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Huang Y, Cai W, Lu Q, Lv J, Wan M, Guan D, Yang S, He S. PMT6 Is Required for SWC4 in Positively Modulating Pepper Thermotolerance. Int J Mol Sci 2023; 24:ijms24054849. [PMID: 36902276 PMCID: PMC10003703 DOI: 10.3390/ijms24054849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 01/31/2023] [Accepted: 02/03/2023] [Indexed: 03/06/2023] Open
Abstract
High temperature stress (HTS), with growth and development impairment, is one of the most important abiotic stresses frequently encountered by plants, in particular solanacaes such as pepper, that mainly distribute in tropical and subtropical regions. Plants activate thermotolerance to cope with this stress; however, the underlying mechanism is currently not fully understood. SWC4, a shared component of SWR1- and NuA4 complexes implicated in chromatin remodeling, was previously found to be involved in the regulation of pepper thermotolerance, but the underlying mechanism remains poorly understood. Herein, PMT6, a putative methyltranferase was originally found to interact with SWC4 by co-immunoprecipitation (Co-IP)-combined LC/MS assay. This interaction was further confirmed by bimolecular fluorescent complimentary (BiFC) and Co-IP assay, and PMT6 was further found to confer SWC4 methylation. By virus-induced gene silencing, it was found that PMT6 silencing significantly reduced pepper basal thermotolerance and transcription of CaHSP24 and significantly reduced the enrichment of chromatin-activation-related H3K9ac, H4K5ac, and H3K4me3 in TSS of CaHSP24, which was previously found to be positively regulated by CaSWC4. By contrast, the overexpression of PMT6 significantly enhanced basal thermotolerance of pepper plants. All these data indicate that PMT6 acts as a positive regulator in pepper thermotolerance, likely by methylating SWC4.
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Affiliation(s)
- Yu Huang
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weiwei Cai
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qiaoling Lu
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jingang Lv
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Meiyun Wan
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Deyi Guan
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Sheng Yang
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (S.Y.); (S.H.)
| | - Shuilin He
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (S.Y.); (S.H.)
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Pristup J, Schaeffeler E, Arjune S, Hofmann U, Santamaria-Araujo JA, Leuthold P, Friedrich N, Nauck M, Mayr S, Haag M, Muerdter T, Marner FJ, Relling MV, Evans WE, Schwarz G, Schwab M. Molybdenum Cofactor Catabolism Unravels the Physiological Role of the Drug Metabolizing Enzyme Thiopurine S-Methyltransferase. Clin Pharmacol Ther 2022; 112:808-816. [PMID: 35538648 PMCID: PMC9474665 DOI: 10.1002/cpt.2637] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/04/2022] [Indexed: 12/14/2022]
Abstract
Therapy of molybdenum cofactor (Moco) deficiency has received US Food and Drug Administration (FDA) approval in 2021. Whereas urothione, the urinary excreted catabolite of Moco, is used as diagnostic biomarker for Moco-deficiency, its catabolic pathway remains unknown. Here, we identified the urothione-synthesizing methyltransferase using mouse liver tissue by anion exchange/size exclusion chromatography and peptide mass fingerprinting. We show that the catabolic Moco S-methylating enzyme corresponds to thiopurine S-methyltransferase (TPMT), a highly polymorphic drug-metabolizing enzyme associated with drug-related hematotoxicity but unknown physiological role. Urothione synthesis was investigated in vitro using recombinantly expressed human TPMT protein, liver lysates from Tpmt wild-type and knock-out (Tpmt-/- ) mice as well as human liver cytosol. Urothione levels were quantified by liquid-chromatography tandem mass spectrometry in the kidneys and urine of mice. TPMT-genotype/phenotype and excretion levels of urothione were investigated in human samples and validated in an independent population-based study. As Moco provides a physiological substrate (thiopterin) of TPMT, thiopterin-methylating activity was associated with TPMT activity determined with its drug substrate (6-thioguanin) in mice and humans. Urothione concentration was extremely low in the kidneys and urine of Tpmt-/- mice. Urinary urothione concentration in TPMT-deficient patients depends on common TPMT polymorphisms, with extremely low levels in homozygous variant carriers (TPMT*3A/*3A) but normal levels in compound heterozygous carriers (TPMT*3A/*3C) as validated in the population-based study. Our work newly identified an endogenous substrate for TPMT and shows an unprecedented link between Moco catabolism and drug metabolism. Moreover, the TPMT example indicates that phenotypic consequences of genetic polymorphisms may differ between drug- and endogenous substrates.
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Affiliation(s)
- Julika Pristup
- Institute of Biochemistry, Department of Chemistry, University of Cologne, 50674 Cologne, Germany
| | - Elke Schaeffeler
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, 72076 Tuebingen, Germany
| | - Sita Arjune
- Institute of Biochemistry, Department of Chemistry, University of Cologne, 50674 Cologne, Germany
| | - Ute Hofmann
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
| | | | - Patrick Leuthold
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
| | - Nele Friedrich
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, University Medicine, 17475 Greifswald, Germany
| | - Matthias Nauck
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, University Medicine, 17475 Greifswald, Germany
| | - Simon Mayr
- Institute of Biochemistry, Department of Chemistry, University of Cologne, 50674 Cologne, Germany
| | - Mathias Haag
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
| | - Thomas Muerdter
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
| | - Franz-Josef Marner
- Institute of Biochemistry, Department of Chemistry, University of Cologne, 50674 Cologne, Germany
| | - Mary V Relling
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, Tennessee 38105-3678, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - William E Evans
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, Tennessee 38105-3678, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Guenter Schwarz
- Institute of Biochemistry, Department of Chemistry, University of Cologne, 50674 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, 72076 Tuebingen, Germany
- Departments of Clinical Pharmacology, Pharmacy and Biochemistry, University Tuebingen, 72076 Tuebingen, Germany
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Dong L, Chen C, Zhang Y, Guo P, Wang Z, Li J, Liu Y, Liu J, Chang R, Li Y, Liang G, Lai W, Sun M, Dougherty U, Bissonnette MB, Wang H, Shen L, Xu MM, Han D. The loss of RNA N 6-adenosine methyltransferase Mettl14 in tumor-associated macrophages promotes CD8 + T cell dysfunction and tumor growth. Cancer Cell 2021; 39:945-957.e10. [PMID: 34019807 DOI: 10.1016/j.ccell.2021.04.016] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 03/07/2021] [Accepted: 04/28/2021] [Indexed: 12/15/2022]
Abstract
Tumor-associated macrophages (TAMs) can dampen the antitumor activity of T cells, yet the underlying mechanism remains incompletely understood. Here, we show that C1q+ TAMs are regulated by an RNA N6-methyladenosine (m6A) program and modulate tumor-infiltrating CD8+ T cells by expressing multiple immunomodulatory ligands. Macrophage-specific knockout of an m6A methyltransferase Mettl14 drives CD8+ T cell differentiation along a dysfunctional trajectory, impairing CD8+ T cells to eliminate tumors. Mettl14-deficient C1q+ TAMs show a decreased m6A abundance on and a higher level of transcripts of Ebi3, a cytokine subunit. In addition, neutralization of EBI3 leads to reinvigoration of dysfunctional CD8+ T cells and overcomes immunosuppressive impact in mice. We show that the METTL14-m6A levels are negatively correlated with dysfunctional T cell levels in patients with colorectal cancer, supporting the clinical relevance of this regulatory pathway. Thus, our study demonstrates how an m6A methyltransferase in TAMs promotes CD8+ T cell dysfunction and tumor progression.
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Affiliation(s)
- Lihui Dong
- Department of Basic Medical Sciences, School of Medicine, Institute for Immunology, Beijing Key Lab for Immunological Research on Chronic Diseases, THU-PKU Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chuanyuan Chen
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences, Beijing 100101, China; College of Future Technology, Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yawei Zhang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences, Beijing 100101, China; College of Future Technology, Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peijin Guo
- Department of Basic Medical Sciences, School of Medicine, Institute for Immunology, Beijing Key Lab for Immunological Research on Chronic Diseases, THU-PKU Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhenghang Wang
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Jian Li
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Yi Liu
- Department of Basic Medical Sciences, School of Medicine, Institute for Immunology, Beijing Key Lab for Immunological Research on Chronic Diseases, THU-PKU Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jun Liu
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Renbao Chang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences, Beijing 100101, China; College of Future Technology, Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yilin Li
- Department of Basic Medical Sciences, School of Medicine, Institute for Immunology, Beijing Key Lab for Immunological Research on Chronic Diseases, THU-PKU Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guanghao Liang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences, Beijing 100101, China; College of Future Technology, Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiyi Lai
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Mengxue Sun
- Department of Basic Medical Sciences, School of Medicine, Institute for Immunology, Beijing Key Lab for Immunological Research on Chronic Diseases, THU-PKU Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Urszula Dougherty
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Marc B Bissonnette
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Lin Shen
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Meng Michelle Xu
- Department of Basic Medical Sciences, School of Medicine, Institute for Immunology, Beijing Key Lab for Immunological Research on Chronic Diseases, THU-PKU Center for Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Dali Han
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences, Beijing 100101, China; College of Future Technology, Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; China National Center for Bioinformation, Beijing, 100101, China.
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Galloway A, Kaskar A, Ditsova D, Atrih A, Yoshikawa H, Gomez-Moreira C, Suska O, Warminski M, Grzela R, Lamond AI, Darzynkiewicz E, Jemielity J, Cowling V. Upregulation of RNA cap methyltransferase RNMT drives ribosome biogenesis during T cell activation. Nucleic Acids Res 2021; 49:6722-6738. [PMID: 34125914 PMCID: PMC8266598 DOI: 10.1093/nar/gkab465] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/09/2021] [Accepted: 05/17/2021] [Indexed: 01/07/2023] Open
Abstract
The m7G cap is ubiquitous on RNAPII-transcribed RNA and has fundamental roles in eukaryotic gene expression, however its in vivo role in mammals has remained unknown. Here, we identified the m7G cap methyltransferase, RNMT, as a key mediator of T cell activation, which specifically regulates ribosome production. During T cell activation, induction of mRNA expression and ribosome biogenesis drives metabolic reprogramming, rapid proliferation and differentiation generating effector populations. We report that RNMT is induced by T cell receptor (TCR) stimulation and co-ordinates the mRNA, snoRNA and rRNA production required for ribosome biogenesis. Using transcriptomic and proteomic analyses, we demonstrate that RNMT selectively regulates the expression of terminal polypyrimidine tract (TOP) mRNAs, targets of the m7G-cap binding protein LARP1. The expression of LARP1 targets and snoRNAs involved in ribosome biogenesis is selectively compromised in Rnmt cKO CD4 T cells resulting in decreased ribosome synthesis, reduced translation rates and proliferation failure. By enhancing ribosome abundance, upregulation of RNMT co-ordinates mRNA capping and processing with increased translational capacity during T cell activation.
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Affiliation(s)
- Alison Galloway
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Aneesa Kaskar
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Dimitrinka Ditsova
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Abdelmadjid Atrih
- FingerPrints Proteomics Facility, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Harunori Yoshikawa
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Carolina Gomez-Moreira
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Olga Suska
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Marcin Warminski
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Renata Grzela
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, and Division of Physics, 02-093 Warsaw, Poland
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Edward Darzynkiewicz
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, and Division of Physics, 02-093 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Victoria H Cowling
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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Han J, Du S, Wu C, Qiu M, Su L, Zhao Z, Cheng S, Tao W. METTL3 participates in glioma development by regulating the methylation level of COL4A1. J BUON 2021; 26:1556-1562. [PMID: 34565019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
PURPOSE The role of RNA methylation in human cancers has emerged. Its biological function in glioma development is explored in the present study. METHODS Differential levels and prognostic potentials of COL4A1 and METTL3 in glioma were analyzed by bioinformatic method. The regulatory effect of METTL3 on COL4A1 was assessed through qRT-PCR, MeRIP and dual-luciferase reporter assay. Their biological functions in influencing proliferative and metastatic capacities of glioma cells were examined by EdU, colony formation and Transwell assay, respectively. RESULTS COL4A1 was upregulated in glioma tissues, and METTL3 was downregulated. Knockdown of METTL3 in U87 and U251 cells could reduce the methylation level of COL4A1 and upregulate its expression level. Intervention of COL4A1 suppressed proliferative and metastatic capacities of glioma cells, while intervention of METTL3 yielded the opposite results. CONCLUSION METTL3 reduces the methylation level of COL4A1 and upregulates its expression level, which further stimulates the malignant development of glioma. METTL3/COL4A1 can be potential therapeutic targets of glioma.
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Affiliation(s)
- Jianguo Han
- Department of Neurosurgery, Shenzhen University General Hospital and Shenzhen University Clinical Medical Academy Centre, Shenzhen University, Shenzhen, China
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Abstract
RNA modification represents one of the most ubiquitous mechanisms of epigenetic regulation and plays an essential role in modulating cell proliferation, differentiation, fate determination, and other biological activities. At present, over 170 types of RNA modification have been discovered in messenger RNA (mRNA) and noncoding RNA (ncRNA). RNA methylation, as an abundant and widely studied epigenetic modification, is crucial for regulating various physiological or pathological states, especially immune responses. Considering the biological significance of T cells as a defense against viral infection and tumor challenge, in this review, we will summarize recent findings of how RNA methylation regulates T cell homeostasis and function, discuss the open questions in this rapidly expanding field of RNA modification, and provide the theoretical basis and potential therapeutic strategies involving targeting of RNA methylation to orchestrate beneficial T cell immune responses.
