in early embryonic lethality, suggesting no functional redundancy among the group. Taken together, these results indicate that the Mrp genes are not a gene family descended from a single ancestral gene, and that each MRP has unique and essential role in the mitoribosome complex. The lack of functional redundancy is surprising given the importance of the mitoribosome for cellular and organismal viability. Further, these data suggest that genomic variants in Mrp genes may be causative for early pregnancy loss and should be evaluated as clinically.
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23
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Plant Ribonuclease J: An Essential Player in Maintaining Chloroplast RNA Quality Control for Gene Expression. PLANTS 2020; 9:plants9030334. [PMID: 32151111 PMCID: PMC7154860 DOI: 10.3390/plants9030334] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 12/27/2022]
Abstract
RNA quality control is an indispensable but poorly understood process that enables organisms to distinguish functional RNAs from nonfunctional or inhibitory ones. In chloroplasts, whose gene expression activities are required for photosynthesis, retrograde signaling, and plant development, RNA quality control is of paramount importance, as transcription is relatively unregulated. The functional RNA population is distilled from this initial transcriptome by a combination of RNA-binding proteins and ribonucleases. One of the key enzymes is RNase J, a 5′→3′ exoribonuclease and an endoribonuclease that has been shown to trim 5′ RNA termini and eliminate deleterious antisense RNA. In the absence of RNase J, embryo development cannot be completed. Land plant RNase J contains a highly conserved C-terminal domain that is found in GT-1 DNA-binding transcription factors and is not present in its bacterial, archaeal, and algal counterparts. The GT-1 domain may confer specificity through DNA and/or RNA binding and/or protein–protein interactions and thus be an element in the mechanisms that identify target transcripts among diverse RNA populations. Further understanding of chloroplast RNA quality control relies on discovering how RNase J is regulated and how its specificity is imparted.
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24
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Abstract
Nonribosomal peptides are assemblages, including antibiotics, of canonical amino acids and other molecules. β-lactam antibiotics act on bacterial cell walls and can be cleaved by β-lactamases. β-lactamase activity in humans has been neglected, even though eighteen enzymes have already been annotated such in human genome. Their hydrolysis activities on antibiotics have not been previously investigated. Here, we report that human cells were able to digest penicillin and this activity was inhibited by β-lactamase inhibitor, i.e. sulbactam. Penicillin degradation in human cells was microbiologically demonstrated on Pneumococcus. We expressed a MBLAC2 human β-lactamase, known as an exosome biogenesis enzyme. It cleaved penicillin and was inhibited by sulbactam. Finally, β-lactamases are widely distributed, archaic, and have wide spectrum, including digesting anticancer and β-lactams, that can be then used as nutriments. The evidence of the other MBLAC2 role as a bona fide β-lactamase allows for reassessment of β-lactams and β-lactamases role in humans.
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25
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Huang J, Wang G. Improved Mammalian Mitochondrial RNA Isolation. Bio Protoc 2019; 9:e3247. [PMID: 33654773 PMCID: PMC7854245 DOI: 10.21769/bioprotoc.3247] [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: 02/24/2019] [Revised: 04/24/2019] [Accepted: 04/30/2019] [Indexed: 11/02/2022] Open
Abstract
Mitochondria have two sets of RNAs. One is encoded in mitochondrial genome, and the other that consists of imported RNAs within mitochondria and cytosolic RNAs associated with mitochondrial outer membrane is encoded in the nucleus. These mitochondrial RNAs play important roles in mitochondrion biosynthesis and signaling in and out of mitochondria. Isolation and analysis of mitochondrial RNAs can provide useful information on understanding the mitochondrial regulation of cellular processes. However, several ribonuclease activities have been found in mitochondria, which will degrade mitochondrial RNAs during the isolation process if they are not properly inactivated. Here, we describe an improved method to inactivate the ribonuclease activities prior to RNA extraction, and thus provide a reliable protocol to isolate mammalian mitochondrial RNAs for quantitative RT-PCR and other assays.
