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Urbelienė N, Tiškus M, Tamulaitienė G, Gasparavičiūtė R, Lapinskaitė R, Jauniškis V, Sūdžius J, Meškienė R, Tauraitė D, Skrodenytė E, Urbelis G, Vaitekūnas J, Meškys R. Cytidine deaminases catalyze the conversion of N( S, O) 4-substituted pyrimidine nucleosides. SCIENCE ADVANCES 2023; 9:eade4361. [PMID: 36735785 PMCID: PMC9897663 DOI: 10.1126/sciadv.ade4361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 01/03/2023] [Indexed: 06/18/2023]
Abstract
Cytidine deaminases (CDAs) catalyze the hydrolytic deamination of cytidine and 2'-deoxycytidine to uridine and 2'-deoxyuridine. Here, we report that prokaryotic homo-tetrameric CDAs catalyze the nucleophilic substitution at the fourth position of N4-acyl-cytidines, N4-alkyl-cytidines, and N4-alkyloxycarbonyl-cytidines, and S4-alkylthio-uridines and O4-alkyl-uridines, converting them to uridine and corresponding amide, amine, carbamate, thiol, or alcohol as leaving groups. The x-ray structure of a metagenomic CDA_F14 and the molecular modeling of the CDAs used in this study show a relationship between the bulkiness of a leaving group and the volume of the binding pocket, which is partly determined by the flexible β3α3 loop of CDAs. We propose that CDAs that are active toward a wide range of substrates participate in salvage and/or catabolism of variously modified pyrimidine nucleosides. This identified promiscuity of CDAs expands the knowledge about the cellular turnover of cytidine derivatives, including the pharmacokinetics of pyrimidine-based prodrugs.
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Affiliation(s)
- Nina Urbelienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av., 10257 Vilnius, Lithuania
| | - Matas Tiškus
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av., 10257 Vilnius, Lithuania
| | - Giedrė Tamulaitienė
- Department of Protein–DNA Interactions, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, 10257 Vilnius, Lithuania
| | - Renata Gasparavičiūtė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av., 10257 Vilnius, Lithuania
| | - Ringailė Lapinskaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av., 10257 Vilnius, Lithuania
- Department of Organic Chemistry, Center for Physical Sciences and Technology, Akademijos 7, LT-08412 Vilnius, Lithuania
| | - Vykintas Jauniškis
- UAB Biomatter Designs (Biomatter), Žirmūnų st. 139A, 09120 Vilnius, Lithuania
| | - Jurgis Sūdžius
- Department of Organic Chemistry, Center for Physical Sciences and Technology, Akademijos 7, LT-08412 Vilnius, Lithuania
| | - Rita Meškienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av., 10257 Vilnius, Lithuania
| | - Daiva Tauraitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av., 10257 Vilnius, Lithuania
| | - Emilija Skrodenytė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av., 10257 Vilnius, Lithuania
| | - Gintaras Urbelis
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av., 10257 Vilnius, Lithuania
- Department of Organic Chemistry, Center for Physical Sciences and Technology, Akademijos 7, LT-08412 Vilnius, Lithuania
| | - Justas Vaitekūnas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av., 10257 Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av., 10257 Vilnius, Lithuania
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Straube H, Niehaus M, Zwittian S, Witte CP, Herde M. Enhanced nucleotide analysis enables the quantification of deoxynucleotides in plants and algae revealing connections between nucleoside and deoxynucleoside metabolism. THE PLANT CELL 2021; 33:270-289. [PMID: 33793855 PMCID: PMC8136904 DOI: 10.1093/plcell/koaa028] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/12/2020] [Indexed: 05/02/2023]
Abstract
Detecting and quantifying low-abundance (deoxy)ribonucleotides and (deoxy)ribonucleosides in plants remains difficult; this is a major roadblock for the investigation of plant nucleotide (NT) metabolism. Here, we present a method that overcomes this limitation, allowing the detection of all deoxy- and ribonucleotides as well as the corresponding nucleosides from the same plant sample. The method is characterized by high sensitivity and robustness enabling the reproducible detection and absolute quantification of these metabolites even if they are of low abundance. Employing the new method, we analyzed Arabidopsis thaliana null mutants of CYTIDINE DEAMINASE, GUANOSINE DEAMINASE, and NUCLEOSIDE HYDROLASE 1, demonstrating that the deoxyribonucleotide (dNT) metabolism is intricately interwoven with the catabolism of ribonucleosides (rNs). In addition, we discovered a function of rN catabolic enzymes in the degradation of deoxyribonucleosides in vivo. We also determined the concentrations of dNTs in several mono- and dicotyledonous plants, a bryophyte, and three algae, revealing a correlation of GC to AT dNT ratios with genomic GC contents. This suggests a link between the genome and the metabolome previously discussed but not experimentally addressed. Together, these findings demonstrate the potential of this new method to provide insight into plant NT metabolism.
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Affiliation(s)
- Henryk Straube
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Markus Niehaus
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Sarah Zwittian
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Claus-Peter Witte
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Marco Herde
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
- Author for correspondence:
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3
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Wang J, Guo Q, Liu L, Wang X. Crystal structure of Arabidopsis thaliana cytidine deaminase. Biochem Biophys Res Commun 2020; 529:659-665. [PMID: 32736689 DOI: 10.1016/j.bbrc.2020.06.084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 06/17/2020] [Indexed: 11/19/2022]
Abstract
Cytidine deaminase (CDA) catalyzes the (deoxy)cytidine deamination to (deoxy)uridine, which involves in the catabolic and salvage pathways of pyrimidine nucleotides in plants. CDA serves as a prototype of the cytidine deaminase superfamily that contains a number of RNA editing enzymes. Arabidopsis thaliana has only one functional CDA, AtCDA1. We solved the crystal structures of AtCDA1, which is a dimeric zinc-containing enzyme and each protomer consists of an N-terminal zinc-binding catalytic domain and a C-terminal non-catalytic domain. Both domains adopt a typical α/β/α sandwich fold. In vitro biochemical assays showed that the ribose moiety of cytidine is required for ligand binding, and structural analyses revealed a conserved catalytic mechanism is adopted by AtCDA1.