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Affiliation(s)
- Yinong Chao
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of Medicine - Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hua-Bing Li
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of Medicine - Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Zhou
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of Medicine - Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Black JJ, Johnson AW. Genetics animates structure: leveraging genetic interactions to study the dynamics of ribosome biogenesis. Curr Genet 2021; 67:729-738. [PMID: 33844044 DOI: 10.1007/s00294-021-01187-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/28/2021] [Accepted: 03/29/2021] [Indexed: 11/26/2022]
Abstract
The assembly of eukaryotic ribosomes follows an assembly line-like pathway in which numerous trans-acting biogenesis factors act on discrete pre-ribosomal intermediates to progressively shape the nascent subunits into their final functional architecture. Recent advances in cryo-electron microscopy have led to high-resolution structures of many pre-ribosomal intermediates; however, these static snapshots do not capture the dynamic transitions between these intermediates. To this end, molecular genetics can be leveraged to reveal how the biogenesis factors drive these dynamic transitions. Here, we briefly review how we recently used the deletion of BUD23 (bud23∆) to understand its role in the assembly of the ribosomal small subunit. The strong growth defect of bud23∆ mutants places a selective pressure on yeast cells for the occurrence of extragenic suppressors that define a network of functional interactions among biogenesis factors. Mapping these suppressing mutations to recently published structures of pre-ribosomal complexes allowed us to contextualize these suppressing mutations and derive a detailed model in which Bud23 promotes a critical transition event to facilitate folding of the central pseudoknot of the small subunit. This mini-review highlights how genetics can be used to understand the dynamics of complex structures, such as the maturing ribosome.
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Affiliation(s)
- Joshua J Black
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Arlen W Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
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Abstract
N6-methyladenosine (m6A) mRNA methylation has been shown to regulate obesity and type 2 diabetes. However, whether METTL3, the key methyltransferase for m6A mRNA methylation, regulates β-cell failure in diabetes has not been fully explored. Here, we show that METTL3 is downregulated under the inflammatory and oxidative stress conditions, and islet β-cell-specific deletion of Mettl3 induces β-cell failure and hyperglycemia, which is likely due to decreased m6A modification and reduced expression of insulin secretion-related genes. Overall, METTL3 might be a potential drug target for the treatment of β-cell failure in diabetes.
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Affiliation(s)
- Xinzhi Li
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Yuze Jiang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Xu Sun
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Yongsen Wu
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Zheng Chen
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China.
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Knüppel R, Trahan C, Kern M, Wagner A, Grünberger F, Hausner W, Quax TEF, Albers SV, Oeffinger M, Ferreira-Cerca S. Insights into synthesis and function of KsgA/Dim1-dependent rRNA modifications in archaea. Nucleic Acids Res 2021; 49:1662-1687. [PMID: 33434266 PMCID: PMC7897474 DOI: 10.1093/nar/gkaa1268] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/01/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
Ribosomes are intricate molecular machines ensuring proper protein synthesis in every cell. Ribosome biogenesis is a complex process which has been intensively analyzed in bacteria and eukaryotes. In contrast, our understanding of the in vivo archaeal ribosome biogenesis pathway remains less characterized. Here, we have analyzed the in vivo role of the almost universally conserved ribosomal RNA dimethyltransferase KsgA/Dim1 homolog in archaea. Our study reveals that KsgA/Dim1-dependent 16S rRNA dimethylation is dispensable for the cellular growth of phylogenetically distant archaea. However, proteomics and functional analyses suggest that archaeal KsgA/Dim1 and its rRNA modification activity (i) influence the expression of a subset of proteins and (ii) contribute to archaeal cellular fitness and adaptation. In addition, our study reveals an unexpected KsgA/Dim1-dependent variability of rRNA modifications within the archaeal phylum. Combining structure-based functional studies across evolutionary divergent organisms, we provide evidence on how rRNA structure sequence variability (re-)shapes the KsgA/Dim1-dependent rRNA modification status. Finally, our results suggest an uncoupling between the KsgA/Dim1-dependent rRNA modification completion and its release from the nascent small ribosomal subunit. Collectively, our study provides additional understandings into principles of molecular functional adaptation, and further evolutionary and mechanistic insights into an almost universally conserved step of ribosome synthesis.
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Affiliation(s)
- Robert Knüppel
- Regensburg Center for Biochemistry, Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Christian Trahan
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec H3A 1A3, Canada
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Michael Kern
- Regensburg Center for Biochemistry, Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Alexander Wagner
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Felix Grünberger
- Chair of Microbiology – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Winfried Hausner
- Chair of Microbiology – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Tessa E F Quax
- Archaeal Virus-Host Interactions, Institute of Biology II, Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Marlene Oeffinger
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec H3A 1A3, Canada
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Sébastien Ferreira-Cerca
- Regensburg Center for Biochemistry, Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
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10
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Zhao D, Luan Y, Shi W, Zhang X, Meng J, Tao J. A Paeonia ostii caffeoyl-CoA O-methyltransferase confers drought stress tolerance by promoting lignin synthesis and ROS scavenging. Plant Sci 2021; 303:110765. [PMID: 33487350 DOI: 10.1016/j.plantsci.2020.110765] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 05/23/2023]
Abstract
Paeonia ostii is an emerging woody oil crop, but drought severely inhibits its growth and promotion in arid or semiarid areas, and little is known about the mechanism governing this inhibition. In this study, the full-length cDNA of a caffeoyl-CoA O-methyltransferase gene (CCoAOMT) from P. ostii was isolated, and determined to be comprised of 987 bp. PoCCoAOMT encoded a 247-amino acid protein, which was located in the nucleus and cytosol. Significantly higher PoCCoAOMT transcription was detected in P. ostii treated with drought stress. Subsequently, the constitutive overexpression of PoCCoAOMT in tobacco significantly conferred drought stress tolerance. Under drought stress, transgenic lines exhibited lower reactive oxygen species (ROS) accumulation, and higher antioxidant enzyme activities and photosynthesis. Moreover, the expression levels of senescence-associated genes were significantly downregulated, whereas the expression levels of lignin biosynthetic genes and PoCCoAOMT were significantly upregulated in transgenic lines. Similarly, transgenic lines produced significantly higher lignin, especially guaiacyl-lignin. These results suggest that PoCCoAOMT is a vital gene in promoting lignin synthesis and ROS scavenging to confer drought stress tolerance in P. ostii.
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Affiliation(s)
- Daqiu Zhao
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Yuting Luan
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Wenbo Shi
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Xiayan Zhang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Jiasong Meng
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Jun Tao
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, Jiangsu, China.
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11
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Hafeez A, Gě Q, Zhāng Q, Lǐ J, Gōng J, Liú R, Shí Y, Shāng H, Liú À, Iqbal MS, Dèng X, Razzaq A, Ali M, Yuán Y, Gǒng W. Multi-responses of O-methyltransferase genes to salt stress and fiber development of Gossypium species. BMC Plant Biol 2021; 21:37. [PMID: 33430775 PMCID: PMC7798291 DOI: 10.1186/s12870-020-02786-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND O-methyltransferases (OMTs) are an important group of enzymes that catalyze the transfer of a methyl group from S-adenosyl-L-methionine to their acceptor substrates. OMTs are divided into several groups according to their structural features. In Gossypium species, they are involved in phenolics and flavonoid pathways. Phenolics defend the cellulose fiber from dreadful external conditions of biotic and abiotic stresses, promoting strength and growth of plant cell wall. RESULTS An OMT gene family, containing a total of 192 members, has been identified and characterized in three main Gossypium species, G. hirsutum, G. arboreum and G. raimondii. Cis-regulatory elements analysis suggested important roles of OMT genes in growth, development, and defense against stresses. Transcriptome data of different fiber developmental stages in Chromosome Substitution Segment Lines (CSSLs), Recombination Inbred Lines (RILs) with excellent fiber quality, and standard genetic cotton cultivar TM-1 demonstrate that up-regulation of OMT genes at different fiber developmental stages, and abiotic stress treatments have some significant correlations with fiber quality formation, and with salt stress response. Quantitative RT-PCR results revealed that GhOMT10_Dt and GhOMT70_At genes had a specific expression in response to salt stress while GhOMT49_At, GhOMT49_Dt, and GhOMT48_At in fiber elongation and secondary cell wall stages. CONCLUSIONS Our results indicate that O-methyltransferase genes have multi-responses to salt stress and fiber development in Gossypium species and that they may contribute to salt tolerance or fiber quality formation in Gossypium.
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Affiliation(s)
- Abdul Hafeez
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- Sindh Agriculture University Tandojam, Hyderabad, Sindh, 70060, Pakistan
| | - Qún Gě
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Qí Zhāng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Jùnwén Lǐ
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Jǔwǔ Gōng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Ruìxián Liú
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Yùzhēn Shí
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Hǎihóng Shāng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Àiyīng Liú
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Muhammad S Iqbal
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Xiǎoyīng Dèng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Abdul Razzaq
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Muharam Ali
- Sindh Agriculture University Tandojam, Hyderabad, Sindh, 70060, Pakistan.
| | - Yǒulù Yuán
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Wànkuí Gǒng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
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12
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Uchida K, Sawada Y, Ochiai K, Sato M, Inaba J, Hirai MY. Identification of a Unique Type of Isoflavone O-Methyltransferase, GmIOMT1, Based on Multi-Omics Analysis of Soybean under Biotic Stress. Plant Cell Physiol 2020; 61:1974-1985. [PMID: 32894761 PMCID: PMC7758036 DOI: 10.1093/pcp/pcaa112] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/25/2020] [Indexed: 05/15/2023]
Abstract
Isoflavonoids are commonly found in leguminous plants. Glycitein is one of the isoflavones produced by soybean. The genes encoding the enzymes in the isoflavone biosynthetic pathway have mostly been identified and characterized. However, the gene(s) for isoflavone O-methyltransferase (IOMT), which catalyzes the last step of glycitein biosynthesis, has not yet been identified. In this study, we conducted multi-omics analyses of fungal-inoculated soybean and indicated that glycitein biosynthesis was induced in response to biotic stress. Moreover, we identified a unique type of IOMT, which participates in glycitein biosynthesis. Soybean seedlings were inoculated with Aspergillus oryzae or Rhizopus oligosporus and sampled daily for 8 d. Multi-omics analyses were conducted using liquid chromatography-tandem mass spectrometry and RNA sequencing. Metabolome analysis revealed that glycitein derivatives increased following fungal inoculation. Transcriptome co-expression analysis identified two candidate IOMTs that were co-expressed with the gene encoding flavonoid 6-hydroxylase (F6H), the key enzyme in glycitein biosynthesis. The enzymatic assay of the two IOMTs using respective recombinant proteins showed that one IOMT, named as GmIOMT1, produced glycitein. Unlike other IOMTs, GmIOMT1 belongs to the cation-dependent OMT family and exhibited the highest activity with Zn2+ among cations tested. Moreover, we demonstrated that GmIOMT1 overexpression increased the levels of glycitein derivatives in soybean hairy roots when F6H was co-expressed. These results strongly suggest that GmIOMT1 participates in inducing glycitein biosynthesis in response to biotic stress.
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Affiliation(s)
- Kai Uchida
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045 Japan
| | - Yuji Sawada
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045 Japan
| | | | - Muneo Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045 Japan
| | - Jun Inaba
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045 Japan
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13
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Cheng Y, Luo H, Izzo F, Pickering BF, Nguyen D, Myers R, Schurer A, Gourkanti S, Brüning JC, Vu LP, Jaffrey SR, Landau DA, Kharas MG. m 6A RNA Methylation Maintains Hematopoietic Stem Cell Identity and Symmetric Commitment. Cell Rep 2020; 28:1703-1716.e6. [PMID: 31412241 PMCID: PMC6818972 DOI: 10.1016/j.celrep.2019.07.032] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/17/2019] [Accepted: 07/11/2019] [Indexed: 12/11/2022] Open
Abstract
Stem cells balance cellular fates through asymmetric and symmetric divisions in order to self-renew or to generate downstream progenitors. Symmetric commitment divisions in stem cells are required for rapid regeneration during tissue damage and stress. The control of symmetric commitment remains poorly defined. Using single-cell RNA sequencing (scRNA-seq) in combination with transcriptomic profiling of HSPCs (hematopoietic stem and progenitor cells) from control and m6A methyltransferase Mettl3 conditional knockout mice, we found that m6A-deficient hematopoietic stem cells (HSCs) fail to symmetrically differentiate. Dividing HSCs are expanded and are blocked in an intermediate state that molecularly and functionally resembles multipotent progenitors. Mechanistically, RNA methylation controls Myc mRNA abundance in differentiating HSCs. We identified MYC as a marker for HSC asymmetric and symmetric commitment. Overall, our results indicate that RNA methylation controls symmetric commitment and cell identity of HSCs and may provide a general mechanism for how stem cells regulate differentiation fate choice. Cheng et al. uncover RNA methylation as a guardian in hematopoietic stem cell (HSC) fate decisions. m6A maintains hematopoietic stem cell symmetric commitment and identity. This study may provide a general mechanism for how RNA methylation controls cellular fate.
