1
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Lin XN, Gai BX, Liu L, Cheng L. Advances in the investigation of N 6-isopentenyl adenosine i 6A RNA modification. Bioorg Med Chem 2024; 110:117838. [PMID: 39018794 DOI: 10.1016/j.bmc.2024.117838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 07/09/2024] [Accepted: 07/09/2024] [Indexed: 07/19/2024]
Abstract
Prenylation (isopentenylation), a key post-transcriptional modification with a hydrophobic prenyl group onto the biomacromolecules such as RNA and proteins, influences their localization and function. Prenyltransferases mediate this process, while cytokinin oxidases degrade the prenylated adenosine in plants. This review summarizes current progress in detecting prenylation modifications in RNA across species and their effects on protein synthesis. Advanced methods have been developed to label and study these modifications in vitro and in vivo, despite challenges posed by the inert chemical properties of prenyl groups. Continued advancements in bioorthogonal chemistry promise new tools for understanding the precise biological functions of prenylated RNA modifications and other related proteins.
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Affiliation(s)
- Xiu-Na Lin
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bo-Xu Gai
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liang Cheng
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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2
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Boughanem H, Böttcher Y, Tomé-Carneiro J, López de Las Hazas MC, Dávalos A, Cayir A, Macias-González M. The emergent role of mitochondrial RNA modifications in metabolic alterations. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1753. [PMID: 35872632 DOI: 10.1002/wrna.1753] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/14/2022] [Accepted: 06/27/2022] [Indexed: 11/11/2022]
Abstract
Mitochondrial epitranscriptomics refers to the modifications occurring in all the different RNA types of mitochondria. Although the number of mitochondrial RNA modifications is less than those in cytoplasm, substantial evidence indicates that they play a critical role in accurate protein synthesis. Recent evidence supported those modifications in mitochondrial RNAs also have crucial implications in mitochondrial-related diseases. In the light of current knowledge about the involvement, the association between mitochondrial RNA modifications and diseases arises from studies focusing on mutations in both mitochondrial and nuclear DNA genes encoding enzymes involved in such modifications. Here, we review the current evidence available for mitochondrial RNA modifications and their role in metabolic disorders, and we also explore the possibility of using them as promising targets for prevention and early detection. Finally, we discuss future directions of mitochondrial epitranscriptomics in these metabolic alterations, and how these RNA modifications may offer a new diagnostic and theragnostic avenue for preventive purposes. This article is categorized under: RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Hatim Boughanem
- Instituto de Investigación Biomédica de Málaga (IBIMA), Unidad de Gestión Clínica de Endocrinología y Nutrición del Hospital Virgen de la Victoria and University of Málaga, Spain.,Instituto de Salud Carlos III (ISCIII), Consorcio CIBER, M.P. Fisiopatología de la Obesidad y Nutrición (CIBERObn), Madrid, Spain
| | - Yvonne Böttcher
- Institute of Clinical Medicine, Department of Clinical Molecular Biology, University of Oslo, Oslo, Norway.,Akershus Universitetssykehus, Medical Department, Lørenskog, Norway
| | - João Tomé-Carneiro
- Laboratory of Functional Foods, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM + CSIC, Madrid, Spain
| | - María-Carmen López de Las Hazas
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM + CSIC, Madrid, Spain
| | - Alberto Dávalos
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM + CSIC, Madrid, Spain
| | - Akin Cayir
- Vocational Health College, Canakkale Onsekiz Mart University, Canakkale, Turkey.,Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus Universitetssykehus, Lørenskog, Norway
| | - Manuel Macias-González
- Instituto de Investigación Biomédica de Málaga (IBIMA), Unidad de Gestión Clínica de Endocrinología y Nutrición del Hospital Virgen de la Victoria and University of Málaga, Spain.,Instituto de Salud Carlos III (ISCIII), Consorcio CIBER, M.P. Fisiopatología de la Obesidad y Nutrición (CIBERObn), Madrid, Spain
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3
