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Zhang J, Wu L, Mu L, Wang Y, Zhao M, Wang H, Li X, Zhao L, Lin C, Zhang H, Gu L. Evolution and post-transcriptional regulation insights of m 6A writers, erasers, and readers in plant epitranscriptome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39167634 DOI: 10.1111/tpj.16996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/30/2024] [Accepted: 08/09/2024] [Indexed: 08/23/2024]
Abstract
As a dynamic and reversible post-transcriptional marker, N6-methyladenosine (m6A) plays an important role in the regulation of biological functions, which are mediated by m6A pathway components including writers (MT-A70, FIP37, VIR and HAKAI family), erasers (ALKBH family) and readers (YTH family). There is an urgent need for a comprehensive analysis of m6A pathway components across species at evolutionary levels. In this study, we identified 4062 m6A pathway components from 154 plant species including green algae, utilizing large-scale phylogenetic to explore their origin and evolution. We discovered that the copy number of writers was conserved among different plant lineages, with notable expansions in the ALKBH and YTH families. Synteny network analysis revealed conserved genomic contexts and lineage-specific transpositions. Furthermore, we used Direct RNA Sequencing (DRS) to reveal the Poly(A) length (PAL) and m6A ratio profiles in six angiosperms species, with a particular focus on the m6A pathway components. The ECT1/2-Poeaece4 sub-branches (YTH family) with unique genomic contexts exhibited significantly higher expression level than genes of other ECT1/2 poeaece sub-branches (ECT1/2-Poeaece1-3), accompanied by lower m6A modification and PAL. Besides, conserved m6A sites distributed in CDS and 3'UTR were detected in the ECT1/2-Poaceae4, and the dual-luciferase assay further demonstrated that these conserved m6A sites in the 3'UTR negatively regulated the expression of Firefly luciferase (LUC) gene. Finally, we developed transcription factor regulatory networks for m6A pathway components, using yeast one-hybrid assay demonstrated that PheBPC1 could interact with the PheECT1/2-5 promoter. Overall, this study presents a comprehensive evolutionary and functional analysis of m6A pathway components and their modifications in plants, providing a valuable resource for future functional analysis in this field.
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Affiliation(s)
- Jun Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lin Wu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lele Mu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuhua Wang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mengna Zhao
- Basic Forestry and Proteomics Research Center, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huiyuan Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiangrong Li
- Basic Forestry and Proteomics Research Center, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liangzhen Zhao
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chentao Lin
- Basic Forestry and Proteomics Research Center, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hangxiao Zhang
- Basic Forestry and Proteomics Research Center, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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Madhwani KR, Sayied S, Ogata CH, Hogan CA, Lentini JM, Mallik M, Dumouchel JL, Storkebaum E, Fu D, O’Connor-Giles KM. tRNA modification enzyme-dependent redox homeostasis regulates synapse formation and memory. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.14.566895. [PMID: 38014328 PMCID: PMC10680711 DOI: 10.1101/2023.11.14.566895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Post-transcriptional modification of RNA regulates gene expression at multiple levels. ALKBH8 is a tRNA modifying enzyme that methylates wobble uridines in specific tRNAs to modulate translation. Through methylation of tRNA-selenocysteine, ALKBH8 promotes selenoprotein synthesis and regulates redox homeostasis. Pathogenic variants in ALKBH8 have been linked to intellectual disability disorders in the human population, but the role of ALKBH8 in the nervous system is unknown. Through in vivo studies in Drosophila, we show that ALKBH8 controls oxidative stress in the brain to restrain synaptic growth and support learning and memory. ALKBH8 null animals lack wobble uridine methylation and exhibit a global reduction in protein synthesis, including a specific decrease in selenoprotein levels. Loss of ALKBH8 or independent disruption of selenoprotein synthesis results in ectopic synapse formation. Genetic expression of antioxidant enzymes fully suppresses synaptic overgrowth in ALKBH8 null animals, confirming oxidative stress as the underlying cause of dysregulation. ALKBH8 animals also exhibit associative learning and memory impairments that are reversed by pharmacological antioxidant treatment. Together, these findings demonstrate the critical role of tRNA modification in redox homeostasis in the nervous system and reveal antioxidants as a potential therapy for ALKBH8-associated intellectual disability.
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Affiliation(s)
| | - Shanzeh Sayied
- Department of Neuroscience, Brown University, Providence, RI, USA
| | | | - Caley A. Hogan
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Jenna M. Lentini
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - Moushami Mallik
- Molecular Neurobiology Laboratory, Donders Institute for Brain, Cognition, and Behaviour, Radboud University, Nijmegen, NL
| | | | - Erik Storkebaum
- Molecular Neurobiology Laboratory, Donders Institute for Brain, Cognition, and Behaviour, Radboud University, Nijmegen, NL
| | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - Kate M. O’Connor-Giles
- Department of Neuroscience, Brown University, Providence, RI, USA
- Carney Institute for Brain Sciences, Brown University, Providence, RI, USA
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3
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Ye L, Yao X, Xu B, Chen W, Lou H, Tong X, Fang S, Zou R, Hu Y, Wang Z, Xiang D, Lin Q, Feng S, Xue X, Guo G. RNA epigenetic modifications in ovarian cancer: The changes, chances, and challenges. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1784. [PMID: 36811232 DOI: 10.1002/wrna.1784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/19/2023] [Accepted: 01/25/2023] [Indexed: 02/23/2023]
Abstract
Ovarian cancer (OC) is the most common female cancer worldwide. Patients with OC have high mortality because of its complex and poorly understood pathogenesis. RNA epigenetic modifications, such as m6 A, m1 A, and m5 C, are closely associated with the occurrence and development of OC. RNA modifications can affect the stability of mRNA transcripts, nuclear export of RNAs, translation efficiency, and decoding accuracy. However, there are few overviews that summarize the link between m6 A RNA modification and OC. Here, we discuss the molecular and cellular functions of different RNA modifications and how their regulation contributes to the pathogenesis of OC. By improving our understanding of the role of RNA modifications in the etiology of OC, we provide new perspectives for their use in OC diagnosis and treatment. This article is categorized under: RNA Processing > RNA Editing and Modification RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Lele Ye
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xuyang Yao
- First Clinical College, Wenzhou Medical University, Wenzhou, China
| | - Binbing Xu
- First Clinical College, Wenzhou Medical University, Wenzhou, China
| | - Wenwen Chen
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Han Lou
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xinya Tong
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Su Fang
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Ruanmin Zou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Yingying Hu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhibin Wang
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Dan Xiang
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qiaoai Lin
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Shiyu Feng
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xiangyang Xue
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Gangqiang Guo
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
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Chu M, Qin Y, Lin X, Ma L, Deng D, Lv D, Fu P, Lin H. A Preliminary Survey of Transfer RNA Modifications and Modifying Enzymes of the Tropical Plant Cocos nucifera L. Genes (Basel) 2023; 14:1287. [PMID: 37372467 DOI: 10.3390/genes14061287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/06/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
The coconut (Cocos nucifera L.) is a commercial crop widely distributed among coastal tropical regions. It provides millions of farmers with food, fuel, cosmetics, folk medicine, and building materials. Among these, oil and palm sugar are representative extracts. However, this unique living species of Cocos has only been preliminarily studied at molecular levels. Benefiting from the genomic sequence data published in 2017 and 2021, we investigated the transfer RNA (tRNA) modifications and modifying enzymes of the coconut in this survey. An extraction method for the tRNA pool from coconut flesh was built. In total, 33 species of modified nucleosides and 66 homologous genes of modifying enzymes were confirmed using a nucleoside analysis using high-performance liquid chromatography combined with high-resolution mass spectrometry (HPLC-HRMS) and homologous protein sequence alignment. The positions of tRNA modifications, including pseudouridines, were preliminarily mapped using a oligonucleotide analysis, and the features of their modifying enzymes were summarized. Interestingly, we found that the gene encoding the modifying enzyme of 2'-O-ribosyladenosine at the 64th position of tRNA (Ar(p)64) was uniquely overexpressed under high-salinity stress. In contrast, most other tRNA-modifying enzymes were downregulated with mining transcriptomic sequencing data. According to previous physiological studies of Ar(p)64, the coconut appears to enhance the quality control of the translation process when subjected to high-salinity stress. We hope this survey can help advance research on tRNA modification and scientific studies of the coconut, as well as thinking of the safety and nutritional value of naturally modified nucleosides.