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Affiliation(s)
- Jinliang Huang
- Ministry of Education Key Laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Geng Wang
- Ministry of Education Key Laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing 100084, China
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26
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Saha S, Sucharita S, Majhi RK, Tiwari A, Ghosh A, Pradhan SK, Patra BK, Dash RR, Nayak RN, Giri SC, Routray P, Kumar A, Kumar G P, Goswami C. TRPA1 is selected as a semi-conserved channel during vertebrate evolution due to its involvement in spermatogenesis. Biochem Biophys Res Commun 2019; 512:295-302. [PMID: 30885439 DOI: 10.1016/j.bbrc.2019.02.121] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 02/22/2019] [Indexed: 11/17/2022]
Abstract
TRPA1 is a non-selective cation channel originated in invertebrates. The genomic locus containing TRPA1 gene remains highly conserved and retained in all vertebrates. TRPA1 gene is evolutionarily selected, yet maintained as a highly diverged protein. Throughout the vertebrate evolution, the extracellular loops of TRPA1 become most diverged indicating that TRPA1 may be involved in detecting large spectrum and uncertain stimulus which is critical for adaptive benefit. We tested the expression of TRPA1 in mature sperm from different vertebrates. This is the first report demonstrating that TRPA1 is expressed endogenously in mature spermatozoa of multiple species representing entire vertebrate phyla. However, its specific localization within sperm remains species-specific. Accordingly, we report that in rodents TRPA1 expression correlates with different stages of spermatogenesis. We propose that presence of endogenous TRPA1 in testes and in mature sperm provides reproductive benefit.
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Affiliation(s)
- Somdatta Saha
- School of Biological Sciences, National Institute of Science Education and Research, Khordha, Jatni, Odisha, 752050, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Samikshya Sucharita
- School of Biological Sciences, National Institute of Science Education and Research, Khordha, Jatni, Odisha, 752050, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Rakesh Kumar Majhi
- School of Biological Sciences, National Institute of Science Education and Research, Khordha, Jatni, Odisha, 752050, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Ankit Tiwari
- School of Biological Sciences, National Institute of Science Education and Research, Khordha, Jatni, Odisha, 752050, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Arijit Ghosh
- School of Biological Sciences, National Institute of Science Education and Research, Khordha, Jatni, Odisha, 752050, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Sunil Kumar Pradhan
- Frozen Semen Bank, Animal Husbandry and Veterinary Services -Odisha, Khapuria, Cuttack, 753010, Odisha, India
| | - Bijay Kumar Patra
- Frozen Semen Bank, Animal Husbandry and Veterinary Services -Odisha, Khapuria, Cuttack, 753010, Odisha, India
| | - Rashmi Ranjan Dash
- Frozen Semen Bank, Animal Husbandry and Veterinary Services -Odisha, Khapuria, Cuttack, 753010, Odisha, India
| | - Rabi Narayan Nayak
- Frozen Semen Bank, Animal Husbandry and Veterinary Services -Odisha, Khapuria, Cuttack, 753010, Odisha, India
| | - Sunil C Giri
- Central Avian Research Institute, Bhubaneswar, 751003, India
| | - Padmanav Routray
- Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751002, India
| | - Abhishek Kumar
- Department of Genetics & Molecular Biology in Botany, Institute of Botany, Christian-Albrechts-University at Kiel, 24118, Germany
| | - Pradeep Kumar G
- Rajiv Gandhi Centre for Biotechnology, Thycaud, Poojappura, Trivandrum, Kerala 695014, India
| | - Chandan Goswami
- School of Biological Sciences, National Institute of Science Education and Research, Khordha, Jatni, Odisha, 752050, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India.
