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Hou G, Wu G, Jiang H, Bai X, Chen Y. RNA-Seq Reveals That Multiple Pathways Are Involved in Tuber Expansion in Tiger Nuts ( Cyperus esculentus L.). Int J Mol Sci 2024; 25:5100. [PMID: 38791140 PMCID: PMC11121407 DOI: 10.3390/ijms25105100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/03/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
The tiger nut (Cyperus esculentus L.) is a usable tuber and edible oil plant. The size of the tubers is a key trait that determines the yield and the mechanical harvesting of tiger nut tubers. However, little is known about the anatomical and molecular mechanisms of tuber expansion in tiger nut plants. This study conducted anatomical and comprehensive transcriptomics analyses of tiger nut tubers at the following days after sowing: 40 d (S1); 50 d (S2); 60 d (S3); 70 d (S4); 90 d (S5); and 110 d (S6). The results showed that, at the initiation stage of a tiger nut tuber (S1), the primary thickening meristem (PTM) surrounded the periphery of the stele and was initially responsible for the proliferation of parenchyma cells of the cortex (before S1) and then the stele (S2-S3). The increase in cell size of the parenchyma cells occurred mainly from S1 to S3 in the cortex and from S3 to S4 in the stele. A total of 12,472 differentially expressed genes (DEGs) were expressed to a greater extent in the S1-S3 phase than in S4-S6 phase. DEGs related to tuber expansion were involved in cell wall modification, vesicle transport, cell membrane components, cell division, the regulation of plant hormone levels, signal transduction, and metabolism. DEGs involved in the biosynthesis and the signaling of indole-3-acetic acid (IAA) and jasmonic acid (JA) were expressed highly in S1-S3. The endogenous changes in IAA and JAs during tuber development showed that the highest concentrations were found at S1 and S1-S3, respectively. In addition, several DEGs were related to brassinosteroid (BR) signaling and the G-protein, MAPK, and ubiquitin-proteasome pathways, suggesting that these signaling pathways have roles in the tuber expansion of tiger nut. Finally, we come to the conclusion that the cortex development preceding stele development in tiger nut tubers. The auxin signaling pathway promotes the division of cortical cells, while the jasmonic acid pathway, brassinosteroid signaling, G-protein pathway, MAPK pathway, and ubiquitin protein pathway regulate cell division and the expansion of the tuber cortex and stele. This finding will facilitate searches for genes that influence tuber expansion and the regulatory networks in developing tubers.
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Affiliation(s)
- Guangshan Hou
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (G.H.); (G.W.); (H.J.)
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guojiang Wu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (G.H.); (G.W.); (H.J.)
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Huawu Jiang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (G.H.); (G.W.); (H.J.)
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xue Bai
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun 666303, China;
| | - Yaping Chen
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (G.H.); (G.W.); (H.J.)
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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Shu Z, Ji Q, He T, Zhou D, Zheng S, Zhou H, He W. Combined metabolome and transcriptome analyses reveal that growing under Red shade affects secondary metabolite content in Huangjinya green tea. Front Genet 2024; 15:1365243. [PMID: 38660681 PMCID: PMC11039865 DOI: 10.3389/fgene.2024.1365243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024] Open
Abstract
Shading treatments impact the tea (Camellia sinensis L.) quality. The sunlight sensitive varieties can be grown under shading nets for better growth and secondary metabolite content. Here, we studied the responses of a sunlight sensitive green tea variety "Huangjinya" by growing under colored shading nets (red, yellow, blue, and black (75% and 95%) shading rates) to find out the most suitable color of the shading net. Red shading was the most promising treatment as it positively affected the weight and length of 100 one-bud-three leaves and reduced the degree and rate of new shoots burn compared to control (natural sunlight). We then explored the comparative metabolomic changes in response to red shading by using UPLC-ESI-MS/MS system. The amino acids and derivatives, flavonoids, and alkaloids were downaccumulated whereas lipids, organic acids, and lignans were upaccumulated in Red shade grown tea samples. The red shading nets caused a decreased catechin, epicatechin, dopamine, and L-tyramine contents but increased caffeine content. We then employed transcriptome sequencing to find key changes in expressions of related genes and pathways. Notably, key genes associated with the phenylpropanoid and flavonoid biosynthesis pathways exhibited complex regulation. These expression changes suggested a potential trend of polymerization or condensation of simple molecules like catechin or pelargonidin into larger molecules like glucoside or proanthocyanidins. Here, Red shading net triggered higher expression of genes enriched in lipid biosynthesis and jasmonic acid biosynthesis, suggesting an interplay of fatty acids and JA in improving tea performance. These findings contribute to the metabolic responses of Huangjinya tea to red shading nets which might have implications for flavor and health benefits. Our data provide a foundation for further exploration and optimization of cultivation practices for this unique tea variety.
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Affiliation(s)
| | | | | | | | | | - Huijuan Zhou
- Lishui Institute of Agricultural and Forestry Sciences, Lishui, Zhejiang, China
| | - Weizhong He
- Lishui Institute of Agricultural and Forestry Sciences, Lishui, Zhejiang, China
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Ľuptáková E, Vigouroux A, Končitíková R, Kopečná M, Zalabák D, Novák O, Salcedo Sarmiento S, Ćavar Zeljković S, Kopečný DJ, von Schwartzenberg K, Strnad M, Spíchal L, De Diego N, Kopečný D, Moréra S. Plant nucleoside N-ribohydrolases: riboside binding and role in nitrogen storage mobilization. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1432-1452. [PMID: 38044809 DOI: 10.1111/tpj.16572] [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: 04/29/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/05/2023]
Abstract
Cells save their energy during nitrogen starvation by selective autophagy of ribosomes and degradation of RNA to ribonucleotides and nucleosides. Nucleosides are hydrolyzed by nucleoside N-ribohydrolases (nucleosidases, NRHs). Subclass I of NRHs preferentially hydrolyzes the purine ribosides while subclass II is more active towards uridine and xanthosine. Here, we performed a crystallographic and kinetic study to shed light on nucleoside preferences among plant NRHs followed by in vivo metabolomic and phenotyping analyses to reveal the consequences of enhanced nucleoside breakdown. We report the crystal structure of Zea mays NRH2b (subclass II) and NRH3 (subclass I) in complexes with the substrate analog forodesine. Purine and pyrimidine catabolism are inseparable because nucleobase binding in the active site of ZmNRH is mediated via a water network and is thus unspecific. Dexamethasone-inducible ZmNRH overexpressor lines of Arabidopsis thaliana, as well as double nrh knockout lines of moss Physcomitrium patents, reveal a fine control of adenosine in contrast to other ribosides. ZmNRH overexpressor lines display an accelerated early vegetative phase including faster root and rosette growth upon nitrogen starvation or osmotic stress. Moreover, the lines enter the bolting and flowering phase much earlier. We observe changes in the pathways related to nitrogen-containing compounds such as β-alanine and several polyamines, which allow plants to reprogram their metabolism to escape stress. Taken together, crop plant breeding targeting enhanced NRH-mediated nitrogen recycling could therefore be a strategy to enhance plant growth tolerance and productivity under adverse growth conditions.
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Affiliation(s)
- Eva Ľuptáková
- Department of Experimental Biology, Faculty of Science, Palacký University, Olomouc, CZ-78371, Czech Republic
| | - Armelle Vigouroux
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, F-91198, France
| | - Radka Končitíková
- Department of Experimental Biology, Faculty of Science, Palacký University, Olomouc, CZ-78371, Czech Republic
| | - Martina Kopečná
- Department of Experimental Biology, Faculty of Science, Palacký University, Olomouc, CZ-78371, Czech Republic
| | - David Zalabák
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences & Palacký University, Šlechtitelů 11, Olomouc, CZ-78371, Czech Republic
| | - Ondřej Novák
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences & Palacký University, Šlechtitelů 11, Olomouc, CZ-78371, Czech Republic
| | - Sara Salcedo Sarmiento
- Czech Advanced Technology and Research Institute, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Sanja Ćavar Zeljković
- Czech Advanced Technology and Research Institute, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Genetic Resources for Vegetables, Medicinal and Special Plants, Crop Research Institute, Šlechtitelů 29, 78371, Olomouc, Czech Republic
| | - David Jaroslav Kopečný
- Department of Experimental Biology, Faculty of Science, Palacký University, Olomouc, CZ-78371, Czech Republic
| | - Klaus von Schwartzenberg
- Institute of Plant Science and Microbiology, Universität Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences & Palacký University, Šlechtitelů 11, Olomouc, CZ-78371, Czech Republic
| | - Lukáš Spíchal
- Czech Advanced Technology and Research Institute, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Nuria De Diego
- Czech Advanced Technology and Research Institute, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - David Kopečný
- Department of Experimental Biology, Faculty of Science, Palacký University, Olomouc, CZ-78371, Czech Republic
| | - Solange Moréra
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, F-91198, France
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Li X, Li C, Chen Z, Wang J, Sun J, Yao J, Chen K, Li Z, Ye H. High-resolution mass spectrometry-based non-targeted metabolomics reveals toxicity of naphthalene on tall fescue and intrinsic molecular mechanisms. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 271:115975. [PMID: 38244514 DOI: 10.1016/j.ecoenv.2024.115975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 01/22/2024]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous at relatively high concentrations by atmospheric deposition, and they are threatening to the environment. In this study, the toxicity of naphthalene on tall fescue and its potential responding mechanism was first studied by integrating approaches. Tall fescue seedlings were exposed to 0, 20, and 100 mg L-1 naphthalene in a hydroponic environment for 9 days, and toxic effects were observed by the studies of general physiological studies, chlorophyll fluorescence, and root morphology. Additionally, Ultra Performance Liquid Chromatography - Electrospray Ionization - High-Resolution Mass Spectrometry (UPLC-ESI-HRMS) was used to depict metabolic profiles of tall fescue under different exposure durations of naphthalene, and the intrinsic molecular mechanism of tall fescue resistance to abiotic stresses. Tall fescue shoots were more sensitive to the toxicity of naphthalene than roots. Low-level exposure to naphthalene inhibited the electron transport from the oxygen-evolving complex (OEC) to D1 protein in tall fescue shoots but induced the growth of roots. Naphthalene induced metabolic change of tall fescue roots in 12 h, and tall fescue roots maintained the level of sphingolipids after long-term exposure to naphthalene, which may play important roles in plant resistance to abiotic stresses.
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Affiliation(s)
- Xuecheng Li
- Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, College of Resources and Environmental Science, South-Central Minzu University, Wuhan 430074, PR China; College of Pharmacy, South-Central Minzu University, Wuhan 430074, PR China
| | - Changyi Li
- Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, College of Resources and Environmental Science, South-Central Minzu University, Wuhan 430074, PR China
| | - Ziyu Chen
- Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, College of Resources and Environmental Science, South-Central Minzu University, Wuhan 430074, PR China; College of Pharmacy, South-Central Minzu University, Wuhan 430074, PR China
| | - Jiahui Wang
- Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, College of Resources and Environmental Science, South-Central Minzu University, Wuhan 430074, PR China
| | - Jie Sun
- Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, College of Resources and Environmental Science, South-Central Minzu University, Wuhan 430074, PR China
| | - Jun Yao
- School of Water Resources & Environment, China University of Geosciences Beijing, Beijing, PR China
| | - Ke Chen
- Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, College of Resources and Environmental Science, South-Central Minzu University, Wuhan 430074, PR China.
| | - Zhenghui Li
- College of Pharmacy, South-Central Minzu University, Wuhan 430074, PR China.
| | - Hengpeng Ye
- Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, College of Resources and Environmental Science, South-Central Minzu University, Wuhan 430074, PR China.
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Kaur R, Chandra J, Varghese B, Keshavkant S. Allantoin: A Potential Compound for the Mitigation of Adverse Effects of Abiotic Stresses in Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:3059. [PMID: 37687306 PMCID: PMC10489999 DOI: 10.3390/plants12173059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/14/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023]
Abstract
Stress-induced alterations vary with the species of plants, the intensity and duration of the exposure, and stressors availability in nature or soil. Purine catabolism acts as an inherent defensive mechanism against various abiotic stresses and plays a pivotal role in the stress acclimatisation of plants. The intermediate metabolite of purine catabolism, allantoin, compensates for soil nitrogen deficiency due to the low carbon/nitrogen ratio, thereby maintaining nitrogen homeostasis and supporting plant growth and development. Allantoin accounts for 90% of the total nitrogenous compound in legumes, while it contributes only 15% in non-leguminous plants. Moreover, studies on a variety of plant species have reported the differential accumulation of allantoin in response to abiotic stresses, endowing allantoin as a stress modulator. Allantoin functions as signalling molecule to stimulate stress-responsive genes (P5CS; pyrroline-5-carboxylase synthase) and ROS (reactive oxygen species) scavenging enzymes (antioxidant). Moreover, it regulates cross-talk between the abscisic acid and jasmonic acid pathway, and maintains ion homeostasis by increasing the accumulation of putrescine and/or spermine, consequently enhancing the tolerance against stress conditions. Further, key enzymes of purine catabolism (xanthine dehydrogenase and allantoinase) have also been explored by constructing various knockdown/knockout mutant lines to decipher their impact on ROS-mediated oxidative injury in plants. Thus, it is established that allantoin serves as a regulatory signalling metabolite in stress protection, and therefore a lower accumulation of allantoin also reduces plant stress tolerance mechanisms. This review gives an account of metabolic regulation and the possible contribution of allantoin as a photo protectant, osmoprotectant, and nitrogen recycler to reduce abiotic-stress-induced impacts on plants.