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Affiliation(s)
- Meng Chu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
- School of Life Sciences, Hainan University, Haikou 570228, China
| | - Yichao Qin
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - Xiuying Lin
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
- School of Life Sciences, Hainan University, Haikou 570228, China
| | - Li Ma
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
- College of Ecology and Environment, Hainan University, Haikou 570228, China
| | - Dehai Deng
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
- College of Ecology and Environment, Hainan University, Haikou 570228, China
| | - Daizhu Lv
- Analysis and Testing Center, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Pengcheng Fu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - Huan Lin
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
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Guo Z, Wang X, Li Y, Xing A, Wu C, Li D, Wang C, de Bures A, Zhang Y, Guo S, Sáez-Vasquez J, Shen Z, Hu Z. Arabidopsis SMO2 modulates ribosome biogenesis by maintaining the RID2 abundance during organ growth. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:96-109. [PMID: 36705084 DOI: 10.1111/tpj.16121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 01/17/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Ribosome biogenesis is a process of making ribosomes that is tightly linked with plant growth and development. Here, through a suppressor screen for the smo2 mutant, we found that lack of a ribosomal stress response mediator, ANAC082 partially restored growth defects of the smo2 mutant, indicating SMO2 is required for the repression of nucleolar stress. Consistently, the smo2 knock-out mutant exhibited typical phenotypes characteristic of ribosome biogenesis mutants, such as pointed leaves, aberrant leaf venation, disrupted nucleolar structure, abnormal distribution of rRNA precursors, and enhanced tolerance to aminoglycoside antibiotics that target ribosomes. SMO2 interacted with ROOT INITIATION DEFECTIVE 2 (RID2), a methyltransferase-like protein required for pre-rRNA processing. SMO2 enhanced RID2 solubility in Escherichia coli and the loss of function of SMO2 in plant cells reduced RID2 abundance, which may result in abnormal accumulation of FIBRILLARIN 1 (FIB1) and NOP56, two key nucleolar proteins, in high-molecular-weight protein complex. Taken together, our results characterized a novel plant ribosome biogenesis factor, SMO2 that maintains the abundance of RID2, thereby sustaining ribosome biogenesis during plant organ growth.
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Affiliation(s)
- Zhengfei Guo
- College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Xiaoyu Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Yan Li
- College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Aiming Xing
- College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Chengyun Wu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
- Sanya Institute of Henan University, 572025, Hainan, Sanya, China
| | - Daojun Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Chunfei Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Anne de Bures
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5096, 66860, Perpignan, France
- Laboratoire Génome et Développement des Plantes, Universite Perpignan Via Domitia, 66860, Perpignan, Unité Mixte de Recherche 5096, France
| | - Yonghong Zhang
- Laboratory of Medicinal Plant, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Academy of Bio-Medicine Research, School of Basic Medicine, Hubei University of Medicine, 442000, Shiyan, China
| | - Siyi Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
- Sanya Institute of Henan University, 572025, Hainan, Sanya, China
| | - Julio Sáez-Vasquez
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5096, 66860, Perpignan, France
- Laboratoire Génome et Développement des Plantes, Universite Perpignan Via Domitia, 66860, Perpignan, Unité Mixte de Recherche 5096, France
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zhubing Hu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
- Sanya Institute of Henan University, 572025, Hainan, Sanya, China
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Cavallin I, Bartosovic M, Skalicky T, Rengaraj P, Demko M, Schmidt-Dengler MC, Drino A, Helm M, Vanacova S. HITS-CLIP analysis of human ALKBH8 reveals interactions with fully processed substrate tRNAs and with specific noncoding RNAs. RNA (NEW YORK, N.Y.) 2022; 28:1568-1581. [PMID: 36192131 PMCID: PMC9670814 DOI: 10.1261/rna.079421.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Transfer RNAs acquire a large plethora of chemical modifications. Among those, modifications of the anticodon loop play important roles in translational fidelity and tRNA stability. Four human wobble U-containing tRNAs obtain 5-methoxycarbonylmethyluridine (mcm5U34) or 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U34), which play a role in decoding. This mark involves a cascade of enzymatic activities. The last step is mediated by alkylation repair homolog 8 (ALKBH8). In this study, we performed a transcriptome-wide analysis of the repertoire of ALKBH8 RNA targets. Using a combination of HITS-CLIP and RIP-seq analyses, we uncover ALKBH8-bound RNAs. We show that ALKBH8 targets fully processed and CCA modified tRNAs. Our analyses uncovered the previously known set of wobble U-containing tRNAs. In addition, both our approaches revealed ALKBH8 binding to several other types of noncoding RNAs, in particular C/D box snoRNAs.
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Affiliation(s)
- Ivana Cavallin
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Marek Bartosovic
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Tomas Skalicky
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Praveenkumar Rengaraj
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Martin Demko
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | | | - Aleksej Drino
- Medical University of Vienna, Center for Anatomy and Cell Biology, 1090 Vienna, Austria
| | - Mark Helm
- Johannes Gutenberg-Universität Mainz, Institute of Pharmaceutical and Biomedical Science (IPBS), D-55128 Mainz, Germany
| | - Stepanka Vanacova
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
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Zhao Y, Guo Q, Cao S, Tian Y, Han K, Sun Y, Li J, Yang Q, Ji Q, Sederoff R, Li Y. Genome-wide identification of the AlkB homologs gene family, PagALKBH9B and PagALKBH10B regulated salt stress response in Populus. FRONTIERS IN PLANT SCIENCE 2022; 13:994154. [PMID: 36204058 PMCID: PMC9530910 DOI: 10.3389/fpls.2022.994154] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
The AlkB homologs (ALKBH) gene family regulates N6-methyladenosine (m6A) RNA methylation and is involved in plant growth and the abiotic stress response. Poplar is an important model plant for studying perennial woody plants. Poplars typically have a long juvenile period of 7-10 years, requiring long periods of time for studies of flowering or mature wood properties. Consequently, functional studies of the ALKBH genes in Populus species have been limited. Based on AtALKBHs sequence similarity with Arabidopsis thaliana, 23 PagALKBHs were identified in the genome of the poplar 84K hybrid genotype (P. alba × P. tremula var. glandulosa), and gene structures and conserved domains were confirmed between homologs. The PagALKBH proteins were classified into six groups based on conserved sequence compared with human, Arabidopsis, maize, rice, wheat, tomato, barley, and grape. All homologs of PagALKBHs were tissue-specific; most were highly expressed in leaves. ALKBH9B and ALKBH10B are m6A demethylases and overexpression of their homologs PagALKBH9B and PagALKBH10B reduced m6A RNA methylation in transgenic lines. The number of adventitious roots and the biomass accumulation of transgenic lines decreased compared with WT. Therefore, PagALKBH9B and PagALKBH10B mediate m6A RNA demethylation and play a regulatory role in poplar growth and development. Overexpression of PagALKBH9B and PagALKBH10B can reduce the accumulation of H2O2 and oxidative damage by increasing the activities of SOD, POD, and CAT, and enhancing protection for Chl a/b, thereby increasing the salt tolerance of transgenic lines. However, overexpression lines were more sensitive to drought stress due to reduced proline content. This research revealed comprehensive information about the PagALKBH gene family and their roles in growth and development and responsing to salt stress of poplar.
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Affiliation(s)
- Ye Zhao
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Qi Guo
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Sen Cao
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Yanting Tian
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Kunjin Han
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Yuhan Sun
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Juan Li
- Natural Resources and Planning Bureau of Yanshan County, Cangzhou, Hebei, China
| | - Qingshan Yang
- Shandong Academy of Forestry, Jinan, Shandong, China
| | - Qingju Ji
- Cangzhou Municipal Forestry Seeding and Cutting Management Center, Cangzhou, China
| | - Ronald Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Yun Li
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
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8
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Cui J, Liu J, Li J, Cheng D, Dai C. Genome-wide sequence identification and expression analysis of N6 -methyladenosine demethylase in sugar beet ( Beta vulgaris L.) under salt stress. PeerJ 2022; 10:e12719. [PMID: 35036097 PMCID: PMC8742538 DOI: 10.7717/peerj.12719] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 12/09/2021] [Indexed: 01/11/2023] Open
Abstract
In eukaryotes, N6 -methyladenosine (m6A) is the most abundant and highly conserved RNA modification. In vivo, m6A demethylase dynamically regulates the m6A level by removing the m6A marker where it plays an important role in plant growth, development and response to abiotic stress. The confirmed m6A demethylases in Arabidopsis thaliana include ALKBH9B and ALKBH10B, both belonging to the ALKB family. In this study, BvALKB family members were identified in sugar beet genome-wide database, and their conserved domains, gene structures, chromosomal locations, phylogeny, conserved motifs and expression of BvALKB genes were analyzed. Almost all BvALKB proteins contained the conserved domain of 2OG-Fe II-Oxy. Phylogenetic analysis suggested that the ten proteins were clustered into five groups, each of which had similar motifs and gene structures. Three Arabidopsis m6A demethylase-homologous proteins (BvALKBH6B, BvALKBH8B and BvALKBH10B) were of particular interest in our study. Expression profile analysis showed that almost all genes were up-regulated or down-regulated to varying degrees under salt stress. More specifically, BvALKBH10B homologous to AtALKBH10B was significantly up-regulated, suggesting that the transcriptional activity of this gene is responsive to salt stress. This study provides a theoretical basis for further screening of m6A demethylase in sugar beet, and also lays a foundation for studying the role of ALKB family proteins in growth, development and response to salinity stress.