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27
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Halpert M, Liveanu V, Glaser F, Schuster G. The Arabidopsis chloroplast RNase J displays both exo- and robust endonucleolytic activities. PLANT MOLECULAR BIOLOGY 2019; 99:17-29. [PMID: 30511330 DOI: 10.1007/s11103-018-0799-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 11/22/2018] [Indexed: 05/17/2023]
Abstract
Arabidopsis chloroplast RNase J displaces both exo- and endo-ribonucleolytic activities and contains a unique GT-1 DNA binding domain. Control of chloroplast gene expression is predominantly at the post-transcriptional level via the coordinated action of nuclear encoded ribonucleases and RNA-binding proteins. The 5' end maturation of mRNAs ascribed to the combined action of 5'→3' exoribonuclease and gene-specific RNA-binding proteins of the pentatricopeptide repeat family and others that impede the progression of this nuclease. The exo- and endoribonuclease RNase J, the only prokaryotic 5'→3' ribonuclease that is commonly present in bacteria, Archaea, as well as in the chloroplasts of higher plants and green algae, has been implicated in this process. Interestingly, in addition to the metalo-β-lactamase and β-CASP domains, RNase J of plants contains a conserved GT-1 domain that was previously characterized in transcription factors that function in light and stress responding genes. Here, we show that the Arabidopsis RNase J (AtRNase J), when analyzed in vitro with synthetic RNAs, displays both 5'→3' exonucleolytic activity, as well as robust endonucleolytic activity as compared to its bacterial homolog RNase J1 of Bacillus subtilis. AtRNase J degraded single-stranded RNA and DNA molecules but displays limited activity on double stranded RNA. The addition of three guanosines at the 5' end of the substrate significantly inhibited the degradation activity, indicating that the sequence and structure of the RNA substrate modulate the ribonucleolytic activity. Mutation of three amino acid in the catalytic reaction center significantly inhibited both the endonucleolytic and exonucleolytic degradation activities, while deletion of the carboxyl GT-1 domain that is unique to the plant RNAse J proteins, had a little or no significant effect. The robust endonucleolytic activity of AtRNase J suggests its involvement in the processing and degradation of RNA in the chloroplast.
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Affiliation(s)
- Michal Halpert
- Faculty of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Varda Liveanu
- Faculty of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Fabian Glaser
- Faculty of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel
- Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Gadi Schuster
- Faculty of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel.
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28
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Pettinati I, Grzechnik P, Ribeiro de Almeida C, Brem J, McDonough MA, Dhir S, Proudfoot NJ, Schofield CJ. Biosynthesis of histone messenger RNA employs a specific 3' end endonuclease. eLife 2018; 7:39865. [PMID: 30507380 PMCID: PMC6303110 DOI: 10.7554/elife.39865] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 11/30/2018] [Indexed: 12/12/2022] Open
Abstract
Replication-dependent (RD) core histone mRNA produced during S-phase is the only known metazoan protein-coding mRNA presenting a 3' stem-loop instead of the otherwise universal polyA tail. A metallo β-lactamase (MBL) fold enzyme, cleavage and polyadenylation specificity factor 73 (CPSF73), is proposed to be the sole endonuclease responsible for 3' end processing of both mRNA classes. We report cellular, genetic, biochemical, substrate selectivity, and crystallographic studies providing evidence that an additional endoribonuclease, MBL domain containing protein 1 (MBLAC1), is selective for 3' processing of RD histone pre-mRNA during the S-phase of the cell cycle. Depletion of MBLAC1 in cells significantly affects cell cycle progression thus identifying MBLAC1 as a new type of S-phase-specific cancer target.