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Affiliation(s)
- Rasleen Kaur
- School of Studies in Biotechnology, Pt. Ravishankar Shukla University, Raipur 492 010, India; (R.K.); (S.K.)
| | - Jipsi Chandra
- Center for Basic Sciences, Pt. Ravishankar Shukla University, Raipur 492 010, India;
| | - Boby Varghese
- Centre for Academic Success in Science and Engineering, University of KwaZulu-Natal, Durban 4001, South Africa
| | - S. Keshavkant
- School of Studies in Biotechnology, Pt. Ravishankar Shukla University, Raipur 492 010, India; (R.K.); (S.K.)
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Sun AZ, Chen JH, Jin XQ, Li H, Guo FQ. Supplementing the Nuclear-Encoded PSII Subunit D1 Induces Dramatic Metabolic Reprogramming in Flag Leaves during Grain Filling in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:3009. [PMID: 37631220 PMCID: PMC10458752 DOI: 10.3390/plants12163009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023]
Abstract
Our previous study has demonstrated that the nuclear-origin supplementation of the PSII core subunit D1 protein stimulates growth and increases grain yields in transgenic rice plants by enhancing photosynthetic efficiency. In this study, the underlying mechanisms have been explored regarding how the enhanced photosynthetic capacity affects metabolic activities in the transgenic plants of rice harboring the integrated transgene RbcSPTP-OspsbA cDNA, cloned from rice, under control of the AtHsfA2 promoter and N-terminal fused with the plastid-transit peptide sequence (PTP) cloned from the AtRbcS. Here, a comparative metabolomic analysis was performed using LC-MS in flag leaves of the transgenic rice plants during the grain-filling stage. Critically, the dramatic reduction in the quantities of nucleotides and certain free amino acids was detected, suggesting that the increased photosynthetic assimilation and grain yield in the transgenic plants correlates with the reduced contents of free nucleotides and the amino acids such as glutamine and glutamic acid, which are cellular nitrogen sources. These results suggest that enhanced photosynthesis needs consuming more free nucleotides and nitrogen sources to support the increase in biomass and yields, as exhibited in transgenic rice plants. Unexpectedly, dramatic changes were measured in the contents of flavonoids in the flag leaves, suggesting that a tight and coordinated relationship exists between increasing photosynthetic assimilation and flavonoid biosynthesis. Consistent with the enhanced photosynthetic efficiency, the substantial increase was measured in the content of starch, which is the primary product of the Calvin-Benson cycle, in the transgenic rice plants under field growth conditions.
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Affiliation(s)
- Ai-Zhen Sun
- The National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (A.-Z.S.); (J.-H.C.); (X.-Q.J.); (H.L.)
| | - Juan-Hua Chen
- The National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (A.-Z.S.); (J.-H.C.); (X.-Q.J.); (H.L.)
| | - Xue-Qi Jin
- The National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (A.-Z.S.); (J.-H.C.); (X.-Q.J.); (H.L.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Han Li
- The National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (A.-Z.S.); (J.-H.C.); (X.-Q.J.); (H.L.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang-Qing Guo
- The National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (A.-Z.S.); (J.-H.C.); (X.-Q.J.); (H.L.)
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Xie H, Zhang P, Jiang C, Wang Q, Guo Y, Zhang X, Huang T, Liu J, Li L, Li H, Wang H, Qin P. Combined transcriptomic and metabolomic analyses of high temperature stress response of quinoa seedlings. BMC PLANT BIOLOGY 2023; 23:292. [PMID: 37264351 DOI: 10.1186/s12870-023-04310-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/23/2023] [Indexed: 06/03/2023]
Abstract
BACKGROUND Quinoa (Chenopodium quinoa Willd.) originates in high altitude areas, such as the Andes, and has some inherent characteristics of cold, drought, and salinity tolerance, but is sensitive to high temperature. RESULTS To gain insight into the response mechanism of quinoa to high temperature stress, we conducted an extensive targeted metabolomic study of two cultivars, Dianli-3101 and Dianli-3051, along with a combined transcriptome analysis. A total of 794 metabolites and 54,200 genes were detected, in which the genes related to photosynthesis were found down-regulated at high temperatures, and two metabolites, lipids and flavonoids, showed the largest changes in differential accumulation. Further analysis of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and transcription factors revealed that quinoa inhibits photosynthesis at high temperatures, and the possible strategies being used for high temperature stress management are regulation of heat stress transcription factors (HSFs) to obtain heat tolerance, and regulation of purine metabolism to enhance stress signals for rapid response to high temperature stress. The tolerant genotype could have an enhanced response through lower purine levels. The induction of the stress response could be mediated by HSF transcription factors. The results of this study may provide theoretical references for understanding the response mechanism of quinoa to high temperature stress, and for screening potential high temperature tolerant target genes and high temperature tolerant strains. CONCLUSIONS These findings reveal the regulation of the transcription factor family HSF and the purinergic pathway in response to high temperature stress to improve quinoa varieties with high temperature tolerance.
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Affiliation(s)
- Heng Xie
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Ping Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Chunhe Jiang
- Academic Affairs Office, Yunnan Agricultural University, Kunming, 650201, China
| | - Qianchao Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Yirui Guo
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Xuesong Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Tingzhi Huang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Junna Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Li Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Hanxue Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Hongxin Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Peng Qin
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China.
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Tang Q, Liu K, Yue C, Luo L, Zeng L, Wu Z. CsXDH1 gene promotes caffeine catabolism induced by continuous strong light in tea plant. HORTICULTURE RESEARCH 2023; 10:uhad090. [PMID: 37342541 PMCID: PMC10277909 DOI: 10.1093/hr/uhad090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 05/01/2023] [Indexed: 06/23/2023]
Abstract
Tea plant (Camellia sinensis) is an important cash crop with extensive adaptability in the world. However, complex environmental factors force a large variation of tea quality-related components. Caffeine is essential for the formation of bitter and fresh flavors in tea, and is the main compound of tea that improves human alertness. Continuous strong light stimulation was observed to cause caffeine reduction in tea leaves, but the mechanism is not clear. In this study, the response of tea plant to light intensity was analysed mainly by multi-omics association, antisense oligodeoxynucleotide (asODN) silencing technique, and in vitro enzyme activity assay. The results revealed multiple strategies for light intensity adaptation in tea plant, among which the regulation of chloroplasts, photosynthesis, porphyrin metabolism, and resistance to oxidative stress were prominent. Caffeine catabolism was enhanced in continuous strong light, which may be a light-adapted strategy due to strict regulation by xanthine dehydrogenase (XDH). asODN silencing and enzymatic activity assays confirmed that CsXDH1 is a protein induced by light intensity to catalyze the substrate xanthine. CsXDH1 asODN silencing resulted in significant up-regulation of both caffeine and theobromine in in vitro enzyme activity assay, but not in vivo. CsXDH1 may act as a coordinator in light intensity adaptation, thus disrupting this balance of caffeine catabolism.
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Affiliation(s)
- Qianhui Tang
- College of Food Science, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Southwest University, Chongqing 400715, China
- Integrative Science Center of Germplasm Creation, Southwest University, Chongqing 401329, China
- Tea Research Institute, Southwest University, Chongqing 400715, China
| | - Keyi Liu
- College of Food Science, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Southwest University, Chongqing 400715, China
- Integrative Science Center of Germplasm Creation, Southwest University, Chongqing 401329, China
- Tea Research Institute, Southwest University, Chongqing 400715, China
| | - Chuan Yue
- College of Food Science, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Southwest University, Chongqing 400715, China
- Integrative Science Center of Germplasm Creation, Southwest University, Chongqing 401329, China
- Tea Research Institute, Southwest University, Chongqing 400715, China
| | - Liyong Luo
- College of Food Science, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Southwest University, Chongqing 400715, China
- Integrative Science Center of Germplasm Creation, Southwest University, Chongqing 401329, China
- Tea Research Institute, Southwest University, Chongqing 400715, China
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Kotajima M, Choi JH, Suzuki H, Suzuki T, Wu J, Hirai H, Nelson DC, Ouchi H, Inai M, Dohra H, Kawagishi H. Identification of Biosynthetic and Metabolic Genes of 2-Azahypoxanthine in Lepista sordida Based on Transcriptomic Analysis. JOURNAL OF NATURAL PRODUCTS 2023; 86:710-718. [PMID: 36802627 DOI: 10.1021/acs.jnatprod.2c00789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
2-Azahypoxanthine was isolated from the fairy ring-forming fungus Lepista sordida as a fairy ring-inducing compound. 2-Azahypoxanthine has an unprecedented 1,2,3-triazine moiety, and its biosynthetic pathway is unknown. The biosynthetic genes for 2-azahypoxanthine formation in L. sordida were predicted by a differential gene expression analysis using MiSeq. The results revealed that several genes in the purine and histidine metabolic pathways and the arginine biosynthetic pathway are involved in the biosynthesis of 2-azahypoxanthine. Furthermore, nitric oxide (NO) was produced by recombinant NO synthase 5 (rNOS5), suggesting that NOS5 can be the enzyme involved in the formation of 1,2,3-triazine. The gene encoding hypoxanthine-guanine phosphoribosyltransferase (HGPRT), one of the major phosphoribosyltransferases of purine metabolism, increased when 2-azahypoxanthine content was the highest. Therefore, we hypothesized that HGPRT might catalyze a reversible reaction between 2-azahypoxanthine and 2-azahypoxanthine-ribonucleotide. We proved the endogenous existence of 2-azahypoxanthine-ribonucleotide in L. sordida mycelia by LC-MS/MS for the first time. Furthermore, it was shown that recombinant HGPRT catalyzed reversible interconversion between 2-azahypoxanthine and 2-azahypoxanthine-ribonucleotide. These findings demonstrate that HGPRT can be involved in the biosynthesis of 2-azahypoxanthine via 2-azahypoxanthine-ribonucleotide generated by NOS5.
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Affiliation(s)
| | | | | | - Tomohiro Suzuki
- Center for Bioscience Research and Education, Utsunomiya University, 350 mine-machi, Utsunomiya, Tochigi 321-8505, Japan
| | | | | | - David C Nelson
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521, United States
| | - Hitoshi Ouchi
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Makoto Inai
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
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10
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Singh S, Chaudhary C, Bharsakale RD, Gazal S, Verma L, Tarannum Z, Behere GT, Giri J, Germain H, Ghosh DK, Sharma AK, Chauhan H. PRpnp, a novel dual activity PNP family protein improves plant vigour and confers multiple stress tolerance in Citrus aurantifolia. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:726-741. [PMID: 36593511 PMCID: PMC10037160 DOI: 10.1111/pbi.13989] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/04/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
Under field conditions, plants are often simultaneously exposed to several abiotic and biotic stresses resulting in significant reductions in growth and yield; thus, developing a multi-stress tolerant variety is imperative. Previously, we reported the neofunctionalization of a novel PNP family protein, Putranjiva roxburghii purine nucleoside phosphorylase (PRpnp) to trypsin inhibitor to cater to the needs of plant defence. However, to date, no study has revealed the potential role and mechanism of either member of this protein group in plant defence. Here, we overexpressed PRpnp in Citrus aurantifolia which showed nuclear-cytoplasmic localization, where it functions in maintaining the intracellular purine reservoir. Overexpression of PRpnp significantly enhanced tolerance to salt, oxidative stress, alkaline pH, drought and two pests, Papilio demoleus and Scirtothrips citri in transgenic plants. Global gene expression studies revealed that PRpnp overexpression up-regulated differentially expressed genes (DEGs) related to ABA- and JA-biosynthesis and signalling, plant defence, growth and development. LC-MS/MS analysis validated higher endogenous ABA and JA accumulation in transgenic plants. Taken together, our results suggest that PRpnp functions by enhancing the endogenous ABA and JA, which interact synergistically and it also inhibits trypsin proteases in the insect gut. Also, like other purine salvage genes, PRpnp also regulates CK metabolism and increases the levels of CK-free bases in transgenic Mexican lime. We also suggest that PRpnp can be used as a potential candidate to develop new varieties with improved plant vigour and enhanced multiple stress resistance.