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Affiliation(s)
- Jie Cui
- Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Junli Liu
- Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Junliang Li
- Harbin Institute of Technology, Harbin, Heilongjiang, China,College of Life and Environmental Science, Wenzhou University, Wenzhou, Zhejiang, China
| | - Dayou Cheng
- Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Cuihong Dai
- Harbin Institute of Technology, Harbin, Heilongjiang, China
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9
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Dannfald A, Favory JJ, Deragon JM. Variations in transfer and ribosomal RNA epitranscriptomic status can adapt eukaryote translation to changing physiological and environmental conditions. RNA Biol 2021; 18:4-18. [PMID: 34159889 PMCID: PMC8677040 DOI: 10.1080/15476286.2021.1931756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 01/27/2023] Open
Abstract
The timely reprogramming of gene expression in response to internal and external cues is essential to eukaryote development and acclimation to changing environments. Chemically modifying molecular receptors and transducers of these signals is one way to efficiently induce proper physiological responses. Post-translation modifications, regulating protein biological activities, are central to many well-known signal-responding pathways. Recently, messenger RNA (mRNA) chemical (i.e. epitranscriptomic) modifications were also shown to play a key role in these processes. In contrast, transfer RNA (tRNA) and ribosomal RNA (rRNA) chemical modifications, although critical for optimal function of the translation apparatus, and much more diverse and quantitatively important compared to mRNA modifications, were until recently considered as mainly static chemical decorations. We present here recent observations that are challenging this view and supporting the hypothesis that tRNA and rRNA modifications dynamically respond to various cell and environmental conditions and contribute to adapt translation to these conditions.
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Affiliation(s)
- Arnaud Dannfald
- CNRS LGDP-UMR5096, Pepignan, France
- Université de Perpignan via Domitia, Perpignan, France
| | - Jean-Jacques Favory
- CNRS LGDP-UMR5096, Pepignan, France
- Université de Perpignan via Domitia, Perpignan, France
| | - Jean-Marc Deragon
- CNRS LGDP-UMR5096, Pepignan, France
- Université de Perpignan via Domitia, Perpignan, France
- Institut Universitaire de France, Paris, France
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10
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Ngoc LNT, Park SJ, Cai J, Huong TT, Lee K, Kang H. RsmD, a Chloroplast rRNA m2G Methyltransferase, Plays a Role in Cold Stress Tolerance by Possibly Affecting Chloroplast Translation in Arabidopsis. PLANT & CELL PHYSIOLOGY 2021; 62:948-958. [PMID: 34015128 DOI: 10.1093/pcp/pcab060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/04/2021] [Accepted: 05/19/2021] [Indexed: 06/12/2023]
Abstract
Ribosomal RNA (rRNA) methylation is a pivotal process in the assembly and activity of ribosomes, which in turn play vital roles in the growth, development and stress responses of plants. Although few methyltransferases responsible for rRNA methylation have been identified in plant chloroplasts, the nature and function of these enzymes in chloroplasts remain largely unknown. In this study, we characterized ArabidopsisRsmD (At3g28460), an ortholog of the methyltransferase responsible for N2-methylguanosine (m2G) modification of 16S rRNA in Escherichia coli. Confocal microscopic analysis of an RsmD- green fluorescent protein fusion protein revealed that RsmD is localized to chloroplasts. Primer extension analysis indicated that RsmD is responsible for m2G methylation at position 915 in the 16S rRNA of Arabidopsis chloroplasts. Under cold stress, rsmd mutant plants exhibited retarded growth, i.e. had shorter roots, lower fresh weight and pale-green leaves, compared with wild-type (WT) plants. However, these phenotypes were not detected in response to drought or salt stress. Notably, the rsmd mutant was hypersensitive to erythromycin or lincomycin and accumulated fewer chloroplast proteins compared with the WT, suggesting that RsmD influences translation in chloroplasts. Complementation lines expressing RsmD in the rsmd mutant background recovered WT phenotypes. Importantly, RsmD harbored RNA methyltransferase activity. Collectively, the findings of this study indicate that RsmD is a chloroplast 16S rRNA methyltransferase responsible for m2G915 modification that plays a role in the adaptation of Arabidopsisto cold stress.
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Affiliation(s)
- Le Nguyen Tieu Ngoc
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, South Korea
- Faculty of Forestry Agriculture, Tay Nguyen University, Buon Ma Thuot, Daklak 63000, Vietnam
| | - Su Jung Park
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, South Korea
| | - Jing Cai
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, South Korea
| | - Trinh Thi Huong
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, South Korea
- The Western Highlands Agriculture and Forestry Science Institute, Buon Ma Thuot, Daklak 63000, Vietnam
| | - Kwanuk Lee
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, South Korea
| | - Hunseung Kang
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, South Korea
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11
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Roles of tRNA metabolism in aging and lifespan. Cell Death Dis 2021; 12:548. [PMID: 34039958 PMCID: PMC8154886 DOI: 10.1038/s41419-021-03838-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 12/17/2022]
Abstract
Transfer RNAs (tRNAs) mainly function as adapter molecules that decode messenger RNAs (mRNAs) during protein translation by delivering amino acids to the ribosome. Traditionally, tRNAs are considered as housekeepers without additional functions. Nevertheless, it has become apparent from biological research that tRNAs are involved in various physiological and pathological processes. Aging is a form of gradual decline in physiological function that ultimately leads to increased vulnerability to multiple chronic diseases and death. Interestingly, tRNA metabolism is closely associated with aging and lifespan. In this review, we summarize the emerging roles of tRNA-associated metabolism, such as tRNA transcription, tRNA molecules, tRNA modifications, tRNA aminoacylation, and tRNA derivatives, in aging and lifespan, aiming to provide new ideas for developing therapeutics and ultimately extending lifespan in humans.
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12
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Lentini JM, Fu D. Monitoring the 5-Methoxycarbonylmethyl-2-Thiouridine (mcm5s2U) Modification Utilizing the Gamma-Toxin Endonuclease. Methods Mol Biol 2021; 2298:197-216. [PMID: 34085247 DOI: 10.1007/978-1-0716-1374-0_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The post-transcriptional modification of tRNAs at the wobble position plays a critical role in proper mRNA decoding and efficient protein synthesis. In particular, certain wobble uridines in eukaryotes are converted to 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U). The mcm5s2U modification modulates decoding during translation by increasing the stringency of the wobble uridine to base pair with its canonical nucleotide partner, thereby restricting decoding to its cognate codon. Here, we outline a technique to monitor wobble uridine status in mcm5s2U-containing tRNAs using the gamma-toxin endonuclease from the yeast Kluyveromyces lactis that naturally cleaves tRNAs containing the mcm5s2U modification. This technique is coupled to Northern blotting or reverse transcription-PCR to enable rapid and sensitive detection of changes in mcm5s2U modification state.
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Affiliation(s)
- Jenna M Lentini
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, USA.
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13
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Marcinkowski M, Pilžys T, Garbicz D, Steciuk J, Zugaj D, Mielecki D, Sarnowski TJ, Grzesiuk E. Human and Arabidopsis alpha-ketoglutarate-dependent dioxygenase homolog proteins-New players in important regulatory processes. IUBMB Life 2020; 72:1126-1144. [PMID: 32207231 DOI: 10.1002/iub.2276] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 02/20/2020] [Accepted: 03/08/2020] [Indexed: 12/31/2022]
Abstract
The family of AlkB homolog (ALKBH) proteins, the homologs of Escherichia coli AlkB 2-oxoglutarate (2OG), and Fe(II)-dependent dioxygenase are involved in a number of important regulatory processes in eukaryotic cells including repair of alkylation lesions in DNA, RNA, and nucleoprotein complexes. There are nine human and thirteen Arabidopsis thaliana ALKBH proteins described, which exhibit diversified functions. Among them, human ALKBH5 and FaT mass and Obesity-associated (FTO) protein and Arabidopsis ALKBH9B and ALKBH10B have been recognized as N6 methyladenine (N6 meA) demethylases, the most abundant posttranscriptional modification in mRNA. The FTO protein is reported to be associated with obesity and type 2 diabetes, and involved in multiple other processes, while ALKBH5 is induced by hypoxia. Arabidopsis ALKBH9B is an N6 meA demethylase influencing plant susceptibility to viral infections via m6 A/A ratio control in viral RNA. ALKBH10B has been discovered to be a functional Arabidopsis homolog of FTO; thus, it is also an RNA N6 meA demethylase involved in plant flowering and several other regulatory processes including control of metabolism. High-throughput mass spectrometry showed multiple sites of human ALKBH phosphorylation. In the case of FTO, the type of modified residue decides about the further processing of the protein. This modification may result in subsequent protein ubiquitination and proteolysis, or in the blocking of these processes. However, the impact of phosphorylation on the other ALKBH function and their downstream pathways remains nearly unexplored in both human and Arabidopsis. Therefore, the investigation of evolutionarily conserved functions of ALKBH proteins and their regulatory impact on important cellular processes is clearly called for.
