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Hinojosa-Cruz A, Díaz-Sánchez ÁG, Díaz-Vilchis A, González-Segura L. Structural and functional properties of uridine 5'-monophosphate synthase from Coffea arabica. Int J Biol Macromol 2024; 259:129226. [PMID: 38184030 DOI: 10.1016/j.ijbiomac.2024.129226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/23/2023] [Accepted: 01/02/2024] [Indexed: 01/08/2024]
Abstract
In higher eukaryotes and plants, the last two sequential steps in the de novo biosynthesis of uridine 5'-monophosphate (UMP) are catalyzed by a bifunctional natural chimeric protein called UMP synthase (UMPS). In higher plants, UMPS consists of two naturally fused enzymes: orotate phosphoribosyltransferase (OPRTase) at N-terminal and orotidine-5'-monophosphate decarboxylase (ODCase) at C-terminal. In this work, we obtained the full functional recombinant protein UMPS from Coffea arabica (CaUMPS) and studied its structure-function relationships. A biochemical and structural characterization of a plant UMPS with its two functional domains is described together with the presentation of the first crystal structure of a plant ODCase at 1.4 Å resolution. The kinetic parameters measured of CaOPRTase and CaODCase domains were comparable to those reported. The crystallographic structure revealed that CaODCase is a dimer that conserves the typical fold observed in other ODCases from prokaryote and eukaryote with a 1-deoxy-ribofuranose-5'-phosphate molecule bound in the active site of one subunit induced a closed conformation. Our results add to the knowledge of one of the key enzymes of the de novo biosynthesis of pyrimidines in plant metabolism and open the door to future applications.
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Affiliation(s)
- Alexis Hinojosa-Cruz
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Ángel G Díaz-Sánchez
- Departamento de Ciencias Químico Biológicas, Instituto de Ciencias Biomédicas, Universidad Autónoma de Ciudad Juárez, Ciudad Juárez 32310, Chihuahua, Mexico
| | - Adelaida Díaz-Vilchis
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Chamilpa, Cuernavaca, Morelos 62240, Mexico
| | - Lilian González-Segura
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico.
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Bellin L, Melzer M, Hilo A, Garza Amaya DL, Keller I, Meurer J, Möhlmann T. Nucleotide Limitation Results in Impaired Photosynthesis, Reduced Growth and Seed Yield Together with Massively Altered Gene Expression. PLANT & CELL PHYSIOLOGY 2023; 64:1494-1510. [PMID: 37329302 DOI: 10.1093/pcp/pcad063] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/04/2023] [Accepted: 06/16/2023] [Indexed: 06/19/2023]
Abstract
Nucleotide limitation and imbalance is a well-described phenomenon in animal research but understudied in the plant field. A peculiarity of pyrimidine de novo synthesis in plants is the complex subcellular organization. Here, we studied two organellar localized enzymes in the pathway, with chloroplast aspartate transcarbamoylase (ATC) and mitochondrial dihydroorotate dehydrogenase (DHODH). ATC knock-downs were most severely affected, exhibiting low levels of pyrimidine nucleotides, a low energy state, reduced photosynthetic capacity and accumulation of reactive oxygen species. Furthermore, altered leaf morphology and chloroplast ultrastructure were observed in ATC mutants. Although less affected, DHODH knock-down mutants showed impaired seed germination and altered mitochondrial ultrastructure. Thus, DHODH might not only be regulated by respiration but also exert a regulatory function on this process. Transcriptome analysis of an ATC-amiRNA line revealed massive alterations in gene expression with central metabolic pathways being downregulated and stress response and RNA-related pathways being upregulated. In addition, genes involved in central carbon metabolism, intracellular transport and respiration were markedly downregulated in ATC mutants, being most likely responsible for the observed impaired growth. We conclude that impairment of the first committed step in pyrimidine metabolism, catalyzed by ATC, leads to nucleotide limitation and by this has far-reaching consequences on metabolism and gene expression. DHODH might closely interact with mitochondrial respiration, as seen in delayed germination, which is the reason for its localization in this organelle.