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Richter F, Plehn JE, Bessler L, Hertler J, Jörg M, Cirzi C, Tuorto F, Friedland K, Helm M. RNA marker modifications reveal the necessity for rigorous preparation protocols to avoid artifacts in epitranscriptomic analysis. Nucleic Acids Res 2022; 50:4201-4215. [PMID: 34850949 PMCID: PMC9071408 DOI: 10.1093/nar/gkab1150] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/31/2021] [Accepted: 11/03/2021] [Indexed: 12/16/2022] Open
Abstract
The accurate definition of an epitranscriptome is endangered by artefacts resulting from RNA degradation after cell death, a ubiquitous yet little investigated process. By tracing RNA marker modifications through tissue preparation protocols, we identified a major blind spot from daily lab routine, that has massive impact on modification analysis in small RNAs. In particular, m6,6A and Am as co-varying rRNA marker modifications, appeared in small RNA fractions following rRNA degradation in vitro and in cellulo. Analysing mouse tissue at different time points post mortem, we tracked the progress of intracellular RNA degradation after cell death, and found it reflected in RNA modification patterns. Differences were dramatic between liver, where RNA degradation commenced immediately after death, and brain, yielding essentially undamaged RNA. RNA integrity correlated with low amounts of co-varying rRNA markers. Thus validated RNA preparations featured differentially modified tRNA populations whose information content allowed a distinction even among the related brain tissues cortex, cerebellum and hippocampus. Inversely, advanced cell death correlated with high rRNA marker content, and correspondingly little with the naïve state of living tissue. Therefore, unless RNA and tissue preparations are executed with utmost care, interpretation of modification patterns in tRNA and small RNA are prone to artefacts.
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Affiliation(s)
- Florian Richter
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5 55128 Mainz, Germany
| | - Johanna E Plehn
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5 55128 Mainz, Germany
| | - Larissa Bessler
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5 55128 Mainz, Germany
| | - Jasmin Hertler
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5 55128 Mainz, Germany
| | - Marko Jörg
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5 55128 Mainz, Germany
| | - Cansu Cirzi
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ) 69120 Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg 69120 Heidelberg, Germany
| | - Francesca Tuorto
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance69120 Heidelberg, Germany
| | - Kristina Friedland
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5 55128 Mainz, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5 55128 Mainz, Germany
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4
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Zhou JB, Wang ED, Zhou XL. Modifications of the human tRNA anticodon loop and their associations with genetic diseases. Cell Mol Life Sci 2021; 78:7087-7105. [PMID: 34605973 PMCID: PMC11071707 DOI: 10.1007/s00018-021-03948-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/07/2021] [Accepted: 09/21/2021] [Indexed: 12/11/2022]
Abstract
Transfer RNAs (tRNAs) harbor the most diverse posttranscriptional modifications. Among such modifications, those in the anticodon loop, either on nucleosides or base groups, compose over half of the identified posttranscriptional modifications. The derivatives of modified nucleotides and the crosstalk of different chemical modifications further add to the structural and functional complexity of tRNAs. These modifications play critical roles in maintaining anticodon loop conformation, wobble base pairing, efficient aminoacylation, and translation speed and fidelity as well as mediating various responses to different stress conditions. Posttranscriptional modifications of tRNA are catalyzed mainly by enzymes and/or cofactors encoded by nuclear genes, whose mutations are firmly connected with diverse human diseases involving genetic nervous system disorders and/or the onset of multisystem failure. In this review, we summarize recent studies about the mechanisms of tRNA modifications occurring at tRNA anticodon loops. In addition, the pathogenesis of related disease-causing mutations at these genes is briefly described.
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Affiliation(s)
- Jing-Bo Zhou
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - En-Duo Wang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China.
- School of Life Science and Technology, ShanghaiTech University, 93 Middle Huaxia Road, Shanghai, 201210, China.
| | - Xiao-Long Zhou
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China.