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Affiliation(s)
- Michał Marcinkowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Tomaš Pilžys
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Damian Garbicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jaroslaw Steciuk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Dorota Zugaj
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Damian Mielecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Tomasz J Sarnowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Elżbieta Grzesiuk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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14
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Pinto R, Vågbø CB, Jakobsson ME, Kim Y, Baltissen MP, O'Donohue MF, Guzmán UH, Małecki JM, Wu J, Kirpekar F, Olsen JV, Gleizes PE, Vermeulen M, Leidel SA, Slupphaug G, Falnes PØ. The human methyltransferase ZCCHC4 catalyses N6-methyladenosine modification of 28S ribosomal RNA. Nucleic Acids Res 2020; 48:830-846. [PMID: 31799605 PMCID: PMC6954407 DOI: 10.1093/nar/gkz1147] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 11/19/2019] [Accepted: 11/25/2019] [Indexed: 01/06/2023] Open
Abstract
RNA methylations are essential both for RNA structure and function, and are introduced by a number of distinct methyltransferases (MTases). In recent years, N6-methyladenosine (m6A) modification of eukaryotic mRNA has been subject to intense studies, and it has been demonstrated that m6A is a reversible modification that regulates several aspects of mRNA function. However, m6A is also found in other RNAs, such as mammalian 18S and 28S ribosomal RNAs (rRNAs), but the responsible MTases have remained elusive. 28S rRNA carries a single m6A modification, found at position A4220 (alternatively referred to as A4190) within a stem–loop structure, and here we show that the MTase ZCCHC4 is the enzyme responsible for introducing this modification. Accordingly, we found that ZCCHC4 localises to nucleoli, the site of ribosome assembly, and that proteins involved in RNA metabolism are overrepresented in the ZCCHC4 interactome. Interestingly, the absence of m6A4220 perturbs codon-specific translation dynamics and shifts gene expression at the translational level. In summary, we establish ZCCHC4 as the enzyme responsible for m6A modification of human 28S rRNA, and demonstrate its functional significance in mRNA translation.
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Affiliation(s)
- Rita Pinto
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0316, Norway
| | - Cathrine B Vågbø
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, NO-7491 Trondheim, Norway.,Proteomics and Modomics Experimental Core (PROMEC), NTNU and the Central Norway Regional Health Authority, NO-7491 Trondheim, Norway
| | - Magnus E Jakobsson
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research (NNF-CPR), University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Yeji Kim
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany.,Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Marijke P Baltissen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen 6500 HB, The Netherlands
| | - Marie-Françoise O'Donohue
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Ulises H Guzmán
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research (NNF-CPR), University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Jędrzej M Małecki
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0316, Norway
| | - Jie Wu
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany.,Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Finn Kirpekar
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Jesper V Olsen
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research (NNF-CPR), University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Pierre-Emmanuel Gleizes
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen 6500 HB, The Netherlands
| | - Sebastian A Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany.,Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Geir Slupphaug
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, NO-7491 Trondheim, Norway.,Proteomics and Modomics Experimental Core (PROMEC), NTNU and the Central Norway Regional Health Authority, NO-7491 Trondheim, Norway
| | - Pål Ø Falnes
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0316, Norway
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15
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Monies D, Vågbø CB, Al-Owain M, Alhomaidi S, Alkuraya FS. Recessive Truncating Mutations in ALKBH8 Cause Intellectual Disability and Severe Impairment of Wobble Uridine Modification. Am J Hum Genet 2019; 104:1202-1209. [PMID: 31079898 DOI: 10.1016/j.ajhg.2019.03.026] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 03/26/2019] [Indexed: 01/17/2023] Open
Abstract
The wobble hypothesis was proposed to explain the presence of fewer tRNAs than possible codons. The wobble nucleoside position in the anticodon stem-loop undergoes a number of modifications that help maintain the efficiency and fidelity of translation. AlkB homolog 8 (ALKBH8) is an atypical member of the highly conserved AlkB family of dioxygenases and is involved in the formation of mcm5s2U, (S)-mchm5U, (R)-mchm5U, mcm5U, and mcm5Um at the anticodon wobble uridines of specific tRNAs. In two multiplex consanguineous families, we identified two homozygous truncating ALKBH8 mutations causing intellectual disability. Analysis of tRNA derived from affected individuals showed the complete absence of these modifications, consistent with the presumptive loss of function of the variants. Our results highlight the sensitivity of the brain to impaired wobble modification and expand the list of intellectual-disability syndromes caused by mutations in genes related to tRNA modification.
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16
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Dixit S, Henderson JC, Alfonzo JD. Multi-Substrate Specificity and the Evolutionary Basis for Interdependence in tRNA Editing and Methylation Enzymes. Front Genet 2019; 10:104. [PMID: 30838029 PMCID: PMC6382703 DOI: 10.3389/fgene.2019.00104] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 01/30/2019] [Indexed: 12/12/2022] Open
Abstract
Among tRNA modification enzymes there is a correlation between specificity for multiple tRNA substrates and heteromultimerization. In general, enzymes that modify a conserved residue in different tRNA sequences adopt a heterodimeric structure. Presumably, such changes in the oligomeric state of enzymes, to gain multi-substrate recognition, are driven by the need to accommodate and catalyze a particular reaction in different substrates while maintaining high specificity. This review focuses on two classes of enzymes where the case for multimerization as a way to diversify molecular recognition can be made. We will highlight several new themes with tRNA methyltransferases and will also discuss recent findings with tRNA editing deaminases. These topics will be discussed in the context of several mechanisms by which heterodimerization may have been achieved during evolution and how these mechanisms might impact modifications in different systems.
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Affiliation(s)
| | | | - Juan D. Alfonzo
- Department of Microbiology, The Ohio State Biochemistry Program, The Center for RNA Biology, The Ohio State University, Columbus, OH, United States
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17
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Borowski R, Dziergowska A, Sochacka E, Leszczynska G. Novel entry to the synthesis of ( S)- and ( R)-5-methoxycarbonylhydroxymethyluridines – a diastereomeric pair of wobble tRNA nucleosides. RSC Adv 2019; 9:40507-40512. [PMID: 35542686 PMCID: PMC9076229 DOI: 10.1039/c9ra08548c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 11/28/2019] [Indexed: 11/30/2022] Open
Abstract
Two novel methods for the preparation of the virtually equimolar mixtures of (S)- and (R)-diastereomers of 5-methoxycarbonylhydroxymethyluridine (mchm5U) have been developed. The first method involved α-hydroxylation of a 5-malonate ester derivative of uridine (5) with SeO2, followed by transformation to (S)- and (R)-5-carboxymethyluridines (cm5U, 8) and, finally, into the corresponding methyl esters. In the second approach, (S)- and (R)-mchm5-uridines were obtained starting from 5-formyluridine derivative (9) by hydrolysis of the imidate salt (11) prepared in the acid catalyzed reaction of 5-cyanohydrin-containing uridine (10b) with methyl alcohol. In both methods, the (S)- and (R) diastereomers of mchm5U were effectively separated by preparative C18 RP HPLC. Two novel methods for the preparation of the virtually equimolar mixtures of (S)- and (R)-diastereomers of 5-methoxycarbonylhydroxymethyluridine (mchm5U) have been developed.![]()
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Affiliation(s)
- Robert Borowski
- Institute of Organic Chemistry
- Lodz University of Technology
- 90-924 Lodz
- Poland
| | | | - Elzbieta Sochacka
- Institute of Organic Chemistry
- Lodz University of Technology
- 90-924 Lodz
- Poland
| | - Grazyna Leszczynska
- Institute of Organic Chemistry
- Lodz University of Technology
- 90-924 Lodz
- Poland
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18
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Roles of Elongator Dependent tRNA Modification Pathways in Neurodegeneration and Cancer. Genes (Basel) 2018; 10:genes10010019. [PMID: 30597914 PMCID: PMC6356722 DOI: 10.3390/genes10010019] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 12/18/2018] [Accepted: 12/20/2018] [Indexed: 02/07/2023] Open
Abstract
Transfer RNA (tRNA) is subject to a multitude of posttranscriptional modifications which can profoundly impact its functionality as the essential adaptor molecule in messenger RNA (mRNA) translation. Therefore, dynamic regulation of tRNA modification in response to environmental changes can tune the efficiency of gene expression in concert with the emerging epitranscriptomic mRNA regulators. Several of the tRNA modifications are required to prevent human diseases and are particularly important for proper development and generation of neurons. In addition to the positive role of different tRNA modifications in prevention of neurodegeneration, certain cancer types upregulate tRNA modification genes to sustain cancer cell gene expression and metastasis. Multiple associations of defects in genes encoding subunits of the tRNA modifier complex Elongator with human disease highlight the importance of proper anticodon wobble uridine modifications (xm⁵U34) for health. Elongator functionality requires communication with accessory proteins and dynamic phosphorylation, providing regulatory control of its function. Here, we summarized recent insights into molecular functions of the complex and the role of Elongator dependent tRNA modification in human disease.
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19
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Lentini JM, Ramos J, Fu D. Monitoring the 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) modification in eukaryotic tRNAs via the γ-toxin endonuclease. RNA (NEW YORK, N.Y.) 2018; 24:749-758. [PMID: 29440318 PMCID: PMC5900570 DOI: 10.1261/rna.065581.118] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 02/06/2018] [Indexed: 06/08/2023]
Abstract
The post-transcriptional modification of tRNA at the wobble position is a universal process occurring in all domains of life. In eukaryotes, the wobble uridine of particular tRNAs is transformed to the 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) modification which is critical for proper mRNA decoding and protein translation. However, current methods to detect mcm5s2U are technically challenging and/or require specialized instrumental expertise. Here, we show that γ-toxin endonuclease from the yeast Kluyveromyces lactis can be used as a probe for assaying mcm5s2U status in the tRNA of diverse eukaryotic organisms ranging from protozoans to mammalian cells. The assay couples the mcm5s2U-dependent cleavage of tRNA by γ-toxin with standard molecular biology techniques such as northern blot analysis or quantitative PCR to monitor mcm5s2U levels in multiple tRNA isoacceptors. The results gained from the γ-toxin assay reveals the evolutionary conservation of the mcm5s2U modification across eukaryotic species. Moreover, we have used the γ-toxin assay to verify uncharacterized eukaryotic Trm9 and Trm112 homologs that catalyze the formation of mcm5s2U. These findings demonstrate the use of γ-toxin as a detection method to monitor mcm5s2U status in diverse eukaryotic cell types for cellular, genetic, and biochemical studies.