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Affiliation(s)
- Yuanming Cheng
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hanzhi Luo
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Franco Izzo
- New York Genome Center, New York, NY, USA; Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Brian F Pickering
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Diu Nguyen
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert Myers
- New York Genome Center, New York, NY, USA; Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Alexandra Schurer
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Saroj Gourkanti
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jens C Brüning
- Department of Mouse Genetics and Metabolism, Institute for Genetics and Center for Molecular Medicine (CMMC), University of Cologne, Zülpicher Strasse 47b, 50674 Cologne, Germany
| | - Ly P Vu
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Terry Fox Laboratory, British Columbia Cancer Research Centre, Vancouver, BC, Canada; Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, BC, Canada
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Dan A Landau
- New York Genome Center, New York, NY, USA; Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
| | - Michael G Kharas
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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14
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Bhat SS, Bielewicz D, Gulanicz T, Bodi Z, Yu X, Anderson SJ, Szewc L, Bajczyk M, Dolata J, Grzelak N, Smolinski DJ, Gregory BD, Fray RG, Jarmolowski A, Szweykowska-Kulinska Z. mRNA adenosine methylase (MTA) deposits m 6A on pri-miRNAs to modulate miRNA biogenesis in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2020; 117:21785-21795. [PMID: 32817553 DOI: 10.1101/557900] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
In Arabidopsis thaliana, the METTL3 homolog, mRNA adenosine methylase (MTA) introduces N6-methyladenosine (m6A) into various coding and noncoding RNAs of the plant transcriptome. Here, we show that an MTA-deficient mutant (mta) has decreased levels of microRNAs (miRNAs) but accumulates primary miRNA transcripts (pri-miRNAs). Moreover, pri-miRNAs are methylated by MTA, and RNA structure probing analysis reveals a decrease in secondary structure within stem-loop regions of these transcripts in mta mutant plants. We demonstrate interaction between MTA and both RNA Polymerase II and TOUGH (TGH), a plant protein needed for early steps of miRNA biogenesis. Both MTA and TGH are necessary for efficient colocalization of the Microprocessor components Dicer-like 1 (DCL1) and Hyponastic Leaves 1 (HYL1) with RNA Polymerase II. We propose that secondary structure of miRNA precursors induced by their MTA-dependent m6A methylation status, together with direct interactions between MTA and TGH, influence the recruitment of Microprocessor to plant pri-miRNAs. Therefore, the lack of MTA in mta mutant plants disturbs pri-miRNA processing and leads to the decrease in miRNA accumulation. Furthermore, our findings reveal that reduced miR393b levels likely contributes to the impaired auxin response phenotypes of mta mutant plants.
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Affiliation(s)
- Susheel Sagar Bhat
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Dawid Bielewicz
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Tomasz Gulanicz
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Zsuzsanna Bodi
- School of Biosciences, Plant Science Division, University of Nottingham, Sutton Bonington, Loughborough LE12 5RD, United Kingdom
| | - Xiang Yu
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Stephen J Anderson
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Lukasz Szewc
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Mateusz Bajczyk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Jakub Dolata
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Natalia Grzelak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Dariusz J Smolinski
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100 Torun, Poland
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Rupert G Fray
- School of Biosciences, Plant Science Division, University of Nottingham, Sutton Bonington, Loughborough LE12 5RD, United Kingdom
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland;
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland;
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15
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Abstract
Like DNA and proteins, RNA is subject to numerous (over 160) covalent modifications which play critical roles to regulate RNA metabolism. Among these modifications, N-methyladenosine (mA) is the most prevalent RNA methylation on mRNA which occurs on around 25% of transcripts. The recent studies demonstrated that mA participates in many aspects of RNA processing, including splicing, nuclear exporting, translation, stabilization, etc. Therefore, it revealed a new layer of regulatory mechanism for gene expression and has been termed "RNA Epigenetics" or "Epitranscriptomics". RNA mA is regulated and exerts its functions by three groups of "mA RNA modifiers" including mA methyltransferases (writers), mA demethylases (erasers), and mA binding proteins (readers). In this review, we would summarize and discuss the current understandings of the roles of the conventional mA RNA modifiers in human cancers.
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Affiliation(s)
- Yanwen Liang
- Department of Life Sciences and Institute of Genomic Sciences, National Yang-Ming University, Taipei, Taiwan, ROC
| | - Guankai Zhan
- Department of Public Health, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Kao-Jung Chang
- Institute of clinical medicine, National Yang-Ming University, Taipei, Taiwan, ROC
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Yi-Ping Yang
- Institute of clinical medicine, National Yang-Ming University, Taipei, Taiwan, ROC
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Lingfang Wang
- Department of Public Health, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jiebo Lin
- Department of Public Health, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Chih-Hung Hsu
- Department of Public Health, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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16
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Uddin MB, Wang Z, Yang C. Dysregulations of Functional RNA Modifications in Cancer, Cancer Stemness and Cancer Therapeutics. Theranostics 2020; 10:3164-3189. [PMID: 32194861 PMCID: PMC7053189 DOI: 10.7150/thno.41687] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/19/2019] [Indexed: 12/11/2022] Open
Abstract
More than a hundred chemical modifications in coding and non-coding RNAs have been identified so far. Many of the RNA modifications are dynamic and reversible, playing critical roles in gene regulation at the posttranscriptional level. The abundance and functions of RNA modifications are controlled mainly by the modification regulatory proteins: writers, erasers and readers. Modified RNA bases and their regulators form intricate networks which are associated with a vast array of diverse biological functions. RNA modifications are not only essential for maintaining the stability and structural integrity of the RNA molecules themselves, they are also associated with the functional outcomes and phenotypic attributes of cells. In addition to their normal biological roles, many of the RNA modifications also play important roles in various diseases particularly in cancer as evidenced that the modified RNA transcripts and their regulatory proteins are aberrantly expressed in many cancer types. This review will first summarize the most commonly reported RNA modifications and their regulations, followed by discussing recent studies on the roles of RNA modifications in cancer, cancer stemness as wells as functional RNA modification machinery as potential cancer therapeutic targets. It is concluded that, while advanced technologies have uncovered the contributions of many of RNA modifications in cancer, the underlying mechanisms are still poorly understood. Moreover, whether and how environmental pollutants, important cancer etiological factors, trigger abnormal RNA modifications and their roles in environmental carcinogenesis remain largely unknown. Further studies are needed to elucidate the mechanism of how RNA modifications promote cell malignant transformation and generation of cancer stem cells, which will lead to the development of new strategies for cancer prevention and treatment.
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Affiliation(s)
| | | | - Chengfeng Yang
- Department of Toxicology and Cancer Biology, College of Medicine, University of Kentucky, Lexington, KY 40536-0305, USA
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17
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Weng YL, Wang X, An R, Cassin J, Vissers C, Liu Y, Liu Y, Xu T, Wang X, Wong SZH, Joseph J, Dore LC, Dong Q, Zheng W, Jin P, Wu H, Shen B, Zhuang X, He C, Liu K, Song H, Ming GL. Epitranscriptomic m 6A Regulation of Axon Regeneration in the Adult Mammalian Nervous System. Neuron 2019; 97:313-325.e6. [PMID: 29346752 DOI: 10.1016/j.neuron.2017.12.036] [Citation(s) in RCA: 253] [Impact Index Per Article: 50.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 11/05/2017] [Accepted: 12/22/2017] [Indexed: 02/07/2023]
Abstract
N6-methyladenosine (m6A) affects multiple aspects of mRNA metabolism and regulates developmental transitions by promoting mRNA decay. Little is known about the role of m6A in the adult mammalian nervous system. Here we report that sciatic nerve lesion elevates levels of m6A-tagged transcripts encoding many regeneration-associated genes and protein translation machinery components in the adult mouse dorsal root ganglion (DRG). Single-base resolution m6A-CLIP mapping further reveals a dynamic m6A landscape in the adult DRG upon injury. Loss of either m6A methyltransferase complex component Mettl14 or m6A-binding protein Ythdf1 globally attenuates injury-induced protein translation in adult DRGs and reduces functional axon regeneration in the peripheral nervous system in vivo. Furthermore, Pten deletion-induced axon regeneration of retinal ganglion neurons in the adult central nervous system is attenuated upon Mettl14 knockdown. Our study reveals a critical epitranscriptomic mechanism in promoting injury-induced protein synthesis and axon regeneration in the adult mammalian nervous system.
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Affiliation(s)
- Yi-Lan Weng
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xu Wang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Ran An
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, State Key Laboratory of Medical Neurobiology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Jessica Cassin
- Human Genetic Pre-graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Caroline Vissers
- Biochemistry, Cellular, and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yuanyuan Liu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Yajing Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Tianlei Xu
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Xinyuan Wang
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; School of Basic Medical Sciences, Fudan University, Shanghai 200040, China
| | - Samuel Zheng Hao Wong
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jessica Joseph
- Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Louis C Dore
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA; Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, USA
| | - Qiang Dong
- Department of Neurology, State Key Laboratory of Medical Neurobiology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Wei Zheng
- National Center for Advancing Translational Sciences, NIH, Bethesda, MD 20892, USA
| | - Peng Jin
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Xiaoxi Zhuang
- Department of Neurobiology, University of Chicago, Chicago, IL 60637, USA
| | - Chuan He
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA; Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, USA
| | - Kai Liu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Hongjun Song
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Human Genetic Pre-graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Biochemistry, Cellular, and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Guo-Li Ming
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry, Cellular, and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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18
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Zhang XS, Ni R, Wang PY, Zhu TT, Sun CJ, Lou HX, Cheng AX. Isolation and functional characterization of two Caffeoyl Coenzyme A 3-O-methyltransferases from the fern species Polypodiodes amoena. Plant Physiol Biochem 2019; 136:169-177. [PMID: 30685696 DOI: 10.1016/j.plaphy.2019.01.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 01/16/2019] [Accepted: 01/16/2019] [Indexed: 06/09/2023]
Abstract
Caffeoyl Coenzyme A 3-O-methyltransferases (CCoAOMTs) catalyze the transfer of a methyl group from S-adenosylmethionine (SAM) to a hydroxyl moiety. CCoAOMTs are important for the synthesis of lignin, which provides much of the rigidity required by tracheophytes to enable the long distance transport of water. So far, no CCoAOMTs has been characterized from the ancient tracheophytes ferns. Here, two genes, each encoding a CCoAOMT (and hence denoted PaCCoAOMT1 and PaCCoAOMT2), were isolated from the fern species Polypodiodes amoena. Sequence comparisons confirmed that the product of each gene resembled enzymes known to be associated with lignin synthesis in higher plants. When either of the genes was heterologously expressed in E. coli, the resulting recombinant protein was able to methylate caffeoyl CoA, along with a number of phenylpropanoids, flavones and flavonols containing two vicinal hydroxyl groups. Their in vitro conversion rate when presented with either caffeoyl CoA or certain flavonoids as substrate was comparable with that of the Medicago sativa MsCCoAOMT. Their constitutive expression in Arabidopsis thaliana boosted the plants' lignin content, but did not affect that of methylated flavonols, indicating that both PaCCoAOMTs contributed to lignin synthesis and that neither was able to methylate flavonols in planta. The transient expression of a PaCCoAOMT-GFP fusion gene in tobacco demonstrated that in planta, PaCCoAOMTs are likely directed to the cytoplasm.
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Affiliation(s)
- Xiao-Shuang Zhang
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China
| | - Rong Ni
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China
| | - Piao-Yi Wang
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China
| | - Ting-Ting Zhu
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China
| | - Chun-Jing Sun
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China
| | - Hong-Xiang Lou
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China
| | - Ai-Xia Cheng
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250012, China.
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Sarkate A, Saini SS, Gaid M, Teotia D, Mir JI, Agrawal PK, Beerhues L, Sircar D. Molecular cloning and functional analysis of a biphenyl phytoalexin-specific O-methyltransferase from apple cell suspension cultures. Planta 2019; 249:677-691. [PMID: 30357505 DOI: 10.1007/s00425-018-3031-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 10/18/2018] [Indexed: 06/08/2023]
Abstract
This manuscript describes the cloning and functional characterization of a biphenyl phytoalexin biosynthetic gene, 3,5-dihydroxybiphenyl O-methyltransferase from elicitor-treated cell cultures of scab resistant apple cultivar 'Florina'. Apples belong to the subtribe Malinae of the Rosaceae family. Biphenyls and dibenzofurans are the specialized phytoalexins of Malinae, of which aucuparin is the most widely distributed biphenyl. The precursor of aucuparin, 3,5-dihydroxybiphenyl, is a benzoate-derived polyketide, which is formed by the sequential condensation of three molecules of malonyl-CoA and one molecule of benzoyl-CoA in a reaction catalyzed by biphenyl synthase (BIS). This 3,5-dihydroxybiphenyl then undergoes sequential 5-O-methylation, 4-hydroxylation, and finally 3-O-methylation to form aucuparin. A cDNA encoding O-methyltransferase (OMT) was isolated and functionally characterized from the cell cultures of scab-resistant apple cultivar 'Florina' (Malus domestica cultivar 'Florina'; MdOMT) after treatment with elicitor prepared from the apple scab causing fungus Venturia inaequalis. MdOMT catalyzed the regiospecific O-methylation of 3,5-dihydroxybiphenyl at the 5-position to form 3-hydroxy-5-methoxybiphenyl. The enzyme showed absolute substrate preference for 3,5-dihydroxybiphenyl. The elicitor-treated apple cell cultures showed transient increases in the MdOMT (GenBank ID MF740747) and MdBIS3 (GenBank ID JQ390523) transcript levels followed by the accumulation of biphenyls (aucuparin and noraucuparin) and dibenzofuran (eriobofuran) phytoalexins. MdOMT fused with N- and C-terminal yellow fluorescent protein showed cytoplasmic localization in the epidermis of Nicotiana benthamiana leaves. In scab inoculated greenhouse-grown 'Florina' plants, the expression of MdOMT was transiently induced in the stem followed by the accumulation of biphenyl phytoalexins.
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Affiliation(s)
- Amol Sarkate
- Plant Molecular Biology Group, Biotechnology Department, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Shashank Sagar Saini
- Plant Molecular Biology Group, Biotechnology Department, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Mariam Gaid
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstrasse 1, 38106, Braunschweig, Germany
| | - Deepa Teotia
- Plant Molecular Biology Group, Biotechnology Department, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Javid Iqbal Mir
- Plant Biotechnology Department, Central Institute of Temperate Horticulture (ICAR-CITH), Srinagar, 190005, Jammu and Kashmir, India
| | | | - Ludger Beerhues
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstrasse 1, 38106, Braunschweig, Germany
| | - Debabrata Sircar
- Plant Molecular Biology Group, Biotechnology Department, Indian Institute of Technology Roorkee, Roorkee, 247667, India.