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5
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Coll-SanMartin L, Davalos V, Piñeyro D, Rosselló-Tortella M, Bueno-Costa A, Setien F, Villanueva A, Granada I, Ruiz-Xiviller N, Kotter A, Helm M, Yokota J, Kawabata-Iwakawa R, Kohno T, Esteller M. Gene Amplification-Associated Overexpression of the Selenoprotein tRNA Enzyme TRIT1 Confers Sensitivity to Arsenic Trioxide in Small-Cell Lung Cancer. Cancers (Basel) 2021; 13:1869. [PMID: 33919717 PMCID: PMC8070726 DOI: 10.3390/cancers13081869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/06/2021] [Accepted: 04/12/2021] [Indexed: 12/16/2022] Open
Abstract
The alteration of RNA modification patterns is emerging as a common feature of human malignancies. If these changes affect key RNA molecules for mRNA translation, such as transfer RNA, they can have important consequences for cell transformation. TRIT1 is the enzyme responsible for the hypermodification of adenosine 37 in the anticodon region of human tRNAs containing serine and selenocysteine. Herein, we show that TRIT1 undergoes gene amplification-associated overexpression in cancer cell lines and primary samples of small-cell lung cancer. From growth and functional standpoints, the induced depletion of TRIT1 expression in amplified cells reduces their tumorigenic potential and downregulates the selenoprotein transcripts. We observed that TRIT1-amplified cells are sensitive to arsenic trioxide, a compound that regulates selenoproteins, whereas reduction of TRIT1 levels confers loss of sensitivity to the drug. Overall, our results indicate a role for TRIT1 as a small-cell lung cancer-relevant gene that, when undergoing gene amplification-associated activation, can be targeted with the differentiation agent arsenic trioxide.
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Affiliation(s)
- Laia Coll-SanMartin
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Barcelona, Spain; (L.C.-S.); (V.D.); (D.P.); (M.R.-T.); (A.B.-C.); (F.S.); (I.G.); (N.R.-X.)
| | - Veronica Davalos
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Barcelona, Spain; (L.C.-S.); (V.D.); (D.P.); (M.R.-T.); (A.B.-C.); (F.S.); (I.G.); (N.R.-X.)
| | - David Piñeyro
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Barcelona, Spain; (L.C.-S.); (V.D.); (D.P.); (M.R.-T.); (A.B.-C.); (F.S.); (I.G.); (N.R.-X.)
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Margalida Rosselló-Tortella
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Barcelona, Spain; (L.C.-S.); (V.D.); (D.P.); (M.R.-T.); (A.B.-C.); (F.S.); (I.G.); (N.R.-X.)
- Germans Trias i Pujol Health Science Research Institute (IGTP), 08916 Barcelona, Spain
| | - Alberto Bueno-Costa
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Barcelona, Spain; (L.C.-S.); (V.D.); (D.P.); (M.R.-T.); (A.B.-C.); (F.S.); (I.G.); (N.R.-X.)
| | - Fernando Setien
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Barcelona, Spain; (L.C.-S.); (V.D.); (D.P.); (M.R.-T.); (A.B.-C.); (F.S.); (I.G.); (N.R.-X.)
| | - Alberto Villanueva
- Group of Chemoresistance and Predictive Factors, Subprogram Against Cancer Therapeutic Resistance (ProCURE), Oncobell Program, IDIBELL, Institut Català d’Oncologia (ICO), L’Hospitalet del Llobregat, 08908 Barcelona, Spain;
| | - Isabel Granada
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Barcelona, Spain; (L.C.-S.); (V.D.); (D.P.); (M.R.-T.); (A.B.-C.); (F.S.); (I.G.); (N.R.-X.)
- Cytogenetics Platform, Hematology Laboratory Service, Institut Català d’Oncologia (ICO)-Hospital Germans Trias i Pujol (IGTP), 08916 Barcelona, Spain
| | - Neus Ruiz-Xiviller
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Barcelona, Spain; (L.C.-S.); (V.D.); (D.P.); (M.R.-T.); (A.B.-C.); (F.S.); (I.G.); (N.R.-X.)
- Cytogenetics Platform, Hematology Laboratory Service, Institut Català d’Oncologia (ICO)-Hospital Germans Trias i Pujol (IGTP), 08916 Barcelona, Spain
| | - Annika Kotter
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität Mainz, 55128 Mainz, Germany; (A.K.); (M.H.)