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Affiliation(s)
- Jenna M Lentini
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York 14627, USA
| | - Jillian Ramos
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York 14627, USA
| | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York 14627, USA
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20
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Wang Y, Pang C, Li X, Hu Z, Lv Z, Zheng B, Chen P. Identification of tRNA nucleoside modification genes critical for stress response and development in rice and Arabidopsis. BMC PLANT BIOLOGY 2017; 17:261. [PMID: 29268705 PMCID: PMC5740945 DOI: 10.1186/s12870-017-1206-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 12/06/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Modification of nucleosides on transfer RNA (tRNA) is important either for correct mRNA decoding process or for tRNA structural stabilization. Nucleoside methylations catalyzed by MTase (methyltransferase) are the most common type among all tRNA nucleoside modifications. Although tRNA modified nucleosides and modification enzymes have been extensively studied in prokaryotic systems, similar research remains preliminary in higher plants, especially in crop species, such as rice (Oryza sativa). Rice is a monocot model plant as well as an important cereal crop, and stress tolerance and yield are of great importance for rice breeding. RESULTS In this study, we investigated how the composition and abundance of tRNA modified nucleosides could change in response to drought, salt and cold stress, as well as in different tissues during the whole growth season in two model plants-O. sativa and Arabidopsis thaliana. Twenty two and 20 MTase candidate genes were identified in rice and Arabidopsis, respectively, by protein sequence homology and conserved domain analysis. Four methylated nucleosides, Am, Cm, m1A and m7G, were found to be very important in stress response both in rice and Arabidopsis. Additionally, three nucleosides,Gm, m5U and m5C, were involved in plant development. Hierarchical clustering analysis revealed consistency on Am, Cm, m1A and m7G MTase candidate genes, and the abundance of the corresponding nucleoside under stress conditions. The same is true for Gm, m5U and m5C modifications and corresponding methylation genes in different tissues during different developmental stages. CONCLUSIONS We identified candidate genes for various tRNA modified nucleosides in rice and Arabidopsis, especially on MTases for methylated nucleosides. Based on bioinformatics analysis, nucleoside abundance assessments and gene expression profiling, we propose four methylated nucleosides (Am, Cm, m1A and m7G) that are critical for stress response in rice and Arabidopsis, and three methylated nucleosides (Gm, m5U and m5C) that might be important during development.
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Affiliation(s)
- Youmei Wang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Chaoqun Pang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xukai Li
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi Province 030801 China
| | - Zhen Hu
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Zhengyi Lv
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Bo Zheng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070 China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Peng Chen
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
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Wang Y, Li D, Gao J, Li X, Zhang R, Jin X, Hu Z, Zheng B, Persson S, Chen P. The 2'-O-methyladenosine nucleoside modification gene OsTRM13 positively regulates salt stress tolerance in rice. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1479-1491. [PMID: 28369540 PMCID: PMC5444449 DOI: 10.1093/jxb/erx061] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Stress induces changes of modified nucleosides in tRNA, and these changes can influence codon-anticodon interaction and therefore the translation of target proteins. Certain nucleoside modification genes are associated with regulation of stress tolerance and immune response in plants. In this study, we found a dramatic increase of 2'-O-methyladenosine (Am) nucleoside in rice seedlings subjected to salt stress and abscisic acid (ABA) treatment. We identified LOC_Os03g61750 (OsTRM13) as a rice candidate methyltransferase for the Am modification. OsTRM13 transcript levels increased significantly upon salt stress and ABA treatment, and the OsTrm13 protein was found to be located primarily to the nucleus. More importantly, OsTRM13 overexpression plants displayed improved salt stress tolerance, and vice versa, OsTRM13 RNA interference (RNAi) plants showed reduced tolerance. Furthermore, OsTRM13 complemented a yeast trm13Δ mutant, deficient in Am synthesis, and the purified OsTrm13 protein catalysed Am nucleoside formation on tRNA-Gly-GCC in vitro. Our results show that OsTRM13, encoding a rice tRNA nucleoside methyltransferase, is an important regulator of salt stress tolerance in rice.
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Affiliation(s)
- Youmei Wang
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China
- Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Dongqin Li
- College of Life Science, HuaZhong Agricultural University, Wuhan 430070, China
| | - Junbao Gao
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China
- Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Xukai Li
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China
- Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Rui Zhang
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China
- Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Xiaohuan Jin
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China
- Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Zhen Hu
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China
- Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
| | - Bo Zheng
- College of Horticulture and Forestry Sciences, HuaZhong Agricultural University, Wuhan 430070, China
| | - Staffan Persson
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China
- Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
- School of Biosciences, University of Melbourne, Parkville 3010 VIC, Australia
| | - Peng Chen
- College of Plant Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China
- Biomass and Bioenergy Research Centre, HuaZhong Agricultural University, Wuhan 430070, China
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Bourgeois G, Létoquart J, van Tran N, Graille M. Trm112, a Protein Activator of Methyltransferases Modifying Actors of the Eukaryotic Translational Apparatus. Biomolecules 2017; 7:biom7010007. [PMID: 28134793 PMCID: PMC5372719 DOI: 10.3390/biom7010007] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 01/16/2017] [Accepted: 01/18/2017] [Indexed: 12/17/2022] Open
Abstract
Post-transcriptional and post-translational modifications are very important for the control and optimal efficiency of messenger RNA (mRNA) translation. Among these, methylation is the most widespread modification, as it is found in all domains of life. These methyl groups can be grafted either on nucleic acids (transfer RNA (tRNA), ribosomal RNA (rRNA), mRNA, etc.) or on protein translation factors. This review focuses on Trm112, a small protein interacting with and activating at least four different eukaryotic methyltransferase (MTase) enzymes modifying factors involved in translation. The Trm112-Trm9 and Trm112-Trm11 complexes modify tRNAs, while the Trm112-Mtq2 complex targets translation termination factor eRF1, which is a tRNA mimic. The last complex formed between Trm112 and Bud23 proteins modifies 18S rRNA and participates in the 40S biogenesis pathway. In this review, we present the functions of these eukaryotic Trm112-MTase complexes, the molecular bases responsible for complex formation and substrate recognition, as well as their implications in human diseases. Moreover, as Trm112 orthologs are found in bacterial and archaeal genomes, the conservation of this Trm112 network beyond eukaryotic organisms is also discussed.
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Affiliation(s)
- Gabrielle Bourgeois
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau CEDEX, France.
| | - Juliette Létoquart
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau CEDEX, France.
- De Duve Institute, Université Catholique de Louvain, avenue Hippocrate 75, 1200 Brussels, Belgium.
| | - Nhan van Tran
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau CEDEX, France.
| | - Marc Graille
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau CEDEX, France.
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Kolaj-Robin O, Séraphin B. Structures and Activities of the Elongator Complex and Its Cofactors. RNA MODIFICATION 2017; 41:117-149. [DOI: 10.1016/bs.enz.2017.03.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Iñigo S, Durand AN, Ritter A, Le Gall S, Termathe M, Klassen R, Tohge T, De Coninck B, Van Leene J, De Clercq R, Cammue BPA, Fernie AR, Gevaert K, De Jaeger G, Leidel SA, Schaffrath R, Van Lijsebettens M, Pauwels L, Goossens A. Glutaredoxin GRXS17 Associates with the Cytosolic Iron-Sulfur Cluster Assembly Pathway. PLANT PHYSIOLOGY 2016; 172:858-873. [PMID: 27503603 PMCID: PMC5047072 DOI: 10.1104/pp.16.00261] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 08/03/2016] [Indexed: 05/12/2023]
Abstract
Cytosolic monothiol glutaredoxins (GRXs) are required in iron-sulfur (Fe-S) cluster delivery and iron sensing in yeast and mammals. In plants, it is unclear whether they have similar functions. Arabidopsis (Arabidopsis thaliana) has a sole class II cytosolic monothiol GRX encoded by GRXS17 Here, we used tandem affinity purification to establish that Arabidopsis GRXS17 associates with most known cytosolic Fe-S assembly (CIA) components. Similar to mutant plants with defective CIA components, grxs17 loss-of-function mutants showed some degree of hypersensitivity to DNA damage and elevated expression of DNA damage marker genes. We also found that several putative Fe-S client proteins directly bind to GRXS17, such as XANTHINE DEHYDROGENASE1 (XDH1), involved in the purine salvage pathway, and CYTOSOLIC THIOURIDYLASE SUBUNIT1 and CYTOSOLIC THIOURIDYLASE SUBUNIT2, both essential for the 2-thiolation step of 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) modification of tRNAs. Correspondingly, profiling of the grxs17-1 mutant pointed to a perturbed flux through the purine degradation pathway and revealed that it phenocopied mutants in the elongator subunit ELO3, essential for the mcm5 tRNA modification step, although we did not find XDH1 activity or tRNA thiolation to be markedly reduced in the grxs17-1 mutant. Taken together, our data suggest that plant cytosolic monothiol GRXs associate with the CIA complex, as in other eukaryotes, and contribute to, but are not essential for, the correct functioning of client Fe-S proteins in unchallenged conditions.