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Affiliation(s)
- Sweta Singh
- Department of Biosciences and BioengineeringIndian Institute of Technology RoorkeeRoorkeeIndia
| | - Chanderkant Chaudhary
- Department of Biosciences and BioengineeringIndian Institute of Technology RoorkeeRoorkeeIndia
| | | | - Snehi Gazal
- Department of Chemistry, Biochemistry and PhysicsUniversité du Québec à Trois‐RivièresTrois‐RivièresQuebecCanada
| | - Lokesh Verma
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Zeba Tarannum
- Department of Biosciences and BioengineeringIndian Institute of Technology RoorkeeRoorkeeIndia
| | | | - Jitender Giri
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Hugo Germain
- Department of Chemistry, Biochemistry and PhysicsUniversité du Québec à Trois‐RivièresTrois‐RivièresQuebecCanada
| | | | - Ashwani K. Sharma
- Department of Biosciences and BioengineeringIndian Institute of Technology RoorkeeRoorkeeIndia
| | - Harsh Chauhan
- Department of Biosciences and BioengineeringIndian Institute of Technology RoorkeeRoorkeeIndia
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11
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Li S, Lin P, Xing H, Li X, Yao Z, Zhang X, Yao X, Yang J, Qin Z. Unveiling the spatial metabolome and anti-atherosclerosis effects of Allium macrostemon Bunge and Allium chinense G. Don. ARAB J CHEM 2023. [DOI: 10.1016/j.arabjc.2023.104772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
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12
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Scully TW, Jiao W, Mittelstädt G, Parker EJ. Structure, mechanism and inhibition of anthranilate phosphoribosyltransferase. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220039. [PMID: 36633281 PMCID: PMC9835598 DOI: 10.1098/rstb.2022.0039] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Anthranilate phosphoribosyltransferase catalyses the second reaction in the biosynthesis of tryptophan from chorismate in microorganisms and plants. The enzyme is homodimeric with the active site located in the hinge region between two domains. A range of structures in complex with the substrates, substrate analogues and inhibitors have been determined, and these have provided insights into the catalytic mechanism of this enzyme. Substrate 5-phospho-d-ribose 1-diphosphate (PRPP) binds to the C-terminal domain and coordinates to Mg2+, in a site completed by two flexible loops. Binding of the second substrate anthranilate is more complex, featuring multiple binding sites along an anthranilate channel. This multi-modal binding is consistent with the substrate inhibition observed at high concentrations of anthranilate. A series of structures predict a dissociative mechanism for the reaction, similar to the reaction mechanisms elucidated for other phosphoribosyltransferases. As this enzyme is essential for some pathogens, efforts have been made to develop inhibitors for this enzyme. To date, the best inhibitors exploit the multiple binding sites for anthranilate. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- Thomas W. Scully
- Ferrier Research Institute, Victoria University of Wellington, Wellington 6140, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Wanting Jiao
- Ferrier Research Institute, Victoria University of Wellington, Wellington 6140, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Gerd Mittelstädt
- Ferrier Research Institute, Victoria University of Wellington, Wellington 6140, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Emily J. Parker
- Ferrier Research Institute, Victoria University of Wellington, Wellington 6140, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
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13
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Chen X, Kim SH, Rhee S, Witte CP. A plastid nucleoside kinase is involved in inosine salvage and control of purine nucleotide biosynthesis. THE PLANT CELL 2023; 35:510-528. [PMID: 36342213 PMCID: PMC9806653 DOI: 10.1093/plcell/koac320] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/02/2022] [Indexed: 05/19/2023]
Abstract
In nucleotide metabolism, nucleoside kinases recycle nucleosides into nucleotides-a process called nucleoside salvage. Nucleoside kinases for adenosine, uridine, and cytidine have been characterized from many organisms, but kinases for inosine and guanosine salvage are not yet known in eukaryotes and only a few such enzymes have been described from bacteria. Here we identified Arabidopsis thaliana PLASTID NUCLEOSIDE KINASE 1 (PNK1), an enzyme highly conserved in plants and green algae belonging to the Phosphofructokinase B family. We demonstrate that PNK1 from A. thaliana is located in plastids and catalyzes the phosphorylation of inosine, 5-aminoimidazole-4-carboxamide-1-β-d-ribose (AICA ribonucleoside), and uridine but not guanosine in vitro, and is involved in inosine salvage in vivo. PNK1 mutation leads to increased flux into purine nucleotide catabolism and, especially in the context of defective uridine degradation, to over-accumulation of uridine and UTP as well as growth depression. The data suggest that PNK1 is involved in feedback regulation of purine nucleotide biosynthesis and possibly also pyrimidine nucleotide biosynthesis. We additionally report that cold stress leads to accumulation of purine nucleotides, probably by inducing nucleotide biosynthesis, but that this adjustment of nucleotide homeostasis to environmental conditions is not controlled by PNK1.
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Affiliation(s)
- Xiaoguang Chen
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Sang-Hoon Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea
| | - Sangkee Rhee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea
| | - Claus-Peter Witte
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
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Melini F, Luziatelli F, Bonini P, Ficca AG, Melini V, Ruzzi M. Optimization of the growth conditions through response surface methodology and metabolomics for maximizing the auxin production by Pantoea agglomerans C1. Front Microbiol 2023; 14:1022248. [PMID: 36970660 PMCID: PMC10030972 DOI: 10.3389/fmicb.2023.1022248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/17/2023] [Indexed: 03/29/2023] Open
Abstract
Introduction The fermentative production of auxin/indole 3-acetate (IAA) using selected Pantoea agglomerans strains can be a promising approach to developing novel plant biostimulants for agriculture use. Methods By integrating metabolomics and fermentation technologies, this study aimed to define the optimal culture conditions to obtain auxin/IAA-enriched plant postbiotics using P. agglomerans strain C1. Metabolomics analysis allowed us to demonstrate that the production of a selected. Results and discussion Array of compounds with plant growth-promoting- (IAA and hypoxanthine) and biocontrol activity (NS-5, cyclohexanone, homo-L-arginine, methyl hexadecenoic acid, and indole-3-carbinol) can be stimulated by cultivating this strain on minimal saline medium amended with sucrose as a carbon source. We applied a three-level-two-factor central composite design (CCD) based response surface methodology (RSM) to explore the impact of the independent variables (rotation speed and medium liquid-to-flask volume ratio) on the production of IAA and IAA precursors. The ANOVA component of the CCD indicated that all the process-independent variables investigated significantly impacted the auxin/IAA production by P. agglomerans strain C1. The optimum values of variables were a rotation speed of 180 rpm and a medium liquid-to-flask volume ratio of 1:10. Using the CCD-RSM method, we obtained a maximum indole auxin production of 208.3 ± 0.4 mg IAAequ/L, which was a 40% increase compared to the growth conditions used in previous studies. Targeted metabolomics allowed us to demonstrate that the IAA product selectivity and the accumulation of the IAA precursor indole-3-pyruvic acid were significantly affected by the increase in the rotation speed and the aeration efficiency.
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Affiliation(s)
- Francesca Melini
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, Viterbo, Italy
- CREA Research Centre for Food and Nutrition, Rome, Italy
| | - Francesca Luziatelli
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, Viterbo, Italy
- *Correspondence: Francesca Luziatelli, ; Maurizio Ruzzi,
| | | | - Anna Grazia Ficca
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, Viterbo, Italy
| | | | - Maurizio Ruzzi
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, Viterbo, Italy
- *Correspondence: Francesca Luziatelli, ; Maurizio Ruzzi,
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15
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Li F, Liu Y, Zhang X, Liu L, Yan Y, Ji X, Kong F, Zhao Y, Li J, Peng T, Sun H, Du Y, Zhao Q. Transcriptome and Metabolome Analyses Reveals the Pathway and Metabolites of Grain Quality Under Phytochrome B in Rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2022; 15:52. [PMID: 36302917 PMCID: PMC9613846 DOI: 10.1186/s12284-022-00600-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Grain size and chalkiness is a critical agronomic trait affecting rice yield and quality. The application of transcriptomics to rice has widened the understanding of complex molecular responsive mechanisms, differential gene expression, and regulatory pathways under varying conditions. Similarly, metabolomics has also contributed drastically for rice trait improvements. As master regulators of plant growth and development, phys influence seed germination, vegetative growth, photoperiodic flowering, shade avoidance responses. OsPHYB can regulate a variety of plant growth and development processes, but little is known about the roles of rice gene OsPHYB in modulating grain development. RESULTS In this study, rice phytochrome B (OsPHYB) was edited using CRISPR/Cas9 technology. We found that OsPHYB knockout increased rice grain size and chalkiness, and increased the contents of amylose, free fatty acids and soluble sugar, while the gel consistency and contents of proteins were reduced in mutant grains. Furthermore, OsPHYB is involved in the regulation of grain size and chalk formation by controlling cell division and complex starch grain morphology. Transcriptomic analysis revealed that loss of OsPHYB function affects multiple metabolic pathways, especially enhancement of glycolysis, fatty acid, oxidative phosphorylation, and antioxidant pathways, as well as differential expression of starch and phytohormone pathways. An analysis of grain metabolites showed an increase in the free fatty acids and lysophosphatidylcholine, whereas the amounts of sugars, alcohols, amino acids and derivatives, organic acids, phenolic acids, alkaloids, nucleotides and derivatives, and flavonoids decreased, which were significantly associated with grain size and chalk formation. CONCLUSIONS Our study reveals that, OsPHYB plays an important regulatory role in the growth and development of rice grains, especially grain size and chalkiness. Furthermore, OsPHYB regulates grain size and chalkiness formation by affecting gene metabolism interaction network. Thus, this study not only revealed that OsPHYB plays a vital role in regulating grain size and chalkiness of rice but reveal new functions and highlighted the importance and value of OsPHYB in rice grain development and provide a new strategy for yield and quality improvement in rice breeding.
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Affiliation(s)
- Fei Li
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Ye Liu
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Xiaohua Zhang
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Lingzhi Liu
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Yun Yan
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Xin Ji
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Fanshu Kong
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Yafan Zhao
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Junzhou Li
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Ting Peng
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Hongzheng Sun
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Yanxiu Du
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China.
| | - Quanzhi Zhao
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China.
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16
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Leong BJ, Folz JS, Bathe U, Clark DG, Fiehn O, Hanson AD. Fluoroacetate distribution, response to fluoridation, and synthesis in juvenile Gastrolobium bilobum plants. PHYTOCHEMISTRY 2022; 202:113356. [PMID: 35934105 DOI: 10.1016/j.phytochem.2022.113356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/23/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Like angiosperms from several other families, the leguminous shrub Gastrolobium bilobum R.Br. produces and accumulates fluoroacetate, indicating that it performs the difficult chemistry needed to make a C-F bond. Bioinformatic analyses indicate that plants lack homologs of the only enzymes known to make a C-F bond, i.e., the Actinomycete flurorinases that form 5'-fluoro-5'-deoxyadenosine from S-adenosylmethionine and fluoride ion. To probe the origin of fluoroacetate in G. bilobum we first showed that fluoroacetate accumulates to millimolar levels in young leaves but not older leaves, stems or roots, that leaf fluoroacetate levels vary >20-fold between individual plants and are not markedly raised by sodium fluoride treatment. Young leaves were fed adenosine-13C-ribose, 13C-serine, or 13C-acetate to test plausible biosynthetic routes to fluoroacetate from S-adenosylmethionine, a C3-pyridoxal phosphate complex, or acetyl-CoA, respectively. Incorporation of 13C into expected metabolites confirmed that all three precursors were taken up and metabolized. Consistent with the bioinformatic evidence against an Actinomycete-type pathway, no adenosine-13C-ribose was converted to 13C-fluoroacetate; nor was the characteristic 4-fluorothreonine product of the Actinomycete pathway detected. Similarly, no 13C from acetate or serine was incorporated into fluoroacetate. While not fully excluding the hypothetical pathways that were tested, these negative labeling data imply that G. bilobum creates the C-F bond by an unprecedented biochemical reaction. Enzyme(s) that mediate such a reaction could be of great value in pharmaceutical and agrochemical manufacturing.
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Affiliation(s)
- Bryan J Leong
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
| | - Jacob S Folz
- West Coast Metabolomics Center, University of California Davis, Davis, CA, USA
| | - Ulschan Bathe
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
| | - David G Clark
- Department of Environmental Horticulture, University of Florida, Gainesville, FL, USA
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California Davis, Davis, CA, USA
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA.
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Piasecka A, Sawikowska A, Jedrzejczak-Rey N, Piślewska-Bednarek M, Bednarek P. Targeted and Untargeted Metabolomic Analyses Reveal Organ Specificity of Specialized Metabolites in the Model Grass Brachypodium distachyon. Molecules 2022; 27:molecules27185956. [PMID: 36144695 PMCID: PMC9506550 DOI: 10.3390/molecules27185956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/02/2022] [Accepted: 09/03/2022] [Indexed: 11/16/2022] Open
Abstract
Brachypodium distachyon, because of its fully sequenced genome, is frequently used as a model grass species. However, its metabolome, which constitutes an indispensable element of complex biological systems, remains poorly characterized. In this study, we conducted comprehensive, liquid chromatography-mass spectrometry (LC-MS)-based metabolomic examination of roots, leaves and spikes of Brachypodium Bd21 and Bd3-1 lines. Our pathway enrichment analysis emphasised the accumulation of specialized metabolites representing the flavonoid biosynthetic pathway in parallel with processes related to nucleotide, sugar and amino acid metabolism. Similarities in metabolite profiles between both lines were relatively high in roots and leaves while spikes showed higher metabolic variance within both accessions. In roots, differences between Bd21 and Bd3-1 lines were manifested primarily in diterpenoid metabolism, while differences within spikes and leaves concerned nucleotide metabolism and nitrogen management. Additionally, sulphate-containing metabolites differentiated Bd21 and Bd3-1 lines in spikes. Structural analysis based on MS fragmentation spectra enabled identification of 93 specialized metabolites. Among them phenylpropanoids and flavonoids derivatives were mainly determined. As compared with closely related barley and wheat species, metabolic profile of Brachypodium is characterized with presence of threonate derivatives of hydroxycinnamic acids.