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität Mainz, 55128 Mainz, Germany; (A.K.); (M.H.)
| | - Jun Yokota
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; (J.Y.); (R.K.-I.); (T.K.)
| | - Reika Kawabata-Iwakawa
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; (J.Y.); (R.K.-I.); (T.K.)
- Division of Integrated Oncology Research, Gunma University Initiative for Advanced Research, Gunma 371-8511, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; (J.Y.); (R.K.-I.); (T.K.)
- Division of Translational Genomics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Tokyo 104-0045, Japan
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Barcelona, Spain; (L.C.-S.); (V.D.); (D.P.); (M.R.-T.); (A.B.-C.); (F.S.); (I.G.); (N.R.-X.)
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), 08036 Barcelona, Spain
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6
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RNA methylations in human cancers. Semin Cancer Biol 2020; 75:97-115. [DOI: 10.1016/j.semcancer.2020.11.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/23/2020] [Accepted: 11/08/2020] [Indexed: 12/24/2022]
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7
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Adami R, Bottai D. S-adenosylmethionine tRNA modification: unexpected/unsuspected implications of former/new players. Int J Biol Sci 2020; 16:3018-3027. [PMID: 33061813 PMCID: PMC7545696 DOI: 10.7150/ijbs.49302] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/10/2020] [Indexed: 12/13/2022] Open
Abstract
S-adenosylmethionine supplies methyl groups to many acceptors, including lipids, proteins, RNA, DNA, and a wide range of small molecules. It acts as the precursor in the biosynthesis of metal ion chelating compounds, such as nicotianamine and phytosiderophores, of the polyamines spermidine and spermine and of some plant hormones. Finally, it is the source of catalytic 5′-deoxyadenosyl radicals. Radical S-adenosylmethionine (SAM) enzymes (RS) represent one of the most abundant groups (more than 100,000) of enzymes, exerting a plethora of biological functions, some of which are still unknown. In this work, we will focus on two RS: CDK5RAP1 and CDKAL1, both of which are involved in tRNA modifications that result in important tRNA folding and stability and in maintaining high translational fidelity. Based on this crucial role, their impairment can be important in the development of different human diseases.
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Affiliation(s)
- Raffaella Adami
- Department of Health Science University of Milan via A. di Rudinì 8 20142 Milan
| | - Daniele Bottai
- Department of Health Science University of Milan via A. di Rudinì 8 20142 Milan
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8
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Liaqat A, Stiller C, Michel M, Sednev MV, Höbartner C. N6‐Isopentenyladenosine in RNA Determines the Cleavage Site of Endonuclease Deoxyribozymes. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006218] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Anam Liaqat
- Institute of Organic Chemistry University of Würzburg Am Hubland 97074 Würzburg Germany
| | - Carina Stiller
- Institute of Organic Chemistry University of Würzburg Am Hubland 97074 Würzburg Germany
| | - Manuela Michel
- Institute of Organic Chemistry University of Würzburg Am Hubland 97074 Würzburg Germany
| | - Maksim V. Sednev
- Institute of Organic Chemistry University of Würzburg Am Hubland 97074 Würzburg Germany
| | - Claudia Höbartner
- Institute of Organic Chemistry University of Würzburg Am Hubland 97074 Würzburg Germany
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9
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Liaqat A, Stiller C, Michel M, Sednev MV, Höbartner C. N 6 -Isopentenyladenosine in RNA Determines the Cleavage Site of Endonuclease Deoxyribozymes. Angew Chem Int Ed Engl 2020; 59:18627-18631. [PMID: 32681686 PMCID: PMC7589339 DOI: 10.1002/anie.202006218] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/29/2020] [Indexed: 12/15/2022]
Abstract
RNA‐cleaving deoxyribozymes can serve as selective sensors and catalysts to examine the modification state of RNA. However, site‐specific endonuclease deoxyribozymes that selectively cleave post‐transcriptionally modified RNA are extremely rare and their specificity over unmodified RNA is low. We report that the native tRNA modification N6‐isopentenyladenosine (i6A) strongly enhances the specificity and has the power to reconfigure the active site of an RNA‐cleaving deoxyribozyme. Using in vitro selection, we identified a DNA enzyme that cleaves i6A‐modified RNA at least 2500‐fold faster than unmodified RNA. Another deoxyribozyme shows unique and unprecedented behaviour by shifting its cleavage site in the presence of the i6A RNA modification. Together with deoxyribozymes that are strongly inhibited by i6A, these results highlight that post‐transcriptional RNA modifications modulate the catalytic activity of DNA in various intricate ways.
