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Zhang S, Fan X, Malde AK, Gilbert RG. Development of a model for granule-bound starch synthase I activity using free-energy calculations. Int J Biol Macromol 2023; 253:127589. [PMID: 37871724 DOI: 10.1016/j.ijbiomac.2023.127589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/11/2023] [Accepted: 10/19/2023] [Indexed: 10/25/2023]
Abstract
Starch is a branched polymer of glucose with two components, both of which have (1 → 4)-α linear links and (1 → 6)-α branch points: amylopectin, of high molecular weight with many short branches, and amylose, of lower molecular weight and only a few long-chain branches. Granule-bound starch synthase I (GBSSI) is one of the main enzymes controlling amylose synthesis and chain-length distribution. As production of different GBSSI mutants is time-consuming and laborious, molecular dynamics (MD) simulations are used here to predict the binding of different GBSSI mutants to a representative amylose fragment. The simulations were atomistic, with explicit solvent and docking, a method successfully used to understand the binding of wild-type GBSSI to amylose fragments. The binding of GBSSI to G5 (a pentasaccharide amylose fragment) is combined with free-energy calculations employing a thermodynamic integration method to predict the effects of mutations on enzyme activity. Ten GBSSI mutants with different enzyme activities were analyzed to find the structural and energy changes among different single amino-acid mutants and their possible relationship to starch characteristics. Comparing the structural changes and the relative binding free energy of G5 to the wild type GBSSI and GBSSI mutants, it was found that mutants with negative binding energy (lower than -2.0 kcal/mol) are more likely to have higher enzyme activity and amylose content compared to the wild type. This theoretical paper used simulations and robust free energy calculations to interpret in planta data with potential predictions as to what mutants might be generated to give desired properties. This study can be used to help develop grains with improved functional properties.
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Affiliation(s)
- Shaobo Zhang
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia; Jiangsu Key Laboratory of Crop Genetics and Physiology, Joint International Research Laboratory of Agriculture and Agri-Product Safety, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xiaolei Fan
- Key Laboratory of Crop Genomics and Molecular Breeding of Jiangsu Province, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Alpeshkumar K Malde
- Institute for Glycomics, Griffith University, Gold Coast, QLD 4222, Australia; School of Environment and Science, Griffith University, Gold Coast, QLD 4222, Australia.
| | - Robert G Gilbert
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia; Jiangsu Key Laboratory of Crop Genetics and Physiology, Joint International Research Laboratory of Agriculture and Agri-Product Safety, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu, Yangzhou University, Yangzhou, Jiangsu 225009, China.
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Wang L, Liu L, Zhao J, Li C, Wu H, Zhao H, Wu Q. Granule-bound starch synthase in plants: Towards an understanding of their evolution, regulatory mechanisms, applications, and perspectives. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 336:111843. [PMID: 37648115 DOI: 10.1016/j.plantsci.2023.111843] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/01/2023]
Abstract
Amylose content (AC) is a significant quality trait in starchy crops, affecting their processing and application by the food and non-food industries. Therefore, fine-tuning AC in these crops has become a focus for breeders. Granule-bound starch synthase (GBSS) is the core enzyme that directly determines the AC levels. Several excellent reviews have summarized key progress in various aspects of GBSS research in recent years, but they mostly focus on cereals. Herein, we provide an in-depth review of GBSS research in monocots and dicots, focusing on the molecular characteristics, evolutionary relationships, expression patterns, molecular regulation mechanisms, and applications. We also discuss future challenges and directions for controlling AC in starchy crops, and found simultaneously increasing both the PTST and GBSS gene expression levels may be an effective strategy to increase amylose content.
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Affiliation(s)
- Lei Wang
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Linling Liu
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Jiali Zhao
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Chenglei Li
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Huala Wu
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Haixia Zhao
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China
| | - Qi Wu
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China.
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3
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Controlled processivity in glycosyltransferases: A way to expand the enzymatic toolbox. Biotechnol Adv 2023; 63:108081. [PMID: 36529206 DOI: 10.1016/j.biotechadv.2022.108081] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/20/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022]
Abstract
Glycosyltransferases (GT) catalyse the biosynthesis of complex carbohydrates which are the most abundant group of molecules in nature. They are involved in several key mechanisms such as cell signalling, biofilm formation, host immune system invasion or cell structure and this in both prokaryotic and eukaryotic cells. As a result, research towards complete enzyme mechanisms is valuable to understand and elucidate specific structure-function relationships in this group of molecules. In a next step this knowledge could be used in GT protein engineering, not only for rational drug design but also for multiple biotechnological production processes, such as the biosynthesis of hyaluronan, cellooligosaccharides or chitooligosaccharides. Generation of these poly- and/or oligosaccharides is possible due to a common feature of several of these GTs: processivity. Enzymatic processivity has the ability to hold on to the growing polymer chain and some of these GTs can even control the number of glycosyl transfers. In a first part, recent advances in understanding the mechanism of various processive enzymes are discussed. To this end, an overview is given of possible engineering strategies for the purpose of new industrial and fundamental applications. In the second part of this review, we focused on specific chain length-controlling mechanisms, i.e., key residues or conserved regions, and this for both eukaryotic and prokaryotic enzymes.