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Affiliation(s)
- Anna Piasecka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland
- Correspondence: (A.P.); (P.B.); Tel.: +48-61-852-85-03 (A.P. & P.B.); Fax: +48-61-852-05-32 (A.P. & P.B.)
| | - Aneta Sawikowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, Wojska Polskiego 28, 60-637 Poznań, Poland
| | - Nicolas Jedrzejczak-Rey
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Mariola Piślewska-Bednarek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Paweł Bednarek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
- Correspondence: (A.P.); (P.B.); Tel.: +48-61-852-85-03 (A.P. & P.B.); Fax: +48-61-852-05-32 (A.P. & P.B.)
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18
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Mair S, Erharter K, Renard E, Brillet K, Brunner M, Lusser A, Kreutz C, Ennifar E, Micura R. Towards a comprehensive understanding of RNA deamination: synthesis and properties of xanthosine-modified RNA. Nucleic Acids Res 2022; 50:6038-6051. [PMID: 35687141 PMCID: PMC9226506 DOI: 10.1093/nar/gkac477] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/28/2022] [Accepted: 05/20/2022] [Indexed: 12/25/2022] Open
Abstract
Nucleobase deamination, such as A-to-I editing, represents an important posttranscriptional modification of RNA. When deamination affects guanosines, a xanthosine (X) containing RNA is generated. However, the biological significance and chemical consequences on RNA are poorly understood. We present a comprehensive study on the preparation and biophysical properties of X-modified RNA. Thermodynamic analyses revealed that base pairing strength is reduced to a level similar to that observed for a G•U replacement. Applying NMR spectroscopy and X-ray crystallography, we demonstrate that X can form distinct wobble geometries with uridine depending on the sequence context. In contrast, X pairing with cytidine occurs either through wobble geometry involving protonated C or in Watson–Crick-like arrangement. This indicates that the different pairing modes are of comparable stability separated by low energetic barriers for switching. Furthermore, we demonstrate that the flexible pairing properties directly affect the recognition of X-modified RNA by reverse transcription enzymes. Primer extension assays and PCR-based sequencing analysis reveal that X is preferentially read as G or A and that the ratio depends on the type of reverse transcriptase. Taken together, our results elucidate important properties of X-modified RNA paving the way for future studies on its biological significance.
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Affiliation(s)
- Stefan Mair
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Kevin Erharter
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Eva Renard
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 67000 Strasbourg, France
| | - Karl Brillet
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 67000 Strasbourg, France
| | - Melanie Brunner
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Alexandra Lusser
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Eric Ennifar
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 67000 Strasbourg, France
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
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Chen L, Jameson GB, Guo Y, Song J, Jameson PE. The LONELY GUY gene family: from mosses to wheat, the key to the formation of active cytokinins in plants. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:625-645. [PMID: 35108444 PMCID: PMC8989509 DOI: 10.1111/pbi.13783] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/06/2022] [Accepted: 01/13/2022] [Indexed: 05/19/2023]
Abstract
LONELY GUY (LOG) was first identified in a screen of rice mutants with defects in meristem maintenance. In plants, LOG codes for cytokinin riboside 5'-monophosphate phosphoribohydrolase, which converts inactive cytokinin nucleotides directly to the active free bases. Many enzymes with the PGGxGTxxE motif have been misannotated as lysine decarboxylases; conversely not all enzymes containing this motif are cytokinin-specific LOGs. As LOG mutants clearly impact yield in rice, we investigated the LOG gene family in bread wheat. By interrogating the wheat (Triticum aestivum) genome database, we show that wheat has multiple LOGs. The close alignment of TaLOG1, TaLOG2 and TaLOG6 with the X-ray structures of two functional Arabidopsis thaliana LOGs allows us to infer that the wheat LOGs 1-11 are functional LOGs. Using RNA-seq data sets, we assessed TaLOG expression across 70 tissue types, their responses to various stressors, the pattern of cis-regulatory elements (CREs) and intron/exon patterns. TaLOG gene family members are expressed variously across tissue types. When the TaLOG CREs are compared with those of the cytokinin dehydrogenases (CKX) and glucosyltransferases (CGT), there is close alignment of CREs between TaLOGs and TaCKXs reflecting the key role of CKX in maintaining cytokinin homeostasis. However, we suggest that the main homeostatic mechanism controlling cytokinin levels in response to biotic and abiotic challenge resides in the CGTs, rather than LOG or CKX. However, LOG transgenics and identified mutants in rice variously impact yield, providing interesting avenues for investigation in wheat.
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Affiliation(s)
- Lei Chen
- School of Life SciencesYantai UniversityYantaiChina
| | | | - Yichu Guo
- School of Life SciencesYantai UniversityYantaiChina
| | - Jiancheng Song
- School of Life SciencesYantai UniversityYantaiChina
- Yantai Jien Biological Science & Technology LtdYEDAYantaiChina
| | - Paula E. Jameson
- School of Life SciencesYantai UniversityYantaiChina
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
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20
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Zhao L, Zhang Y, Wang L, Liu X, Zhang J, He Z. Stereoselective metabolomic and lipidomic responses of lettuce (Lactuca sativa L.) exposing to chiral triazole fungicide tebuconazole. Food Chem 2022; 371:131209. [PMID: 34598121 DOI: 10.1016/j.foodchem.2021.131209] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/12/2021] [Accepted: 09/20/2021] [Indexed: 02/05/2023]
Abstract
In this study, non-targeted and targeted metabolomics/lipidomics studies based on UPLC-QTOF-MS and UPLC-MS/MS were carried out to clarify the effects of tebuconazole and its different enantiomers on lettuce metabolites and lipids. Slight enantioselective degradation of tebuconazole was observed and six degradation metabolites were tentatively identified. The endogenous metabolites involved in carbohydrate metabolism, amino acid metabolism, nucleic acid metabolism, phenylpropanoid and flavonoid metabolism, vitamins, and lipid metabolism were significantly affected with enantioselectivity by tebuconazole exposure. Nucleotide metabolism and nicotinic acid metabolic network were significantly activated by the stimulation of tebuconazole. Rac- and (-)-R-tebuconazole caused the down-regulation of soluble sugars and subsequent amino acids and organic acids. Overall, lettuce exposed to tebuconazole was shown to have a significant impact on plant metabolism and lipid metabolism, with notable stereoselectivity. The results showed stereoselective toxicity of tebuconazole and provided a better understanding of its metabolomic and lipidomic effects on lettuce.
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Affiliation(s)
- Liuqing Zhao
- Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Ministry of Agriculture, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Yanwei Zhang
- Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Ministry of Agriculture, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Lu Wang
- Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Ministry of Agriculture, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Xiaowei Liu
- Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Ministry of Agriculture, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Jingran Zhang
- SCIEX, Analytical Instrument Trading Co., Ltd, Beijing 100015, China
| | - Zeying He
- Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Ministry of Agriculture, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China.
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21
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Gupta K, Rishishwar R, Dasgupta I. The interplay of plant hormonal pathways and geminiviral proteins: partners in disease development. Virus Genes 2022; 58:1-14. [PMID: 35034268 DOI: 10.1007/s11262-021-01881-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 11/28/2021] [Indexed: 10/19/2022]
Abstract
Viruses belonging to the family Geminiviridae infect plants and are responsible for a number of diseases of crops in the tropical and sub-tropical regions of the World. The innate immune response of the plant assists in its defense against such viral pathogens by the recognition of pathogen/microbe-associated molecular patterns through pattern-recognition receptors. Phytohormone signalling pathways play a vital role in plant defense responses against these devastating viruses. Geminiviruses, however, have developed counter-defense strategies that prevail over the above defense pathways. The proteins encoded by geminiviruses act as suppressors of plant immunity by interacting with the signalling components of several hormones. In this review we focus on the molecular interplay of phytohormone pathways and geminiviral infection and try to find interesting parallels with similar mechanisms known in other plant-infecting viruses and strengthen the argument that this interplay is necessary for disease development.
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Affiliation(s)
- Kanika Gupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, -110021, India
| | - Rashmi Rishishwar
- Department of Botany, Bhagat Singh Government P.G. College, Jaora, Ratlam, Madhya Pradesh, 457226, India
| | - Indranil Dasgupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, -110021, India.
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22
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Matsunaga S, Yamasaki Y, Mega R, Toda Y, Akashi K, Tsujimoto H. Metabolome Profiling of Heat Priming Effects, Senescence, and Acclimation of Bread Wheat Induced by High Temperatures at Different Growth Stages. Int J Mol Sci 2021; 22:ijms222313139. [PMID: 34884945 PMCID: PMC8658393 DOI: 10.3390/ijms222313139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 11/16/2022] Open
Abstract
Our previous study described stage-specific responses of ‘Norin 61’ bread wheat to high temperatures from seedling to tillering (GS1), tillering to flowering (GS2), flowering to full maturity stage (GS3), and seedling to full maturity stage (GS1–3). The grain development phase lengthened in GS1 plants; source tissue decreased in GS2 plants; rapid senescence occurred in GS3 plants; all these effects occurred in GS1–3 plants. The present study quantified 69 flag leaf metabolites during early grain development to reveal the effects of stage-specific high-temperature stress and identify markers that predict grain weight. Heat stresses during GS2 and GS3 showed the largest shifts in metabolite contents compared with the control, followed by GS1–3 and GS1. The GS3 plants accumulated nucleosides related to the nucleotide salvage pathway, beta-alanine, and serotonin. Accumulation of these compounds in GS1 plants was significantly lower than in the control, suggesting that the reduction related to the high-temperature priming effect observed in the phenotype (i.e., inhibition of senescence). The GS2 plants accumulated a large quantity of free amino acids, indicating residual effects of the previous high-temperature treatment and recovery from stress. However, levels in GS1–3 plants tended to be close to those in the control, indicating an acclimation response. Beta-alanine, serotonin, tryptophan, proline, and putrescine are potential molecular markers that predict grain weight due to their correlation with agronomic traits.
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Affiliation(s)
- Sachiko Matsunaga
- United Graduate School of Agricultural Sciences, Tottori University, 4-101 Koyama-Cho Minami, Tottori 680-8553, Japan;
| | - Yuji Yamasaki
- Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori 680-0001, Japan;
| | - Ryosuke Mega
- Graduate School of Science & Technology for Innovation, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan;
| | - Yusuke Toda
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan;
| | - Kinya Akashi
- Faculty of Agricultural Sciences, Tottori University, 4-101 Koyama-Cho Minami, Tottori 680-8553, Japan;
| | - Hisashi Tsujimoto
- Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori 680-0001, Japan;
- Correspondence: ; Tel.: +81-857-21-7213; Fax: +81-857-29-6199
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23
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Initiation of cytosolic plant purine nucleotide catabolism involves a monospecific xanthosine monophosphate phosphatase. Nat Commun 2021; 12:6846. [PMID: 34824243 PMCID: PMC8616923 DOI: 10.1038/s41467-021-27152-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 11/02/2021] [Indexed: 12/05/2022] Open
Abstract
In plants, guanosine monophosphate (GMP) is synthesized from adenosine monophosphate via inosine monophosphate and xanthosine monophosphate (XMP) in the cytosol. It has been shown recently that the catabolic route for adenylate-derived nucleotides bifurcates at XMP from this biosynthetic route. Dephosphorylation of XMP and GMP by as yet unknown phosphatases can initiate cytosolic purine nucleotide catabolism. Here we show that Arabidopsis thaliana possesses a highly XMP-specific phosphatase (XMPP) which is conserved in vascular plants. We demonstrate that XMPP catalyzes the irreversible entry reaction of adenylate-derived nucleotides into purine nucleotide catabolism in vivo, whereas the guanylates enter catabolism via an unidentified GMP phosphatase and guanosine deaminase which are important to maintain purine nucleotide homeostasis. We also present a crystal structure and mutational analysis of XMPP providing a rationale for its exceptionally high substrate specificity, which is likely required for the efficient catalysis of the very small XMP pool in vivo. Dephosphorylation of xanthosine monophosphate (XMP) initiates purine nucleotide catabolism in plant cells. Here the authors identify an XMP phosphatase from Arabidopsis that channels XMP towards catabolism in vivo and demonstrate the structural basis for its XMP specificity.
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24
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Dabravolski SA, Isayenkov SV. Evolution of the Cytokinin Dehydrogenase (CKX) Domain. J Mol Evol 2021; 89:665-677. [PMID: 34757471 DOI: 10.1007/s00239-021-10035-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 10/30/2021] [Indexed: 01/05/2023]
Abstract
Plant hormone cytokinins are important regulators of plant development, response to environmental stresses and interplay with other plant hormones. Cytokinin dehydrogenases (CKXs) are proteins responsible for the irreversible break-down of cytokinins to the adenine and aldehyde. Even though plant CKXs have been extensively studied, homologous proteins from other taxa remain mainly uncharacterised. Here we present our study on the molecular evolution and divergence of the CKX from bacteria, fungi, amoeba and viridiplantae. Although CKXs are present in eukaryotes and prokaryotes, they are missing in algae and metazoan taxa. The prevalent domain architecture consists of the FAD-binding and cytokinin binding domains, whereas some bacteria appear to have only cytokinin binding domain proteins. The CKXs play important role in the various aspects of plant life including control of plant development, response to biotic and abiotic stress, influence nutrition. Results of our study suggested that CKX originates from the FAD-linked C-terminal oxidase and has a defence-oriented function. The obtained results significantly extend the current understanding of the cytokinin dehydrogenases structure-function from the relationship to homologues from other taxa and provide a starting point baseline for their future functional characterization.