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Affiliation(s)
- Sabrina Iñigo
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Astrid Nagels Durand
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Andrés Ritter
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Sabine Le Gall
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Martin Termathe
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Roland Klassen
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Takayuki Tohge
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Barbara De Coninck
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Jelle Van Leene
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Rebecca De Clercq
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Bruno P A Cammue
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Alisdair R Fernie
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Kris Gevaert
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Sebastian A Leidel
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Raffael Schaffrath
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Mieke Van Lijsebettens
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Laurens Pauwels
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
| | - Alain Goossens
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., B.D.C., J.V.L., R.D.C., B.P.A.C., G.D.J., M.V.L., L.P., A.G.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (S.I., A.N.D., A.R., S.L.G., J.V.L., R.D.C., G.D.J., M.V.L., L.P., A.G.);Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany (M.T., S.A.L.);Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, D-34132 Kassel, Germany (R.K., R.S.);Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany (T.T., A.R.F.);Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium (B.D.C., B.P.A.C.);Cells-in-Motion Cluster of Excellence (M.T., S.A.L.) and Faculty of Medicine (S.A.L.), University of Muenster, 48149 Muenster, Germany;Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium (K.G.); andDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium (K.G.)
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25
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Burgess A, David R, Searle IR. Deciphering the epitranscriptome: A green perspective. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:822-835. [PMID: 27172004 PMCID: PMC5094531 DOI: 10.1111/jipb.12483] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 05/10/2016] [Indexed: 05/13/2023]
Abstract
The advent of high-throughput sequencing technologies coupled with new detection methods of RNA modifications has enabled investigation of a new layer of gene regulation - the epitranscriptome. With over 100 known RNA modifications, understanding the repertoire of RNA modifications is a huge undertaking. This review summarizes what is known about RNA modifications with an emphasis on discoveries in plants. RNA ribose modifications, base methylations and pseudouridylation are required for normal development in Arabidopsis, as mutations in the enzymes modifying them have diverse effects on plant development and stress responses. These modifications can regulate RNA structure, turnover and translation. Transfer RNA and ribosomal RNA modifications have been mapped extensively and their functions investigated in many organisms, including plants. Recent work exploring the locations, functions and targeting of N6 -methyladenosine (m6 A), 5-methylcytosine (m5 C), pseudouridine (Ψ), and additional modifications in mRNAs and ncRNAs are highlighted, as well as those previously known on tRNAs and rRNAs. Many questions remain as to the exact mechanisms of targeting and functions of specific modified sites and whether these modifications have distinct functions in the different classes of RNAs.
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Affiliation(s)
- Alice Burgess
- School of Biological Sciences, The University of Adelaide, South Australia,, 5005, Australia
- School of Agriculture, Food and Wine, The Waite Research Institute, The University of Adelaide, South Australia,, 5005, Australia
| | - Rakesh David
- School of Biological Sciences, The University of Adelaide, South Australia,, 5005, Australia
- School of Agriculture, Food and Wine, The Waite Research Institute, The University of Adelaide, South Australia,, 5005, Australia
| | - Iain Robert Searle
- School of Biological Sciences, The University of Adelaide, South Australia,, 5005, Australia.
- School of Agriculture, Food and Wine, The Waite Research Institute, The University of Adelaide, South Australia,, 5005, Australia.
- The University of Adelaide and Shanghai Jiao Tong University Joint International Centre for Agriculture and Health, Joint International Research Laboratory of Metabolic & Developmental Sciences, Adelaide, Australia.
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26
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Horning BD, Suciu RM, Ghadiri DA, Ulanovskaya OA, Matthews ML, Lum KM, Backus KM, Brown SJ, Rosen H, Cravatt BF. Chemical Proteomic Profiling of Human Methyltransferases. J Am Chem Soc 2016; 138:13335-13343. [PMID: 27689866 DOI: 10.1021/jacs.6b07830] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Methylation is a fundamental mechanism used in Nature to modify the structure and function of biomolecules, including proteins, DNA, RNA, and metabolites. Methyl groups are predominantly installed into biomolecules by a large and diverse class of S-adenosyl methionine (SAM)-dependent methyltransferases (MTs), of which there are ∼200 known or putative members in the human proteome. Deregulated MT activity contributes to numerous diseases, including cancer, and several MT inhibitors are in clinical development. Nonetheless, a large fraction of the human MT family remains poorly characterized, underscoring the need for new technologies to characterize MTs and their inhibitors in native biological systems. Here, we describe a suite of S-adenosyl homocysteine (SAH) photoreactive probes and their application in chemical proteomic experiments to profile and enrich a large number of MTs (>50) from human cancer cell lysates with remarkable specificity over other classes of proteins. We further demonstrate that the SAH probes can enrich MT-associated proteins and be used to screen for and assess the selectivity of MT inhibitors, leading to the discovery of a covalent inhibitor of nicotinamide N-methyltransferase (NNMT), an enzyme implicated in cancer and metabolic disorders. The chemical proteomics probes and methods for their utilization reported herein should prove of value for the functional characterization of MTs, MT complexes, and MT inhibitors in mammalian biology and disease.
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Affiliation(s)
- Benjamin D Horning
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Radu M Suciu
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Darian A Ghadiri
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Olesya A Ulanovskaya
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Megan L Matthews
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Kenneth M Lum
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Keriann M Backus
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Steven J Brown
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Hugh Rosen
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Benjamin F Cravatt
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
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27
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Zhang B, Li B, Chen D, Zong J, Sun F, Qu H, Liang C. Transcriptional Regulation of Aerobic Metabolism in Pichia pastoris Fermentation. PLoS One 2016; 11:e0161502. [PMID: 27537181 PMCID: PMC4990298 DOI: 10.1371/journal.pone.0161502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Accepted: 08/05/2016] [Indexed: 11/18/2022] Open
Abstract
In this study, we investigated the classical fermentation process in Pichia pastoris based on transcriptomics. We utilized methanol in pichia yeast cell as the focus of our study, based on two key steps: limiting carbon source replacement (from glycerol to methonal) and fermentative production of exogenous proteins. In the former, the core differential genes in co-expression net point to initiation of aerobic metabolism and generation of peroxisome. The transmission electron microscope (TEM) results showed that yeast gradually adapted methanol induction to increased cell volume, and decreased density, via large number of peroxisomes. In the fermentative production of exogenous proteins, the Gene Ontology (GO) mapping results show that PAS_chr2-1_0582 played a vital role in regulating aerobic metabolic drift. In order to confirm the above results, we disrupted PAS_chr2-1_0582 by homologous recombination. Alcohol consumption was equivalent to one fifth of the normal control, and fewer peroxisomes were observed in Δ0582 strain following methanol induction. In this study we determined the important core genes and GO terms regulating aerobic metabolic drift in Pichia, as well as developing new perspectives for the continued development within this field.
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Affiliation(s)
- Biao Zhang
- Institute of Frontier Medical Science of Jilin University, Changchun 130021, P.R. China
| | - Baizhi Li
- Institute of Frontier Medical Science of Jilin University, Changchun 130021, P.R. China
| | - Dai Chen
- NovelBio Bio-Pharm Technology Co., Ltd, Shanghai 200000, P.R. China
| | - Jie Zong
- NovelBio Bio-Pharm Technology Co., Ltd, Shanghai 200000, P.R. China
| | - Fei Sun
- Institute of Frontier Medical Science of Jilin University, Changchun 130021, P.R. China
| | - Huixin Qu
- Institute of Frontier Medical Science of Jilin University, Changchun 130021, P.R. China
| | - Chongyang Liang
- Institute of Frontier Medical Science of Jilin University, Changchun 130021, P.R. China
- * E-mail:
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28
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Karlsborn T, Tükenmez H, Mahmud AKMF, Xu F, Xu H, Byström AS. Elongator, a conserved complex required for wobble uridine modifications in eukaryotes. RNA Biol 2015; 11:1519-28. [PMID: 25607684 DOI: 10.4161/15476286.2014.992276] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Elongator is a 6 subunit protein complex highly conserved in eukaryotes. The role of this complex has been controversial as the pleiotropic phenotypes of Elongator mutants have implicated the complex in several cellular processes. However, in yeast there is convincing evidence that the primary and probably only role of this complex is in formation of the 5-methoxycarbonylmethyl (mcm(5)) and 5-carbamoylmethyl (ncm(5)) side chains on uridines at wobble position in tRNA. In this review we summarize the cellular processes that have been linked to the Elongator complex and discuss its role in tRNA modification and regulation of translation. We also describe additional gene products essential for formation of ncm(5) and mcm(5) side chains at U34 and their influence on Elongator activity.