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Affiliation(s)
- Leo Bellin
- Pflanzenphysiologie, Fachbereich Biologie, Universität Kaiserslautern, Erwin-Schrödinger-Straße, Kaiserslautern D-67663, Germany
| | - Michael Melzer
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Corrensstrasse 3, Seeland, OT Gatersleben 06466, Germany
| | - Alexander Hilo
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Corrensstrasse 3, Seeland, OT Gatersleben 06466, Germany
| | - Diana Laura Garza Amaya
- Pflanzenphysiologie, Fachbereich Biologie, Universität Kaiserslautern, Erwin-Schrödinger-Straße, Kaiserslautern D-67663, Germany
| | - Isabel Keller
- Pflanzenphysiologie, Fachbereich Biologie, Universität Kaiserslautern, Erwin-Schrödinger-Straße, Kaiserslautern D-67663, Germany
| | - Jörg Meurer
- Plant Sciences, Department Biology I, Ludwig-Maximilians-University Munich, Großhaderner Straße 2-4, Planegg-Martinsried 82152, Germany
| | - Torsten Möhlmann
- Pflanzenphysiologie, Fachbereich Biologie, Universität Kaiserslautern, Erwin-Schrödinger-Straße, Kaiserslautern D-67663, Germany
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Niu Y, Liu L. RNA pseudouridine modification in plants. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6431-6447. [PMID: 37581601 DOI: 10.1093/jxb/erad323] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/11/2023] [Indexed: 08/16/2023]
Abstract
Pseudouridine is one of the well-known chemical modifications in various RNA species. Current advances to detect pseudouridine show that the pseudouridine landscape is dynamic and affects multiple cellular processes. Although our understanding of this post-transcriptional modification mainly depends on yeast and human models, the recent findings provide strong evidence for the critical role of pseudouridine in plants. Here, we review the current knowledge of pseudouridine in plant RNAs, including its synthesis, degradation, regulatory mechanisms, and functions. Moreover, we propose future areas of research on pseudouridine modification in plants.
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Affiliation(s)
- Yanli Niu
- Laboratory of Cell Signal Transduction, School of Basic Medical Sciences, Henan University, Kaifeng 475001, China
| | - Lingyun Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475001, China
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Du M, Yin Z, Xu K, Huang Y, Xu Y, Wen W, Zhang Z, Xu H, Wu X. Integrated mass spectrometry imaging and metabolomics reveals sublethal effects of indoxacarb on the red fire ant Solenopsis invicta. PEST MANAGEMENT SCIENCE 2023; 79:3122-3132. [PMID: 37013793 DOI: 10.1002/ps.7489] [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: 11/03/2022] [Revised: 03/26/2023] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Indoxacarb, representing an efficient insecticide, is normally made into a bait to spread the poison among red fire ants so that it can be widely applied in the prevention and control of Solenopsis invicta. However, the potential toxicity mechanism of S. invicta in response to indoxacarb remains to be explored. In this study, we integrated mass spectrometry imaging (MSI) and untargeted metabolomics methods to reveal disturbed metabolic expression levels and spatial distribution within the whole-body tissue of S. invicta treated with indoxacarb. RESULTS Metabolomics results showed a significantly altered level of metabolites after indoxacarb treatment, such as carbohydrates, amino acids and pyrimidine and derivatives. Additionally, the spatial distribution and regulation of several crucial metabolites resulting from the metabolic pathway and lipids can be visualized using label-free MSI methods. Specifically, xylitol, aspartate, and uracil were distributed throughout the whole body of S. invicta, while sucrose-6'-phosphate and glycerol were mainly distributed in the abdomen of S. invicta, and thymine was distributed in the head and chest of S. invicta. Taken together, the integrated MSI and metabolomics results indicated that the toxicity mechanism of indoxacarb in S. invicta is closely associated with the disturbance in several key metabolic pathways, such as pyrimidine metabolism, aspartate metabolism, pentose and glucuronate interconversions, and inhibited energy synthesis. CONCLUSION Collectively, these findings provide a new perspective for the understanding of toxicity assessment between targeted organisms S. invicta and pesticides. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Mingyi Du
- National Key Laboratory of Green Pesticide and Key Laboratory of Natural Pesticide and Chemical Biology of the Ministry of Education, South China Agricultural University, Guangzhou, China