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Affiliation(s)
- Ilaria Pettinati
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Pawel Grzechnik
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | | | - Jurgen Brem
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | | | - Somdutta Dhir
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Nick J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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29
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Huang J, Liu P, Wang G. Regulation of mitochondrion-associated cytosolic ribosomes by mammalian mitochondrial ribonuclease T2 (RNASET2). J Biol Chem 2018; 293:19633-19644. [PMID: 30385512 PMCID: PMC6314140 DOI: 10.1074/jbc.ra118.005433] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/15/2018] [Indexed: 11/12/2022] Open
Abstract
Mitochondrial proteins are encoded in both mitochondrial and nuclear genomes. The expression levels of these two pools of mitochondrial genes are co-regulated and synchronized. Import and assembly of the nucleus-encoded oxidative phosphorylation (OXPHOS) subunits affect protein synthesis in the mitochondrial matrix by engaging the mitochondrial ribosomes. How the ribosomes at the outside of mitochondria are regulated by mitochondria, however, remains mostly unexplored. Here, using an array of biochemical assays and genetic knockdown and overexpression in HEK293 or mouse cells, we show that cytosolic rRNAs that are associated with the mitochondrial outer membrane have very different decay patterns from those of both endoplasmic reticulum–associated and –nonassociated cytosolic rRNAs. Mitochondrial intermembrane space RNase T2 (RNASET2), which has been previously shown to degrade mitochondrial RNAs, is also responsible for selective degradation of the cytosolic rRNAs on the outer membrane. We noted that the degradation activity also has a positive effect on nuclear transcription of rRNAs, suggesting a compensatory feedback mechanism, and affects protein translations in and out of mitochondria. These findings establish a mechanism for the co-regulation of gene expression programs inside and outside of mitochondria in mammalian cells.
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Affiliation(s)
- Jinliang Huang
- From the Ministry of Education Key Laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Peipei Liu
- From the Ministry of Education Key Laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Geng Wang
- From the Ministry of Education Key Laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing 100084, China
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30
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Pietras Z, Wojcik MA, Borowski LS, Szewczyk M, Kulinski TM, Cysewski D, Stepien PP, Dziembowski A, Szczesny RJ. Dedicated surveillance mechanism controls G-quadruplex forming non-coding RNAs in human mitochondria. Nat Commun 2018; 9:2558. [PMID: 29967381 PMCID: PMC6028389 DOI: 10.1038/s41467-018-05007-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 06/08/2018] [Indexed: 12/13/2022] Open
Abstract
The GC skew in vertebrate mitochondrial genomes results in synthesis of RNAs that are prone to form G-quadruplexes (G4s). Such RNAs, although mostly non-coding, are transcribed at high rates and are degraded by an unknown mechanism. Here we describe a dedicated mechanism of degradation of G4-containing RNAs, which is based on cooperation between mitochondrial degradosome and quasi-RNA recognition motif (qRRM) protein GRSF1. This cooperation prevents accumulation of G4-containing transcripts in human mitochondria. In vitro reconstitution experiments show that GRSF1 promotes G4 melting that facilitates degradosome-mediated decay. Among degradosome and GRSF1 regulated transcripts we identified one that undergoes post-transcriptional modification. We show that GRSF1 proteins form a distinct qRRM group found only in vertebrates. The appearance of GRSF1 coincided with changes in the mitochondrial genome, which allows the emergence of G4-containing RNAs. We propose that GRSF1 appearance is an evolutionary adaptation enabling control of G4 RNA.
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Affiliation(s)
- Zbigniew Pietras
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Laboratory of RNA Biology and Functional Genomics, Pawinskiego 5A, 02-106, Warsaw, Poland.,International Institute of Molecular and Cell Biology, Laboratory of Protein Structure, Ks. Trojdena 4, 02-109, Warsaw, Poland
| | - Magdalena A Wojcik
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Laboratory of RNA Biology and Functional Genomics, Pawinskiego 5A, 02-106, Warsaw, Poland.,Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Pawinskiego 5A, 02-106, Warsaw, Poland
| | - Lukasz S Borowski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Laboratory of RNA Biology and Functional Genomics, Pawinskiego 5A, 02-106, Warsaw, Poland.,Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Pawinskiego 5A, 02-106, Warsaw, Poland
| | - Maciej Szewczyk
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Laboratory of RNA Biology and Functional Genomics, Pawinskiego 5A, 02-106, Warsaw, Poland.,Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Pawinskiego 5A, 02-106, Warsaw, Poland
| | - Tomasz M Kulinski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Laboratory of RNA Biology and Functional Genomics, Pawinskiego 5A, 02-106, Warsaw, Poland
| | - Dominik Cysewski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Laboratory of RNA Biology and Functional Genomics, Pawinskiego 5A, 02-106, Warsaw, Poland
| | - Piotr P Stepien
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Laboratory of RNA Biology and Functional Genomics, Pawinskiego 5A, 02-106, Warsaw, Poland.,Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Pawinskiego 5A, 02-106, Warsaw, Poland
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Laboratory of RNA Biology and Functional Genomics, Pawinskiego 5A, 02-106, Warsaw, Poland. .,Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Pawinskiego 5A, 02-106, Warsaw, Poland.
| | - Roman J Szczesny
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Laboratory of RNA Biology and Functional Genomics, Pawinskiego 5A, 02-106, Warsaw, Poland. .,Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Pawinskiego 5A, 02-106, Warsaw, Poland.