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Affiliation(s)
- Jia Wang
- CAS Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Haidian, Beijing, 100093, China; Graduate School, University of Chinese Academy of Sciences, Shijingshan, Beijing, 100049, China
| | - Qi Guo
- CAS Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Haidian, Beijing, 100093, China; Graduate School, University of Chinese Academy of Sciences, Shijingshan, Beijing, 100049, China
| | - Lin Liu
- School of Life Sciences, Anhui University, Hefei, Anhui, 230601, China
| | - Xiao Wang
- School of Life Sciences, Anhui University, Hefei, Anhui, 230601, China.
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Searing AM, Satyanarayan MB, O′Donnell JP, Lu Y. Two organelle RNA recognition motif proteins affect distinct sets of RNA editing sites in the Arabidopsis thaliana plastid. PLANT DIRECT 2020; 4:e00213. [PMID: 32259001 PMCID: PMC7132558 DOI: 10.1002/pld3.213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/12/2019] [Accepted: 03/13/2020] [Indexed: 06/01/2023]
Abstract
Plastid and mitochondrial RNAs in vascular plants are subjected to cytidine-to-uridine editing. The model plant species Arabidopsis thaliana (Arabidopsis) has two nuclear-encoded plastid-targeted organelle RNA recognition motif (ORRM) proteins: ORRM1 and ORRM6. In the orrm1 mutant, 21 plastid RNA editing sites were affected but none are essential to photosynthesis. In the orrm6 mutants, two plastid RNA editing sites were affected: psbF-C77 and accD-C794. Because psbF encodes the β subunit of cytochrome b 559 in photosystem II, which is essential to photosynthesis, the orrm6 mutants were much smaller than the wild type. In addition, the orrm6 mutants had pale green leaves and reduced photosynthetic efficiency. To investigate the functional relationship between ORRM1 and ORRM6, we generated orrm1 orrm6 double homozygous mutants. Morphological and physiological analyses showed that the orrm1 orrm6 double mutants had a smaller plant size, reduced chlorophyll contents, and decreased photosynthetic efficiency, similar to the orrm6 single mutants. Although the orrm1 orrm6 double mutants adopted the phenotype of the orrm6 single mutants, the total number of plastid RNA editing sites affected in the orrm1 orrm6 double mutants was the sum of the sites affected in the orrm1 and orrm6 single mutants. These data suggest that ORRM1 and ORRM6 are in charge of distinct sets of plastid RNA editing sites and that simultaneous mutations in ORRM1 and ORRM6 genes do not cause additional reduction in editing extent at other plastid RNA editing sites.
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Affiliation(s)
- Audrey M. Searing
- Department of Biological SciencesWestern Michigan UniversityKalamazooMIUSA
| | | | - James P. O′Donnell
- Department of Biological SciencesWestern Michigan UniversityKalamazooMIUSA
| | - Yan Lu
- Department of Biological SciencesWestern Michigan UniversityKalamazooMIUSA
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Niu M, Wang Y, Wang C, Lyu J, Wang Y, Dong H, Long W, Wang D, Kong W, Wang L, Guo X, Sun L, Hu T, Zhai H, Wang H, Wan J. ALR encoding dCMP deaminase is critical for DNA damage repair, cell cycle progression and plant development in rice. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5773-5786. [PMID: 29186482 DOI: 10.1093/jxb/erx380] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 09/26/2017] [Indexed: 06/07/2023]
Abstract
Deoxycytidine monophosphate deaminase (dCMP deaminase, DCD) is crucial to the production of dTTP needed for DNA replication and damage repair. However, the effect of DCD deficiency and its molecular mechanism are poorly understood in plants. Here, we isolated and characterized a rice albinic leaf and growth retardation (alr) mutant that is manifested by albinic leaves, dwarf stature and necrotic lesions. Map-based cloning and complementation revealed that ALR encodes a DCD protein. OsDCD was expressed ubiquitously in all tissues. Enzyme activity assays showed that OsDCD catalyses conversion of dCMP to dUMP, and the ΔDCD protein in the alr mutant is a loss-of-function protein that lacks binding ability. We report that alr plants have typical DCD-mediated imbalanced dNTP pools with decreased dTTP; exogenous dTTP recovers the wild-type phenotype. A comet assay and Trypan Blue staining showed that OsDCD deficiency causes accumulation of DNA damage in the alr mutant, sometimes leading to cell apoptosis. Moreover, OsDCD deficiency triggered cell cycle checkpoints and arrested cell progression at the G1/S-phase. The expression of nuclear and plastid genome replication genes was down-regulated under decreased dTTP, and together with decreased cell proliferation and defective chloroplast development in the alr mutant this demonstrated the molecular and physiological roles of DCD-mediated dNTP pool balance in plant development.