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20
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Chen W, Taylor MC, Barrow RA, Croyal M, Masle J. Loss of Phosphoethanolamine N-Methyltransferases Abolishes Phosphatidylcholine Synthesis and Is Lethal. Plant Physiol 2019; 179:124-142. [PMID: 30381317 PMCID: PMC6324220 DOI: 10.1104/pp.18.00694] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/19/2018] [Indexed: 05/21/2023]
Abstract
Plants use several pathways to synthesize phosphatidylcholine (PC), the major phospholipid of eukaryotic cells. PC has important structural and signaling roles. One pathway plants use for synthesis is the phospho-base methylation pathway, which forms the head-group phosphocholine through the triple methylation of phosphoethanolamine (PEA) catalyzed by phosphoethanolamine N-methyltransferases (PEAMTs). Our understanding of that pathway and its physiological importance remains limited. We recently reported that disruption of Arabidopsis thaliana PEAMT1/NMT1 and PEAMT3/NMT3 induces severe PC deficiency leading to dwarfism and impaired development. However, the double nmt1 nmt3 knock-out mutant is viable. Here, we show that this is enabled by residual PEAMT activity through a third family member, NMT2. The triple nmt1 nmt2 nmt3 knock-out mutant cannot synthesize PC from PEA and is lethal. This shows that, unlike mammals and yeast, Arabidopsis cannot form PC from phosphatidyl ethanolamine (PE), and demonstrates that methylation of PEA is the sole, and vital, entry point to PC synthesis. We further show that Arabidopsis has evolved an expanded family of four nonredundant PEAMTs through gene duplication and alternate use of the NMT2 promoter. NMT2 encodes two PEAMT variants, which greatly differ in their ability to perform the initial phospho-base methylation of PEA. Five amino acids at the N terminus of PEAMTs are shown to each be critical for the catalysis of that step committing to PC synthesis. As a whole, these findings open new avenues for enzymatic engineering and the exploration of ways to better tune phosphocholine and PC synthesis to environmental conditions for improved plant performance.
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Affiliation(s)
- Weihua Chen
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Matthew C Taylor
- Land and Water Flagship, Commonwealth Scientific and Industrial Research Organization, Canberra, Australian Capital Territory 2601, Australia
| | - Russell A Barrow
- Research School of Chemistry, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Mikaël Croyal
- CRNH Nantes, Mass Spectrometry Core facility, 8 Quai Moncousu BP-70721, Nantes cedex 1, France
| | - Josette Masle
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
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21
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Doxtader KA, Wang P, Scarborough AM, Seo D, Conrad NK, Nam Y. Structural Basis for Regulation of METTL16, an S-Adenosylmethionine Homeostasis Factor. Mol Cell 2018; 71:1001-1011.e4. [PMID: 30197297 PMCID: PMC6367934 DOI: 10.1016/j.molcel.2018.07.025] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 06/25/2018] [Accepted: 07/20/2018] [Indexed: 12/12/2022]
Abstract
S-adenosylmethionine (SAM) is an essential metabolite that acts as a cofactor for most methylation events in the cell. The N6-methyladenosine (m6A) methyltransferase METTL16 controls SAM homeostasis by regulating the abundance of SAM synthetase MAT2A mRNA in response to changing intracellular SAM levels. Here we present crystal structures of METTL16 in complex with MAT2A RNA hairpins to uncover critical molecular mechanisms underlying the regulated activity of METTL16. The METTL16-RNA complex structures reveal atomic details of RNA substrates that drive productive methylation by METTL16. In addition, we identify a polypeptide loop in METTL16 near the SAM binding site with an autoregulatory role. We show that mutations that enhance or repress METTL16 activity in vitro correlate with changes in MAT2A mRNA levels in cells. Thus, we demonstrate the structural basis for the specific activity of METTL16 and further suggest the molecular mechanisms by which METTL16 efficiency is tuned to regulate SAM homeostasis.
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Affiliation(s)
- Katelyn A Doxtader
- Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ping Wang
- Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Anna M Scarborough
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Dahee Seo
- Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nicholas K Conrad
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yunsun Nam
- Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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22
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Růžička K, Zhang M, Campilho A, Bodi Z, Kashif M, Saleh M, Eeckhout D, El‐Showk S, Li H, Zhong S, De Jaeger G, Mongan NP, Hejátko J, Helariutta Y, Fray RG. Identification of factors required for m 6 A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI. New Phytol 2017; 215:157-172. [PMID: 28503769 PMCID: PMC5488176 DOI: 10.1111/nph.14586] [Citation(s) in RCA: 251] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 03/19/2017] [Indexed: 05/04/2023]
Abstract
N6-adenosine methylation (m6 A) of mRNA is an essential process in most eukaryotes, but its role and the status of factors accompanying this modification are still poorly understood. Using combined methods of genetics, proteomics and RNA biochemistry, we identified a core set of mRNA m6 A writer proteins in Arabidopsis thaliana. The components required for m6 A in Arabidopsis included MTA, MTB, FIP37, VIRILIZER and the E3 ubiquitin ligase HAKAI. Downregulation of these proteins led to reduced relative m6 A levels and shared pleiotropic phenotypes, which included aberrant vascular formation in the root, indicating that correct m6 A methylation plays a role in developmental decisions during pattern formation. The conservation of these proteins amongst eukaryotes and the demonstration of a role in writing m6 A for the E3 ubiquitin ligase HAKAI is likely to be of considerable relevance beyond the plant sciences.
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Affiliation(s)
- Kamil Růžička
- Functional Genomics and Proteomics of PlantsCentral European Institute of Technology and National Centre for Biomolecular ResearchMasaryk University62500BrnoCzech Republic
- Institute of BiotechnologyUniversity of Helsinki00014HelsinkiFinland
| | - Mi Zhang
- Plant Sciences DivisionSchool of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughboroughLE12 5RDUK
| | - Ana Campilho
- Institute of BiotechnologyUniversity of Helsinki00014HelsinkiFinland
- Research Center in Biodiversity and Genetic ResourcesUniversity of Porto4485‐661 VairãoPortugal
| | - Zsuzsanna Bodi
- Plant Sciences DivisionSchool of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughboroughLE12 5RDUK
| | - Muhammad Kashif
- Institute of BiotechnologyUniversity of Helsinki00014HelsinkiFinland
| | - Mária Saleh
- Functional Genomics and Proteomics of PlantsCentral European Institute of Technology and National Centre for Biomolecular ResearchMasaryk University62500BrnoCzech Republic
| | - Dominique Eeckhout
- Department of Plant Systems BiologyVIB9052GentBelgium
- Department of Plant Biotechnology and BioinformaticsGhent University9052GentBelgium
| | - Sedeer El‐Showk
- Institute of BiotechnologyUniversity of Helsinki00014HelsinkiFinland
| | - Hongying Li
- Plant Sciences DivisionSchool of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughboroughLE12 5RDUK
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess PlateauMinistry of AgricultureTaiyuanShanxi030031China
| | - Silin Zhong
- Plant Sciences DivisionSchool of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughboroughLE12 5RDUK
- The State Key Laboratory of AgrobiotechnologyThe School of Life SciencesThe Chinese University of Hong KongHong KongChina
| | - Geert De Jaeger
- Department of Plant Systems BiologyVIB9052GentBelgium
- Department of Plant Biotechnology and BioinformaticsGhent University9052GentBelgium
| | - Nigel P. Mongan
- School of Veterinary Medicine and SciencesUniversity of NottinghamSutton BoningtonLoughboroughLE12 5RDUK
| | - Jan Hejátko
- Functional Genomics and Proteomics of PlantsCentral European Institute of Technology and National Centre for Biomolecular ResearchMasaryk University62500BrnoCzech Republic
| | - Ykä Helariutta
- Institute of BiotechnologyUniversity of Helsinki00014HelsinkiFinland
- Sainsbury LaboratoryUniversity of CambridgeCambridgeCB2 1LRUK
| | - Rupert G. Fray
- Plant Sciences DivisionSchool of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughboroughLE12 5RDUK
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23
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Qu L, Wu C, Zhang F, Wu Y, Fang C, Jin C, Liu X, Luo J. Rice putative methyltransferase gene OsTSD2 is required for root development involving pectin modification. J Exp Bot 2016; 67:5349-5362. [PMID: 27497286 PMCID: PMC5049386 DOI: 10.1093/jxb/erw297] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Pectin synthesis and modification are vital for plant development, although the underlying mechanisms are still not well understood. Here, we report the functional characterization of the OsTSD2 gene, which encodes a putative methyltransferase in rice. All three independent T-DNA insertion lines of OsTSD2 displayed dwarf phenotypes and serial alterations in different zones of the root. These alterations included abnormal cellular adhesion and schizogenous aerenchyma formation in the meristematic zone, inhibited root elongation in the elongation zone, and higher lateral root density in the mature zone. Immunofluorescence (with LM19) and Ruthenium Red staining of the roots showed that unesterified homogalacturonan (HG) was increased in Ostsd2 mutants. Biochemical analysis of cell wall pectin polysaccharides revealed that both the monosaccharide composition and the uronic acid content were decreased in Ostsd2 mutants. Increased endogenous ABA content and opposite roles performed by ABA and IAA in regulating cellular adhesion in the Ostsd2 mutants suggested that OsTSD2 is required for root development in rice through a pathway involving pectin synthesis/modification. A hypothesis to explain the relationship among OsTSD2, pectin methylesterification, and root development is proposed, based on pectin's function in regional cell extension/division in a zone-dependent manner.
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Affiliation(s)
- Lianghuan Qu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunyan Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Fei Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yangyang Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Chuanying Fang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Cheng Jin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xianqing Liu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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24
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Fu KY, Li Q, Zhou LT, Meng QW, Lü FG, Guo WC, Li GQ. Knockdown of juvenile hormone acid methyl transferase severely affects the performance of Leptinotarsa decemlineata (Say) larvae and adults. Pest Manag Sci 2016; 72:1231-1241. [PMID: 26299648 DOI: 10.1002/ps.4103] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Revised: 07/22/2015] [Accepted: 08/13/2015] [Indexed: 06/04/2023]
Abstract
BACKGROUND Juvenile hormone (JH) plays a critical role in the regulation of metamorphosis in Leptinotarsa decemlineata, a notorious defoliator of potato. JH acid methyltransferase (JHAMT) is involved in one of the final steps of JH biosynthesis. RESULTS A putative JHAMT cDNA (LdJHAMT) was cloned. Two double-stranded RNAs (dsRNAs) (dsJHAMT1 and dsJHAMT2) against LdJHAMT were constructed and bacterially expressed. Experiments were conducted to investigate the effectiveness of RNAi in both second- and fourth-instar larvae. Dietary introduction of dsJHAMT1 and dsJHAMT2 successfully knocked down the target gene, lowered JH titre in the haemolymph and reduced the transcript of Krüppel homologue 1 gene. Ingestion of dsJHAMT caused larval death and weight loss, shortened larval developmental period and impaired pupation. Moreover, the dsJHAMT-fed pupae exhibited lower adult emergence rates. The resulting adults weighed an average of 50 mg less than the control group, and the females did not deposit eggs. Application of pyriproxyfen to the dsJHAMT-fed insects rescued all the negative effects. CONCLUSIONS LdJHAMT expresses functional JHAMT enzyme. The RNAi targeting LdJHAMT could be used for control of L. decemlineata. © 2015 Society of Chemical Industry.
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Affiliation(s)
- Kai-Yun Fu
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Qian Li
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Li-Tao Zhou
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Qing-Wei Meng
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Feng-Gong Lü
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Wen-Chao Guo
- Department of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Guo-Qing Li
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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25
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Linde T, Zoglowek M, Lübeck M, Frisvad JC, Lübeck PS. The global regulator LaeA controls production of citric acid and endoglucanases in Aspergillus carbonarius. J Ind Microbiol Biotechnol 2016; 43:1139-47. [PMID: 27169528 DOI: 10.1007/s10295-016-1781-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 04/28/2016] [Indexed: 01/11/2023]
Abstract
The global regulatory protein LaeA is known for regulating the production of many kinds of secondary metabolites in Aspergillus species, as well as sexual and asexual reproduction, and morphology. In Aspergillus carbonarius, it has been shown that LaeA regulates production of ochratoxin. We have investigated the regulatory effect of LaeA on production of citric acid and cellulolytic enzymes in A. carbonarius. Two types of A. carbonarius strains, having laeA knocked out or overexpressed, were constructed and tested in fermentation. The knockout of laeA significantly decreased the production of citric acid and endoglucanases, but did not reduce the production of beta-glucosidases or xylanases. The citric acid accumulation was reduced with 74-96 % compared to the wild type. The endoglucanase activity was reduced with 51-78 %. Overexpression of LaeA seemed not to have an effect on citric acid production or on cellulose or xylanase activity.
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Affiliation(s)
- Tore Linde
- Section for Sustainable Biotechnology, Aalborg University, A.C. Meyers Vaenge 15, 2450, Copenhagen SV, Denmark
| | - Marta Zoglowek
- Carlsberg Research Laboratory, Yeast & Fermentation, Group Commercial, Gamle Carlsberg Vej 4, 1799, Copenhagen V, Denmark
| | - Mette Lübeck
- Section for Sustainable Biotechnology, Aalborg University, A.C. Meyers Vaenge 15, 2450, Copenhagen SV, Denmark
| | - Jens Christian Frisvad
- DTU, Institute for System-biologi, Fungal Chemodiversity, Søltofts Plads, 2800, Kgs. Lyngby, Denmark
| | - Peter Stephensen Lübeck
- Section for Sustainable Biotechnology, Aalborg University, A.C. Meyers Vaenge 15, 2450, Copenhagen SV, Denmark.