- Key Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Zhibin Yin
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Kaijie Xu
- National Key Laboratory of Green Pesticide and Key Laboratory of Natural Pesticide and Chemical Biology of the Ministry of Education, South China Agricultural University, Guangzhou, China
| | - Yudi Huang
- National Key Laboratory of Green Pesticide and Key Laboratory of Natural Pesticide and Chemical Biology of the Ministry of Education, South China Agricultural University, Guangzhou, China
| | - Yizhu Xu
- National Key Laboratory of Green Pesticide and Key Laboratory of Natural Pesticide and Chemical Biology of the Ministry of Education, South China Agricultural University, Guangzhou, China
| | - Wenlin Wen
- National Key Laboratory of Green Pesticide and Key Laboratory of Natural Pesticide and Chemical Biology of the Ministry of Education, South China Agricultural University, Guangzhou, China
| | - Zhixiang Zhang
- National Key Laboratory of Green Pesticide and Key Laboratory of Natural Pesticide and Chemical Biology of the Ministry of Education, South China Agricultural University, Guangzhou, China
| | - Hanhong Xu
- National Key Laboratory of Green Pesticide and Key Laboratory of Natural Pesticide and Chemical Biology of the Ministry of Education, South China Agricultural University, Guangzhou, China
| | - Xinzhou Wu
- National Key Laboratory of Green Pesticide and Key Laboratory of Natural Pesticide and Chemical Biology of the Ministry of Education, South China Agricultural University, Guangzhou, China
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Sircar S, Parekh N. Meta-analysis of drought-tolerant genotypes in Oryza sativa: A network-based approach. PLoS One 2019; 14:e0216068. [PMID: 31059518 PMCID: PMC6502313 DOI: 10.1371/journal.pone.0216068] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 04/12/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Drought is a severe environmental stress. It is estimated that about 50% of the world rice production is affected mainly by drought. Apart from conventional breeding strategies to develop drought-tolerant crops, innovative computational approaches may provide insights into the underlying molecular mechanisms of stress response and identify drought-responsive markers. Here we propose a network-based computational approach involving a meta-analytic study of seven drought-tolerant rice genotypes under drought stress. RESULTS Co-expression networks enable large-scale analysis of gene-pair associations and tightly coupled clusters that may represent coordinated biological processes. Considering differentially expressed genes in the co-expressed modules and supplementing external information such as resistance/tolerance QTLs, transcription factors, network-based topological measures, we identify and prioritize drought-adaptive co-expressed gene modules and potential candidate genes. Using the candidate genes that are well-represented across the datasets as 'seed' genes, two drought-specific protein-protein interaction networks (PPINs) are constructed with up- and down-regulated genes. Cluster analysis of the up-regulated PPIN revealed ABA signalling pathway as a central process in drought response with a probable crosstalk with energy metabolic processes. Tightly coupled gene clusters representing up-regulation of core cellular respiratory processes and enhanced degradation of branched chain amino acids and cell wall metabolism are identified. Cluster analysis of down-regulated PPIN provides a snapshot of major processes associated with photosynthesis, growth, development and protein synthesis, most of which are shut down during drought. Differential regulation of phytohormones, e.g., jasmonic acid, cell wall metabolism, signalling and posttranslational modifications associated with biotic stress are elucidated. Functional characterization of topologically important, drought-responsive uncharacterized genes that may play a role in important processes such as ABA signalling, calcium signalling, photosynthesis and cell wall metabolism is discussed. Further transgenic studies on these genes may help in elucidating their biological role under stress conditions. CONCLUSION Currently, a large number of resources for rice functional genomics exist which are mostly underutilized by the scientific community. In this study, a computational approach integrating information from various resources such as gene co-expression networks, protein-protein interactions and pathway-level information is proposed to provide a systems-level view of complex drought-responsive processes across the drought-tolerant genotypes.