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Affiliation(s)
- Mei Niu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, China
| | - Yihua Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, China
| | - Chunming Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, China
| | - Jia Lyu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, China
| | - Yunlong Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, China
| | - Hui Dong
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, China
| | - Wuhua Long
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, China
| | - Di Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, China
| | - Weiyi Kong
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, China
| | - Liwei Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, China
| | - Xiuping Guo
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, China
| | - Liting Sun
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, China
| | - Tingting Hu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, China
| | - Huqu Zhai
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, China
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, China
| | - Haiyang Wang
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, China
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, China
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, China
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Hackett JB, Lu Y. Whole-transcriptome RNA-seq, gene set enrichment pathway analysis, and exon coverage analysis of two plastid RNA editing mutants. PLANT SIGNALING & BEHAVIOR 2017; 12:e1312242. [PMID: 28387567 PMCID: PMC5501230 DOI: 10.1080/15592324.2017.1312242] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 03/18/2017] [Accepted: 03/23/2017] [Indexed: 06/02/2023]
Abstract
In land plants, plastid and mitochondrial RNAs are subject to post-transcriptional C-to-U RNA editing. T-DNA insertions in the ORGANELLE RNA RECOGNITION MOTIF PROTEIN6 gene resulted in reduced photosystem II (PSII) activity and smaller plant and leaf sizes. Exon coverage analysis of the ORRM6 gene showed that orrm6-1 and orrm6-2 are loss-of-function mutants. Compared to other ORRM proteins, ORRM6 affects a relative small number of RNA editing sites. Sanger sequencing of reverse transcription-PCR products of plastid transcripts revealed 2 plastid RNA editing sites that are substantially affected in the orrm6 mutants: psbF-C77 and accD-C794. The psbF gene encodes the β subunit of cytochrome b559, an essential component of PSII. The accD gene encodes the β subunit of acetyl-CoA carboxylase, a protein required in plastid fatty acid biosynthesis. Whole-transcriptome RNA-seq demonstrated that editing at psbF-C77 is nearly absent and the editing extent at accD-C794 was significantly reduced. Gene set enrichment pathway analysis showed that expression of multiple gene sets involved in photosynthesis, especially photosynthetic electron transport, is significantly upregulated in both orrm6 mutants. The upregulation could be a mechanism to compensate for the reduced PSII electron transport rate in the orrm6 mutants. These results further demonstrated that Organelle RNA Recognition Motif protein ORRM6 is required in editing of specific RNAs in the Arabidopsis (Arabidopsis thaliana) plastid.
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Affiliation(s)
- Justin B. Hackett
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, USA
| | - Yan Lu
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, USA
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Sánchez-Quitian ZA, Rodrigues-Junior V, Rehm JG, Eichler P, Barbosa Trivella DB, Bizarro CV, Basso LA, Santos DS. Functional and structural evidence for the catalytic role played by glutamate-47 residue in the mode of action of Mycobacterium tuberculosis cytidine deaminase. RSC Adv 2015. [DOI: 10.1039/c4ra13748e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Glutamate-47 plays a catalytic role in the mode of action ofMycobacterium tuberculosiscytidine deaminase.
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Affiliation(s)
- Zilpa Adriana Sánchez-Quitian
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF)
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB)
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
- Porto Alegre
- Brazil
| | - Valnês Rodrigues-Junior
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF)
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB)
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
- Porto Alegre
- Brazil
| | - Jacqueline Gonçalves Rehm
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF)
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB)
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
- Porto Alegre
- Brazil
| | - Paula Eichler
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF)
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB)
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
- Porto Alegre
- Brazil
| | | | - Cristiano Valim Bizarro
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF)
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB)
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
- Porto Alegre
- Brazil
| | - Luiz Augusto Basso
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF)
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB)
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
- Porto Alegre
- Brazil
| | - Diogenes Santiago Santos
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF)
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB)
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
- Porto Alegre
- Brazil
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Xu J, Deng Y, Li Q, Zhu X, He Z. STRIPE2 encodes a putative dCMP deaminase that plays an important role in chloroplast development in rice. J Genet Genomics 2014; 41:539-48. [PMID: 25438698 DOI: 10.1016/j.jgg.2014.05.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 05/08/2014] [Accepted: 05/09/2014] [Indexed: 12/20/2022]
Abstract
Mutants with abnormal leaf coloration are good genetic materials for understanding the mechanism of chloroplast development and chlorophyll biosynthesis. In this study, a rice mutant st2 (stripe2) with stripe leaves was identified from the γ-ray irradiated mutant pool. The st2 mutant exhibited decreased accumulation of chlorophyll and aberrant chloroplasts. Genetic analysis indicated that the st2 mutant was controlled by a single recessive locus. The ST2 gene was finely confined to a 27-kb region on chromosome 1 by the map-based cloning strategy and a 5-bp deletion in Os01g0765000 was identified by sequence analysis. The deletion happened in the joint of exon 3 and intron 3 and led to new spliced products of mRNA. Genetic complementation confirmed that Os01g0765000 is the ST2 gene. We found that the ST2 gene was expressed ubiquitously. Subcellular localization assay showed that the ST2 protein was located in mitochondria. ST2 belongs to the cytidine deaminase-like family and possibly functions as the dCMP deaminase, which catalyzes the formation of dUMP from dCMP by deamination. Additionally, exogenous application of dUMP could partially rescue the st2 phenotype. Therefore, our study identified a putative dCMP deaminase as a novel regulator in chloroplast development for the first time.
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Affiliation(s)
- Jing Xu
- National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yiwen Deng
- National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qun Li
- National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xudong Zhu
- China National Rice Research Institute, Hangzhou 31006, China.
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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Takenaka M, Zehrmann A, Verbitskiy D, Härtel B, Brennicke A. RNA editing in plants and its evolution. Annu Rev Genet 2014; 47:335-52. [PMID: 24274753 DOI: 10.1146/annurev-genet-111212-133519] [Citation(s) in RCA: 247] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA editing alters the identity of nucleotides in RNA molecules such that the information for a protein in the mRNA differs from the prediction of the genomic DNA. In chloroplasts and mitochondria of flowering plants, RNA editing changes C nucleotides to U nucleotides; in ferns and mosses, it also changes U to C. The approximately 500 editing sites in mitochondria and 40 editing sites in plastids of flowering plants are individually addressed by specific proteins, genes for which are amplified in plant species with organellar RNA editing. These proteins contain repeat elements that bind to cognate RNA sequence motifs just 5' to the edited nucleotide. In flowering plants, the site-specific proteins interact selectively with individual members of a different, smaller family of proteins. These latter proteins may be connectors between the site-specific proteins and the as yet unknown deaminating enzymatic activity.