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31
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Levin M, Stark M, Assaraf YG. The JmjN domain as a dimerization interface and a targeted inhibitor of KDM4 demethylase activity. Oncotarget 2018; 9:16861-16882. [PMID: 29682190 PMCID: PMC5908291 DOI: 10.18632/oncotarget.24717] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 02/25/2018] [Indexed: 12/14/2022] Open
Abstract
Histone methylation is regulated to shape the epigenome by modulating DNA compaction, thus playing central roles in fundamental chromatin-based processes including transcriptional regulation, DNA repair and cell proliferation. Histone methylation is erased by demethylases including the well-established KDM4 subfamily members, however, little is known about their dimerization capacity and its impact on their demethylase activity. Using the powerful bimolecular fluorescence complementation technique, we herein show the in situ formation of human KDM4A and KDM4C homodimers and heterodimers in nuclei of live transfectant cells and evaluate their H3K9me3 demethylation activity. Using size exclusion HPLC as well as Western blot analysis, we show that endogenous KDM4C undergoes dimerization under physiological conditions. Importantly, we identify the JmjN domain as the KDM4C dimerization interface and pin-point specific charged residues therein to be essential for this dimerization. We further demonstrate that KDM4A/C dimerization is absolutely required for their demethylase activity which was abolished by the expression of free JmjN peptides. In contrast, KDM4B does not dimerize and functions as a monomer, and hence was not affected by free JmjN expression. KDM4 proteins are overexpressed in numerous malignancies and their pharmacological inhibition or depletion in cancer cells was shown to impair tumor cell proliferation, invasion and metastasis. Thus, the KDM4 dimer-interactome emerging from the present study bears potential implications for cancer therapeutics via selective inhibition of KDM4A/C demethylase activity using JmjN-based peptidomimetics.
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Affiliation(s)
- May Levin
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Michal Stark
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Yehuda G Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
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Liu P, Huang J, Zheng Q, Xie L, Lu X, Jin J, Wang G. Mammalian mitochondrial RNAs are degraded in the mitochondrial intermembrane space by RNASET2. Protein Cell 2017; 8:735-749. [PMID: 28730546 PMCID: PMC5636749 DOI: 10.1007/s13238-017-0448-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 07/06/2017] [Indexed: 10/28/2022] Open
Abstract
Mammalian mitochondrial genome encodes a small set of tRNAs, rRNAs, and mRNAs. The RNA synthesis process has been well characterized. How the RNAs are degraded, however, is poorly understood. It was long assumed that the degradation happens in the matrix where transcription and translation machineries reside. Here we show that contrary to the assumption, mammalian mitochondrial RNA degradation occurs in the mitochondrial intermembrane space (IMS) and the IMS-localized RNASET2 is the enzyme that degrades the RNAs. This provides a new paradigm for understanding mitochondrial RNA metabolism and transport.
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Affiliation(s)
- Peipei Liu
- MOE Key laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jinliang Huang
- MOE Key laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qian Zheng
- MOE Key laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Leiming Xie
- MOE Key laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xinping Lu
- MOE Key laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jie Jin
- MOE Key laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Geng Wang
- MOE Key laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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Polyadenylation and degradation of RNA in the mitochondria. Biochem Soc Trans 2017; 44:1475-1482. [PMID: 27911729 DOI: 10.1042/bst20160126] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 06/24/2016] [Accepted: 06/28/2016] [Indexed: 12/20/2022]
Abstract
Mitochondria have their own gene expression machinery and the relative abundance of RNA products in these organelles in animals is mostly dictated by their rate of degradation. The molecular mechanisms regulating the differential accumulation of the transcripts in this organelle remain largely elusive. Here, we summarize the present knowledge of how RNA is degraded in human mitochondria and describe the coexistence of stable poly(A) tails and the nonabundant tails, which have been suggested to play a role in the RNA degradation process.