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Affiliation(s)
- Sanchari Sircar
- Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India
| | - Nita Parekh
- Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India
- * E-mail:
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Ahkami A, Scholz U, Steuernagel B, Strickert M, Haensch KT, Druege U, Reinhardt D, Nouri E, von Wirén N, Franken P, Hajirezaei MR. Comprehensive transcriptome analysis unravels the existence of crucial genes regulating primary metabolism during adventitious root formation in Petunia hybrida. PLoS One 2014; 9:e100997. [PMID: 24978694 PMCID: PMC4076263 DOI: 10.1371/journal.pone.0100997] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 06/01/2014] [Indexed: 11/18/2022] Open
Abstract
To identify specific genes determining the initiation and formation of adventitious roots (AR), a microarray-based transcriptome analysis in the stem base of the cuttings of Petunia hybrida (line W115) was conducted. A microarray carrying 24,816 unique, non-redundant annotated sequences was hybridized to probes derived from different stages of AR formation. After exclusion of wound-responsive and root-regulated genes, 1,354 of them were identified which were significantly and specifically induced during various phases of AR formation. Based on a recent physiological model distinguishing three metabolic phases in AR formation, the present paper focuses on the response of genes related to particular metabolic pathways. Key genes involved in primary carbohydrate metabolism such as those mediating apoplastic sucrose unloading were induced at the early sink establishment phase of AR formation. Transcriptome changes also pointed to a possible role of trehalose metabolism and SnRK1 (sucrose non-fermenting 1- related protein kinase) in sugar sensing during this early step of AR formation. Symplastic sucrose unloading and nucleotide biosynthesis were the major processes induced during the later recovery and maintenance phases. Moreover, transcripts involved in peroxisomal beta-oxidation were up-regulated during different phases of AR formation. In addition to metabolic pathways, the analysis revealed the activation of cell division at the two later phases and in particular the induction of G1-specific genes in the maintenance phase. Furthermore, results point towards a specific demand for certain mineral nutrients starting in the recovery phase.
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Affiliation(s)
- Amirhossein Ahkami
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, United States of America
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | | | | | - Klaus-Thomas Haensch
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Grossbeeren & Erfurt, Germany
| | - Uwe Druege
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Grossbeeren & Erfurt, Germany
| | - Didier Reinhardt
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Eva Nouri
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Nicolaus von Wirén
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Philipp Franken
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Grossbeeren & Erfurt, Germany
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Jørgensen MS, Skovlund DA, Johannesen PF, Mortensen UH. A novel platform for heterologous gene expression in Trichoderma reesei (Teleomorph Hypocrea jecorina). Microb Cell Fact 2014; 13:33. [PMID: 24602241 PMCID: PMC4015775 DOI: 10.1186/1475-2859-13-33] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 02/10/2014] [Indexed: 12/16/2022] Open
Abstract
Background The industrially applied filamentous fungus Trichoderma reesei has received substantial interest due to its highly efficient synthesis apparatus of cellulytic enzymes. However, the production of heterologous enzymes in T. reesei still remains low mainly due to lack of tools for genetic engineering. Results In this study we present new genetic tools for T. reesei to further expand its use in industrial production. We have developed an expression platform where genes are inserted into a versatile expression vector via highly efficient uracil-excision cloning and subsequently inserted into a defined position in the T. reesei genome ensuring that enzyme production from different transformants can be directly compared. The ade2 locus was selected as integration site since ade2 mutants develop red pigment that facilitates easy and rapid detection of correctly targeted transformants. In addition, our system includes a tku70 disruption to increase gene targeting efficiency and a new bidirectional marker, pyr2, for iterative gene targeting. The dual selection system, color and prototrophism, ensures that correct transformants containing the desired gene inserted into the defined expression site can be selected with an efficiency approaching 100%. Conclusions The new genetic tools we have developed are suitable for high-throughput integration of genes into the genome of T. reesei and can easily be combined with techniques for generation of defined mutants. Moreover, the usability of the novel expression system with ade2 as integration site was confirmed by expression of a Thermomyces lanuginosus lipase.