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Affiliation(s)
- Mizuki Takenaka
- Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany; , , , ,
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Shibu MA, Yang HH, Lo CT, Lin HS, Liu SY, Peng KC. Characterization of a novel resistance-related deoxycytidine deaminase from Brassica oleracea var. capitata. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:1796-1801. [PMID: 24475736 DOI: 10.1021/jf4048513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Brassica oleracea deoxycytidine deaminase (BoDCD), a deoxycytidine deaminase (DCD, EC 3.5.4.14) enzyme, is known to play an important role in the Trichoderma harzianum ETS 323 mediated resistance mechanism in young leaves of B. oleracea var. capitata during Rhizoctonia solani infection. BoDCD potentially neutralizes cytotoxic products of host lipoxygenase activity, and thereby BoDCD restricts the hypersensitivity-related programmed cell death induced in plants during the initial stages of infection. To determine the biochemical characteristics and to partially elucidate the designated functional properties of BoDCD, the enzyme was cloned into an Escherichia coli expression system, and its potential to neutralize the toxic analogues of 2'-deoxycytidine (dC) was examined. BoDCD transformants of E. coli cells were found to be resistant to 2'-deoxycytidine analogues at all of the concentrations tested. The BoDCD enzyme was also overexpressed as a histidine-tagged protein and purified using nickel chelating affinity chromatography. The molecular weight of BoDCD was determined to be 20.8 kDa as visualized by SDS-PAGE. The substrate specificity and other kinetic properties show that BoDCD is more active in neutralizing cytotoxic cytosine β-d-arabinofuranoside than in deaminating 2'-deoxycytinde to 2'-deoxyuridine in nucleic acids or in metabolizing cytidine to uridine. The optimal temperature and pH of the enzyme were 27 °C and 7.5. The Km and Vmax values of BoDCD were, respectively, 91.3 μM and 1.475 mM for its natural substrate 2'-deoxycytidine and 63 μM and 2.072 mM for cytosine β-d-arabinofuranoside. The phenomenon of neutralization of cytotoxic dC analogues by BoDCD is discussed in detail on the basis of enzyme biochemical properties.
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Affiliation(s)
- Marthandam Asokan Shibu
- Department of Life Science and the Institute of Biotechnology, National Dong Hwa University , Hualien 97401, Taiwan, Republic of China
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Kolesnikov AA, Gerasimov ES. Diversity of mitochondrial genome organization. BIOCHEMISTRY (MOSCOW) 2013; 77:1424-35. [PMID: 23379519 DOI: 10.1134/s0006297912130020] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In this review, we discuss types of mitochondrial genome structural organization (architecture), which includes the following characteristic features: size and the shape of DNA molecule, number of encoded genes, presence of cryptogenes, and editing of primary transcripts.
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Affiliation(s)
- A A Kolesnikov
- Biological Faculty, Lomonosov Moscow State University, Moscow, 119234, Russia.
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Cai Y, Li H, Hao L, Li G, Xie P, Chen J. Identification of cda gene in bighead carp and its expression in response to microcystin-LR. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2012; 79:206-213. [PMID: 22264741 DOI: 10.1016/j.ecoenv.2012.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 12/28/2011] [Accepted: 01/03/2012] [Indexed: 05/31/2023]
Abstract
Microcystin-LR (MCLR) is a widespread cyanotoxin, which can influence genes transcription and cause nucleic acid damage in different organisms. To identify MCLR induced transcriptionally changed hepatic genes in bighead carp by subtractive suppression hybridization, we obtained the cDNA fragment of cda. Then we cloned its full-length cDNA, which encodes a cytidine deaminase (CDA). 3D structure prediction showed that the 3D structure and amino acid residues related to function sites of bighead carp CDA were highly conserved. Bighead carp CDA shared high identities with other CDA sequences, and evolved closely to non-mammalian CDAs. Bighead carp expressed cda in all tested tissues under normal situation, and changed its expression profile in a time inversely dependent and dose dependent manner to MCLR, so as to protect itself from MCLR induced toxic damage. These indicated that cda might be involved in anti-MCLR response, especially in the regulation of cytidine and dexocytidine metabolism pathway.
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Affiliation(s)
- Yan Cai
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory for Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Huiying Li
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory for Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Le Hao
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory for Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Guangyu Li
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory for Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Ping Xie
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory for Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Jun Chen
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory for Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China.
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14
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Castandet B, Araya A. RNA editing in plant organelles. Why make it easy? BIOCHEMISTRY (MOSCOW) 2011; 76:924-31. [DOI: 10.1134/s0006297911080086] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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Chateigner-Boutin AL, Small I. Organellar RNA editing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:493-506. [PMID: 21957039 DOI: 10.1002/wrna.72] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
RNA editing is a term used for a number of mechanistically different processes that alter the nucleotide sequence of RNA molecules to differ from the gene sequence. RNA editing occurs in a wide variety of organisms and is particularly frequent in organelle transcripts of eukaryotes. The discontiguous phylogenetic distribution of mRNA editing, the mechanistic differences observed in different organisms, and the nonhomologous editing machinery described in different taxonomic groups all suggest that RNA editing has appeared independently several times. This raises questions about the selection pressures acting to maintain editing that are yet to be completely resolved. Editing tends to be frequent in organisms with atypical organelle genomes and acts to correct the effect of DNA mutations that would otherwise compromise the synthesis of functional proteins. Additional functions of editing in generating protein diversity or regulating gene expression have been proposed but so far lack widespread experimental evidence, at least in organelles.