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Affiliation(s)
- Siarhei A Dabravolski
- Department of Clinical Diagnostics, Vitebsk State Academy of Veterinary Medicine [UO VGAVM], Dovatora str. 7/11, 21002, Vitebsk, Belarus
| | - Stanislav V Isayenkov
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China.
- Department of Plant Food Products and Biofortification, Institute of Food Biotechnology and Genomics, NAS of Ukraine, Osipovskogo str., 2a, Kyiv-123, Kyiv, 04123, Ukraine.
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25
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Nguyen HN, Nguyen TQ, Kisiala AB, Emery RJN. Beyond transport: cytokinin ribosides are translocated and active in regulating the development and environmental responses of plants. PLANTA 2021; 254:45. [PMID: 34365553 DOI: 10.1007/s00425-021-03693-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 08/01/2021] [Indexed: 06/13/2023]
Abstract
Riboside type cytokinins are key components in cytokinin metabolism, transport, and sensitivity, making them important functional signals in plant growth and development and environmental stress responses. Cytokinin (CKs) are phytohormones that regulate multiple processes in plants and are critical for agronomy, as they are involved in seed filling and plant responses to biotic and abiotic stress. Among the over 30 identified CKs, there is uncertainty about the roles of many of the individual CK structural forms. Cytokinin free bases (CKFBs), have been studied in great detail, but, by comparison, roles of riboside-type CKs (CKRs) in CK metabolism and associated signaling pathways and their distal impacts on plant physiology remain largely unknown. Here, recent findings on CKR abundance, transport and localization, are summarized, and their importance in planta is discussed. The history of CKR analyses is reviewed, in the context of the determination of CK metabolic pathways, and research on CKR affinity for CK receptors, all of which yield essential insights into their functions. Recent studies suggest that CKR forms are a lot more than a group of transport CKs and, beyond this, they play important roles in plant development and responses to environmental stress. In this context, this review discusses the involvement of CKRs in plant development, and highlight the less anticipated functions of CKRs in abiotic stress tolerance. Based on this, possible mechanisms for CKR modes of action are proposed and experimental approaches to further uncover their roles and future biotechnological applications are suggested.
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Affiliation(s)
- Hai Ngoc Nguyen
- Department of Biology, Trent University, Peterborough, ON, K9L 0G2, Canada.
| | - Thien Quoc Nguyen
- Department of Biology, Trent University, Peterborough, ON, K9L 0G2, Canada
| | - Anna B Kisiala
- Department of Biology, Trent University, Peterborough, ON, K9L 0G2, Canada
| | - R J Neil Emery
- Department of Biology, Trent University, Peterborough, ON, K9L 0G2, Canada
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26
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Suh JH, Tang X, Zhang Y, Gmitter FG, Wang Y. Metabolomic Analysis Provides New Insight Into Tolerance of Huanglongbing in Citrus. FRONTIERS IN PLANT SCIENCE 2021; 12:710598. [PMID: 34421957 PMCID: PMC8371912 DOI: 10.3389/fpls.2021.710598] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 06/30/2021] [Indexed: 05/17/2023]
Abstract
There have been efforts to develop citrus cultivars that are tolerant of Huanglongbing (HLB), a catastrophic phloem-limited disease. Previous studies demonstrated that continuous plant growth with phloem regeneration is one of the major characteristics of HLB tolerance. In this study, the metabolic mechanisms of HLB tolerance in citrus were elucidated using a multiple pathway-targeted metabolomic approach. Comparative analysis of healthy and infected HLB-tolerant and HLB-sensitive mandarin cultivars (Citrus reticulata) revealed differentially expressed metabolic responses among different groups. Pathway enrichment analysis indicated aspartate and glutamate metabolism, purine metabolism, and biosynthesis of plant hormones were upregulated in the tolerant group, except salicylic acid signaling. Catabolic pathways linked to energy-yielding metabolism were also upregulated in the tolerant group. These metabolisms and pathways were interconnected with each other, unveiling a pivotal metabolic network associated with HLB tolerance. In the network, auxins and cytokinins, the plant hormones responsible for plant growth and phloem regeneration, were accumulated. In addition, purine metabolites serving as energy carriers and nitrogen sources of plants were increased. Only salicylic acid-related metabolites for plant defense responses were decreased in the tolerant group. Our findings may evidence the strategy of HLB-tolerant cultivars that sustain plant growth and phloem formation rather than displaying direct plant defense to overcome the disease.
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Affiliation(s)
| | | | | | | | - Yu Wang
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
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27
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Gotarkar D, Longkumer T, Yamamoto N, Nanda AK, Iglesias T, Li L, Miro B, Blanco Gonzalez E, Montes Bayon M, Olsen KM, Hsing YC, Kohli A. A drought-responsive rice amidohydrolase is the elusive plant guanine deaminase with the potential to modulate the epigenome. PHYSIOLOGIA PLANTARUM 2021; 172:1853-1866. [PMID: 33749847 PMCID: PMC8360030 DOI: 10.1111/ppl.13392] [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: 12/29/2020] [Revised: 02/16/2021] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
Drought stress in plants causes differential expression of numerous genes. One of these differentially expressed genes in rice is a specific amidohydrolase. We characterized this amidohydrolase gene on the rice chromosome 12 as the first plant guanine deaminase (OsGDA1). The biochemical activity of GDA is known from tea and coffee plants where its catalytic product, xanthine, is the precursor for theine and caffeine. However, no plant gene that is coding for GDA is known so far. Recombinant OsGDA1 converted guanine to xanthine in vitro. Measurement of guanine and xanthine contents in the OsGDA1 knockout (KO) line and in the wild type Tainung 67 rice plants also suggested GDA activity in vivo. The content of cellular xanthine is important because of its catabolic products allantoin, ureides, and urea which play roles in water and nitrogen stress tolerance among others. The identification of OsGDA1 fills a critical gap in the S-adenosyl-methionine (SAM) to xanthine pathway. SAM is converted to S-adenosyl-homocysteine (SAH) and finally to xanthine. SAH is a potent inhibitor of DNA methyltransferases, the reduction of which leads to increased DNA methylation and gene silencing in Arabidopsis. We report that the OsGDA1 KO line exhibited a decrease in SAM, SAH and adenosine and an increase in rice genome methylation. The OsGDA1 protein phylogeny combined with mutational protein destabilization analysis suggested artificial selection for null mutants, which could affect genome methylation as in the KO line. Limited information on genes that may affect epigenetics indirectly requires deeper insights into such a role and effect of purine catabolism and related genetic networks.
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Affiliation(s)
- Dhananjay Gotarkar
- Strategic Innovation PlatformInternational Rice Research InstituteMakatiPhilippines
| | | | - Naoki Yamamoto
- Strategic Innovation PlatformInternational Rice Research InstituteMakatiPhilippines
| | - Amrit Kaur Nanda
- Strategic Innovation PlatformInternational Rice Research InstituteMakatiPhilippines
| | - Tamara Iglesias
- Faculty of Chemistry, Department of Physical and Analytical ChemistryUniversity of OviedoOviedoAsturiasSpain
| | - Lin‐Feng Li
- Department of BiologyWashington UniversitySt. LouisMissouriUSA
| | - Berta Miro
- Strategic Innovation PlatformInternational Rice Research InstituteMakatiPhilippines
| | - Elisa Blanco Gonzalez
- Faculty of Chemistry, Department of Physical and Analytical ChemistryUniversity of OviedoOviedoAsturiasSpain
| | - Maria Montes Bayon
- Faculty of Chemistry, Department of Physical and Analytical ChemistryUniversity of OviedoOviedoAsturiasSpain
| | | | | | - Ajay Kohli
- Strategic Innovation PlatformInternational Rice Research InstituteMakatiPhilippines
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28
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Sizova I, Kelterborn S, Verbenko V, Kateriya S, Hegemann P. Chlamydomonas POLQ is necessary for CRISPR/Cas9-mediated gene targeting. G3 (BETHESDA, MD.) 2021; 11:jkab114. [PMID: 33836052 PMCID: PMC8495919 DOI: 10.1093/g3journal/jkab114] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/18/2021] [Indexed: 02/06/2023]
Abstract
The use of CRISPR/Cas endonucleases has revolutionized gene editing techniques for research on Chlamydomonas reinhardtii. To better utilize the CRISPR/Cas system, it is essential to develop a more comprehensive understanding of the DNA repair pathways involved in genome editing. In this study, we have analyzed contributions from canonical KU80/KU70-dependent nonhomologous end-joining (cNHEJ) and DNA polymerase theta (POLQ)-mediated end joining on SpCas9-mediated untemplated mutagenesis and homology-directed repair (HDR)/gene inactivation in Chlamydomonas. Using CRISPR/SpCas9 technology, we generated DNA repair-defective mutants ku80, ku70, polQ for gene targeting experiments. Our results show that untemplated repair of SpCas9-induced double strand breaks results in mutation spectra consistent with an involvement of both KU80/KU70 and POLQ. In addition, the inactivation of POLQ was found to negatively affect HDR of the inactivated paromomycin-resistant mut-aphVIII gene when donor single-stranded oligos were used. Nevertheless, mut-aphVIII was still repaired by homologous recombination in these mutants. POLQ inactivation suppressed random integration of transgenes co-transformed with the donor ssDNA. KU80 deficiency did not affect these events but instead was surprisingly found to stimulate HDR/gene inactivation. Our data suggest that in Chlamydomonas, POLQ is the main contributor to CRISPR/Cas-induced HDR and random integration of transgenes, whereas KU80/KU70 potentially plays a secondary role. We expect our results will lead to improvement of genome editing in C. reinhardtii and can be used for future development of algal biotechnology.
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Affiliation(s)
- Irina Sizova
- Experimental Biophysics, Institute of Biology, Humboldt University of Berlin, Berlin D-10099, Germany
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre “Kurchatov Institute”, Gatchina 188300, Russia
- Kurchatov Genome Center - PNPI, Gatchina 188300, Russia
| | - Simon Kelterborn
- Experimental Biophysics, Institute of Biology, Humboldt University of Berlin, Berlin D-10099, Germany
| | - Valeriy Verbenko
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre “Kurchatov Institute”, Gatchina 188300, Russia
- Kurchatov Genome Center - PNPI, Gatchina 188300, Russia
| | - Suneel Kateriya
- Laboratory of Optobiology School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Peter Hegemann
- Experimental Biophysics, Institute of Biology, Humboldt University of Berlin, Berlin D-10099, Germany
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29
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Guyon‐Debast A, Alboresi A, Terret Z, Charlot F, Berthier F, Vendrell‐Mir P, Casacuberta JM, Veillet F, Morosinotto T, Gallois J, Nogué F. A blueprint for gene function analysis through Base Editing in the model plant Physcomitrium (Physcomitrella) patens. THE NEW PHYTOLOGIST 2021; 230:1258-1272. [PMID: 33421132 PMCID: PMC8048939 DOI: 10.1111/nph.17171] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/21/2020] [Indexed: 05/14/2023]
Abstract
CRISPR-Cas9 has proven to be highly valuable for genome editing in plants, including the model plant Physcomitrium patens. However, the fact that most of the editing events produced using the native Cas9 nuclease correspond to small insertions and deletions is a limitation. CRISPR-Cas9 base editors enable targeted mutation of single nucleotides in eukaryotic genomes and therefore overcome this limitation. Here, we report two programmable base-editing systems to induce precise cytosine or adenine conversions in P. patens. Using cytosine or adenine base editors, site-specific single-base mutations can be achieved with an efficiency up to 55%, without off-target mutations. Using the APT gene as a reporter of editing, we could show that both base editors can be used in simplex or multiplex, allowing for the production of protein variants with multiple amino-acid changes. Finally, we set up a co-editing selection system, named selecting modification of APRT to report gene targeting (SMART), allowing up to 90% efficiency site-specific base editing in P. patens. These two base editors will facilitate gene functional analysis in P. patens, allowing for site-specific editing of a given base through single sgRNA base editing or for in planta evolution of a given gene through the production of randomly mutagenised variants using multiple sgRNA base editing.