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Affiliation(s)
| | | | | | - Uffe H Mortensen
- Department of Systems Biology, Center for Microbial Biotechnology, Technical University of Denmark, Building 223, DK-2800 Lyngby, Denmark.
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8
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De novo pyrimidine biosynthesis in the oomycete plant pathogen Phytophthora infestans. Gene 2014; 537:312-21. [DOI: 10.1016/j.gene.2013.12.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 11/21/2013] [Accepted: 12/04/2013] [Indexed: 11/21/2022]
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9
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Qin L, Shi H, Xia H, Chen L, Yao Q, Chen K. Comparative proteomic analysis of midgut proteins from male and female Bombyx mori (Lepidoptera: Bombycidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2014; 14:ieu088. [PMID: 25502033 PMCID: PMC5633941 DOI: 10.1093/jisesa/ieu088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Many biological phenotypes of male and female silkworms (Bombyx mori) are quite different, and one of the major differences is the growth rate at various larval stages. Nutrient utilization by midgut varies with sexes. However, the molecular basis of this variation is not clear. To understand the molecular mechanism, comparative proteomic approach was employed to investigate the variation of midgut proteomes between male and female silkworms. Totally, 32 proteins that were grouped into four categories were differentially expressed and subsequently identified by mass spectrometry. Gene ontology analysis revealed that these proteins were attributed with biological functions such as binding, catalytic, and transporter, and these proteins were involved in biological process such as cellular process, localization, and metabolic process. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that these proteins were involved in pathways such as glycolysis, gluconeogenesis, oxidative phosphorylation, and purine metabolism. At transcription level, the expressional variation was confirmed for six identified proteins including muscle glycogen phosphorylase, uridine 5'-monophosphate synthase, cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha, ATP synthase, thiol peroxiredoxin, and serpin-2. This study provides useful information for understanding the mechanisms of nutrient absorption and the protein-protein interaction in the silkworm.
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Affiliation(s)
- Lvgao Qin
- Institute of Life Sciences, Jiangsu University, 301 Xuefu Rd., Zhenjiang 212013, Jiangsu Province, People's Republic of China
| | - Haifeng Shi
- Institute of Life Sciences, Jiangsu University, 301 Xuefu Rd., Zhenjiang 212013, Jiangsu Province, People's Republic of China
| | - Hengchuan Xia
- Institute of Life Sciences, Jiangsu University, 301 Xuefu Rd., Zhenjiang 212013, Jiangsu Province, People's Republic of China
| | - Liang Chen
- Institute of Life Sciences, Jiangsu University, 301 Xuefu Rd., Zhenjiang 212013, Jiangsu Province, People's Republic of China
| | - Qin Yao
- Institute of Life Sciences, Jiangsu University, 301 Xuefu Rd., Zhenjiang 212013, Jiangsu Province, People's Republic of China
| | - Keping Chen
- Institute of Life Sciences, Jiangsu University, 301 Xuefu Rd., Zhenjiang 212013, Jiangsu Province, People's Republic of China
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Chen CT, Slocum RD. Expression and functional analysis of aspartate transcarbamoylase and role of de novo pyrimidine synthesis in regulation of growth and development in Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2008; 46:150-9. [PMID: 18053734 DOI: 10.1016/j.plaphy.2007.10.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2007] [Indexed: 05/09/2023]
Abstract