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Marchand CH, Vanacker H, Collin V, Issakidis-Bourguet E, Maréchal PL, Decottignies P. Thioredoxin targets in Arabidopsis roots. Proteomics 2010; 10:2418-28. [DOI: 10.1002/pmic.200900835] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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17
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Carviel JL, Al-Daoud F, Neumann M, Mohammad A, Provart NJ, Moeder W, Yoshioka K, Cameron RK. Forward and reverse genetics to identify genes involved in the age-related resistance response in Arabidopsis thaliana. MOLECULAR PLANT PATHOLOGY 2009; 10:621-34. [PMID: 19694953 PMCID: PMC6640485 DOI: 10.1111/j.1364-3703.2009.00557.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
SUMMARY Age-related resistance (ARR) occurs in numerous plant species, often resulting in increased disease resistance as plants mature. ARR in Arabidopsis to Pseudomonas syringae pv. tomato is associated with intercellular salicylic acid (SA) accumulation and the transition to flowering. Forward and reverse genetic screens were performed to identify genes required for ARR and to investigate the mechanism of the ARR response. Infiltration of SA into the intercellular space of the ARR-defective mutant iap1-1 (important for the ARR pathway) partially restored ARR function. Inter- and intracellular SA accumulation was reduced in the mutant iap1-1 compared with the wild-type, and the SA regulatory gene EDS1 was also required for ARR. Combining microarray analysis with reverse genetics using T-DNA insertion lines, four additional ARR genes were identified as contributing to ARR: two plant-specific transcription factors of the NAC family [ANAC055 (At3g15500) and ANAC092 (At5g39610)], a UDP-glucose glucosyltransferase [UGT85A1 (At1g22400)] and a cytidine deaminase [CDA1 (At2g19570)]. These four genes and IAP1 are also required for ARR to Hyaloperonospora parasitica. IAP1 encodes a key component of ARR that acts upstream of SA accumulation and possibly downstream of UGT85A1, CDA1 and the two NAC transcription factors (ANAC055, ANAC092).
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Affiliation(s)
- Jessie L Carviel
- Department of Biology, McMaster University, Hamilton, ON, Canada, L8S 4K1
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Du P, Li Y. Prediction of C-to-U RNA editing sites in plant mitochondria using both biochemical and evolutionary information. J Theor Biol 2008; 253:579-86. [PMID: 18511083 DOI: 10.1016/j.jtbi.2008.04.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Revised: 04/06/2008] [Accepted: 04/09/2008] [Indexed: 01/30/2023]
Abstract
Although cytidine-to-uridine conversions in plant mitochondria were discovered 18 years ago, it was still an enigmatic process. Since the sequencing projects of plant mitochondrial genomes are providing more and more available sequences, the requirements of computationally identifying C-to-U RNA editing sites are also increasing. By incorporating both evolutionary and biochemical information, we developed a novel algorithm for predicting C-to-U RNA editing sites in plant mitochondria. The algorithm has been implemented as an online service called CURE (Cytidine-to-Uridine Recognizing Editor). CURE performs better than other methods that are based on only biochemical or only evolutionary information. CURE also provides the ability of predicting C-to-U RNA editing sites in non-coding regions and the synonymous C-to-U RNA editing sites in coding regions that are impossible for other methods. Furthermore, CURE can carry out prediction directly on the entire mitochondria genome sequence. The prediction results of CURE suggest the functional importance of synonymous RNA editing sites, which was neglected before. The CURE service can be accessed at http://bioinfo.au.tsinghua.edu.cn/cure.
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Affiliation(s)
- Pufeng Du
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China.
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Takenaka M, van der Merwe JA, Verbitskiy D, Neuwirt J, Zehrmann A, Brennicke A. RNA Editing in Plant Mitochondria. NUCLEIC ACIDS AND MOLECULAR BIOLOGY 2008. [DOI: 10.1007/978-3-540-73787-2_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Takenaka M, Verbitskiy D, van der Merwe JA, Zehrmann A, Brennicke A. The process of RNA editing in plant mitochondria. Mitochondrion 2008; 8:35-46. [PMID: 18326075 DOI: 10.1016/j.mito.2007.09.004] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
RNA editing changes more than 400 cytidines to uridines in the mRNAs of mitochondria in flowering plants. In other plants such as ferns and mosses, RNA editing reactions changing C to U and U to C are observed at almost equal frequencies. Development of transfection systems with isolated mitochondria and of in vitro systems with extracts from mitochondria has considerably improved our understanding of the recognition of specific editing sites in the last few years. These assays have also yielded information about the biochemical parameters, but the enzymes involved have not yet been identified. Here we summarize our present understanding of the process of RNA editing in flowering plant mitochondria.
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Couldridge C, Newbury HJ, Ford-Lloyd B, Bale J, Pritchard J. Exploring plant responses to aphid feeding using a full Arabidopsis microarray reveals a small number of genes with significantly altered expression. BULLETIN OF ENTOMOLOGICAL RESEARCH 2007; 97:523-32. [PMID: 17916270 DOI: 10.1017/s0007485307005160] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The aim of this study was to determine which Arabidopsis thaliana (L.) genes had significantly altered expression following 2-36 h of infestation by the aphid Myzus persicae (Sulzer). Six biological replicates were performed for both control and treatment at each time point, allowing rigorous statistical analysis of any changes. Only two genes showed altered expression after 2 h (one up- and one down-regulated) while two were down-regulated and twenty three were up-regulated at 36 h. The transcript annotation allowed classification of the significantly altered genes into a number of classes, including those involved in cell wall modification, carbon metabolism and signalling. Additionally, a number of genes were implicated in oxidative stress and defence against other pathogens. Five genes could not currently be assigned any function. The changes in gene expression are discussed in relation to current models of plant-insect interactions.