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Affiliation(s)
- Tony Karlsborn
- a Department of Molecular Biology ; Umeå University; Umeå , Sweden
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29
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Karlsborn T, Tükenmez H, Chen C, Byström AS. Familial dysautonomia (FD) patients have reduced levels of the modified wobble nucleoside mcm5s2U in tRNA. Biochem Biophys Res Commun 2014; 454:441-5. [DOI: 10.1016/j.bbrc.2014.10.116] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 10/21/2014] [Indexed: 12/30/2022]
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Zdżalik D, Vågbø CB, Kirpekar F, Davydova E, Puścian A, Maciejewska AM, Krokan HE, Klungland A, Tudek B, van den Born E, Falnes PØ. Protozoan ALKBH8 oxygenases display both DNA repair and tRNA modification activities. PLoS One 2014; 9:e98729. [PMID: 24914785 PMCID: PMC4051686 DOI: 10.1371/journal.pone.0098729] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 05/07/2014] [Indexed: 11/29/2022] Open
Abstract
The ALKBH family of Fe(II) and 2-oxoglutarate dependent oxygenases comprises enzymes that display sequence homology to AlkB from E. coli, a DNA repair enzyme that uses an oxidative mechanism to dealkylate methyl and etheno adducts on the nucleobases. Humans have nine different ALKBH proteins, ALKBH1–8 and FTO. Mammalian and plant ALKBH8 are tRNA hydroxylases targeting 5-methoxycarbonylmethyl-modified uridine (mcm5U) at the wobble position of tRNAGly(UCC). In contrast, the genomes of some bacteria encode a protein with strong sequence homology to ALKBH8, and robust DNA repair activity was previously demonstrated for one such protein. To further explore this apparent functional duality of the ALKBH8 proteins, we have here enzymatically characterized a panel of such proteins, originating from bacteria, protozoa and mimivirus. All the enzymes showed DNA repair activity in vitro, but, interestingly, two protozoan ALKBH8s also catalyzed wobble uridine modification of tRNA, thus displaying a dual in vitro activity. Also, we found the modification status of tRNAGly(UCC) to be unaltered in an ALKBH8 deficient mutant of Agrobacterium tumefaciens, indicating that bacterial ALKBH8s have a function different from that of their eukaryotic counterparts. The present study provides new insights on the function and evolution of the ALKBH8 family of proteins.
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Affiliation(s)
- Daria Zdżalik
- Department of Biosciences, University of Oslo, Oslo, Norway
- Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Cathrine B. Vågbø
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Finn Kirpekar
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Erna Davydova
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Alicja Puścian
- Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
- Department of Neurophysiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | | | - Hans E. Krokan
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Arne Klungland
- Clinic for Diagnostics and Intervention and Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Barbara Tudek
- Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | - Pål Ø. Falnes
- Department of Biosciences, University of Oslo, Oslo, Norway
- * E-mail:
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31
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Hori H. Methylated nucleosides in tRNA and tRNA methyltransferases. Front Genet 2014; 5:144. [PMID: 24904644 PMCID: PMC4033218 DOI: 10.3389/fgene.2014.00144] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 05/04/2014] [Indexed: 12/26/2022] Open
Abstract
To date, more than 90 modified nucleosides have been found in tRNA and the biosynthetic pathways of the majority of tRNA modifications include a methylation step(s). Recent studies of the biosynthetic pathways have demonstrated that the availability of methyl group donors for the methylation in tRNA is important for correct and efficient protein synthesis. In this review, I focus on the methylated nucleosides and tRNA methyltransferases. The primary functions of tRNA methylations are linked to the different steps of protein synthesis, such as the stabilization of tRNA structure, reinforcement of the codon-anticodon interaction, regulation of wobble base pairing, and prevention of frameshift errors. However, beyond these basic functions, recent studies have demonstrated that tRNA methylations are also involved in the RNA quality control system and regulation of tRNA localization in the cell. In a thermophilic eubacterium, tRNA modifications and the modification enzymes form a network that responses to temperature changes. Furthermore, several modifications are involved in genetic diseases, infections, and the immune response. Moreover, structural, biochemical, and bioinformatics studies of tRNA methyltransferases have been clarifying the details of tRNA methyltransferases and have enabled these enzymes to be classified. In the final section, the evolution of modification enzymes is discussed.
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Affiliation(s)
- Hiroyuki Hori
- Department of Materials Science and Biotechnology, Applied Chemistry, Graduate School of Science and Engineering, Ehime University Matsuyama, Japan
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32
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Affiliation(s)
- Guanqun Zheng
- Department of Chemistry and
Institute for Biophysical Dynamics, The
University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United
States
| | - Ye Fu
- Department of Chemistry and
Institute for Biophysical Dynamics, The
University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United
States
| | - Chuan He
- Department of Chemistry and
Institute for Biophysical Dynamics, The
University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United
States
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33
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Affiliation(s)
- Guanqun Zheng
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago , 929 East 57th Street, Chicago, Illinois 60637, United States
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El Yacoubi B, Bailly M, de Crécy-Lagard V. Biosynthesis and Function of Posttranscriptional Modifications of Transfer RNAs. Annu Rev Genet 2012; 46:69-95. [DOI: 10.1146/annurev-genet-110711-155641] [Citation(s) in RCA: 380] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Basma El Yacoubi
- Department of Microbiology and Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611-0700;
| | - Marc Bailly
- Department of Microbiology and Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611-0700;
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611-0700;
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Salinas T, Duby F, Larosa V, Coosemans N, Bonnefoy N, Motte P, Maréchal-Drouard L, Remacle C. Co-evolution of mitochondrial tRNA import and codon usage determines translational efficiency in the green alga Chlamydomonas. PLoS Genet 2012; 8:e1002946. [PMID: 23028354 PMCID: PMC3447967 DOI: 10.1371/journal.pgen.1002946] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 07/26/2012] [Indexed: 11/26/2022] Open
Abstract
Mitochondria from diverse phyla, including protozoa, fungi, higher plants, and humans, import tRNAs from the cytosol in order to ensure proper mitochondrial translation. Despite the broad occurrence of this process, our understanding of tRNA import mechanisms is fragmentary, and crucial questions about their regulation remain unanswered. In the unicellular green alga Chlamydomonas, a precise correlation was found between the mitochondrial codon usage and the nature and amount of imported tRNAs. This led to the hypothesis that tRNA import might be a dynamic process able to adapt to the mitochondrial genome content. By manipulating the Chlamydomonas mitochondrial genome, we introduced point mutations in order to modify its codon usage. We find that the codon usage modification results in reduced levels of mitochondrial translation as well as in subsequent decreased levels and activities of respiratory complexes. These effects are linked to the consequential limitations of the pool of tRNAs in mitochondria. This indicates that tRNA mitochondrial import cannot be rapidly regulated in response to a novel genetic context and thus does not appear to be a dynamic process. It rather suggests that the steady-state levels of imported tRNAs in mitochondria result from a co-evolutive adaptation between the tRNA import mechanism and the requirements of the mitochondrial translation machinery. Mitochondria are endosymbiotic organelles involved in diverse fundamental cellular processes. They contain their own genome that encodes a few but essential proteins (e.g. proteins of the respiratory chain complexes). Their synthesis requires functional mitochondrial translational machinery that necessitates a full set of transfer RNAs (tRNAs). As mitochondrial genomes of various organisms do not code for the complete set of tRNA genes, nucleus-encoded tRNAs have to be imported into mitochondria to compensate. Mitochondrial import of tRNAs is highly specific and tailored to the mitochondrial needs. Because transformation of the mitochondrial genome is possible in Chlamydomonas, we used this green alga as model to know if a fine regulation of the tRNA import process is possible so that the tRNA population can rapidly adapt to codon usage changes in mitochondria. Here we provide evidence that the regulation of tRNA mitochondrial import process is not dynamic but is rather the result of a co-evolutive process between the import and the mitochondrial codon bias in order to optimize the mitochondrial translation efficiency.