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26
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Al-Hadid Q, Roy K, Chanfreau G, Clarke SG. Methylation of yeast ribosomal protein Rpl3 promotes translational elongation fidelity. RNA 2016; 22:489-98. [PMID: 26826131 PMCID: PMC4793205 DOI: 10.1261/rna.054569.115] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 12/14/2015] [Indexed: 05/05/2023]
Abstract
Rpl3, a highly conserved ribosomal protein, is methylated at histidine 243 by the Hpm1 methyltransferase in Saccharomyces cerevisiae. Histidine 243 lies close to the peptidyl transferase center in a functionally important region of Rpl3 designated as the basic thumb that coordinates the decoding, peptidyl transfer, and translocation steps of translation elongation. Hpm1 was recently implicated in ribosome biogenesis and translation. However, the biological role of methylation of its Rpl3 substrate has not been identified. Here we interrogate the role of Rpl3 methylation at H243 by investigating the functional impact of mutating this histidine residue to alanine (rpl3-H243A). Akin to Hpm1-deficient cells, rpl3-H243A cells accumulate 35S and 23S pre-rRNA precursors to a similar extent, confirming an important role for histidine methylation in pre-rRNA processing. In contrast, Hpm1-deficient cells but not rpl3-H243A mutants show perturbed levels of ribosomal subunits. We show that Hpm1 has multiple substrates in different subcellular fractions, suggesting that methylation of proteins other than Rpl3 may be important for controlling ribosomal subunit levels. Finally, translational fidelity assays demonstrate that like Hpm1-deficient cells, rpl3-H243A mutants have defects in translation elongation resulting in decreased translational accuracy. These data suggest that Rpl3 methylation at H243 is playing a significant role in translation elongation, likely via the basic thumb, but has little impact on ribosomal subunit levels. Hpm1 is therefore a multifunctional methyltransferase with independent roles in ribosome biogenesis and translation.
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Affiliation(s)
- Qais Al-Hadid
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Kevin Roy
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Guillaume Chanfreau
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Steven G Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
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27
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Nakamoto M, Schmit AC, Heintz D, Schaller H, Ohta D. Diversification of sterol methyltransferase enzymes in plants and a role for β-sitosterol in oriented cell plate formation and polarized growth. Plant J 2015; 84:860-74. [PMID: 26426526 DOI: 10.1111/tpj.13043] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 09/16/2015] [Accepted: 09/18/2015] [Indexed: 05/06/2023]
Abstract
Phytosterols are classified into C24-ethylsterols and C24-methylsterols according to the different C24-alkylation levels conferred by two types of sterol methyltransferases (SMTs). The first type of SMT (SMT1) is widely conserved, whereas the second type (SMT2) has diverged in charophytes and land plants. The Arabidopsis smt2 smt3 mutant is defective in the SMT2 step, leading to deficiency in C24-ethylsterols while the C24-methylsterol pathway is unchanged. smt2 smt3 plants exhibit severe dwarfism and abnormal development throughout their life cycle, with irregular cell division followed by collapsed cell files. Preprophase bands are occasionally formed in perpendicular directions in adjacent cells, and abnormal phragmoplasts with mislocalized KNOLLE syntaxin and tubulin are observed. Defects in auxin-dependent processes are exemplified by mislocalizations of the PIN2 auxin efflux carrier due to disrupted cell division and failure to distribute PIN2 asymmetrically after cytokinesis. Although endocytosis of PIN2-GFP from the plasma membrane (PM) is apparently unaffected in smt2 smt3, strong inhibition of the endocytic recycling is associated with a remarkable reduction in the level of PIN2-GFP on the PM. Aberrant localization of the cytoplasmic linker associated protein (CLASP) and microtubules is implicated in the disrupted endocytic recycling in smt2 smt3. Exogenous C24-ethylsterols partially recover lateral root development and auxin distribution in smt2 smt3 roots. These results indicate that C24-ethylsterols play a crucial role in division plane determination, directional auxin transport, and polar growth. It is proposed that the divergence of SMT2 genes together with the ability to produce C24-ethylsterols were critical events to achieve polarized growth in the plant lineage.
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Affiliation(s)
- Masatoshi Nakamoto
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 599-8531, Sakai, Japan
| | - Anne-Catherine Schmit
- Institut de Biologie Moléculaire des Plantes, CNRS, UPR2357, Conventionné Avec l'Université de Strasbourg, 67084, Strasbourg, France
| | - Dimitri Heintz
- Institut de Biologie Moléculaire des Plantes, CNRS, UPR2357, Conventionné Avec l'Université de Strasbourg, 67084, Strasbourg, France
| | - Hubert Schaller
- Institut de Biologie Moléculaire des Plantes, CNRS, UPR2357, Conventionné Avec l'Université de Strasbourg, 67084, Strasbourg, France
| | - Daisaku Ohta
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 599-8531, Sakai, Japan
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Abstract
PURPOSE Given the toxic nature and narrow therapeutic index of traditional chemotherapeutics, better methods of dose and therapy selection are critical. Pharmacological methods, including pharmacogenomics and pharmacokinetics, offer a practical method to enrich drug exposure, reduce toxicity, and improve quality of life for patients. METHODS PubMed and key abstracts from the American Society of Clinical Oncology (ASCO) and American Association for Cancer Research (AACR) were searched until July 2015 for clinical data relating to pharmacogenomic- and/or pharmacokinetic-guided dosing of anticancer drugs. RESULTS Based on the results returned from a thorough search of the literature and the plausibility of utilizing pharmacogenomic and/or pharmacokinetic methods to personalize chemotherapy dosing, we identified several chemotherapeutic agents with the potential for therapy individualization. We highlight the available data, clinical validity, and utility of using pharmacogenomics to personalize therapy for tamoxifen, 5-fluorouracil, mercaptopurine, and irinotecan, in addition to using pharmacokinetics to personalize dosing for 5-fluorouracil, busulfan, methotrexate, taxanes, and topotecan. CONCLUSION A concerted effort should be made by researchers to further elucidate the role of pharmacological methods in personalizing chemotherapy dosing to optimize the risk-benefit profile. Clinicians should be aware of the clinical validity, utility, and availability of pharmacogenomic- and pharmacokinetic-guided therapies in clinical practice, to ultimately allow optimal dosing for each and every cancer patient.
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Affiliation(s)
- Jai N Patel
- Department of Cancer Pharmacology, Levine Cancer Institute, Carolinas HealthCare System, 1021 Morehead Medical Drive, Charlotte, NC, 28204, USA.
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Haziza S, Magnani R, Lan D, Keinan O, Saada A, Hershkovitz E, Yanay N, Cohen Y, Nevo Y, Houtz RL, Sheffield VC, Golan H, Parvari R. Calmodulin Methyltransferase Is Required for Growth, Muscle Strength, Somatosensory Development and Brain Function. PLoS Genet 2015; 11:e1005388. [PMID: 26247364 PMCID: PMC4527749 DOI: 10.1371/journal.pgen.1005388] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 06/23/2015] [Indexed: 01/11/2023] Open
Abstract
Calmodulin lysine methyl transferase (CaM KMT) is ubiquitously expressed and highly conserved from plants to vertebrates. CaM is frequently trimethylated at Lys-115, however, the role of CaM methylation in vertebrates has not been studied. CaM KMT was found to be homozygously deleted in the 2P21 deletion syndrome that includes 4 genes. These patients present with cystinuria, severe intellectual disabilities, hypotonia, mitochondrial disease and facial dysmorphism. Two siblings with deletion of three of the genes included in the 2P21 deletion syndrome presented with cystinuria, hypotonia, a mild/moderate mental retardation and a respiratory chain complex IV deficiency. To be able to attribute the functional significance of the methylation of CaM in the mouse and the contribution of CaM KMT to the clinical presentation of the 2p21deletion patients, we produced a mouse model lacking only CaM KMT with deletion borders as in the human 2p21deletion syndrome. No compensatory activity for CaM methylation was found. Impairment of complexes I and IV, and less significantly III, of the mitochondrial respiratory chain was more pronounced in the brain than in muscle. CaM KMT is essential for normal body growth and somatosensory development, as well as for the proper functioning of the adult mouse brain. Developmental delay was demonstrated for somatosensory function and for complex behavior, which involved both basal motor function and motivation. The mutant mice also had deficits in motor learning, complex coordination and learning of aversive stimuli. The mouse model contributes to the evaluation of the role of methylated CaM. CaM methylation appears to have a role in growth, muscle strength, somatosensory development and brain function. The current study has clinical implications for human patients. Patients presenting slow growth and muscle weakness that could result from a mitochondrial impairment and mental retardation should be considered for sequence analysis of the CaM KMT gene. Calmodulin (CaM) is a highly abundant, ubiquitous, small protein, which plays a major role in the transmission of calcium signals to target proteins in eukaryotes. Hundreds of CaM targets are known, and their respective cellular functions include signaling, metabolism, cytoskeletal regulation, and ion channel regulation, to name but a few. CaM is frequently modified after translation, including frequently trimethylation at a single amino acid, however, the role of this methylation is not known. Human patients with a homozygous deletion of the gene that methylates CaM, CaM-KMT, are known, but they also have a deletion of additional genes. Thus, to study the role of CaM–KMT, we produced a mouse model in which CaM-KMT is the only deleted gene, with the deletion constructed as in the human patients. The model proved to reveal the function of methylation of CaM, since CaM was found to be non-methylated and the methylation of CaM found to be important in growth, muscle strength, somatosensory development and brain function. The current study also has clinical implications for human patients. Patients presenting slow growth and muscle weakness that could result from a mitochondrial impairment and mental retardation should be considered for sequence analysis of the CaM KMT gene.
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Affiliation(s)
- Sitvanit Haziza
- Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Roberta Magnani
- Department of Horticulture, University of Kentucky, Lexington, Kentucky, United States of America
| | - Dima Lan
- Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Omer Keinan
- Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ann Saada
- Department of Genetic and Metabolic Diseases, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Eli Hershkovitz
- Pediatric Endocrinology & Metabolism Unit, Soroka Medical Center, Beer Sheva, Israel
| | - Nurit Yanay
- Pediatric Neuromuscular Laboratory and Pediatric Neurology Unit Hadassah, Hebrew University Medical Center, Jerusalem, Israel
| | - Yoram Cohen
- Pesticides and Mycotoxins Division, Aminolab, Weizmann Science Park, Ness Ziona, Israel
| | - Yoram Nevo
- Pediatric Neuromuscular Laboratory and Pediatric Neurology Unit Hadassah, Hebrew University Medical Center, Jerusalem, Israel
- Institute of Neurology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Robert L. Houtz
- Department of Horticulture, University of Kentucky, Lexington, Kentucky, United States of America
| | - Val C. Sheffield
- Department of Pediatrics, Division of Medical Genetics and Hughes Medical Institute, University of Iowa, Iowa City, Iowa, United States of America
| | - Hava Golan
- Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ruti Parvari
- Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- National Institute of Biotechnology in the Negev, Ben Gurion University of the Negev, Beer Sheva, Israel
- * E-mail:
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Haag S, Kretschmer J, Bohnsack MT. WBSCR22/Merm1 is required for late nuclear pre-ribosomal RNA processing and mediates N7-methylation of G1639 in human 18S rRNA. RNA 2015; 21:180-7. [PMID: 25525153 PMCID: PMC4338346 DOI: 10.1261/rna.047910.114] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 11/11/2014] [Indexed: 05/10/2023]
Abstract
Ribosomal (r)RNAs are extensively modified during ribosome synthesis and their modification is required for the fidelity and efficiency of translation. Besides numerous small nucleolar RNA-guided 2'-O methylations and pseudouridinylations, a number of individual RNA methyltransferases are involved in rRNA modification. WBSCR22/Merm1, which is affected in Williams-Beuren syndrome and has been implicated in tumorigenesis and metastasis formation, was recently shown to be involved in ribosome synthesis, but its molecular functions have remained elusive. Here we show that depletion of WBSCR22 leads to nuclear accumulation of 3'-extended 18SE pre-rRNA intermediates resulting in impaired 18S rRNA maturation. We map the 3' ends of the 18SE pre-rRNA intermediates accumulating after depletion of WBSCR22 and in control cells using 3'-RACE and deep sequencing. Furthermore, we demonstrate that WBSCR22 is required for N(7)-methylation of G1639 in human 18S rRNA in vivo. Interestingly, the catalytic activity of WBSCR22 is not required for 18S pre-rRNA processing, suggesting that the key role of WBSCR22 in 40S subunit biogenesis is independent of its function as an RNA methyltransferase.