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Affiliation(s)
- C Couldridge
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
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22
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Salone V, Rüdinger M, Polsakiewicz M, Hoffmann B, Groth-Malonek M, Szurek B, Small I, Knoop V, Lurin C. A hypothesis on the identification of the editing enzyme in plant organelles. FEBS Lett 2007; 581:4132-8. [PMID: 17707818 DOI: 10.1016/j.febslet.2007.07.075] [Citation(s) in RCA: 190] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2007] [Revised: 07/20/2007] [Accepted: 07/30/2007] [Indexed: 11/28/2022]
Abstract
RNA editing in plant organelles is an enigmatic process leading to conversion of cytidines into uridines. Editing specificity is determined by proteins; both those known so far are pentatricopeptide repeat (PPR) proteins. The enzyme catalysing RNA editing in plants is still totally unknown. We propose that the DYW domain found in many higher plant PPR proteins is the missing catalytic domain. This hypothesis is based on two compelling observations: (i) the DYW domain contains invariant residues that match the active site of cytidine deaminases; (ii) the phylogenetic distribution of the DYW domain is strictly correlated with RNA editing.
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Abstract
To analyze the C-to-U conversion of RNA editing in plant mitochondria, complementary methods are required, which include in vivo, in organello, and in vitro approaches. The major obstacle for in vitro assays is the generally observed fragility of the activity in mitochondrial lysates and the corresponding low activity. If seen at all, this activity is often in the range of a few percent conversion of the added templates. We have developed a sensitive assay system using mismatch analysis that allows detection of such low conversion rates. With this assay mitochondrial lysate preparations could be established from pea shoots and cauliflower inflorescences, which can be employed for the in vitro analysis of specificity requirements and biochemical parameters of RNA editing in plant mitochondria.
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Maize haplotype with a helitron-amplified cytidine deaminase gene copy. BMC Genet 2006; 7:52. [PMID: 17094807 PMCID: PMC1657028 DOI: 10.1186/1471-2156-7-52] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2006] [Accepted: 11/09/2006] [Indexed: 12/23/2022] Open
Abstract
Background Genetic maps are based on recombination of orthologous gene sequences between different strains of the same species. Therefore, it was unexpected to find extensive non-collinearity of genes between different inbred strains of maize. Interestingly, disruption of gene collinearity can be caused among others by a rolling circle-type copy and paste mechanism facilitated by Helitrons. However, understanding the role of this type of gene amplification has been hampered by the lack of finding intact gene sequences within Helitrons. Results By aligning two haplotypes of the z1C1 locus of maize we found a Helitron that contains two genes, one encoding a putative cytidine deaminase and one a hypothetical protein with part of a 40S ribosomal protein. The cytidine deaminase gene, called ZmCDA3, has been copied from the ZmCDA1 gene on maize chromosome 7 about 4.5 million years ago (mya) after maize was formed by whole-genome duplication from two progenitors. Inbred lines contain gene copies of both progenitors, the ZmCDA1 and ZmCDA2 genes. Both genes diverged when the progenitors of maize split and are derived from the same progenitor as the rice OsCDA1 gene. The ZmCDA1 and ZmCDA2 genes are both transcribed in leaf and seed tissue, but transcripts of the paralogous ZmCDA3 gene have not been found yet. Based on their protein structure the maize CDA genes encode a nucleoside deaminase that is found in bacterial systems and is distinct from the mammalian RNA and/or DNA modifying enzymes. Conclusion The conservation of a paralogous gene sequence encoding a cytidine deaminase gene over 4.5 million years suggests that Helitrons could add functional gene sequences to new chromosomal positions and thereby create new haplotypes. However, the function of such paralogous gene copies cannot be essential because they are not present in all maize strains. However, it is interesting to note that maize hybrids can outperform their inbred parents. Therefore, certain haplotypes may function only in combination with other haplotypes or under specialized environmental conditions.
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Zrenner R, Stitt M, Sonnewald U, Boldt R. Pyrimidine and purine biosynthesis and degradation in plants. ANNUAL REVIEW OF PLANT BIOLOGY 2006; 57:805-36. [PMID: 16669783 DOI: 10.1146/annurev.arplant.57.032905.105421] [Citation(s) in RCA: 359] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Nucleotide metabolism operates in all living organisms, embodies an evolutionarily ancient and indispensable complex of metabolic pathways and is of utmost importance for plant metabolism and development. In plants, nucleotides can be synthesized de novo from 5-phosphoribosyl-1-pyrophosphate and simple molecules (e.g., CO(2), amino acids, and tetrahydrofolate), or be derived from preformed nucleosides and nucleobases via salvage reactions. Nucleotides are degraded to simple metabolites, and this process permits the recycling of phosphate, nitrogen, and carbon into central metabolic pools. Despite extensive biochemical knowledge about purine and pyrimidine metabolism, comprehensive studies of the regulation of this metabolism in plants are only starting to emerge. Here we review progress in molecular aspects and recent studies on the regulation and manipulation of nucleotide metabolism in plants.
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Affiliation(s)
- Rita Zrenner
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam OT Golm, Germany.