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Affiliation(s)
- Anam Liaqat
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Carina Stiller
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Manuela Michel
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Maksim V Sednev
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Claudia Höbartner
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
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10
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Dabravolski S. Multi-faceted nature of the tRNA isopentenyltransferase. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 47:475-485. [PMID: 32345433 DOI: 10.1071/fp19255] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/26/2019] [Indexed: 06/11/2023]
Abstract
Transfer RNA isopentenylation an adenine 37 position (A37) is a universal modification known in prokaryotes and eukaryotes. A set of highly homologous enzymes catalyse a series of reactions, leading to tRNA modifications, aimed to increase adaptation to environmental condition through the control of translation efficiency and reading frame maintenance. Transfer RNA-isopentenylation-related (TI-related) functions are well studied in bacteria, mitochondria of yeast and human, but completely unexplored in plants. Transfer RNA-isopentenylation-unrelated (TI-unrelated) functions participate in adaptation to environmental stresses via the regulation of sterol metabolism, gene silencing/suppression and amyloid fibrils formation. TI-unrelated functions are mostly studied in yeast. Finally, the degradation of A37-modified tRNA releases a set of bioactive compounds known as cis-cytokinins. Although all organisms are able to produce cis-cytokinins, its physiological role is still a matter of debates. For several species of bacteria and fungi, cis-cytokinins are known to play a crucial role in pathogenesis. In mammalian and human models cis-cytokinins have tumour-suppressing and anti-inflammation effects. This review aims to summarise current knowledge of the TI-related and TI-unrelated functions and main bioactive by-products of isopentenylated tRNA degradation.
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Affiliation(s)
- Siarhei Dabravolski
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelu 27, 78371 Olomouc, Czech Republic.
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11
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Leonardi A, Evke S, Lee M, Melendez JA, Begley TJ. Epitranscriptomic systems regulate the translation of reactive oxygen species detoxifying and disease linked selenoproteins. Free Radic Biol Med 2019; 143:573-593. [PMID: 31476365 PMCID: PMC7650020 DOI: 10.1016/j.freeradbiomed.2019.08.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 02/07/2023]
Abstract
Here we highlight the role of epitranscriptomic systems in post-transcriptional regulation, with a specific focus on RNA modifying writers required for the incorporation of the 21st amino acid selenocysteine during translation, and the pathologies linked to epitranscriptomic and selenoprotein defects. Epitranscriptomic marks in the form of enzyme-catalyzed modifications to RNA have been shown to be important signals regulating translation, with defects linked to altered development, intellectual impairment, and cancer. Modifications to rRNA, mRNA and tRNA can affect their structure and function, while the levels of these dynamic tRNA-specific epitranscriptomic marks are stress-regulated to control translation. The tRNA for selenocysteine contains five distinct epitranscriptomic marks and the ALKBH8 writer for the wobble uridine (U) has been shown to be vital for the translation of the glutathione peroxidase (GPX) and thioredoxin reductase (TRXR) family of selenoproteins. The reactive oxygen species (ROS) detoxifying selenocysteine containing proteins are a prime examples of how specialized translation can be regulated by specific tRNA modifications working in conjunction with distinct codon usage patterns, RNA binding proteins and specific 3' untranslated region (UTR) signals. We highlight the important role of selenoproteins in detoxifying ROS and provide details on how epitranscriptomic marks and selenoproteins can play key roles in and maintaining mitochondrial function and preventing disease.
