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Cui Q, Liu Q, Fan Y, Wang C, Li Y, Li S, Zhang J, Rao G. Functional differentiation of olive PLP_deC genes: insights into metabolite biosynthesis and genetic improvement at the whole-genome level. PLANT CELL REPORTS 2024; 43:127. [PMID: 38652203 DOI: 10.1007/s00299-024-03212-z] [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: 02/23/2024] [Accepted: 04/01/2024] [Indexed: 04/25/2024]
Abstract
KEY MESSAGE This study identified 16 pyridoxal phosphate-dependent decarboxylases in olive at the whole-genome level, conducted analyses on their physicochemical properties, evolutionary relationships and characterized their activity. Group II pyridoxal phosphate-dependent decarboxylases (PLP_deC II) mediate the biosynthesis of characteristic olive metabolites, such as oleuropein and hydroxytyrosol. However, there have been no report on the functional differentiation of this gene family at the whole-genome level. This study conducted an exploration of the family members of PLP_deC II at the whole-genome level, identified 16 PLP_deC II genes, and analyzed their gene structure, physicochemical properties, cis-acting elements, phylogenetic evolution, and gene expression patterns. Prokaryotic expression and enzyme activity assays revealed that OeAAD2 and OeAAD4 could catalyze the decarboxylation reaction of tyrosine and dopa, resulting in the formation of their respective amine compounds, but it did not catalyze phenylalanine and tryptophan. Which is an important step in the synthetic pathway of hydroxytyrosol and oleuropein. This finding established the foundational data at the molecular level for studying the functional aspects of the olive PLP_deC II gene family and provided essential gene information for genetic improvement of olive.
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Affiliation(s)
- Qizhen Cui
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Qingqing Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yutong Fan
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Chenhe Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yufei Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Shuyuan Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Jianguo Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Guodong Rao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
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Cherry A, Fisher B, Branch W, Peralta C, Gilliam L, Pahom O, Liebold C, Marshall J. Proteomic Analysis of Arachis hypogaea Seeds from Different Maturity Classes. PLANTS (BASEL, SWITZERLAND) 2024; 13:1111. [PMID: 38674520 PMCID: PMC11054812 DOI: 10.3390/plants13081111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024]
Abstract
Physiological maturity impacts seed quality through various mechanisms including vigor, desiccation tolerance, dormancy induction, synthesis of raw materials (including seed storage proteins), and the reorganization of metabolisms. Peanut seed development can be classified into seven classes with four incremental stages per class. Based on the mesocarp color, the final three stages are commonly referred to as "orange", "brown", and "black". In 2017, freshly harvested pods from one genotype of runner market-type peanuts grown under conventional practices were obtained from the University of Georgia research facility. The pods were removed from the plant material and 'pod blasted' to reveal the mesocarp. After separation, the remainder of the pod outer layer was removed, and the seeds were segregated for proteomic analysis. The raw peanuts were analyzed by bottom-up LC-MS/MS proteomics, which was conducted by the Proteomics Resource Center at the Rockefeller University, to identify the significant protein composition differences in each maturity class. The proteomic data revealed differentially expressed proteins as a function of maturity class with multiple functions including plant defense, metabolism, cell signaling, nutrient accumulation, and packaging. Understanding the processes needed for seed maturation will enable peanut scientists to evaluate the traits needed for robust germination, hardiness of the seed in response to disease, and nutrient quality.
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Affiliation(s)
- Ashley Cherry
- Department of Mathematics, Lubbock Christian University, Lubbock, TX 79407, USA; (A.C.); (B.F.)
| | - Brian Fisher
- Department of Mathematics, Lubbock Christian University, Lubbock, TX 79407, USA; (A.C.); (B.F.)