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27
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Hegeman CE, Hayes ML, Hanson MR. Substrate and cofactor requirements for RNA editing of chloroplast transcripts in Arabidopsis in vitro. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2005; 42:124-32. [PMID: 15773858 DOI: 10.1111/j.1365-313x.2005.02360.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
None of the macromolecular components of the chloroplast RNA editing apparatus has yet been identified. In order to facilitate biochemical purification and characterization of the chloroplast RNA editing apparatus, we have identified conditions suitable for production of chloroplast extracts from the model plant Arabidopsis that are capable of editing exogenous substrates produced by in vitro transcription. A simple poisoned primer extension assay readily quantified editing extent of mutated and wild-type substrates. Maximum editing efficiency typically varied from 10 to 40% with different chloroplast preparations. Substrates carrying as little as 47 nt surrounding the psbE editing site were as efficiently edited as longer substrates. Editing activity was stimulated when either ATP, CTP, or dCTP was provided to the extract, an unusual observation also recently seen with plant mitochondrial editing extracts. Editing was sensitive to a zinc chelator, also a characteristic of the mammalian APOBEC editing enzyme, which is a zinc-dependent cytidine deaminase.
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Affiliation(s)
- Carla E Hegeman
- Department of Molecular Biology and Genetics, Cornell University, Biotechnology Building, Ithaca, NY 14853, USA
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Takenaka M, Neuwirt J, Brennicke A. Complex cis-elements determine an RNA editing site in pea mitochondria. Nucleic Acids Res 2004; 32:4137-44. [PMID: 15295040 PMCID: PMC514384 DOI: 10.1093/nar/gkh763] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2004] [Revised: 07/26/2004] [Accepted: 07/26/2004] [Indexed: 11/14/2022] Open
Abstract
The cis-requirements for the first editing site in the atp9 mRNA from pea mitochondria were investigated in an in vitro RNA editing system. Template RNAs deleted 5' of -20 are edited correctly, but with decreased efficiency. Deletions between -20 and the edited nucleotide abolish editing activity. Substitution of the sequences 3' of the editing site has little effect, which suggests that the major determinants reside upstream. Stepwise mutated RNA sequences were used as templates or competitors that divide the cis-elements into several distinct regions. In the template RNAs, mutation of the sequence between -40 and -35 reduces the editing activity, while the region from -15 to -5 is essential for the editing reaction. In competition experiments the upstream region can be titrated, while the essential sequence near the editing site is largely resistant to excess competitor. This observation suggests that either one trans-factor attaches to these separate cis-regions with different affinities or two distinct trans-factors bind to these sequences, and one of which is present in limited amounts, whereas the other one is more abundant in the lysate.
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Takenaka M, Brennicke A. In vitro RNA editing in pea mitochondria requires NTP or dNTP, suggesting involvement of an RNA helicase. J Biol Chem 2003; 278:47526-33. [PMID: 12970369 DOI: 10.1074/jbc.m305341200] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To analyze the biochemical parameters of RNA editing in plant mitochondria and to eventually characterize the enzymes involved we developed a novel in vitro system. The high sensitivity of the mismatch-specific thymine glycosylase is exploited to facilitate reliable quantitative evaluation of the in vitro RNA editing products. A pea mitochondrial lysate correctly processes a C to U editing site in the cognate atp9 template. Reaction conditions were determined for a number of parameters, which allow first conclusions on the proteins involved. The apparent tolerance against specific Zn2+ chelators argues against the involvement of a cytidine deaminase enzyme, the theoretically most straightforward catalysator of the deamination reaction. Participation of a transaminase was investigated by testing potential amino group receptors, but none of these increased the RNA editing reaction. Most notable is the requirement of the RNA editing activity for NTPs. Any NTP or dNTP can substitute for ATP to the optimal concentration of 15 mm. This observation suggests the participation of an RNA helicase in the predicted RNA editing protein complex of plant mitochondria.
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31
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Stasolla C, Katahira R, Thorpe TA, Ashihara H. Purine and pyrimidine nucleotide metabolism in higher plants. JOURNAL OF PLANT PHYSIOLOGY 2003; 160:1271-95. [PMID: 14658380 DOI: 10.1078/0176-1617-01169] [Citation(s) in RCA: 201] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Purine and pyrimidine nucleotides participate in many biochemical processes in plants. They are building blocks for nucleic acid synthesis, an energy source, precursors for the synthesis of primary products, such as sucrose, polysaccharides, phospholipids, as well as secondary products. Therefore, biosynthesis and metabolism of nucleotides are of fundamental importance in the growth and development of plants. Nucleotides are synthesized both from amino acids and other small molecules via de novo pathways, and from preformed nucleobases and nucleosides by salvage pathways. In this article the biosynthesis, interconversion and degradation of purine and pyrimidine nucleotides in higher plants are reviewed. This description is followed by an examination of physiological aspects of nucleotide metabolism in various areas of growth and organized development in plants, including embryo maturation and germination, in vitro organogenesis, storage organ development and sprouting, leaf senescence, and cultured plant cells. The effects of environmental factors on nucleotide metabolism are also described. This review ends with a brief discussion of molecular studies on nucleotide synthesis and metabolism.
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Affiliation(s)
- Claudio Stasolla
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
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Binder S, Brennicke A. Gene expression in plant mitochondria: transcriptional and post-transcriptional control. Philos Trans R Soc Lond B Biol Sci 2003; 358:181-8; discussion 188-9. [PMID: 12594926 PMCID: PMC1693100 DOI: 10.1098/rstb.2002.1179] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The informational content of the mitochondrial genome in plants is, although small, essential for each cell. Gene expression in these organelles involves a number of distinct transcriptional and post-transcriptional steps. The complex post-transcriptional processes of plant mitochondria such as 5' and 3' RNA processing, intron splicing, RNA editing and controlled RNA stability extensively modify individual steady-state RNA levels and influence the mRNA quantities available for translation. In this overview of the processes in mitochondrial gene expression, we focus on confirmed and potential sites of regulatory interference and discuss the evolutionary origins of the transcriptional and post-transcriptional processes.