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Affiliation(s)
- Anouchka Guyon‐Debast
- Institut Jean‐Pierre BourginINRAEAgroParisTechUniversité Paris‐SaclayVersailles78000France
| | | | | | - Florence Charlot
- Institut Jean‐Pierre BourginINRAEAgroParisTechUniversité Paris‐SaclayVersailles78000France
| | - Floriane Berthier
- Institut Jean‐Pierre BourginINRAEAgroParisTechUniversité Paris‐SaclayVersailles78000France
| | - Pol Vendrell‐Mir
- Centre for Research in Agricultural Genomics CSIC‐IRTA‐UAB‐UBCampus UAB, Edifici CRAG, BellaterraBarcelona08193Spain
| | - Josep M. Casacuberta
- Centre for Research in Agricultural Genomics CSIC‐IRTA‐UAB‐UBCampus UAB, Edifici CRAG, BellaterraBarcelona08193Spain
| | - Florian Veillet
- IGEPPINRAE, Institut AgroUniversité de RennesPloudaniel29260France
| | | | | | - Fabien Nogué
- Institut Jean‐Pierre BourginINRAEAgroParisTechUniversité Paris‐SaclayVersailles78000France
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30
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Zhou S, Xing Y, Yuan X, Wu G, Zhu X, Wu D. Cytotoxicity and action mechanisms of polycyclic aromatic hydrocarbons by a miniature electrochemical detection system. Biomed Microdevices 2021; 23:19. [PMID: 33770288 DOI: 10.1007/s10544-021-00560-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2021] [Indexed: 11/28/2022]
Abstract
The effects of six polycyclic aromatic hydrocarbons (PAHs) on the activity of V79 cells were studied by using a miniature electrochemical system based on graphene oxide quantum dots and multiwall carbon nanotubes modified anodized screen printed carbon electrode. The cytotoxicity sequence of PAHs on V79 cells was different with guanine/xanthine (G/X), adenine (A), hypoxanthine (HX), and the end product of purine nucleotide catabolism, uric acid (UA), as biomarkers. The IC50 values measured with UA as the biomarker were the lowest, indicating that UA in cells was more sensitive to PAHs. The cytotoxicity sequence with G/X as the biomarker was the same as that of the MTT assay: pyrene > phenanthrene > benzo[a]pyrene > fluoranthene > fluorene > naphthalene. The cytotoxicity sequences measured by different biomarkers varied, which related to different structures that may influence the expression of the cellular aryl hydrocarbon receptor, gap junctional intercellular communication, and p53 protein. PAHs with different structures played varied roles in cell development and differentiation. Additionally, the electrochemical method was more sensitive than the MTT assay. The miniature electrochemical system enabled the simultaneous detection of four signals in cells, providing more information for multi-parameter evaluation and toxic mechanism study of PAHs and other pollutants.
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Affiliation(s)
- Shi Zhou
- School of Environment, Northeast Normal University, 130117, Changchun, Jilin, China.,College of Pharmacy, Jiamusi University, 154007, Jiamusi, Heilongjiang, China
| | - Yi Xing
- School of Environment, Northeast Normal University, 130117, Changchun, Jilin, China
| | - Xing Yuan
- School of Environment, Northeast Normal University, 130117, Changchun, Jilin, China
| | - Guanlan Wu
- School of Environment, Northeast Normal University, 130117, Changchun, Jilin, China
| | - Xiaolin Zhu
- School of Environment, Northeast Normal University, 130117, Changchun, Jilin, China.
| | - Dongmei Wu
- College of Pharmacy, Jiamusi University, 154007, Jiamusi, Heilongjiang, China.
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Delgado-García E, Piedras P, Gómez-Baena G, García-Magdaleno IM, Pineda M, Gálvez-Valdivieso G. Nucleoside Metabolism Is Induced in Common Bean During Early Seedling Development. FRONTIERS IN PLANT SCIENCE 2021; 12:651015. [PMID: 33841480 PMCID: PMC8027947 DOI: 10.3389/fpls.2021.651015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
Nucleoside hydrolases (NSH; nucleosidases) catalyze the cleavage of nucleosides into ribose and free nucleobases. These enzymes have been postulated as key elements controlling the ratio between nucleotide salvage and degradation. Moreover, they play a pivotal role in ureidic legumes by providing the substrate for the synthesis of ureides. Furthermore, nucleotide metabolism has a crucial role during germination and early seedling development, since the developing seedlings require high amount of nucleotide simultaneously to the mobilization of nutrient in cotyledons. In this study, we have cloned two nucleosidases genes from Phaseolus vulgaris, PvNSH1 and PvNSH2, expressed them as recombinant proteins, and characterized their catalytic activities. Both enzymes showed a broad range of substrate affinity; however, PvNSH1 exhibited the highest activity with uridine, followed by xanthosine, whereas PvNSH2 hydrolyses preferentially xanthosine and shows low activity with uridine. The study of the regulation of nucleosidases during germination and early postgerminative development indicated that nucleosidases are induced in cotyledons and embryonic axes just after the radicle emergence, coincident with the induction of nucleases activity and the synthesis of ureides in the embryonic axes, with no remarkable differences in the level of expression of both nucleosidase genes. In addition, nucleosides and nucleobase levels were determined as well in cotyledons and embryonic axes. Our results suggest that PvNSH1 and PvNSH2 play an important role in the mobilization of nutrients during this crucial stage of plant development.
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Affiliation(s)
- Elena Delgado-García
- Departamento de Botánica, Ecología y Fisiología Vegetal. Grupo de Fisiología Molecular y Biotecnología de Plantas. Campus de Excelencia Internacional en Agroalimentación, Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, Córdoba, Spain
| | - Pedro Piedras
- Departamento de Botánica, Ecología y Fisiología Vegetal. Grupo de Fisiología Molecular y Biotecnología de Plantas. Campus de Excelencia Internacional en Agroalimentación, Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, Córdoba, Spain
| | - Guadalupe Gómez-Baena
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional en Agroalimentación, Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, Córdoba, Spain
| | - Isabel M. García-Magdaleno
- Servicio Central de Apoyo a la Investigación (SCAI), Unidad de Espectrometría de Masas y Cromatografía, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Manuel Pineda
- Departamento de Botánica, Ecología y Fisiología Vegetal. Grupo de Fisiología Molecular y Biotecnología de Plantas. Campus de Excelencia Internacional en Agroalimentación, Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, Córdoba, Spain
| | - Gregorio Gálvez-Valdivieso
- Departamento de Botánica, Ecología y Fisiología Vegetal. Grupo de Fisiología Molecular y Biotecnología de Plantas. Campus de Excelencia Internacional en Agroalimentación, Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, Córdoba, Spain
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Bakr RO, El-Behairy MF, Elissawy AM, Elimam H, Fayed MAA. New Adenosine Derivatives from Aizoon canariense L.: In Vitro Anticholinesterase, Antimicrobial, and Cytotoxic Evaluation of Its Extracts. Molecules 2021; 26:1198. [PMID: 33668096 PMCID: PMC7956659 DOI: 10.3390/molecules26051198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 01/11/2023] Open
Abstract
Aizoaceae is a large succulent family characterized by many psychoactive species. Aizoon canariense L., a wild neglected plant traditionally used in gastrointestinal ailments, has been the subject of a limited number of phytochemical and biological studies. Therefore, herein, we investigated the in vitro cytotoxic, antimicrobial, and anticholinesteraseactivity of the aerial parts of A. canariense L. and analyzed the phytochemical compositions of the lipoidal and alkaloidal fractions. Petroleum ether extract showed the presence of behenic and tricosylic acid, while an in-depth investigation of the alkaloidal fraction revealed the identification of new adenine based alkaloids (1-5), which were isolated and identified for the first time from Aizoon canariense L. Their structures were elucidated based on extensive spectroscopic analyses. The alkaloidal extract showed a powerful cytotoxic effect (IC50 14-28 μg/mL), with the best effect against colon carcinoma, followed by liver and breast carcinomas. The alkaloidal extract also had a potent effect against Candida albicans and Escherichia coli, with minimum inhibitory concentrations (MIC) values of 312.5 and 625 µg/mL. The in vitro anticholinesterase activity was potent, with IC50 < 200 ng/mL for the tested extracts compared with 27.29 ± 0.49 ng/mL for tacrine.
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Affiliation(s)
- Riham O. Bakr
- Department of Pharmacognosy, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza 11787, Egypt;
| | - Mohammed F. El-Behairy
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Sadat City, Sadat 32897, Egypt;
| | - Ahmed M. Elissawy
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt;
- Center for Drug Discovery Research and Development, Ain Shams University, Cairo 11566, Egypt
| | - Hanan Elimam
- Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, Sadat 32897, Egypt;
| | - Marwa A. A. Fayed
- Department of Pharmacognosy, Faculty of Pharmacy, University of Sadat City, Sadat 32897, Egypt
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Liu L, Sanchez-Arcos C, Pohnert G, Wei D. Untargeted Metabolomics Unveil Changes in Autotrophic and Mixotrophic Galdieria sulphuraria Exposed to High-Light Intensity. Int J Mol Sci 2021; 22:ijms22031247. [PMID: 33513853 PMCID: PMC7865508 DOI: 10.3390/ijms22031247] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 11/16/2022] Open
Abstract
The thermoacidophilic red alga Galdieria sulphuraria has been optimizing a photosynthetic system for low-light conditions over billions of years, thriving in hot and acidic endolithic habitats. The growth of G. sulphuraria in the laboratory is very much dependent on light and substrate supply. Here, higher cell densities in G. sulphuraria under high-light conditions were obtained, although reductions in photosynthetic pigments were observed, which indicated this alga might be able to relieve the effects caused by photoinhibition. We further describe an extensive untargeted metabolomics study to reveal metabolic changes in autotrophic and mixotrophic G. sulphuraria grown under high and low light intensities. The up-modulation of bilayer lipids, that help generate better-ordered lipid domains (e.g., ergosterol) and keep optimal membrane thickness and fluidity, were observed under high-light exposure. Moreover, high-light conditions induced changes in amino acids, amines, and amide metabolism. Compared with the autotrophic algae, higher accumulations of osmoprotectant sugars and sugar alcohols were recorded in the mixotrophic G. sulphuraria. This response can be interpreted as a measure to cope with stress due to the high concentration of organic carbon sources. Our results indicate how G. sulphuraria can modulate its metabolome to maintain energetic balance and minimize harmful effects under changing environments.
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Affiliation(s)
- Lu Liu
- School of Food Science and Engineering, South China University of Technology, Wushan Rd. 381, Guangzhou 510641, China;
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Carlos Sanchez-Arcos
- Aquatic Chemical Ecology, Cologne Biocenter, University of Cologne, 50674 Cologne, Germany;
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich Schiller University Jena, Lessingstr. 8, 07743 Jena, Germany;
| | - Georg Pohnert
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich Schiller University Jena, Lessingstr. 8, 07743 Jena, Germany;
| | - Dong Wei
- School of Food Science and Engineering, South China University of Technology, Wushan Rd. 381, Guangzhou 510641, China;
- Research Institute for Food Nutrition and Human Health, Guangzhou 510640, China
- Correspondence: ; Tel.: +86-20-8711-3849
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Ou Z, Ouzounis C, Wang D, Sun W, Li J, Chen W, Marlière P, Danchin A. A Path toward SARS-CoV-2 Attenuation: Metabolic Pressure on CTP Synthesis Rules the Virus Evolution. Genome Biol Evol 2020; 12:2467-2485. [PMID: 33125064 PMCID: PMC7665462 DOI: 10.1093/gbe/evaa229] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2020] [Indexed: 02/06/2023] Open
Abstract
In the context of the COVID-19 pandemic, we describe here the singular metabolic background that constrains enveloped RNA viruses to evolve toward likely attenuation in the long term, possibly after a step of increased pathogenicity. Cytidine triphosphate (CTP) is at the crossroad of the processes allowing SARS-CoV-2 to multiply, because CTP is in demand for four essential metabolic steps. It is a building block of the virus genome, it is required for synthesis of the cytosine-based liponucleotide precursors of the viral envelope, it is a critical building block of the host transfer RNAs synthesis and it is required for synthesis of dolichol-phosphate, a precursor of viral protein glycosylation. The CCA 3'-end of all the transfer RNAs required to translate the RNA genome and further transcripts into the proteins used to build active virus copies is not coded in the human genome. It must be synthesized de novo from CTP and ATP. Furthermore, intermediary metabolism is built on compulsory steps of synthesis and salvage of cytosine-based metabolites via uridine triphosphate that keep limiting CTP availability. As a consequence, accidental replication errors tend to replace cytosine by uracil in the genome, unless recombination events allow the sequence to return to its ancestral sequences. We document some of the consequences of this situation in the function of viral proteins. This unique metabolic setup allowed us to highlight and provide a raison d'être to viperin, an enzyme of innate antiviral immunity, which synthesizes 3'-deoxy-3',4'-didehydro-CTP as an extremely efficient antiviral nucleotide.