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Bruni F, Lightowlers RN, Chrzanowska-Lightowlers ZM. Human mitochondrial nucleases. FEBS J 2017; 284:1767-1777. [PMID: 27926991 PMCID: PMC5484287 DOI: 10.1111/febs.13981] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 11/22/2016] [Accepted: 11/30/2016] [Indexed: 12/26/2022]
Abstract
Mitochondria are cytosolic organelles that have many essential roles including ATP production via oxidative phosphorylation, apoptosis, iron‐sulfur cluster biogenesis, heme and steroid synthesis, calcium homeostasis, and regulation of cellular redox state. One of the unique features of these organelles is the presence of an extrachromosomal mitochondrial genome (mtDNA), together with all the machinery required to replicate and transcribe mtDNA. The accurate maintenance of mitochondrial gene expression is essential for correct organellar metabolism, and is in part dependent on the levels of mtDNA and mtRNA, which are regulated by balancing synthesis against degradation. It is clear that although a number of mitochondrial nucleases have been identified, not all those responsible for the degradation of DNA or RNA have been characterized. Recent investigations, however, have revealed the contribution that mutations in the genes coding for these enzymes has made to causing pathogenic mitochondrial diseases.
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Affiliation(s)
- Francesco Bruni
- The Wellcome Trust Centre for Mitochondrial Research, The Medical School, Newcastle University, UK
| | - Robert N Lightowlers
- The Wellcome Trust Centre for Mitochondrial Research, The Medical School, Newcastle University, UK
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Hierarchical RNA Processing Is Required for Mitochondrial Ribosome Assembly. Cell Rep 2016; 16:1874-90. [PMID: 27498866 DOI: 10.1016/j.celrep.2016.07.031] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 06/20/2016] [Accepted: 07/13/2016] [Indexed: 11/24/2022] Open
Abstract
The regulation of mitochondrial RNA processing and its importance for ribosome biogenesis and energy metabolism are not clear. We generated conditional knockout mice of the endoribonuclease component of the RNase P complex, MRPP3, and report that it is essential for life and that heart and skeletal-muscle-specific knockout leads to severe cardiomyopathy, indicating that its activity is non-redundant. Transcriptome-wide parallel analyses of RNA ends (PARE) and RNA-seq enabled us to identify that in vivo 5' tRNA cleavage precedes 3' tRNA processing, and this is required for the correct biogenesis of the mitochondrial ribosomal subunits. We identify that mitoribosomal biogenesis proceeds co-transcriptionally because large mitoribosomal proteins can form a subcomplex on an unprocessed RNA containing the 16S rRNA. Taken together, our data show that RNA processing links transcription to translation via assembly of the mitoribosome.
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Abstract
Oxidative phosphorylation (OXPHOS) is the mechanism whereby ATP, the major energy source for the cell, is produced by harnessing cellular respiration in the mitochondrion. This is facilitated by five multi-subunit complexes housed within the inner mitochondrial membrane. These complexes, with the exception of complex II, are of a dual genetic origin, requiring expression from nuclear and mitochondrial genes. Mitochondrially encoded mRNA is translated on the mitochondrial ribosome (mitoribosome) and the recent release of the near atomic resolution structure of the mammalian mitoribosome has highlighted its peculiar features. However, whereas some aspects of mitochondrial translation are understood, much is to be learnt about the presentation of mitochondrial mRNA to the mitoribosome, the biogenesis of the machinery, the exact role of the membrane, the constitution of the translocon/insertion machinery and the regulation of translation in the mitochondrion. This review addresses our current knowledge of mammalian mitochondrial gene expression, highlights key questions and indicates how defects in this process can result in profound mitochondrial disease.
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