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Affiliation(s)
- Sara Haag
- Centre for Biochemistry and Molecular Cell Biology, Georg-August-University, 37073 Göttingen, Germany
| | - Jens Kretschmer
- Centre for Biochemistry and Molecular Cell Biology, Georg-August-University, 37073 Göttingen, Germany
| | - Markus T Bohnsack
- Centre for Biochemistry and Molecular Cell Biology, Georg-August-University, 37073 Göttingen, Germany Göttingen Centre for Molecular Biosciences, Georg-August-University, 37073 Göttingen, Germany
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Van Ekert E, Powell CA, Shatters RG, Borovsky D. Control of larval and egg development in Aedes aegypti with RNA interference against juvenile hormone acid methyl transferase. J Insect Physiol 2014; 70:143-150. [PMID: 25111689 DOI: 10.1016/j.jinsphys.2014.08.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Revised: 07/31/2014] [Accepted: 08/02/2014] [Indexed: 06/03/2023]
Abstract
RNA interference (RNAi) is a powerful approach for elucidating gene functions in a variety of organisms, including mosquitoes and many other insects. Little has been done, however, to harness this approach in order to control adult and larval mosquitoes. Juvenile hormone (JH) plays a pivotal role in the control of reproduction in adults and metamorphism in larval mosquitoes. This report describes an approach to control Aedes aegypti using RNAi against JH acid methyl transferase (AeaJHAMT), the ultimate enzyme in the biosynthetic pathway of JH III that converts JH acid III (JHA III) into JH III. In female A. aegypti that were injected or fed jmtA dsRNA targeting the AeaJHAMT gene (jmtA) transcript, egg development was inhibited in 50% of the treated females. In mosquito larvae that were fed transgenic Pichia pastoris cells expressing long hair pin (LHP) RNA, adult eclosion was delayed by 3 weeks causing high mortality. Northern blot analyses and qPCR studies show that jmtA dsRNA causes inhibition of jmtA transcript in adults and larvae, which is consistent with the observed inhibition of egg maturation and larval development. Taken together, these results suggest that jmtA LHP RNA expressed in heat inactivated genetically modified P. pastoris cells could be used to control mosquito populations in the marsh.
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Affiliation(s)
- Evelien Van Ekert
- Indian River Research and Education Center, University of Florida, FL 34945, USA
| | - Charles A Powell
- Indian River Research and Education Center, University of Florida, FL 34945, USA
| | | | - Dov Borovsky
- Borovsky Consulting, 135 36th Court, Vero Beach, FL 32968, USA.
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32
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Abstract
Biological responses due to nutrient deprivation in the nematode Caenorhabditis elegans, including L1 diapause and autophagy during dauer formation, can be mediated through the linked DAF-2/insulin/IGF receptor and target-of-rapamycin (TOR) kinase pathways. Here we discuss how altered insulin/TOR signaling may underlie the previously reported phenotypes of worms with a null mutation in the pcm-1 gene that results in reduced autophagy during dauer formation and decreased L1 arrest survival. PCM-1 encodes a protein repair methyltransferase and mutants of the encoding pcm-1 gene are incapable of converting spontaneously damaged l-isoaspartyl residues in cellular proteins to normal forms by this pathway. We speculate that PCM-1 may function either directly or indirectly as an inhibitor of insulin/TOR signaling, perhaps in a role to balance autophagy with alternative protein degradation pathways that may be more specific for recognizing age-damaged proteins.
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Affiliation(s)
- Tara A Gomez
- Department of Chemistry and Biochemistry, Molecular Biology Institute, University of California, Los Angeles, California 90095, USA
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Pandey M, Sahay S, Tiwari P, Upadhyay DS, Sultana S, Gupta KP. Involvement of EZH2, SUV39H1, G9a and associated molecules in pathogenesis of urethane induced mouse lung tumors: potential targets for cancer control. Toxicol Appl Pharmacol 2014; 280:296-304. [PMID: 25168426 DOI: 10.1016/j.taap.2014.08.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 08/04/2014] [Accepted: 08/14/2014] [Indexed: 01/13/2023]
Abstract
In the present study, we showed the correlation of EZH2, SUV39H1 or G9a expression and histone modifications with the urethane induced mouse lung tumorigenesis in the presence or absence of antitumor agent, inositol hexaphosphate (IP6). Tumorigenesis and the molecular events involved therein were studied at 1, 4, 12 or 36 weeks after the exposure. There were no tumors at 1 or 4 weeks but tumors started appearing at 12 weeks and grew further till 36 weeks after urethane exposure. Among the molecular events, upregulation of EZH2 and SUV39H1 expressions appeared to be time dependent, but G9a expression was altered significantly only at later stages of 12 or 36 weeks. Alteration in miR-138 expression supports the upregulation of its target, EZH2. H3K9me2, H3K27me3 or H4K20me3 was found to be altered at 12 or 36 weeks. However, ChIP analysis of p16 and MLH1 promoters showed their binding with H3K9me2 and H3K27me3 which was maximum at 36 weeks. Thus, histone modification and their interactions with gene promoter resulted in the reduced expression of p16 and MLH1. IP6 prevented the incidence and the size of urethane induced lung tumors. IP6 also prevented the urethane induced alterations in EZH2, SUV39H1, G9a expressions and histone modifications. Our results suggest that the alterations in the histone modification pathways involving EZH2 and SUV39H1 expressions are among the early events in urethane induced mouse lung tumorigenesis and could be exploited for cancer control.
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Affiliation(s)
- Manuraj Pandey
- Carcinogenesis Laboratory, CSIR-Indian Institute of Toxicology Research, Mahatma Gandhi Marg, Lucknow -226001, India
| | - Satya Sahay
- Carcinogenesis Laboratory, CSIR-Indian Institute of Toxicology Research, Mahatma Gandhi Marg, Lucknow -226001, India
| | - Prakash Tiwari
- Carcinogenesis Laboratory, CSIR-Indian Institute of Toxicology Research, Mahatma Gandhi Marg, Lucknow -226001, India
| | - Daya S Upadhyay
- Laboratory Animals Services, CSIR-Central Drug Research Institute, Sitapur Road, Lucknow, India
| | - Sarwat Sultana
- Dept. Medical Elementology and Toxicology, Jamia Hamdard, Hamdard Nagar, New Delhi, India
| | - Krishna P Gupta
- Carcinogenesis Laboratory, CSIR-Indian Institute of Toxicology Research, Mahatma Gandhi Marg, Lucknow -226001, India.
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Al-Sady B, Madhani HD, Narlikar GJ. Division of labor between the chromodomains of HP1 and Suv39 methylase enables coordination of heterochromatin spread. Mol Cell 2013; 51:80-91. [PMID: 23849629 DOI: 10.1016/j.molcel.2013.06.013] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 05/15/2013] [Accepted: 06/20/2013] [Indexed: 01/22/2023]
Abstract
In Schizosaccharomyces pombe, heterochromatin spread, which is marked by histone 3 lysine 9 methylation (H3K9me), requires the chromodomains (CDs) of the H3K9 methylase Suv39/Clr4 and the HP1/Swi6 protein. It is unclear how the actions of these two H3K9me-recognizing CDs are coordinated. We find that the intrinsic preference of Suv39/Clr4 is to generate dimethylated H3K9 product. The recognition of pre-existing H3K9me marks by the CD of Suv39/Clr4 stimulates overall catalysis, enabling the accumulation of small amounts of trimethylated product in vivo. Coincidentally, the Suv39/Clr4 CD, unlike the HP1/Swi6 CD, has been shown to prefer the trimethyl state over the dimethyl state. We show that this preference enables efficient heterochromatin spread in vivo by reducing competition with HP1 proteins for the more prevalent dimethyl state. Our results reveal a strategy by which "writers" and "readers" of a chromatin mark exploit different methylation states on the same residue in order to facilitate collaboration and avoid competition.
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Affiliation(s)
- Bassem Al-Sady
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
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35
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Millán M, Castro-Fernández M, Ampuero J, Romero-Gómez M. [Myelotoxicity due to interaction between azathioprine and allopurinol in a patient with Crohn's disease]. Gastroenterol Hepatol 2013; 36:298-299. [PMID: 23274032 DOI: 10.1016/j.gastrohep.2012.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 10/15/2012] [Indexed: 06/01/2023]
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Latrasse D, Jégu T, Meng PH, Mazubert C, Hudik E, Delarue M, Charon C, Crespi M, Hirt H, Raynaud C, Bergounioux C, Benhamed M. Dual function of MIPS1 as a metabolic enzyme and transcriptional regulator. Nucleic Acids Res 2013; 41:2907-17. [PMID: 23341037 PMCID: PMC3597657 DOI: 10.1093/nar/gks1458] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 12/07/2012] [Accepted: 12/14/2012] [Indexed: 12/16/2022] Open
Abstract
Because regulation of its activity is instrumental either to support cell proliferation and growth or to promote cell death, the universal myo-inositol phosphate synthase (MIPS), responsible for myo-inositol biosynthesis, is a critical enzyme of primary metabolism. Surprisingly, we found this enzyme to be imported in the nucleus and to interact with the histone methyltransferases ATXR5 and ATXR6, raising the question of whether MIPS1 has a function in transcriptional regulation. Here, we demonstrate that MIPS1 binds directly to its promoter to stimulate its own expression by locally inhibiting the spreading of ATXR5/6-dependent heterochromatin marks coming from a transposable element. Furthermore, on activation of pathogen response, MIPS1 expression is reduced epigenetically, providing evidence for a complex regulatory mechanism acting at the transcriptional level. Thus, in plants, MIPS1 appears to have evolved as a protein that connects cellular metabolism, pathogen response and chromatin remodeling.
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Affiliation(s)
- David Latrasse
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France, Institute of Horticulture, Guizhou Academy of Agricultural Sciences, GuiYang, Guizhou Province, 550006, P.R. China, Institut des Sciences du Végétal, UPR CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France and URGV Plant Genomics, INRA/CNRS/University of Evry, 2 rue Gaston Cremieux, 91057 Evry, France
| | - Teddy Jégu
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France, Institute of Horticulture, Guizhou Academy of Agricultural Sciences, GuiYang, Guizhou Province, 550006, P.R. China, Institut des Sciences du Végétal, UPR CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France and URGV Plant Genomics, INRA/CNRS/University of Evry, 2 rue Gaston Cremieux, 91057 Evry, France
| | - Pin-Hong Meng
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France, Institute of Horticulture, Guizhou Academy of Agricultural Sciences, GuiYang, Guizhou Province, 550006, P.R. China, Institut des Sciences du Végétal, UPR CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France and URGV Plant Genomics, INRA/CNRS/University of Evry, 2 rue Gaston Cremieux, 91057 Evry, France
| | - Christelle Mazubert
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France, Institute of Horticulture, Guizhou Academy of Agricultural Sciences, GuiYang, Guizhou Province, 550006, P.R. China, Institut des Sciences du Végétal, UPR CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France and URGV Plant Genomics, INRA/CNRS/University of Evry, 2 rue Gaston Cremieux, 91057 Evry, France
| | - Elodie Hudik
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France, Institute of Horticulture, Guizhou Academy of Agricultural Sciences, GuiYang, Guizhou Province, 550006, P.R. China, Institut des Sciences du Végétal, UPR CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France and URGV Plant Genomics, INRA/CNRS/University of Evry, 2 rue Gaston Cremieux, 91057 Evry, France
| | - Marianne Delarue
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France, Institute of Horticulture, Guizhou Academy of Agricultural Sciences, GuiYang, Guizhou Province, 550006, P.R. China, Institut des Sciences du Végétal, UPR CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France and URGV Plant Genomics, INRA/CNRS/University of Evry, 2 rue Gaston Cremieux, 91057 Evry, France
| | - Céline Charon
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France, Institute of Horticulture, Guizhou Academy of Agricultural Sciences, GuiYang, Guizhou Province, 550006, P.R. China, Institut des Sciences du Végétal, UPR CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France and URGV Plant Genomics, INRA/CNRS/University of Evry, 2 rue Gaston Cremieux, 91057 Evry, France
| | - Martin Crespi
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France, Institute of Horticulture, Guizhou Academy of Agricultural Sciences, GuiYang, Guizhou Province, 550006, P.R. China, Institut des Sciences du Végétal, UPR CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France and URGV Plant Genomics, INRA/CNRS/University of Evry, 2 rue Gaston Cremieux, 91057 Evry, France
| | - Heribert Hirt
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France, Institute of Horticulture, Guizhou Academy of Agricultural Sciences, GuiYang, Guizhou Province, 550006, P.R. China, Institut des Sciences du Végétal, UPR CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France and URGV Plant Genomics, INRA/CNRS/University of Evry, 2 rue Gaston Cremieux, 91057 Evry, France
| | - Cécile Raynaud
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France, Institute of Horticulture, Guizhou Academy of Agricultural Sciences, GuiYang, Guizhou Province, 550006, P.R. China, Institut des Sciences du Végétal, UPR CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France and URGV Plant Genomics, INRA/CNRS/University of Evry, 2 rue Gaston Cremieux, 91057 Evry, France
| | - Catherine Bergounioux
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France, Institute of Horticulture, Guizhou Academy of Agricultural Sciences, GuiYang, Guizhou Province, 550006, P.R. China, Institut des Sciences du Végétal, UPR CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France and URGV Plant Genomics, INRA/CNRS/University of Evry, 2 rue Gaston Cremieux, 91057 Evry, France
| | - Moussa Benhamed
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France, Institute of Horticulture, Guizhou Academy of Agricultural Sciences, GuiYang, Guizhou Province, 550006, P.R. China, Institut des Sciences du Végétal, UPR CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France and URGV Plant Genomics, INRA/CNRS/University of Evry, 2 rue Gaston Cremieux, 91057 Evry, France
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Zueva E, Allan RS, Cammas F, Schreiber HA, Masson V, Belz GT, Roche D, Maison C, Quivy JP, Almouzni G, Amigorena S. [Epigenetic control of Th2 helper cell differentiation by the Suv39h1/HP1α pathway]. Med Sci (Paris) 2012; 28:1032-4. [PMID: 23290393 DOI: 10.1051/medsci/20122812003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Benítez-Páez A, Villarroya M, Armengod ME. The Escherichia coli RlmN methyltransferase is a dual-specificity enzyme that modifies both rRNA and tRNA and controls translational accuracy. RNA 2012; 18:1783-1795. [PMID: 22891362 PMCID: PMC3446703 DOI: 10.1261/rna.033266.112] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 06/26/2012] [Indexed: 05/28/2023]
Abstract
Modifying RNA enzymes are highly specific for substrate-rRNA or tRNA-and the target position. In Escherichia coli, there are very few multisite acting enzymes, and only one rRNA/tRNA dual-specificity enzyme, pseudouridine synthase RluA, has been identified to date. Among the tRNA-modifying enzymes, the methyltransferase responsible for the m(2)A synthesis at purine 37 in a tRNA set still remains unknown. m(2)A is also present at position 2503 in the peptidyl transferase center of 23S RNA, where it is introduced by RlmN, a radical S-adenosyl-L-methionine (SAM) enzyme. Here, we show that E. coli RlmN is a dual-specificity enzyme that catalyzes methylation of both rRNA and tRNA. The ΔrlmN mutant lacks m(2)A in both RNA types, whereas the expression of recombinant RlmN from a plasmid introduced into this mutant restores tRNA modification. Moreover, RlmN performs m(2)A(37) synthesis in vitro using a tRNA chimera as a substrate. This chimera has also proved useful to characterize some tRNA identity determinants for RlmN and other tRNA modification enzymes. Our data suggest that RlmN works in a late step during tRNA maturation by recognizing a precise 3D structure of tRNA. RlmN inactivation increases the misreading of a UAG stop codon. Since loss of m(2)A(37) from tRNA is expected to produce a hyperaccurate phenotype, we believe that the error-prone phenotype exhibited by the ΔrlmN mutant is due to loss of m(2)A from 23S rRNA and, accordingly, that the m(2)A2503 modification plays a crucial role in the proofreading step occurring at the peptidyl transferase center.