Aspartate transcarbamoylase (ATCase, EC 2.1.3.2) catalyzes the committed step in the de novo synthesis of uridine-5'-monophosphate (UMP), from which all other pyrimidine nucleotides are made. In Arabidopsis, ATCase is encoded by a single PYRB gene, whose expression was regulated by tissue pyrimidine availability. RT-PCR and PYRB:GUS expression profiles showed markedly increased expression of PYRB in root tissues during the first 5days after germination, as seed pyrimidine reserves were exhausted and de novo synthesis was required to support new growth. Growth of seedlings in the presence of the ATCase inhibitor N-(phosphonacetyl)-l-aspartate (PALA) resulted in complete developmental arrest at the day 5 stage, which was reversible upon addition of exogenous uracil. Arabidopsis RNAi lines exhibiting 70-95% reductions in PYRB transcript and ATCase protein levels had delayed growth and development, produced smaller plants with reduced root to shoot biomass ratios, few flowers, and siliques that produced smaller seeds with greatly reduced viability, compared with wild type plants. The severity of the phenotype was correlated with the extent of PYRB silencing and was reversible by pyrimidine addition. These results suggest that de novo synthesis is required, although minimal activities, supplemented by efficient salvaging pathway activities, are able to meet metabolic demands for pyrimdines during growth and development. Coordinate changes in expression of salvage and catabolic pathway genes in RNAi plants indicate that pyrimidine metabolism responds dynamically to changes in tissue pyrimidine availability.
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Affiliation(s)
- Celine T Chen
- Department of Biological Sciences, Goucher College, Baltimore, MD 21204-2794, USA
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11
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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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12
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Schröder M, Giermann N, Zrenner R. Functional analysis of the pyrimidine de novo synthesis pathway in solanaceous species. PLANT PHYSIOLOGY 2005; 138:1926-38. [PMID: 16024685 PMCID: PMC1183384 DOI: 10.1104/pp.105.063693] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2005] [Revised: 05/14/2005] [Accepted: 05/16/2005] [Indexed: 05/03/2023]
Abstract
Pyrimidines are particularly important in dividing tissues as building blocks for nucleic acids, but they are equally important for many biochemical processes, including sucrose and cell wall polysaccharide metabolism. In recent years, the molecular organization of nucleotide biosynthesis in plants has been analyzed. Here, we present a functional analysis of the pyrimidine de novo synthesis pathway. Each step in the pathway was investigated using transgenic plants with reduced expression of the corresponding gene to identify controlling steps and gain insights into the phenotypic and metabolic consequences. Inhibition of expression of 80% based on steady-state mRNA level did not lead to visible phenotypes. Stepwise reduction of protein abundance of Asp transcarbamoylase or dihydro orotase resulted in a corresponding inhibition of growth. This was not accompanied by pleiotropic effects or by changes in the developmental program. A more detailed metabolite analysis revealed slightly different responses in roots and shoots of plants with decreased abundance of proteins involved in pyrimidine de novo synthesis. Whereas in leaves the nucleotide and amino acid levels were changed only in the very strong inhibited plants, the roots show a transient increase of these metabolites in intermediate plants followed by a decrease in the strong inhibited plants. Growth analysis revealed that elongation rates and number of organs per plant were reduced, without large changes in the average cell size. It is concluded that reduced pyrimidine de novo synthesis is compensated for by reduction in growth rates, and the remaining nucleotide pools are sufficient for running basic metabolic processes.