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Affiliation(s)
- Stefan Binder
- Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany
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Fey J, Weil JH, Tomita K, Cosset A, Dietrich A, Small I, Maréchal-Drouard L. Role of editing in plant mitochondrial transfer RNAs. Gene 2002; 286:21-4. [PMID: 11943456 DOI: 10.1016/s0378-1119(01)00817-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Editing in plant mitochondria consists in C to U changes and mainly affects messenger RNAs, thus providing the correct genetic information for the biosynthesis of mitochondrial (mt) proteins. But editing can also affect some of the plant mt tRNAs encoded by the mt genome. In dicots, a C to U editing event corrects a C:A mismatch into a U:A base pair in the acceptor stem of mt tRNA(Phe) (GAA). In larch mitochondria, three C to U editing events restore U:A base pairs in the acceptor stem, D stem and anticodon stem, respectively, of mt tRNA(His) (GUG). For both these mt RNA(Phe) and tRNA(His), editing of the precursors is a prerequisite for their processing into mature tRNAs. In potato mt tRNA(Cys) (GCA), editing converts a C28:U42 mismatch in the anticodon stem into a U28:U42 non-canonical base pair, and reverse transcriptase minisequencing has shown that the mature mt tRNA(Cys) is fully edited. In the bryophyte Marchantia polymorpha this U residue is encoded in the mt genome and evolutionary studies suggest that restoration of a U28 residue is necessary when it is not encoded in the gene. However, in vitro studies have shown that neither processing of the precursor, nor aminoacylation of tRNA(Cys), requires C to U editing at this position. But sequencing of the purified mt tRNA(Cys) has shown that Psi is present at position 28, indicating that C to U editing is a prerequisite for the subsequent isomerization of U into Psi at position 28.
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MESH Headings
- Cytidine/genetics
- Cytidine/metabolism
- Mitochondria/genetics
- Plants/genetics
- Pseudouridine/genetics
- Pseudouridine/metabolism
- RNA Editing
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- RNA, Transfer, Cys/genetics
- RNA, Transfer, Cys/metabolism
- RNA, Transfer, His/genetics
- RNA, Transfer, His/metabolism
- RNA, Transfer, Phe/genetics
- RNA, Transfer, Phe/metabolism
- Uridine/genetics
- Uridine/metabolism
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Affiliation(s)
- J Fey
- Institut de Biologie Moléculaire des Plantes, CNRS, 12 rue du Général Zimmer, 67084 Strasbourg, France
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Hirose T, Sugiura M. Involvement of a site-specific trans-acting factor and a common RNA-binding protein in the editing of chloroplast mRNAs: development of a chloroplast in vitro RNA editing system. EMBO J 2001; 20:1144-52. [PMID: 11230137 PMCID: PMC145495 DOI: 10.1093/emboj/20.5.1144] [Citation(s) in RCA: 146] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2000] [Revised: 01/15/2001] [Accepted: 01/15/2001] [Indexed: 11/13/2022] Open
Abstract
RNA editing in higher plant chloroplasts involves C-->U conversion at approximately 30 specific sites. An in vitro system supporting accurate editing has been developed from tobacco chloroplasts. Mutational analysis of substrate mRNAs derived from tobacco chloroplast psbL and ndhB mRNAs confirmed the participation of cis-acting elements that had previously been identified in vivo. Competition analysis revealed the existence of site-specific trans-acting factors interacting with the corresponding upstream cis-elements. A chloroplast protein of 25 kDa was found to be specifically associated with the cis-element involved in psbL mRNA editing. Immunological analyses revealed that an additional factor, the chloroplast RNA-binding protein cp31, is also required for RNA editing at multiple sites. This combination of site-specific and common RNA-binding proteins recognizes editing sites in chloroplasts.
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Affiliation(s)
- Tetsuro Hirose
- Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan Present address: Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 295 Congress Avenue, BCMM 133, New Haven, CT 06536, USA Present address: Graduate School of Natural Sciences, Nagoya City University, Nagoya 467-8501, Japan Corresponding author e-mail:
| | - Masahiro Sugiura
- Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan Present address: Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 295 Congress Avenue, BCMM 133, New Haven, CT 06536, USA Present address: Graduate School of Natural Sciences, Nagoya City University, Nagoya 467-8501, Japan Corresponding author e-mail:
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Chester A, Scott J, Anant S, Navaratnam N. RNA editing: cytidine to uridine conversion in apolipoprotein B mRNA. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1494:1-13. [PMID: 11072063 DOI: 10.1016/s0167-4781(00)00219-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
RNA editing is a post-transcriptional process that changes the informational capacity within the RNA. These processes include alterations made by nucleotide deletion, insertion and base conversion. A to I and C to U conversion occurs in mammals and these editing events are catalysed by RNA binding deaminases. C to U editing of apoB mRNA was the first mammalian editing event to be identified. The minimal protein complex necessary for apoB mRNA editing has been determined and consists of APOBEC-1 and ACF. Overexpression of APOBEC-1 in transgenic animals caused liver dysplasia and APOBEC-1 has been identified in neurofibromatosis type 1 tumours, suggesting that RNA editing may be another mechanism for tumourigenesis. Several APOBEC-1-like proteins have been identified, including a family of APOBEC-1-related proteins with unknown function on chromosome 22. This review summarises the different types of RNA editing and discusses the current status of C to U apoB mRNA editing. This knowledge is very important in understanding the structure and function of these related proteins and their role in biology.
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Affiliation(s)
- A Chester
- MRC Molecular Medicine, Clinical Science Centre, Imperial College School of Medicine, Hammersmith Hospital, London, UK
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