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Affiliation(s)
- Alfonso Benítez-Páez
- Laboratorio de Genética Molecular, Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain
- Bioinformatic Analysis Group—GABi, Centro de Investigación y Desarrollo en Biotecnología, Bogotá D.C., 111221 Colombia
| | - Magda Villarroya
- Laboratorio de Genética Molecular, Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain
| | - M.-Eugenia Armengod
- Laboratorio de Genética Molecular, Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Unidad 721, Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain
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O’Hanlon KA, Margison GP, Hatch A, Fitzpatrick DA, Owens RA, Doyle S, Jones GW. Molecular characterization of an adaptive response to alkylating agents in the opportunistic pathogen Aspergillus fumigatus. Nucleic Acids Res 2012; 40:7806-20. [PMID: 22669901 PMCID: PMC3439912 DOI: 10.1093/nar/gks522] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An adaptive response to alkylating agents based upon the conformational change of a methylphosphotriester (MPT) DNA repair protein to a transcriptional activator has been demonstrated in a number of bacterial species, but this mechanism appears largely absent from eukaryotes. Here, we demonstrate that the human pathogen Aspergillus fumigatus elicits an adaptive response to sub-lethal doses of the mono-functional alkylating agent N-methyl-N'-nitro-N-nitrosoguanidine (MNNG). We have identified genes that encode MPT and O(6)-alkylguanine DNA alkyltransferase (AGT) DNA repair proteins; deletions of either of these genes abolish the adaptive response and sensitize the organism to MNNG. In vitro DNA repair assays confirm the ability of MPT and AGT to repair methylphosphotriester and O(6)-methylguanine lesions respectively. In eukaryotes, the MPT protein is confined to a select group of fungal species, some of which are major mammalian and plant pathogens. The evolutionary origin of the adaptive response is bacterial and rooted within the Firmicutes phylum. Inter-kingdom horizontal gene transfer between Firmicutes and Ascomycete ancestors introduced the adaptive response into the Fungal kingdom. Our data constitute the first detailed characterization of the molecular mechanism of the adaptive response in a lower eukaryote and has applications for development of novel fungal therapeutics targeting this DNA repair system.
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Affiliation(s)
- Karen A. O’Hanlon
- Biotechnology Laboratory, Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland, Cancer Research-UK Carcinogenesis Group, Paterson Institute for Cancer Research, University of Manchester, Manchester M20 4BX, UK, Genome Evolution Laboratory and Yeast Genetics Laboratory, Department of Biology, National University of Ireland Maynooth, Maynooth, County Kildare, Ireland
| | - Geoffrey P. Margison
- Biotechnology Laboratory, Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland, Cancer Research-UK Carcinogenesis Group, Paterson Institute for Cancer Research, University of Manchester, Manchester M20 4BX, UK, Genome Evolution Laboratory and Yeast Genetics Laboratory, Department of Biology, National University of Ireland Maynooth, Maynooth, County Kildare, Ireland
| | - Amy Hatch
- Biotechnology Laboratory, Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland, Cancer Research-UK Carcinogenesis Group, Paterson Institute for Cancer Research, University of Manchester, Manchester M20 4BX, UK, Genome Evolution Laboratory and Yeast Genetics Laboratory, Department of Biology, National University of Ireland Maynooth, Maynooth, County Kildare, Ireland
| | - David A. Fitzpatrick
- Biotechnology Laboratory, Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland, Cancer Research-UK Carcinogenesis Group, Paterson Institute for Cancer Research, University of Manchester, Manchester M20 4BX, UK, Genome Evolution Laboratory and Yeast Genetics Laboratory, Department of Biology, National University of Ireland Maynooth, Maynooth, County Kildare, Ireland
| | - Rebecca A. Owens
- Biotechnology Laboratory, Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland, Cancer Research-UK Carcinogenesis Group, Paterson Institute for Cancer Research, University of Manchester, Manchester M20 4BX, UK, Genome Evolution Laboratory and Yeast Genetics Laboratory, Department of Biology, National University of Ireland Maynooth, Maynooth, County Kildare, Ireland
| | - Sean Doyle
- Biotechnology Laboratory, Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland, Cancer Research-UK Carcinogenesis Group, Paterson Institute for Cancer Research, University of Manchester, Manchester M20 4BX, UK, Genome Evolution Laboratory and Yeast Genetics Laboratory, Department of Biology, National University of Ireland Maynooth, Maynooth, County Kildare, Ireland
| | - Gary W. Jones
- Biotechnology Laboratory, Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland, Cancer Research-UK Carcinogenesis Group, Paterson Institute for Cancer Research, University of Manchester, Manchester M20 4BX, UK, Genome Evolution Laboratory and Yeast Genetics Laboratory, Department of Biology, National University of Ireland Maynooth, Maynooth, County Kildare, Ireland
- *To whom correspondence should be addressed. Tel: +353 1 708 3839; Fax: +353 1 708 3845;
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Heaslip AT, Nishi M, Stein B, Hu K. The motility of a human parasite, Toxoplasma gondii, is regulated by a novel lysine methyltransferase. PLoS Pathog 2011; 7:e1002201. [PMID: 21909263 PMCID: PMC3164638 DOI: 10.1371/journal.ppat.1002201] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2010] [Accepted: 06/23/2011] [Indexed: 11/29/2022] Open
Abstract
Protozoa in the phylum Apicomplexa are a large group of obligate intracellular parasites. Toxoplasma gondii and other apicomplexan parasites, such as Plasmodium falciparum, cause diseases by reiterating their lytic cycle, comprising host cell invasion, parasite replication, and parasite egress. The successful completion of the lytic cycle requires that the parasite senses changes in its environment and switches between the non-motile (for intracellular replication) and motile (for invasion and egress) states appropriately. Although the signaling pathway that regulates the motile state switch is critical to the pathogenesis of the diseases caused by these parasites, it is not well understood. Here we report a previously unknown mechanism of regulating the motility activation in Toxoplasma, mediated by a protein lysine methyltransferase, AKMT (for Apical complex lysine (K) methyltransferase). AKMT depletion greatly inhibits activation of motility, compromises parasite invasion and egress, and thus severely impairs the lytic cycle. Interestingly, AKMT redistributes from the apical complex to the parasite body rapidly in the presence of egress-stimulating signals that increase [Ca2+] in the parasite cytoplasm, suggesting that AKMT regulation of parasite motility might be accomplished by the precise temporal control of its localization in response to environmental changes. Toxoplasma gondii is one of the most successful human parasites, infecting ∼20% of the total world population. It is the most common cause of congenital neurological defects in humans, and an agent for devastating opportunistic infections in immunocompromised patients. To cause diseases, Toxoplasma gondii and other related parasites, such as Plasmodium falciparum, must reiterate their lytic cycle, comprising host cell infection, intracellular replication and parasite egress. At each step of the lytic cycle, the parasite tightly regulates its motility, being completely immotile while intracellular, and becoming highly motile as it leaves the host cell. Changes in local ionic conditions are known to trigger this rapid transition from immotile to motile. In this study, we report a previously unknown mechanism of regulating the motility activation in Toxoplasma, mediated by a novel protein lysine methyltransferase, AKMT (for Apical complex lysine (K) methyltransferase). The depletion of this protein greatly inhibits the parasite's ability to invade into and egress from the host cell due to impaired motility activation. Interestingly, the localization of AKMT in the parasite is sensitive to egress-stimulating signals, suggesting that AKMT regulation of parasite motility might be accomplished by the precise temporal control of its localization in response to environmental changes.
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Affiliation(s)
- Aoife T. Heaslip
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Manami Nishi
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Barry Stein
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Ke Hu
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
- * E-mail:
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Rebelo AP, Dillon LM, Moraes CT. Mitochondrial DNA transcription regulation and nucleoid organization. J Inherit Metab Dis 2011; 34:941-51. [PMID: 21541724 DOI: 10.1007/s10545-011-9330-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 03/28/2011] [Accepted: 03/31/2011] [Indexed: 12/18/2022]
Abstract
Mitochondrial biogenesis is a complex process depending on both nuclear and mitochondrial DNA (mtDNA) transcription regulation to tightly coordinate mitochondrial levels and the cell's energy demand. The energy requirements for a cell to support its metabolic function can change in response to varying physiological conditions, such as, proliferation and differentiation. Therefore, mitochondrial transcription regulation is constantly being modulated in order to establish efficient mitochondrial oxidative metabolism and proper cellular function. The aim of this article is to review the function of major protein factors that are directly involved in the process of mtDNA transcription regulation, as well as, the importance of mitochondrial nucleoid structure and its influence on mtDNA segregation and transcription regulation. Here, we discuss the current knowledge on the molecular mode of action of transcription factors comprising the mitochondrial transcriptional machinery, as well as the action of nuclear receptors on regulatory regions of the mtDNA.
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Affiliation(s)
- Adriana P Rebelo
- Departments of Neurology, University of Miami Miller School of Medicine, 1095 NW 14th Terrace, Miami, FL 33136, USA
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Widiez T, Hartman TG, Dudai N, Yan Q, Lawton M, Havkin-Frenkel D, Belanger FC. Functional characterization of two new members of the caffeoyl CoA O-methyltransferase-like gene family from Vanilla planifolia reveals a new class of plastid-localized O-methyltransferases. Plant Mol Biol 2011; 76:475-88. [PMID: 21629984 DOI: 10.1007/s11103-011-9772-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Accepted: 03/22/2011] [Indexed: 05/19/2023]
Abstract
Caffeoyl CoA O-methyltransferases (OMTs) have been characterized from numerous plant species and have been demonstrated to be involved in lignin biosynthesis. Higher plant species are known to have additional caffeoyl CoA OMT-like genes, which have not been well characterized. Here, we identified two new caffeoyl CoA OMT-like genes by screening a cDNA library from specialized hair cells of pods of the orchid Vanilla planifolia. Characterization of the corresponding two enzymes, designated Vp-OMT4 and Vp-OMT5, revealed that in vitro both enzymes preferred as a substrate the flavone tricetin, yet their sequences and phylogenetic relationships to other enzymes are distinct from each other. Quantitative analysis of gene expression indicated a dramatic tissue-specific expression pattern for Vp-OMT4, which was highly expressed in the hair cells of the developing pod, the likely location of vanillin biosynthesis. Although Vp-OMT4 had a lower activity with the proposed vanillin precursor, 3,4-dihydroxybenzaldehyde, than with tricetin, the tissue specificity of expression suggests it may be a candidate for an enzyme involved in vanillin biosynthesis. In contrast, the Vp-OMT5 gene was mainly expressed in leaf tissue and only marginally expressed in pod hair cells. Phylogenetic analysis suggests Vp-OMT5 evolved from a cyanobacterial enzyme and it clustered within a clade in which the sequences from eukaryotic species had predicted chloroplast transit peptides. Transient expression of a GFP-fusion in tobacco demonstrated that Vp-OMT5 was localized in the plastids. This is the first flavonoid OMT demonstrated to be targeted to the plastids.
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Affiliation(s)
- Thomas Widiez
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, 59 Dudley Road, New Brunswick, NJ 08901, USA
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Mahmoudi T, Boj SF, Hatzis P, Li VSW, Taouatas N, Vries RGJ, Teunissen H, Begthel H, Korving J, Mohammed S, Heck AJR, Clevers H. The leukemia-associated Mllt10/Af10-Dot1l are Tcf4/β-catenin coactivators essential for intestinal homeostasis. PLoS Biol 2010; 8:e1000539. [PMID: 21103407 PMCID: PMC2982801 DOI: 10.1371/journal.pbio.1000539] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Accepted: 10/01/2010] [Indexed: 01/07/2023] Open
Abstract
Wnt signaling maintains the undifferentiated state of intestinal crypt progenitor cells by inducing the formation of nuclear TCF4/β-catenin complexes. In colorectal cancer, activating mutations in Wnt pathway components cause inappropriate activation of TCF4/β-catenin-driven transcription. Despite the passage of a decade after the discovery of TCF4 and β-catenin as the molecular effectors of the Wnt signal, few transcriptional activators essential and unique to the regulation of this transcription program have been found. Using proteomics, we identified the leukemia-associated Mllt10/Af10 and the methyltransferase Dot1l as Tcf4/β-catenin interactors in mouse small intestinal crypts. Mllt10/Af10-Dot1l, essential for transcription elongation, are recruited to Wnt target genes in a β-catenin-dependent manner, resulting in H3K79 methylation over their coding regions in vivo in proliferative crypts of mouse small intestine in colorectal cancer and Wnt-inducible HEK293T cells. Depletion of MLLT10/AF10 in colorectal cancer and Wnt-inducible HEK293T cells followed by expression array analysis identifies MLLT10/AF10 and DOT1L as essential activators to a large extent dedicated to Wnt target gene regulation. In contrast, previously published β-catenin coactivators p300 and BRG1 displayed a more pleiotropic target gene expression profile controlling Wnt and other pathways. tcf4, mllt10/af10, and dot1l are co-expressed in Wnt-driven tissues in zebrafish and essential for Wnt-reporter activity. Intestinal differentiation defects in apc-mutant zebrafish can be rescued by depletion of Mllt10 and Dot1l, establishing these genes as activators downstream of Apc in Wnt target gene activation in vivo. Morpholino-depletion of mllt10/af10-dot1l in zebrafish results in defects in intestinal homeostasis and a significant reduction in the in vivo expression of direct Wnt target genes and in the number of proliferative intestinal epithelial cells. We conclude that Mllt10/Af10-Dot1l are essential, largely dedicated activators of Wnt-dependent transcription, critical for maintenance of intestinal proliferation and homeostasis. The methyltransferase DOT1L may present an attractive candidate for drug targeting in colorectal cancer.