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Affiliation(s)
- Andrea Leonardi
- Colleges of Nanoscale Science and Engineering, University at Albany, State University of New York, Albany, NY, USA
| | - Sara Evke
- Colleges of Nanoscale Science and Engineering, State University of New York Polytechnic Institute, Albany, NY, USA
| | - May Lee
- Colleges of Nanoscale Science and Engineering, State University of New York Polytechnic Institute, Albany, NY, USA
| | - J Andres Melendez
- Colleges of Nanoscale Science and Engineering, State University of New York Polytechnic Institute, Albany, NY, USA.
| | - Thomas J Begley
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA; RNA Institute, University at Albany, State University of New York, Albany, NY, USA.
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12
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Yamamoto T, Fujimura A, Wei FY, Shinojima N, Kuroda JI, Mukasa A, Tomizawa K. 2-Methylthio Conversion of N6-Isopentenyladenosine in Mitochondrial tRNAs by CDK5RAP1 Promotes the Maintenance of Glioma-Initiating Cells. iScience 2019; 21:42-56. [PMID: 31654853 PMCID: PMC6820277 DOI: 10.1016/j.isci.2019.10.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 06/04/2019] [Accepted: 10/02/2019] [Indexed: 12/26/2022] Open
Abstract
2-Methylthio-N6-isopentenyl modification of adenosine (ms2i6A) is an evolutionally conserved modification found in mitochondrial (mt)-tRNAs. Cdk5 regulatory subunit-associated protein 1 (CDK5RAP1) specifically converts N6-isopentenyladenosine (i6A) to ms2i6A at position A37 of four mt-DNA-encoded tRNAs, and the modification regulates efficient mitochondrial translation and energy metabolism in mammals. Here, we report that the ms2 conversion mediated by CDK5RAP1 in mt-tRNAs is required to sustain glioma-initiating cell (GIC)-related traits. CDK5RAP1 maintained the self-renewal capacity, undifferentiated state, and tumorigenic potential of GICs. This regulation was not related to the translational control of mt-proteins. CDK5RAP1 abrogated the antitumor effect of i6A by converting i6A to ms2i6A and protected GICs from excessive autophagy triggered by i6A. The elevated activity of CDK5RAP1 contributed to the amelioration of the tumor-suppressive effect of i6A and promoted GIC maintenance. This work demonstrates that CDK5RAP1 is crucial for the detoxification of endogenous i6A and that GICs readily utilize this mechanism for survival. CDK5RAP1 is required to sustain the growth of GICs through ms2 modification of i6A Deficit of CDK5RAP1 inhibits the growth of GIC through i6A accumulation CDK5RAP1 detoxifies i6A by conversion into ms2i6A in the mitochondria of GICs Mitochondria serve as antidotal machinery against i6A in GICs
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Affiliation(s)
- Takahiro Yamamoto
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan; Department of Neurosurgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Atsushi Fujimura
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan; Department of Physiology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan; Neutron Therapy Research Center, Okayama University, Okayama 700-8558, Japan
| | - Fan-Yan Wei
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Naoki Shinojima
- Department of Neurosurgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Jun-Ichiro Kuroda
- Department of Neurosurgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Akitake Mukasa
- Department of Neurosurgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan; Center for Metabolic Regulation of Healthy Aging, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan; Neutron Therapy Research Center, Okayama University, Okayama 700-8558, Japan.