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Affiliation(s)
- Michael Schröder
- Botanisches Institut, Im Neuenheimer Feld 360, Ruprecht-Karls-Universität Heidelberg, 69120 Heidelberg, Germany
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Hewitt MM, Carr JM, Williamson CL, Slocum RD. Effects of phosphate limitation on expression of genes involved in pyrimidine synthesis and salvaging in Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2005; 43:91-9. [PMID: 15820655 DOI: 10.1016/j.plaphy.2005.01.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2004] [Accepted: 01/03/2005] [Indexed: 05/01/2023]
Abstract
Arabidopsis seedlings grown for 14 d without phosphate (P) exhibited stunted growth and other visible symptoms associated with P deficiency. RNA contents in shoots decreased nearly 90%, relative to controls. In shoots, expression of Pht1;2, encoding an inducible high-affinity phosphate transporter, increased threefold, compared with controls, and served as a molecular marker for P limitation. Transcript levels for five enzymes (aspartate transcarbamoylase, ATCase, EC 2.1.3.2; carbamoyl phosphate synthetase, CPSase, EC 6.3.5.5); UMP synthase, EC 2.4.1.10, EC 4.1.1.23; uracil phosphoribosyltransferase, UPRTase, EC 2.4.2.9; UMP kinase, EC 2.7.1.14) increased 2-10-fold in response to P starvation in shoots. These enzymes, which utilize phosphorylated intermediates at putative regulated steps in de novo synthesis and salvaging pathways leading to UMP and pyrimidine nucleotide formation, appear to be coordinately regulated, at the level of gene expression. This response may facilitate pyrimidine nucleotide synthesis under P limitation in this plant. Expression of P-dependent and P-independent phosphoribosyl pyrophosphate (PRPP) synthases (PRS2 and PRS3, respectively) which provide PRPP, the phosphoribosyl donor in UMP synthesis via both de novo and salvaging pathways, was differentially regulated in response to P limitation. PRS2 mRNA levels increased twofold in roots and shoots of P-starved plants, while PRS3 was constitutively-expressed. PRS3 may play a novel role in providing PRPP to cellular metabolism under low P availability.
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Affiliation(s)
- Matthew M Hewitt
- Department of Biological Sciences, Goucher College, Baltimore, MD 21204-2794, USA
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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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Boldt R, Zrenner R. Purine and pyrimidine biosynthesis in higher plants. PHYSIOLOGIA PLANTARUM 2003; 117:297-304. [PMID: 12654029 DOI: 10.1034/j.1399-3054.2003.00030.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Purine and pyrimidine nucleotides have important functions in a multitude of biochemical and developmental processes during the life cycle of a plant. In higher plants the processes of nucleotide metabolism are poorly understood, but it is in principle accepted that nucleotides are essential constituents of fundamental biological functions. Despite of its significance, higher plant nucleotide metabolism has been poorly explored during the last 10-20 years (Suzuki and Takahashi 1977, Schubert 1986, Wagner and Backer 1992). But considerable progress was made on purine biosynthesis in nodules of ureide producing tropical legumes, where IMP-synthesis plays a dominant role in primary nitrogen metabolism (Atkins and Smith 2000, Smith and Atkins 2002). Besides these studies on tropical legumes, this review emphasises on progress made in analysing the function in planta of genes involved in purine and pyrimidine biosynthesis and their impact on metabolism and development.
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Affiliation(s)
- Ralf Boldt
- University of Rostock Department of Bioscience -Plant Physiology, Albert-Einstein-Str.3, D-18051 Rostock, Germany Max Plank Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Golm, Germany
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Ullrich A, Knecht W, Piskur J, Löffler M. Plant dihydroorotate dehydrogenase differs significantly in substrate specificity and inhibition from the animal enzymes. FEBS Lett 2002; 529:346-50. [PMID: 12372626 DOI: 10.1016/s0014-5793(02)03425-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The mitochondrial membrane bound dihydroorotate dehydrogenase (DHODH; EC 1.3.99.11) catalyzes the fourth step of pyrimidine biosynthesis. By the present correction of a known cDNA sequence for Arabidopsis thaliana DHODH we revealed the importance of the very C-terminal part for its catalytic activity and the reason why--in contrast to mammalian and insect species--the recombinant plant flavoenzyme was unaccessible to date for in vitro characterization. Structure-activity relationship studies explained that potent inhibitors of animal DHODH do not significantly affect the plant enzyme. These difference could be exploited for a novel approach to herb or pest growth control by limitation of pyrimidine nucleotide pools.