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Affiliation(s)
- Tokameh Mahmoudi
- Hubrecht Institute and University Medical Centre Utrecht, Utrecht, The Netherlands.
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Neelakandan AK, Nguyen HTM, Kumar R, Tran LSP, Guttikonda SK, Quach TN, Aldrich DL, Nes WD, Nguyen HT. Molecular characterization and functional analysis of Glycine max sterol methyl transferase 2 genes involved in plant membrane sterol biosynthesis. Plant Mol Biol 2010; 74:503-18. [PMID: 20865301 DOI: 10.1007/s11103-010-9692-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2010] [Accepted: 09/11/2010] [Indexed: 05/29/2023]
Abstract
Sterol C24 methyltransferase (SMT2) genes governing the pattern of phytosterols synthesized in higher plants have been studied in Glycine seedlings and wild-type and engineered Arabidopsis thaliana plants. The SMT2 genes of soybean (SMT2-1 and SMT2-2) previously cloned and characterized (Neelakandan et al. 2009) were shown to complement the SMT deficient cvp1 mutant Arabidopsis plants, consistent with their role in regulation of 24-alkyl sterol-controlled plant physiology. Further analysis of these genes showed that environmental cues, including dehydration, cold, and abscisic acid induced differential changes in transcript levels of the SMT2 during soybean seedling growth. Sterol analyses of transgenic Arabidopsis seeds originating in variant constructs of AtHMGR1, GmSMT1, and GmSMT2 engineered in seeds showed relevant modifications in the ratio of 24-methyl to 24-ethyl sterol in the direction of sitosterol formation. To provide insight into the structural features of the sterol gene that affects transcript regulation, the upstream promoter sequences of soybean SMT2 genes were cloned and characterized. Sequence analysis revealed several important cis-elements and transcription factor binding sites. The analysis of promoter-GUS fusions in transgenic Arabidopsis plants revealed shared and distinct expression features in different developmental stages and tissues. The data are interpreted to imply that SMT2 is an important contributor to normal plant growth and development.
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Affiliation(s)
- Anjanasree K Neelakandan
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA
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Yusuf MA, Kumar D, Rajwanshi R, Strasser RJ, Tsimilli-Michael M, Sarin NB. Overexpression of gamma-tocopherol methyl transferase gene in transgenic Brassica juncea plants alleviates abiotic stress: physiological and chlorophyll a fluorescence measurements. Biochim Biophys Acta 2010. [PMID: 20144585 DOI: 10.1016/j.bbabio.2010.02.002l] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/24/2023]
Abstract
Tocopherols (vitamin E) are lipid soluble antioxidants synthesized by plants and some cyanobacteria. We have earlier reported that overexpression of the gamma-tocopherol methyl transferase (gamma-TMT) gene from Arabidopsis thaliana in transgenic Brassica juncea plants resulted in an over six-fold increase in the level of alpha-tocopherol, the most active form of all the tocopherols. Tocopherol levels have been shown to increase in response to a variety of abiotic stresses. In the present study on Brassica juncea, we found that salt, heavy metal and osmotic stress induced an increase in the total tocopherol levels. Measurements of seed germination, shoot growth and leaf disc senescence showed that transgenic Brassica juncea plants overexpressing the gamma-TMT gene had enhanced tolerance to the induced stresses. Analysis of the chlorophyll a fluorescence rise kinetics, from the initial "O" level to the "P" (the peak) level, showed that there were differential effects of the applied stresses on different sites of the photosynthetic machinery; further, these effects were alleviated in the transgenic (line 16.1) Brassica juncea plants. We show that alpha-tocopherol plays an important role in the alleviation of stress induced by salt, heavy metal and osmoticum in Brassica juncea.
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Affiliation(s)
- Mohd Aslam Yusuf
- School of Life Sciences, Jawaharlal Nehru University, New Delhi-110067, India
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Reimann M, Lee S, Loddenkemper C, Dörr JR, Tabor V, Aichele P, Stein H, Dörken B, Jenuwein T, Schmitt CA. Tumor stroma-derived TGF-beta limits myc-driven lymphomagenesis via Suv39h1-dependent senescence. Cancer Cell 2010; 17:262-72. [PMID: 20227040 DOI: 10.1016/j.ccr.2009.12.043] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Revised: 11/27/2009] [Accepted: 12/31/2009] [Indexed: 01/31/2023]
Abstract
Activated RAS/BRAF oncogenes induce cellular senescence as a tumor-suppressive barrier in early cancer development, at least in part, via an oncogene-evoked DNA damage response (DDR). In contrast, Myc activation-although producing a DDR as well-is known to primarily elicit an apoptotic countermeasure. Using the Emu-myc transgenic mouse lymphoma model, we show here in vivo that apoptotic lymphoma cells activate macrophages to secrete transforming growth factor beta (TGF-beta) as a critical non-cell-autonomous inducer of cellular senescence. Accordingly, neutralization of TGF-beta action, like genetic inactivation of the senescence-related histone methyltransferase Suv39h1, significantly accelerates Myc-driven tumor development via cancellation of cellular senescence. These findings, recapitulated in human aggressive B cell lymphomas, demonstrate that tumor-prompted stroma-derived signals may limit tumorigenesis by feedback senescence induction.
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Affiliation(s)
- Maurice Reimann
- Charité - Universitätsmedizin Berlin/Molekulares Krebsforschungszentrum der Charité - MKFZ, 13353 Berlin, Germany
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Benarroch D, Jankowska-Anyszka M, Stepinski J, Darzynkiewicz E, Shuman S. Cap analog substrates reveal three clades of cap guanine-N2 methyltransferases with distinct methyl acceptor specificities. RNA 2010; 16:211-20. [PMID: 19926722 PMCID: PMC2802030 DOI: 10.1261/rna.1872110] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The Tgs proteins are structurally homologous AdoMet-dependent eukaryal enzymes that methylate the N2 atom of 7-methyl guanosine nucleotides. They have an imputed role in the synthesis of the 2,2,7-trimethylguanosine (TMG) RNA cap. Here we exploit a collection of cap-like substrates to probe the repertoire of three exemplary Tgs enzymes, from mammalian, protozoan, and viral sources, respectively. We find that human Tgs (hTgs1) is a bona fide TMG synthase adept at two separable transmethylation steps: (1) conversion of m(7)G to m(2,7)G, and (2) conversion of m(2,7)G to m(2,2,7)G. hTgs1 is unable to methylate G or m(2)G, signifying that both steps require an m(7)G cap. hTgs1 utilizes a broad range of m(7)G nucleotides, including mono-, di-, tri-, and tetraphosphate derivatives as well as cap dinucleotides with triphosphate or tetraphosphate bridges. In contrast, Giardia lamblia Tgs (GlaTgs2) exemplifies a different clade of guanine-N2 methyltransferase that synthesizes only a dimethylguanosine (DMG) cap structure and cannot per se convert DMG to TMG under any conditions tested. Methylation of benzyl(7)G and ethyl(7)G nucleotides by hTgs1 and GlaTgs2 underscored the importance of guanine N7 alkylation in providing a key pi-cation interaction in the methyl acceptor site. Mimivirus Tgs (MimiTgs) shares with the Giardia homolog the ability to catalyze only a single round of methyl addition at guanine-N2, but is distinguished by its capacity for guanine-N2 methylation in the absence of prior N7 methylation. The relaxed cap specificity of MimiTgs is revealed at alkaline pH. Our findings highlight both stark and subtle differences in acceptor specificity and reaction outcomes among Tgs family members.
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Affiliation(s)
- Delphine Benarroch
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
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Sato K, Nishikubo N, Mashino Y, Yoshitomi K, Zhou J, Kajita S, Katayama Y. Immunohistochemical localization of enzymes that catalyze the long sequential pathways of lignin biosynthesis during differentiation of secondary xylem tissues of hybrid aspen (Populus sieboldii x Populus grandidentata). Tree Physiol 2009; 29:1599-1606. [PMID: 19910325 DOI: 10.1093/treephys/tpp069] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We have investigated the spatial localization of enzymes that catalyze the sequential pathways of lignin biosynthesis in developing secondary xylem tissues of hybrid aspen (Populus sieboldii Miq. x Populus grandidentata Michx.) using immunohistochemical techniques. The enzymes phenylalanine ammonia-lyase, caffeic acid 3-O-methyltransferase and 4-coumarate:CoA ligase in the common phenylpropanoid pathway, cinnamyl-alcohol dehydrogenase (CAD) and peroxidase in the specific lignin pathway, 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAHPS) in the shikimate pathway and glutamine synthetase (GS) in the nitrogen reassimilation system were abundantly localized in the 6th to 9th wood fibers away from cambium; these wood fibers are likely undergoing the most intense lignification. Only weak immunolabeling of enzymes involved in the general phenylpropanoid and specific lignin pathways was detected in the cells near the cambium; lignification of these cells has likely been initiated after primary cell wall formation. In contrast, distinct localization of DAHPS and GS was observed around the cambium, which may be involved not only in lignin biosynthesis, but also in amino acid and protein synthesis, which are essential for cell survival. Our observations suggest that co-localization of enzymes related to the sequential shikimate, general phenylpropanoid and specific lignin branch pathways and to the nitrogen recycling system is associated with cell wall lignification of wood fibers during secondary xylem development.
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Affiliation(s)
- Kanna Sato
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
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An D, Apidianakis Y, Boechat AL, Baldini RL, Goumnerov BC, Rahme LG. The pathogenic properties of a novel and conserved gene product, KerV, in proteobacteria. PLoS One 2009; 4:e7167. [PMID: 19779606 PMCID: PMC2744870 DOI: 10.1371/journal.pone.0007167] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Accepted: 08/19/2009] [Indexed: 12/27/2022] Open
Abstract
Identification of novel virulence factors is essential for understanding bacterial pathogenesis and designing antibacterial strategies. In this study, we uncover such a factor, termed KerV, in Proteobacteria. Experiments carried out in a variety of eukaryotic host infection models revealed that the virulence of a Pseudomonas aeruginosa kerV null mutant was compromised when it interacted with amoebae, plants, flies, and mice. Bioinformatics analyses indicated that KerV is a hypothetical methyltransferase and is well-conserved across numerous Proteobacteria, including both well-known and emerging pathogens (e.g., virulent Burkholderia, Escherichia, Shigella, Vibrio, Salmonella, Yersinia and Brucella species). Furthermore, among the 197 kerV orthologs analyzed in this study, about 89% reside in a defined genomic neighborhood, which also possesses essential DNA replication and repair genes and detoxification gene. Finally, infection of Drosophila melanogaster with null mutants demonstrated that KerV orthologs are also crucial in Vibrio cholerae and Yersinia pseudotuberculosis pathogenesis. Our findings suggested that KerV has a novel and broad significance as a virulence factor in pathogenic Proteobacteria and it might serve as a new target for antibiotic drug design.
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Affiliation(s)
- Dingding An
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Shriners Research Institute, Boston, Massachusetts, United States of America
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Yiorgos Apidianakis
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Shriners Research Institute, Boston, Massachusetts, United States of America
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ana Laura Boechat
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Regina L. Baldini
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Boyan C. Goumnerov
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Laurence G. Rahme
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Shriners Research Institute, Boston, Massachusetts, United States of America
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: .
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Cao F, Li X, Hiew S, Brady H, Liu Y, Dou Y. Dicer independent small RNAs associate with telomeric heterochromatin. RNA 2009; 15:1274-81. [PMID: 19460867 PMCID: PMC2704082 DOI: 10.1261/rna.1423309] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Accepted: 04/06/2009] [Indexed: 05/25/2023]
Abstract
Small RNAs play important roles in the establishment and maintenance of heterochromatin structures. We show the presence of telomere specific small RNAs (tel-sRNAs) in mouse embryonic stem cells that are approximately 24 nucleotides in length, Dicer-independent, and 2'-O-methylated at the 3' terminus. The tel-sRNAs are asymmetric with specificity toward telomere G-rich strand, and evolutionarily conserved from protozoan to mammalian cells. Furthermore, tel-sRNAs are up-regulated in cells that carry null mutation of H3K4 methyltransferase MLL (Mll((-/-))) and down-regulated in cells that carry null mutations of histone H3K9 methyltransferase SUV39H (Suv39h1/h2((-/-))), suggesting that they are subject to epigenetic regulation. These results support that tel-sRNAs are heterochromatin associated pi-like small RNAs.
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Affiliation(s)
- Fang Cao
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
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