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Affiliation(s)
- Zhihua Ou
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China
| | - Christos Ouzounis
- Biological Computation and Process Laboratory, Centre for Research and Technology Hellas, Chemical Process and Energy Resources Institute, Thessalonica, Greece
| | - Daxi Wang
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China
| | - Wanying Sun
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Junhua Li
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China
| | - Weijun Chen
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China.,BGI PathoGenesis Pharmaceutical Technology, BGI-Shenzhen, Shenzhen, China
| | - Philippe Marlière
- TESSSI, The European Syndicate of Synthetic Scientists and Industrialists, Paris, France
| | - Antoine Danchin
- Kodikos Labs, Institut Cochin, Paris, France.,School of Biomedical Sciences, Li KaShing Faculty of Medicine, Hong Kong University, Pokfulam, Hong Kong
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35
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A comparative UHPLC-Q/TOF-MS-based eco-metabolomics approach reveals temperature adaptation of four Nepenthes species. Sci Rep 2020; 10:21861. [PMID: 33318532 PMCID: PMC7736350 DOI: 10.1038/s41598-020-78873-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 11/30/2020] [Indexed: 12/15/2022] Open
Abstract
Nepenthes, as the largest family of carnivorous plants, is found with an extensive geographical distribution throughout the Malay Archipelago, specifically in Borneo, Philippines, and Sumatra. Highland species are able to tolerate cold stress and lowland species heat stress. Our current understanding on the adaptation or survival mechanisms acquired by the different Nepenthes species to their climatic conditions at the phytochemical level is, however, limited. In this study, we applied an eco-metabolomics approach to identify temperature stressed individual metabolic fingerprints of four Nepenthes species: the lowlanders N. ampullaria, N. rafflesiana and N. northiana, and the highlander N. minima. We hypothesized that distinct metabolite regulation patterns exist between the Nepenthes species due to their adaptation towards different geographical and altitudinal distribution. Our results revealed not only distinct temperature stress induced metabolite fingerprints for each Nepenthes species, but also shared metabolic response and adaptation strategies. The interspecific responses and adaptation of N. rafflesiana and N. northiana likely reflected their natural habitat niches. Moreover, our study also indicates the potential of lowlanders, especially N. ampullaria and N. rafflesiana, to produce metabolites needed to deal with increased temperatures, offering hope for the plant genus and future adaption in times of changing climate.
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36
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Ghosh Biswas R, Fortier-McGill B, Akhter M, Soong R, Ning P, Bastawrous M, Jenne A, Schmidig D, De Castro P, Graf S, Kuehn T, Busse F, Struppe J, Fey M, Heumann H, Boenisch H, Gundy M, Simpson MJ, Simpson AJ. Ex vivo Comprehensive Multiphase NMR of whole organisms: A complementary tool to in vivo NMR. Anal Chim Acta X 2020; 6:100051. [PMID: 33392494 PMCID: PMC7772632 DOI: 10.1016/j.acax.2020.100051] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/29/2020] [Accepted: 06/23/2020] [Indexed: 12/15/2022] Open
Abstract
Nuclear Magnetic Resonance (NMR) spectroscopy is a non-invasive analytical technique which allows for the study of intact samples. Comprehensive Multiphase NMR (CMP-NMR) combines techniques and hardware from solution state and solid state NMR to allow for the holistic analysis of all phases (i.e. solutions, gels and solids) in unaltered samples. This study is the first to apply CMP-NMR to deceased, intact organisms and uses 13C enriched Daphnia magna (water fleas) as an example. D. magna are commonly used model organisms for environmental toxicology studies. As primary consumers, they are responsible for the transfer of nutrients across trophic levels, and a decline in their population can potentially impact the entire freshwater aquatic ecosystem. Though in vivo research is the ultimate tool to understand an organism’s most biologically relevant state, studies are limited by conditions (i.e. oxygen requirements, limited experiment time and reduced spinning speed) required to keep the organisms alive, which can negatively impact the quality of the data collected. In comparison, ex vivo CMP-NMR is beneficial in that; organisms do not need oxygen (eliminating air holes in rotor caps and subsequent evaporation); samples can be spun faster, leading to improved spectral resolution; more biomass per sample can be analyzed; and experiments can be run for longer. In turn, higher quality ex vivo NMR, can provide more comprehensive NMR assignments, which in many cases could be transferred to better understand less resolved in vivo signals. This manuscript is divided into three sections: 1) multiphase spectral editing techniques, 2) detailed metabolic assignments of 2D NMR of 13C enriched D. magna and 3) multiphase biological changes over different life stages, ages and generations of D. magna. In summary, ex vivo CMP-NMR proves to be a very powerful approach to study whole organisms in a comprehensive manner and should provide very complementary information to in vivo based research. Comprehensive Multiphase NMR detects all phases (solid/liquid/gel) in whole samples. Deceased organisms are not subjected to the limitations of in vivo NMR studies. 2D ex vivo NMR offer increased spectral resolution, improving metabolite assignment. Holistic analysis shows biological changes in D. magna over different life stages. Ex vivo NMR can be a complementary tool for in vivo NMR metabolomic studies.
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Affiliation(s)
- Rajshree Ghosh Biswas
- University of Toronto Scarborough, Department of Physical & Environmental Sciences, 1265, Military Trail, M1C 1A4, ON, Canada
| | - Blythe Fortier-McGill
- University of Toronto Scarborough, Department of Physical & Environmental Sciences, 1265, Military Trail, M1C 1A4, ON, Canada
| | - Mohammad Akhter
- University of Toronto Scarborough, Department of Physical & Environmental Sciences, 1265, Military Trail, M1C 1A4, ON, Canada
| | - Ronald Soong
- University of Toronto Scarborough, Department of Physical & Environmental Sciences, 1265, Military Trail, M1C 1A4, ON, Canada
| | - Paris Ning
- University of Toronto Scarborough, Department of Physical & Environmental Sciences, 1265, Military Trail, M1C 1A4, ON, Canada
| | - Monica Bastawrous
- University of Toronto Scarborough, Department of Physical & Environmental Sciences, 1265, Military Trail, M1C 1A4, ON, Canada
| | - Amy Jenne
- University of Toronto Scarborough, Department of Physical & Environmental Sciences, 1265, Military Trail, M1C 1A4, ON, Canada
| | - Daniel Schmidig
- Bruker Switzerland AG, Industriestrasse 26, 8117, Fällanden, Switzerland
| | - Peter De Castro
- Bruker Switzerland AG, Industriestrasse 26, 8117, Fällanden, Switzerland
| | - Stephan Graf
- Bruker Switzerland AG, Industriestrasse 26, 8117, Fällanden, Switzerland
| | - Till Kuehn
- Bruker Switzerland AG, Industriestrasse 26, 8117, Fällanden, Switzerland
| | - Falko Busse
- Bruker Biospin GmbH, Silberstreifen 4, 76287, Rheinstetten, Germany
| | - Jochem Struppe
- Bruker Corporation, 15 Fortune Drive, Billerica, MA, 01821-3991, USA
| | - Michael Fey
- Bruker Corporation, 15 Fortune Drive, Billerica, MA, 01821-3991, USA
| | - Hermann Heumann
- Silantes GmbH, Gollierstrasse 70c, D-80339, München, Germany
| | - Holger Boenisch
- Silantes GmbH, Gollierstrasse 70c, D-80339, München, Germany
| | - Marcel Gundy
- Silantes GmbH, Gollierstrasse 70c, D-80339, München, Germany
| | - Myrna J Simpson
- University of Toronto Scarborough, Department of Physical & Environmental Sciences, 1265, Military Trail, M1C 1A4, ON, Canada
| | - André J Simpson
- University of Toronto Scarborough, Department of Physical & Environmental Sciences, 1265, Military Trail, M1C 1A4, ON, Canada
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Cader MZ, de Almeida Rodrigues RP, West JA, Sewell GW, Md-Ibrahim MN, Reikine S, Sirago G, Unger LW, Iglesias-Romero AB, Ramshorn K, Haag LM, Saveljeva S, Ebel JF, Rosenstiel P, Kaneider NC, Lee JC, Lawley TD, Bradley A, Dougan G, Modis Y, Griffin JL, Kaser A. FAMIN Is a Multifunctional Purine Enzyme Enabling the Purine Nucleotide Cycle. Cell 2020; 180:278-295.e23. [PMID: 31978345 PMCID: PMC6978800 DOI: 10.1016/j.cell.2019.12.017] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 11/18/2019] [Accepted: 12/12/2019] [Indexed: 12/11/2022]
Abstract
Mutations in FAMIN cause arthritis and inflammatory bowel disease in early childhood, and a common genetic variant increases the risk for Crohn's disease and leprosy. We developed an unbiased liquid chromatography-mass spectrometry screen for enzymatic activity of this orphan protein. We report that FAMIN phosphorolytically cleaves adenosine into adenine and ribose-1-phosphate. Such activity was considered absent from eukaryotic metabolism. FAMIN and its prokaryotic orthologs additionally have adenosine deaminase, purine nucleoside phosphorylase, and S-methyl-5′-thioadenosine phosphorylase activity, hence, combine activities of the namesake enzymes of central purine metabolism. FAMIN enables in macrophages a purine nucleotide cycle (PNC) between adenosine and inosine monophosphate and adenylosuccinate, which consumes aspartate and releases fumarate in a manner involving fatty acid oxidation and ATP-citrate lyase activity. This macrophage PNC synchronizes mitochondrial activity with glycolysis by balancing electron transfer to mitochondria, thereby supporting glycolytic activity and promoting oxidative phosphorylation and mitochondrial H+ and phosphate recycling. An unbiased LC-MS screen reveals FAMIN as a purine nucleoside enzyme FAMIN combines adenosine phosphorylase with ADA-, PNP-, and MTAP-like activities FAMIN enables a purine nucleotide cycle (PNC) preventing cytoplasmic acidification The FAMIN-dependent PNC balances the glycolysis-mitochondrial redox interface
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Affiliation(s)
- M Zaeem Cader
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Rodrigo Pereira de Almeida Rodrigues
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - James A West
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, UK
| | - Gavin W Sewell
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Muhammad N Md-Ibrahim
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Stephanie Reikine
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Giuseppe Sirago
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Lukas W Unger
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Ana Belén Iglesias-Romero
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Katharina Ramshorn
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Lea-Maxie Haag
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Svetlana Saveljeva
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Jana-Fabienne Ebel
- Institute of Clinical Molecular Biology, Christian Albrechts University, Campus Kiel, 24105 Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian Albrechts University, Campus Kiel, 24105 Kiel, Germany
| | - Nicole C Kaneider
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - James C Lee
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | | | - Allan Bradley
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Infectious Diseases, Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Yorgo Modis
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Julian L Griffin
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, UK
| | - Arthur Kaser
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK.
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Nguyen J, Schein J, Hunt K, Tippmann-Feightner J, Rapp M, Stoffer-Bittner A, Nalam V, Funk A, Schultes N, Mourad G. The Nicotiana sylvestris nucleobase cation symporter 1 retains a dicot solute specificity profile. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.plgene.2020.100226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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39
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Bonini P, Rouphael Y, Miras-Moreno B, Lee B, Cardarelli M, Erice G, Cirino V, Lucini L, Colla G. A Microbial-Based Biostimulant Enhances Sweet Pepper Performance by Metabolic Reprogramming of Phytohormone Profile and Secondary Metabolism. FRONTIERS IN PLANT SCIENCE 2020; 11:567388. [PMID: 33224160 PMCID: PMC7674627 DOI: 10.3389/fpls.2020.567388] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/15/2020] [Indexed: 05/05/2023]
Abstract
Microbial-based biostimulants can improve crop productivity by modulating cell metabolic pathways including hormonal balance. However, little is known about the microbial-mediated molecular changes causing yield increase. The present study elucidates the metabolomic modulation occurring in pepper (Capsicum annuum L.) leaves at the vegetative and reproductive phenological stages, in response to microbial-based biostimulants. The arbuscular mycorrhizal fungi Rhizoglomus irregularis and Funneliformis mosseae, as well as Trichoderma koningii, were used in this work. The application of endophytic fungi significantly increased total fruit yield by 23.7% compared to that of untreated plants. Multivariate statistics indicated that the biostimulant treatment substantially altered the shape of the metabolic profile of pepper. Compared to the untreated control, the plants treated with microbial biostimulants presented with modified gibberellin, auxin, and cytokinin patterns. The biostimulant treatment also induced secondary metabolism and caused carotenoids, saponins, and phenolic compounds to accumulate in the plants. Differential metabolomic signatures indicated diverse and concerted biochemical responses in the plants following the colonization of their roots by beneficial microorganisms. The above findings demonstrated a clear link between microbial-mediated yield increase and a strong up-regulation of hormonal and secondary metabolic pathways associated with growth stimulation and crop defense to environmental stresses.