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13
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de Crécy-Lagard V, Boccaletto P, Mangleburg CG, Sharma P, Lowe TM, Leidel SA, Bujnicki JM. Matching tRNA modifications in humans to their known and predicted enzymes. Nucleic Acids Res 2019; 47:2143-2159. [PMID: 30698754 PMCID: PMC6412123 DOI: 10.1093/nar/gkz011] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/28/2018] [Accepted: 01/10/2019] [Indexed: 12/25/2022] Open
Abstract
tRNA are post-transcriptionally modified by chemical modifications that affect all aspects of tRNA biology. An increasing number of mutations underlying human genetic diseases map to genes encoding for tRNA modification enzymes. However, our knowledge on human tRNA-modification genes remains fragmentary and the most comprehensive RNA modification database currently contains information on approximately 20% of human cytosolic tRNAs, primarily based on biochemical studies. Recent high-throughput methods such as DM-tRNA-seq now allow annotation of a majority of tRNAs for six specific base modifications. Furthermore, we identified large gaps in knowledge when we predicted all cytosolic and mitochondrial human tRNA modification genes. Only 48% of the candidate cytosolic tRNA modification enzymes have been experimentally validated in mammals (either directly or in a heterologous system). Approximately 23% of the modification genes (cytosolic and mitochondrial combined) remain unknown. We discuss these 'unidentified enzymes' cases in detail and propose candidates whenever possible. Finally, tissue-specific expression analysis shows that modification genes are highly expressed in proliferative tissues like testis and transformed cells, but scarcely in differentiated tissues, with the exception of the cerebellum. Our work provides a comprehensive up to date compilation of human tRNA modifications and their enzymes that can be used as a resource for further studies.
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Affiliation(s)
- Valérie de Crécy-Lagard
- Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA
- Cancer and Genetic Institute, University of Florida, Gainesville, FL 32611, USA
| | - Pietro Boccaletto
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland
| | - Carl G Mangleburg
- Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Puneet Sharma
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany
- Cells-in-Motion Cluster of Excellence, University of Muenster, 48149 Muenster, Germany
| | - Todd M Lowe
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Sebastian A Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany
- Cells-in-Motion Cluster of Excellence, University of Muenster, 48149 Muenster, Germany
- Research Group for RNA Biochemistry, Institute of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznań, Poland
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14
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Mon EE, Wei FY, Ahmad RNR, Yamamoto T, Moroishi T, Tomizawa K. Regulation of mitochondrial iron homeostasis by sideroflexin 2. J Physiol Sci 2018; 69:359-373. [PMID: 30570704 PMCID: PMC6373408 DOI: 10.1007/s12576-018-0652-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/10/2018] [Indexed: 02/08/2023]
Abstract
Mitochondrial iron is indispensable for heme biosynthesis and iron–sulfur cluster assembly. Several mitochondrial transmembrane proteins have been implicated to function in the biosynthesis of heme and iron–sulfur clusters by transporting reaction intermediates. However, several mitochondrial proteins related to iron metabolism remain uncharacterized. Here, we show that human sideroflexin 2 (SFXN2), a member of the SFXN protein family, is involved in mitochondrial iron metabolism. SFXN2 is an evolutionarily conserved protein that localized to mitochondria via its transmembrane domain. SFXN2-knockout (KO) cells had an increased mitochondrial iron content, which was associated with decreases in the heme content and heme-dependent enzyme activities. By contrast, the activities of iron–sulfur cluster-dependent enzymes were unchanged in SFXN2-KO cells. Moreover, abnormal iron metabolism impaired mitochondrial respiration in SFXN2-KO cells and accelerated iron-mediated death of these cells. Our findings demonstrate that SFXN2 functions in mitochondrial iron metabolism by regulating heme biosynthesis.
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Affiliation(s)
- Ei Ei Mon
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Honjo 1-1-1, Chuo-Ku, Kumamoto, 860-8556, Japan
| | - Fan-Yan Wei
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Honjo 1-1-1, Chuo-Ku, Kumamoto, 860-8556, Japan. .,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Kawaguchi, 332-0012, Japan.
| | - Raja Norazireen Raja Ahmad
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Honjo 1-1-1, Chuo-Ku, Kumamoto, 860-8556, Japan
| | - Takahiro Yamamoto
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Honjo 1-1-1, Chuo-Ku, Kumamoto, 860-8556, Japan
| | - Toshiro Moroishi
- Department of Molecular Enzymology, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan.,Center for Metabolic Regulation of Healthy Aging, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Kawaguchi, 332-0012, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Honjo 1-1-1, Chuo-Ku, Kumamoto, 860-8556, Japan. .,Center for Metabolic Regulation of Healthy Aging, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan. .,Neutron Therapy Research Center, Okayama University, Okayama, 700-8558, Japan.