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Affiliation(s)
- Alexandra Ullrich
- Institute for Physiological Chemistry, Philipps-University, Karl-von-Frisch-Strasse 1, D-35033 Marburg, Germany.
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Giermann N, Schröder M, Ritter T, Zrenner R. Molecular analysis of de novo pyrimidine synthesis in solanaceous species. PLANT MOLECULAR BIOLOGY 2002; 50:393-403. [PMID: 12369616 DOI: 10.1023/a:1019854531254] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The de novo synthesis of pyrimidine nucleotides in plants has been analysed on a molecular level with special focus on cDNA cloning and structure analysis of all genes involved and their expression pattern during development. The exhaustive cloning of all cDNAs resulted from screening with heterologous cDNAs or by using complementation strategies with Escherichia coli mutants and subsequent enzyme activity measurements. Southern hybridization and comparison with the Arabidopsis genome reveals plant specific aspects and a simple genomic organization of pyrimidine synthesis in plants, which is superimposed by the postulated, complex subcellular compartmentalization. Northern hybridization evinces coordinated expression of all genes under developmental control during tobacco leaf growth.
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MESH Headings
- Arabidopsis/genetics
- Aspartate Carbamoyltransferase/genetics
- Aspartate Carbamoyltransferase/metabolism
- Blotting, Northern
- Carbamoyl-Phosphate Synthase (Ammonia)/genetics
- Carbamoyl-Phosphate Synthase (Ammonia)/metabolism
- Cloning, Molecular
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Plant/chemistry
- DNA, Plant/genetics
- Dihydroorotate Dehydrogenase
- Escherichia coli/genetics
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Enzymologic
- Gene Expression Regulation, Plant
- Genes/genetics
- Genetic Complementation Test
- Genome, Plant
- Molecular Sequence Data
- Mutation
- Oxidoreductases/genetics
- Oxidoreductases/metabolism
- Oxidoreductases Acting on CH-CH Group Donors
- Plant Leaves/enzymology
- Plant Leaves/genetics
- Plant Leaves/growth & development
- Pyrimidines/biosynthesis
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Sequence Analysis, DNA
- Solanum tuberosum/enzymology
- Solanum tuberosum/genetics
- Solanum tuberosum/metabolism
- Nicotiana/enzymology
- Nicotiana/genetics
- Nicotiana/metabolism
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Affiliation(s)
- Norbert Giermann
- Botanisches Institut, Ruprecht-Karls-Universität Heidelberg, Germany
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Santoso D, Thornburg R. Fluoroorotic acid-selected Nicotiana plumbaginifolia cell lines with a stable thymine starvation phenotype have lost the thymine-regulated transcriptional program. PLANT PHYSIOLOGY 2000; 123:1517-24. [PMID: 10938367 PMCID: PMC59107 DOI: 10.1104/pp.123.4.1517] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/1999] [Accepted: 03/28/2000] [Indexed: 05/20/2023]
Abstract
We have selected 143 independent Nicotiana plumbaginifolia cell lines that survive in the presence of 5-fluoroorotic acid. These lines show several diverse phenotypes. The majority of these cell lines showed reduced levels of UMP synthase. However, one particular phenotype, which represents 14% of the total independent lines (20 cell lines), showed an unexpected, high level of UMP synthase and was therefore analyzed in detail. The selected cell lines showed no differences with wild-type cells with respect to uptake of orotic acid, affinity of UMP synthase for its substrates, or UMP synthase gene-copy number. Alternative detoxification mechanisms were also excluded. The elevated enzyme activity was correlated with elevated UMP synthase protein levels as well as elevated UMP synthase mRNA levels. In contrast to wild-type cell lines, the fluoroorotic acid-selected cell lines did not respond to thymine or to other biochemicals that affect thymine levels. In addition, there was also a concomitant up-regulation of aspartate transcarbamoylase, however, dihydroorotase and dihydroorotate dehydrogenase are not up-regulated in these cell lines.
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Affiliation(s)
- D Santoso
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
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