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Affiliation(s)
- Paolo Bonini
- Next Generation Agronomics Laboratory (NGAlab), La Riera de Gaia, Tarragona, Spain
- *Correspondence: Paolo Bonini,
| | - Youssef Rouphael
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Begoña Miras-Moreno
- Department for Sustainable Food Process, Research Centre for Nutrigenomics and Proteomics, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Byungha Lee
- Next Generation Agronomics Laboratory (NGAlab), La Riera de Gaia, Tarragona, Spain
| | - Mariateresa Cardarelli
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria, Centro di ricerca Orticoltura e Florovivaismo, Pontecagnano Faiano, Italy
| | | | | | - Luigi Lucini
- Department for Sustainable Food Process, Research Centre for Nutrigenomics and Proteomics, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Giuseppe Colla
- Department of Agriculture and Forest Sciences, Università degli Studi della Tuscia, Viterbo, Italy
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Uawisetwathana U, Chevallier OP, Xu Y, Kamolsukyeunyong W, Nookaew I, Somboon T, Toojinda T, Vanavichit A, Goodacre R, Elliott CT, Karoonuthaisiri N. Global metabolite profiles of rice brown planthopper-resistant traits reveal potential secondary metabolites for both constitutive and inducible defenses. Metabolomics 2019; 15:151. [PMID: 31741127 DOI: 10.1007/s11306-019-1616-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 11/11/2019] [Indexed: 10/25/2022]
Abstract
INTRODUCTION Brown planthopper (BPH) is a phloem feeding insect that causes annual disease outbreaks, called hopper burn in many countries throughout Asia, resulting in severe damage to rice production. Currently, mechanistic understanding of BPH resistance in rice plant is limited, which has caused slow progression on developing effective rice varieties as well as effective farming practices against BPH infestation. OBJECTIVE To reveal rice metabolic responses during 8 days of BPH attack, this study examined polar metabolome extracts of BPH-susceptible (KD) and its BPH-resistant isogenic line (IL308) rice leaves. METHODS Ultra high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QToF-MS) was combined with multi-block PCA to analyze potential metabolites in response to BPH attack. RESULTS This multivariate statistical model revealed different metabolic response patterns between the BPH-susceptible and BPH-resistant varieties during BPH infestation. The metabolite responses of the resistant IL308 variety occurred on Day 1, which was significantly earlier than those of the susceptible KD variety which showed an induced response by Days 4 and 8. BPH infestation caused metabolic perturbations in purine, phenylpropanoid, flavonoid, and terpenoid pathways. While found in both susceptible and resistant rice varieties, schaftoside (1.8 fold), iso-schaftoside (1.7 fold), rhoifolin (3.4 fold) and apigenin 6-C-α-L-arabinoside-8-C-β-L-arabinoside levels (1.6 fold) were significantly increased in the resistant variety by Day 1 post-infestation. 20-hydroxyecdysone acetate (2.5 fold) and dicaffeoylquinic acid (4.7 fold) levels were considerably higher in the resistant rice variety than those in the susceptible variety, both before and after infestation, suggesting that these secondary metabolites play important roles in inducible and constitutive defenses against the BPH infestation. CONCLUSIONS These potential secondary metabolites will be useful as metabolite markers and/or bioactive compounds for effective and durable approaches to address the BPH problem.
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Affiliation(s)
- Umaporn Uawisetwathana
- Microarray Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Pathumthani, 12120, Thailand.
| | - Olivier P Chevallier
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, Northern Ireland, UK
| | - Yun Xu
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 3BX, UK
| | - Wintai Kamolsukyeunyong
- Rice Gene Discovery and Utilization Laboratory, Innovative Plant Biotechnology and Precision Agriculture Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, Thailand
| | - Intawat Nookaew
- College of Medicine, Department Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Thapakorn Somboon
- Microarray Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Pathumthani, 12120, Thailand
| | - Theerayut Toojinda
- Rice Gene Discovery and Utilization Laboratory, Innovative Plant Biotechnology and Precision Agriculture Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, Thailand
- Integrative Crop Biotechnology and Management Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, Thailand
| | - Apichart Vanavichit
- Agronomy Department, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom, Thailand
| | - Royston Goodacre
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 3BX, UK
| | - Christopher T Elliott
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, Northern Ireland, UK
| | - Nitsara Karoonuthaisiri
- Microarray Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Pathumthani, 12120, Thailand
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Abd El-Daim IA, Bejai S, Meijer J. Bacillus velezensis 5113 Induced Metabolic and Molecular Reprogramming during Abiotic Stress Tolerance in Wheat. Sci Rep 2019; 9:16282. [PMID: 31704956 PMCID: PMC6841942 DOI: 10.1038/s41598-019-52567-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 10/18/2019] [Indexed: 12/21/2022] Open
Abstract
Abiotic stresses are main limiting factors for agricultural production around the world. Plant growth promoting rhizobacteria (PGPR) have been shown to improve abiotic stress tolerance in several plants. However, the molecular and physiological changes connected with PGPR priming of stress management are poorly understood. The present investigation aimed to explore major metabolic and molecular changes connected with the ability of Bacillus velezensis 5113 to mediate abiotic stress tolerance in wheat. Seedlings treated with Bacillus were exposed to heat, cold/freezing or drought stress. Bacillus improved wheat survival in all stress conditions. SPAD readings showed higher chlorophyll content in 5113-treated stressed seedlings. Metabolite profiling using NMR and ESI-MS provided evidences for metabolic reprograming in 5113-treated seedlings and showed that several common stress metabolites were significantly accumulated in stressed wheat. Two-dimensional gel electrophoresis of wheat leaves resolved more than 300 proteins of which several were differentially expressed between different treatments and that cold stress had a stronger impact on the protein pattern compared to heat and drought. Peptides maps or sequences were used for database searches which identified several homologs. The present study suggests that 5113 treatment provides systemic effects that involve metabolic and regulatory functions supporting both growth and stress management.
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Affiliation(s)
- Islam A Abd El-Daim
- Department of Plant Biology, Uppsala Biocenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE75007, Uppsala, Sweden. .,Department of Microbiology, Soils, Water and Environment Research Institute, Agricultural Research Centre, Giza, Egypt. .,Institute of Biology, Environmental and Rural Sciences (IBERS) Aberystwyth University, Aberystwyth, UK.
| | - Sarosh Bejai
- Department of Plant Biology, Uppsala Biocenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE75007, Uppsala, Sweden
| | - Johan Meijer
- Department of Plant Biology, Uppsala Biocenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE75007, Uppsala, Sweden.
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Li P, Lei K, Li Y, He X, Wang S, Liu R, Ji L, Hou B. Identification and characterization of the first cytokinin glycosyltransferase from rice. RICE (NEW YORK, N.Y.) 2019; 12:19. [PMID: 30923923 PMCID: PMC6439077 DOI: 10.1186/s12284-019-0279-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/21/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Cytokinins are one of the five major hormones families in plants and are important for their normal growth and environmental adaptability. In plants, cytokinins are mostly present as glycosides in plants, and their glycosylation modifications are catalyzed by family 1 glycosyltransferases. Current research on cytokinin glycosylation has focused on the biochemical identification of enzymes and the analysis of metabolites in Arabidopsis. There are few studies that examine how cytokinin glycosylation affects its synthesis and accumulation in plants. It is particularly important to understand these processes in food crops such as rice (Oryza sativa); however, to date, cytokinin glycosyltransferase genes in rice have not been reported. RESULTS In this study, we identified eight rice genes that were functionally homologous to an Arabidopsis cytokinin glycosyltransferase gene. These genes were cloned and expressed in a prokaryotic system to obtain their purified proteins. Through enzymatic analysis and liquid chromatography-mass spectrometry, a single rice glycosyltransferase, Os6, was identified that glycosylated cytokinin in vitro. Os6 was overexpressed in Arabidopsis, and the extraction of cytokinin glycosides showed that Os6 is functionally active in planta. CONCLUSIONS The identification and characterization of the first cytokinin glycosyltransferase from rice is important for future studies on the cytokinin metabolic pathway in rice. An improved understanding of rice cytokinin glycosyltransferases may facilitate genetic improvements in rice quality.
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Affiliation(s)
- Pan Li
- College of Pharmacy, Liaocheng University, Liaocheng, 252000, Shandong, China
- College of Life Science, Shandong University, Qingdao, 250000, Shandong, China
| | - Kang Lei
- College of Pharmacy, Liaocheng University, Liaocheng, 252000, Shandong, China
| | - Yanjie Li
- College of Life Science, Shandong University, Qingdao, 250000, Shandong, China
| | - Xingrui He
- College of Pharmacy, Liaocheng University, Liaocheng, 252000, Shandong, China
| | - Shuo Wang
- College of Pharmacy, Liaocheng University, Liaocheng, 252000, Shandong, China
| | - Renmin Liu
- College of Pharmacy, Liaocheng University, Liaocheng, 252000, Shandong, China
| | - Lusha Ji
- College of Pharmacy, Liaocheng University, Liaocheng, 252000, Shandong, China.
| | - Bingkai Hou
- College of Life Science, Shandong University, Qingdao, 250000, Shandong, China.
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Guzmán-Zapata D, Sandoval-Vargas JM, Macedo-Osorio KS, Salgado-Manjarrez E, Castrejón-Flores JL, Oliver-Salvador MDC, Durán-Figueroa NV, Nogué F, Badillo-Corona JA. Efficient Editing of the Nuclear APT Reporter Gene in Chlamydomonas reinhardtii via Expression of a CRISPR-Cas9 Module. Int J Mol Sci 2019; 20:E1247. [PMID: 30871076 PMCID: PMC6429146 DOI: 10.3390/ijms20051247] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 03/04/2019] [Accepted: 03/07/2019] [Indexed: 12/20/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeat/CRISPR-associated protein 9 (CRISPR/Cas9) technology is a versatile and useful tool to perform genome editing in different organisms ranging from bacteria and yeast to plants and mammalian cells. For a couple of years, it was believed that the system was inefficient and toxic in the alga Chlamydomonas reinhardtii. However, recently the system has been successfully implemented in this model organism, albeit relying mostly on the electroporation of ribonucleoproteins (RNPs) into cell wall deficient strains. This requires a constant source of RNPs and limits the application of the technology to strains that are not necessarily the most relevant from a biotechnological point of view. Here, we show that transient expression of the Streptococcus pyogenes Cas9 gene and sgRNAs, targeted to the single-copy nuclear apt9 gene, encoding an adenine phosphoribosyl transferase (APT), results in efficient disruption at the expected locus. Introduction of indels to the apt9 locus results in cell insensitivity to the otherwise toxic compound 2-fluoroadenine (2-FA). We have used agitation with glass beads and particle bombardment to introduce the plasmids carrying the coding sequences for Cas9 and the sgRNAs in a cell-walled strain of C. reinhardtii (CC-125). Using sgRNAs targeting exons 1 and 3 of apt9, we obtained disruption efficiencies of 3 and 30% on preselected 2-FA resistant colonies, respectively. Our results show that transient expression of Cas9 and a sgRNA can be used for editing of the nuclear genome inexpensively and at high efficiency. Targeting of the APT gene could potentially be used as a pre-selection marker for multiplexed editing or disruption of genes of interest.
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Affiliation(s)
- Daniel Guzmán-Zapata
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología. Av. Acueducto S/N., Col. Barrio La Laguna Ticomán, 07340 Mexico City, Mexico.
| | - José M Sandoval-Vargas
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología. Av. Acueducto S/N., Col. Barrio La Laguna Ticomán, 07340 Mexico City, Mexico.
| | - Karla S Macedo-Osorio
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología. Av. Acueducto S/N., Col. Barrio La Laguna Ticomán, 07340 Mexico City, Mexico.
| | - Edgar Salgado-Manjarrez
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología. Av. Acueducto S/N., Col. Barrio La Laguna Ticomán, 07340 Mexico City, Mexico.
| | - José L Castrejón-Flores
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología. Av. Acueducto S/N., Col. Barrio La Laguna Ticomán, 07340 Mexico City, Mexico.
| | - María Del Carmen Oliver-Salvador
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología. Av. Acueducto S/N., Col. Barrio La Laguna Ticomán, 07340 Mexico City, Mexico.
| | - Noé V Durán-Figueroa
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología. Av. Acueducto S/N., Col. Barrio La Laguna Ticomán, 07340 Mexico City, Mexico.
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France.
| | - Jesús A Badillo-Corona
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología. Av. Acueducto S/N., Col. Barrio La Laguna Ticomán, 07340 Mexico City, Mexico.
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Abstract
Transition state theory teaches that chemically stable mimics of enzymatic transition states will bind tightly to their cognate enzymes. Kinetic isotope effects combined with computational quantum chemistry provides enzymatic transition state information with sufficient fidelity to design transition state analogues. Examples are selected from various stages of drug development to demonstrate the application of transition state theory, inhibitor design, physicochemical characterization of transition state analogues, and their progress in drug development.
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Affiliation(s)
- Vern L. Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
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da Fonseca-Pereira P, Neri-Silva R, Cavalcanti JHF, Brito DS, Weber APM, Araújo WL, Nunes-Nesi A. Data-Mining Bioinformatics: Connecting Adenylate Transport and Metabolic Responses to Stress. TRENDS IN PLANT SCIENCE 2018; 23:961-974. [PMID: 30287161 DOI: 10.1016/j.tplants.2018.09.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/30/2018] [Accepted: 09/07/2018] [Indexed: 06/08/2023]
Abstract
Adenine nucleotides are essential in countless processes within the cellular metabolism. In plants, ATP is mainly produced in chloroplasts and mitochondria through photophosphorylation and oxidative phosphorylation, respectively. Thus, efficient adenylate transport systems are required for intracellular energy partitioning between the cell organelles. Adenylate carriers present in different subcellular compartments have been previously identified and biochemically characterized in plants. Here, by using data-mining bioinformatics tools, we propose how, and to what extent, these carriers integrate energy metabolism within a plant cell under different environmental conditions. We demonstrate that the expression pattern of the corresponding genes is variable under different environmental conditions, suggesting that specific adenylate carriers have distinct and nonredundant functions in plants.
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Affiliation(s)
- Paula da Fonseca-Pereira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil; These authors contributed equally to this work
| | - Roberto Neri-Silva
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil; These authors contributed equally to this work
| | - João Henrique F Cavalcanti
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil; Max-Panck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Danielle S Brito
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-Universität, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil; Max-Panck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.
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