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15
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Wei Y, Chen L, Xu H, Xie C, Zhou Y, Zhou F. Mitochondrial Dysfunctions Regulated Radioresistance through Mitochondria-to-Nucleus Retrograde Signaling Pathway of NF-κB/PI3K/AKT2/mTOR. Radiat Res 2018; 190:204-215. [PMID: 29863983 DOI: 10.1667/rr15021.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We investigated the relationship between significantly different genes of the mitochondria-to-nucleus retrograde signaling pathway (RTG) in H1299 ρ0 cells (mtDNA depleted cell) and compared their radiosensitivity to that of parental ρ+ cells, to determine the possible intervention targets of radiosensitization. ρ0 cells were depleted of mitochondrial DNA by chronic culturing in ethidium bromide at low concentration. Radiosensitivity was analyzed using clonogenic assay. Western blot was used to analyze the cell cycle-related proteins, serine/threonine kinase ataxia telangiectasia mutant (ATM), ataxia telangiectasia and Rad3-related protein (ATR) and cyclin B1 (CCNB1). The γ-H2AX foci were detected using confocal fluorescence microscopy. RNA samples were hybridized using the Agilent human genome expression microarray. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database was used for Gene Ontology (GO) Consortium and pathway annotations of differentially expressed genes, respectively. The H1299 ρ0 cells were found to be more radioresistant than ρ+ cells. The ATP production of H1299 ρ0 cells was lower than that of the ρ+ cells before or after irradiation. Both H1299 ρ0 and ρ+ cells had higher ROS levels after irradiation, however, the radiation-induced ROS production in ρ0 cells was significantly lower than in ρ+ cells. In addition, the percentage of apoptosis in H1299 ρ0 cells was lower than in ρ+ cells after 6 Gy irradiation. As for the cell cycle and DNA damage response-related proteins ATM, ATR and CCNB1, the expression levels in ρ0 cells were significantly higher than in ρ+ cells, and there were less γ-H2AX foci in the ρ0 than ρ+ cells after irradiation. Furthermore, the results of the human genome expression microarray demonstrated that the phosphorylated protein levels of the NF-κB/PI3K/AKT2/mTOR signaling pathway were increased after 6 Gy irradiation and were decreased after treatment with the AKT2-specific inhibitor MK-2206 combined with radiation in H1299 ρ0 cells. MK-2206 treatment also led to an increase in pro-apoptotic proteins. In conclusion, these results demonstrate that mtDNA depletion might activate the mitochondria-to-nucleus retrograde signaling pathway of NF-κB/PI3K/AKT2/mTOR and induce radioresistance in H1299 ρ0 cells by evoking mitochondrial dysfunctions.
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Affiliation(s)
- Yuehua Wei
- a Department of Radiation and Medical Oncology.,b Hubei Key Laboratory of Tumor Biological Behaviors.,d Cancer Center, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Lulu Chen
- a Department of Radiation and Medical Oncology.,b Hubei Key Laboratory of Tumor Biological Behaviors.,c Hubei Clinical Cancer Study Centre, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China.,d Cancer Center, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Hui Xu
- a Department of Radiation and Medical Oncology.,b Hubei Key Laboratory of Tumor Biological Behaviors.,c Hubei Clinical Cancer Study Centre, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
| | - Conghua Xie
- a Department of Radiation and Medical Oncology.,b Hubei Key Laboratory of Tumor Biological Behaviors.,c Hubei Clinical Cancer Study Centre, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
| | - Yunfeng Zhou
- a Department of Radiation and Medical Oncology.,b Hubei Key Laboratory of Tumor Biological Behaviors.,c Hubei Clinical Cancer Study Centre, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
| | - Fuxiang Zhou
- a Department of Radiation and Medical Oncology.,b Hubei Key Laboratory of Tumor Biological Behaviors.,c Hubei Clinical Cancer Study Centre, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
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