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Affiliation(s)
- Thalia Salinas
- Génétique des Microorganismes, Department of Life Sciences, Institute of Botany, University of Li?ge, Li?ge, Belgium
- Institut de Biologie Moléculaire des Plantes, UPR 2357, Centre National de la Recherche Scientifique, University of Strasbourg, Strasbourg, France
| | - Francéline Duby
- Génétique des Microorganismes, Department of Life Sciences, Institute of Botany, University of Li?ge, Li?ge, Belgium
| | - Véronique Larosa
- Génétique des Microorganismes, Department of Life Sciences, Institute of Botany, University of Li?ge, Li?ge, Belgium
| | - Nadine Coosemans
- Génétique des Microorganismes, Department of Life Sciences, Institute of Botany, University of Li?ge, Li?ge, Belgium
| | - Nathalie Bonnefoy
- Centre de Génétique Moléculaire, UPR3404, FRC3115, Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
| | - Patrick Motte
- Functional Genomics and Plant Molecular Imaging, Department of Life Sciences, Institute of Botany, University of Li?ge, Li?ge, Belgium
| | - Laurence Maréchal-Drouard
- Institut de Biologie Moléculaire des Plantes, UPR 2357, Centre National de la Recherche Scientifique, University of Strasbourg, Strasbourg, France
- * E-mail: (LM-D); (CR)
| | - Claire Remacle
- Génétique des Microorganismes, Department of Life Sciences, Institute of Botany, University of Li?ge, Li?ge, Belgium
- * E-mail: (LM-D); (CR)
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36
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The potential of 2-oxoglutarate oxygenases acting on nucleic acids as therapeutic targets. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.ddstr.2012.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Patil A, Chan CTY, Dyavaiah M, Rooney JP, Dedon PC, Begley TJ. Translational infidelity-induced protein stress results from a deficiency in Trm9-catalyzed tRNA modifications. RNA Biol 2012; 9:990-1001. [PMID: 22832247 DOI: 10.4161/rna.20531] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Correct codon-anticodon pairing promotes translational fidelity, with these interactions greatly facilitated by modified nucleosides found in tRNA. We hypothesized that wobble uridine modifications catalyzed by tRNA methyltransferase 9 (Trm9) are essential for translational fidelity. In support, we have used phenotypic, reporter and protein-based assays to demonstrate increased translational infidelity in trm9Δ Saccharomyces cerevisiae cells. Codon reengineering studies suggest that Trm9-catalyzed tRNA modifications promote fidelity during the translation of specific genes, those rich in arginine and glutamic acid codons from mixed boxes. Using quantitative tRNA modification analysis, we determined that trm9Δ cells are only deficient in 2 of 23 tRNA modifications, with those 2, 5-methoxycarbonylmethyluridine (mcm ( 5) U) and 5-methoxycarbonylmethyl-2-thiouridine (mcm ( 5) s ( 2) U), classified as key determinants of translational fidelity. We also show that in the absence of mcm ( 5) U and mcm ( 5) s ( 2) U, the resulting translational infidelity promotes protein errors and activation of unfolded protein and heat shock responses. These data support a model in which Trm9-catalyzed tRNA modifications promote fidelity during the translation of specific transcripts, with decreased wobble base modification leading to translational infidelity, protein errors and activation of protein stress response pathways.
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Affiliation(s)
- Ashish Patil
- Cancer Research Center, University at Albany, State University of New York, Rensselaer, NY, USA
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Meza TJ, Moen MN, Vågbø CB, Krokan HE, Klungland A, Grini PE, Falnes PØ. The DNA dioxygenase ALKBH2 protects Arabidopsis thaliana against methylation damage. Nucleic Acids Res 2012; 40:6620-31. [PMID: 22532610 PMCID: PMC3413135 DOI: 10.1093/nar/gks327] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The Escherichia coli AlkB protein (EcAlkB) is a DNA repair enzyme which reverses methylation damage such as 1-methyladenine (1-meA) and 3-methylcytosine (3-meC). The mammalian AlkB homologues ALKBH2 and ALKBH3 display EcAlkB-like repair activity in vitro, but their substrate specificities are different, and ALKBH2 is the main DNA repair enzyme for 1-meA in vivo. The genome of the model plant Arabidopsis thaliana encodes several AlkB homologues, including the yet uncharacterized protein AT2G22260, which displays sequence similarity to both ALKBH2 and ALKBH3. We have here characterized protein AT2G22260, by us denoted ALKBH2, as both our functional studies and bioinformatics analysis suggest it to be an orthologue of mammalian ALKBH2. The Arabidopsis ALKBH2 protein displayed in vitro repair activities towards methyl and etheno adducts in DNA, and was able to complement corresponding repair deficiencies of the E. coli alkB mutant. Interestingly, alkbh2 knock-out plants were sensitive to the methylating agent methylmethanesulphonate (MMS), and seedlings from these plants developed abnormally when grown in the presence of MMS. The present study establishes ALKBH2 as an important enzyme for protecting Arabidopsis against methylation damage in DNA, and suggests its homologues in other plants to have a similar function.
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Affiliation(s)
- Trine J Meza
- Department of Molecular Biosciences, University of Oslo, P.O. Box 1041 Blindern, N-0316 Oslo, Norway
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Winczura A, Zdżalik D, Tudek B. Damage of DNA and proteins by major lipid peroxidation products in genome stability. Free Radic Res 2012; 46:442-59. [PMID: 22257221 DOI: 10.3109/10715762.2012.658516] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Oxidative stress and lipid peroxidation (LPO) accompanying infections and chronic inflammation may induce several human cancers. LPO products are characterized by carbohydrate chains of different length, reactive aldehyde groups and double bonds, which make these molecules reactive to nucleic acids, proteins and cellular thiols. LPO-derived adducts to DNA bases form etheno-type and propano-type exocyclic rings, which have profound mutagenic potential, and are elevated in several cancer-prone diseases. Adducts of long chain LPO products to DNA bases inhibit transcription. Elimination from DNA of LPO-induced lesions is executed by several repair systems: base excision repair (BER), direct reversal by AlkB family proteins, nucleotide excision repair (NER) and recombination. Modifications of proteins with LPO products may regulate cellular processes like apoptosis, cell signalling and senescence. This review summarizes consequences of LPO products' presence in cell, particularly 4-hydroxy-2-nonenal, in terms of genomic stability.
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Affiliation(s)
- Alicja Winczura
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 02-106 Warsaw, Poland
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40
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Mielecki D, Zugaj DŁ, Muszewska A, Piwowarski J, Chojnacka A, Mielecki M, Nieminuszczy J, Grynberg M, Grzesiuk E. Novel AlkB dioxygenases--alternative models for in silico and in vivo studies. PLoS One 2012; 7:e30588. [PMID: 22291995 PMCID: PMC3265494 DOI: 10.1371/journal.pone.0030588] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 12/19/2011] [Indexed: 11/21/2022] Open
Abstract
Background ALKBH proteins, the homologs of Escherichia coli AlkB dioxygenase, constitute a direct, single-protein repair system, protecting cellular DNA and RNA against the cytotoxic and mutagenic activity of alkylating agents, chemicals significantly contributing to tumor formation and used in cancer therapy. In silico analysis and in vivo studies have shown the existence of AlkB homologs in almost all organisms. Nine AlkB homologs (ALKBH1–8 and FTO) have been identified in humans. High ALKBH levels have been found to encourage tumor development, questioning the use of alkylating agents in chemotherapy. The aim of this work was to assign biological significance to multiple AlkB homologs by characterizing their activity in the repair of nucleic acids in prokaryotes and their subcellular localization in eukaryotes. Methodology and Findings Bioinformatic analysis of protein sequence databases identified 1943 AlkB sequences with eight new AlkB subfamilies. Since Cyanobacteria and Arabidopsis thaliana contain multiple AlkB homologs, they were selected as model organisms for in vivo research. Using E. coli alkB− mutant and plasmids expressing cyanobacterial AlkBs, we studied the repair of methyl methanesulfonate (MMS) and chloroacetaldehyde (CAA) induced lesions in ssDNA, ssRNA, and genomic DNA. On the basis of GFP fusions, we investigated the subcellular localization of ALKBHs in A. thaliana and established its mostly nucleo-cytoplasmic distribution. Some of the ALKBH proteins were found to change their localization upon MMS treatment. Conclusions Our in vivo studies showed highly specific activity of cyanobacterial AlkB proteins towards lesions and nucleic acid type. Subcellular localization and translocation of ALKBHs in A. thaliana indicates a possible role for these proteins in the repair of alkyl lesions. We hypothesize that the multiplicity of ALKBHs is due to their involvement in the metabolism of nucleo-protein complexes; we find their repair by ALKBH proteins to be economical and effective alternative to degradation and de novo synthesis.
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Affiliation(s)
- Damian Mielecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Dorota Ł. Zugaj
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Jan Piwowarski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Aleksandra Chojnacka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Marcin Mielecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Jadwiga Nieminuszczy
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Marcin Grynberg
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
- * E-mail: (MG); (EG)
| | - Elżbieta Grzesiuk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
- * E-mail: (MG); (EG)
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Graille M, Figaro S, Kervestin S, Buckingham RH, Liger D, Heurgué-Hamard V. Methylation of class I translation termination factors: structural and functional aspects. Biochimie 2012; 94:1533-43. [PMID: 22266024 DOI: 10.1016/j.biochi.2012.01.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 01/07/2012] [Indexed: 12/23/2022]
Abstract
During protein synthesis, release of polypeptide from the ribosome occurs when an in frame termination codon is encountered. Contrary to sense codons, which are decoded by tRNAs, stop codons present in the A-site are recognized by proteins named class I release factors, leading to the release of newly synthesized proteins. Structures of these factors bound to termination ribosomal complexes have recently been obtained, and lead to a better understanding of stop codon recognition and its coordination with peptidyl-tRNA hydrolysis in bacteria. Release factors contain a universally conserved GGQ motif which interacts with the peptidyl-transferase centre to allow peptide release. The Gln side chain from this motif is methylated, a feature conserved from bacteria to man, suggesting an important biological role. However, methylation is catalysed by completely unrelated enzymes. The function of this motif and its post-translational modification will be discussed in the context of recent structural and functional studies.
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Affiliation(s)
- Marc Graille
- IBBMC, Université Paris-Sud 11, CNRS UMR8619, Orsay Cedex, F-91405, France.
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