| | - William Branch
- Institute of Plant Breeding, Genetics, and Genomics, Tifton Campus, The University of Georgia, Crop and Soil Sciences, Tifton, GA 31793, USA;
| | - Christopher Peralta
- The Proteomics Resource Center, Rockefeller University, New York, NY 10065, USA;
| | - Lissa Gilliam
- Biochemistry Research Laboratory, Lubbock Christian University, Lubbock, TX 79407, USA;
| | - Olga Pahom
- Honors College, Lubbock Christian University, Lubbock, TX 79407, USA;
| | | | - Julie Marshall
- Department of Chemistry and Biochemistry, Lubbock Christian University, Lubbock, TX 79407, USA
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Zhou Y, Liao L, Liu X, Liu B, Chen X, Guo Y, Huang C, Zhao Y, Zeng Z. Crystal structure of Oryza sativa TDC reveals the substrate specificity for TDC-mediated melatonin biosynthesis. J Adv Res 2020; 24:501-511. [PMID: 32595985 PMCID: PMC7306523 DOI: 10.1016/j.jare.2020.06.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 04/20/2020] [Accepted: 06/08/2020] [Indexed: 01/01/2023] Open
Abstract
Plant tryptophan decarboxylase (TDC) is a type II Pyridoxal-5'-phosphate-dependent decarboxylase (PLP_DC) that could be used as a target to genetically improve crops. However, lack of accurate structural information on plant TDC hampers the understanding of its decarboxylation mechanisms. In the present study, the crystal structures of Oryza sativa TDC (OsTDC) in its complexes with pyridoxal-5'-phosphate, tryptamine and serotonin were determined. The structures provide detailed interaction information between TDC and its substrates. The Y359 residue from the loop gate is a proton donor and forms a Lewis acid-base pair with serotonin/tryptamine, which is associated with product release. The H214 residue is responsible for PLP binding and proton transfer, and its proper interaction with Y359 is essential for OsTDC enzyme activity. The extra hydrogen bonds formed between the 5-hydroxyl group of serotonin and the backbone carboxyl groups of F104 and P105 explain the discrepancy between the catalytic activity of TDC in tryptophan and in 5-hydroxytryptophan. In addition, an evolutionary analysis revealed that type II PLP_DC originated from glutamic acid decarboxylase, potentially as an adaptive evolution of mechanism in organisms in extreme environments. This study is, to our knowledge, the first to present a detailed analysis of the crystal structure of OsTDC in these complexes. The information regarding the catalytic mechanism described here could facilitate the development of protocols to regulate melatonin levels and thereby contribute to crop improvement efforts to improve food security worldwide.
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Affiliation(s)
- Yuanze Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Lijing Liao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xikai Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Biao Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinxin Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yan Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Chuanlong Huang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210014, China
| | - Yucheng Zhao
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210014, China
| | - Zhixiong Zeng
- Shandong Provincial Key Laboratory of Microbial Engineering, College of Bioengineering, Qilu University of Technology, Jinan 250353, China
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Zhang L, Jiao C, Cao Y, Cheng X, Wang J, Jin Q, Cai Y. Comparative Analysis and Expression Patterns of the PLP_deC Genes in Dendrobium officinale. Int J Mol Sci 2019; 21:E54. [PMID: 31861760 PMCID: PMC6981363 DOI: 10.3390/ijms21010054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 11/30/2022] Open
Abstract
Studies have shown that the type II pyridoxal phosphate-dependent decarboxylase (PLP_deC) genes produce secondary metabolites and flavor volatiles in plants, and TDC (tryptophan decarboxylase), a member of the PLP_deC family, plays an important role in the biosynthesis of terpenoid indole alkaloids (TIAs). In this study, we identified eight PLP_deC genes in Dendrobium officinale (D. officinale) and six in Phalaenopsis equestris (P. equestris), and their structures, physicochemical properties, response elements, evolutionary relationships, and expression patterns were preliminarily predicted and analyzed. The results showed that PLP_deC genes play important roles in D. officinale and respond to different exogenous hormone treatments; additionally, the results support the selection of appropriate candidates for further functional characterization of PLP_deC genes in D. officinale.
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Affiliation(s)
- Lei Zhang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (L.Z.); (C.J.); (X.C.)
- Anhui Provincial Engineering Technology Reserach Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
| | - Chunyan Jiao
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (L.Z.); (C.J.); (X.C.)
- Anhui Provincial Engineering Technology Reserach Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
| | - Yunpeng Cao
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China;
- Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha 410004, China
| | - Xi Cheng
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (L.Z.); (C.J.); (X.C.)
- Anhui Provincial Engineering Technology Reserach Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
| | - Jian Wang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (L.Z.); (C.J.); (X.C.)
- Anhui Provincial Engineering Technology Reserach Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
| | - Qing Jin
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (L.Z.); (C.J.); (X.C.)
- Anhui Provincial Engineering Technology Reserach Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (L.Z.); (C.J.); (X.C.)
- Anhui Provincial Engineering Technology Reserach Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
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