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4
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Willems P, Huang J, Messens J, Van Breusegem F. Functionally annotating cysteine disulfides and metal binding sites in the plant kingdom using AlphaFold2 predicted structures. Free Radic Biol Med 2023; 194:220-229. [PMID: 36493985 DOI: 10.1016/j.freeradbiomed.2022.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/14/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Deep learning algorithms such as AlphaFold2 predict three-dimensional protein structure with high confidence. The recent release of more than 200 million structural models provides an unprecedented resource for functional protein annotation. Here, we used AlphaFold2 predicted structures of fifteen plant proteomes to functionally and evolutionary analyze cysteine residues in the plant kingdom. In addition to identification of metal ligands coordinated by cysteine residues, we systematically analyzed cysteine disulfides present in these structural predictions. Our analysis demonstrates most of these predicted disulfides are trustworthy due their high agreement (∼96%) with those present in X-ray and NMR protein structures, their characteristic disulfide stereochemistry, the biased subcellular distribution of their proteins and a higher degree of oxidation of their respective cysteines as measured by proteomics. Adopting an evolutionary perspective, zinc binding sites are increasingly present at the expense of iron-sulfur clusters in plants. Interestingly, disulfide formation is increased in secreted proteins of land plants, likely promoting sequence evolution to adapt to changing environments encountered by plants. In summary, Alphafold2 predicted structural models are a rich source of information for studying the role of cysteines residues in proteins of interest and for protein redox biology in general.
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Affiliation(s)
- Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9052, Ghent, Belgium; Center for Medical Biotechnology, VIB, 9052, Ghent, Belgium.
| | - Jingjing Huang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Joris Messens
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
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Sharma V, Jahan K, Kumar P, Puri A, Sharma VK, Mishra A, Bharatam PV, Sharma D, Rishi V, Roy J. Mechanistic insights into granule-bound starch synthase I (GBSSI.L539P) allele in high amylose starch biosynthesis in wheat (Triticum aestivum L.). Funct Integr Genomics 2022; 23:20. [PMID: 36564499 DOI: 10.1007/s10142-022-00923-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 12/01/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022]
Abstract
Amylose fraction of grain starch is correlated with a type of resistant starch with better nutritional quality. Granule-bound starch synthase I (GBSSI) is the known starch synthase, responsible for elongation of linear amylose chains. GBSSI expression, activity, and binding to starch and other proteins are the key factors that can affect amylose content. Previously, a QTL, qhams7A.1 carrying GBSSI mutant allele, was identified through QTL mapping using F2 population of the high amylose mutant line, 'TAC 75'. This high amylose mutant line has >2-fold higher amylose content than wild variety 'C 306'. In this study, we characterized this novel mutant allele, GBSSI.L539P. In vitro starch synthase activity of GBSSI.L539P showed improved activity than the wild type (GBSSI-wt). When expressed in yeast glycogen synthase mutants (Δgsy1gsy2), GBSSI-wt and GBSSI.L539P partially complemented the glycogen synthase (gsy1gsy2) activity in yeast. Structural analysis by circular dichroism (CD) and homology modelling showed no significant structural distortion in the mutant enzyme. Molecular docking studies suggested that the residue Leu539 is distant from the catalytic active site (ADP binding pocket) and had no detectable conformational changes in active site. Both wild and mutant enzymes were assayed for starch binding in vitro, and demonstrating higher affinity of the GBSSI.L539P mutant for starch than the wild type. The present study indicated that distant residue (L539P) influenced GBSSI activity by affecting its starch-binding ability. Therefore, it may be a potential molecular target for enhanced amylose content in grain.
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Affiliation(s)
- Vinita Sharma
- National Agri-Food Biotechnology Institute (NABI), SAS Nagar, Sector-81, Mohali, 140306, Punjab, India.,Department of Biological Sciences, Indian Institute of Science Education & Research (IISER) Mohali, SAS Nagar, Sector-81, Mohali, 140306, Punjab, India
| | - Kousar Jahan
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Sector-67, Mohali, Punjab, 160062, India
| | - Prashant Kumar
- National Agri-Food Biotechnology Institute (NABI), SAS Nagar, Sector-81, Mohali, 140306, Punjab, India
| | - Anuradhika Puri
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Vishnu K Sharma
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Sector-67, Mohali, Punjab, 160062, India
| | - Ankita Mishra
- National Agri-Food Biotechnology Institute (NABI), SAS Nagar, Sector-81, Mohali, 140306, Punjab, India
| | - P V Bharatam
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Sector-67, Mohali, Punjab, 160062, India
| | - Deepak Sharma
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Vikas Rishi
- National Agri-Food Biotechnology Institute (NABI), SAS Nagar, Sector-81, Mohali, 140306, Punjab, India
| | - Joy Roy
- National Agri-Food Biotechnology Institute (NABI), SAS Nagar, Sector-81, Mohali, 140306, Punjab, India.
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6
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Luo Z, Wang Z. The role of starch granule-associated proteins in enhancing the strength of indica rice starch gels. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.107826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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7
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Li Y, Karim H, Wang B, Guzmán C, Harwood W, Xu Q, Zhang Y, Tang H, Jiang Y, Qi P, Deng M, Ma J, Lan J, Wang J, Chen G, Lan X, Wei Y, Zheng Y, Jiang Q. Regulation of Amylose Content by Single Mutations at an Active Site in the Wx-B1 Gene in a Tetraploid Wheat Mutant. Int J Mol Sci 2022; 23:ijms23158432. [PMID: 35955567 PMCID: PMC9368913 DOI: 10.3390/ijms23158432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/21/2022] [Accepted: 07/26/2022] [Indexed: 01/15/2023] Open
Abstract
The granule-bound starch synthase I (GBSSI) encoded by the waxy gene is responsible for amylose synthesis in the endosperm of wheat grains. In the present study, a novel Wx-B1 null mutant line, M3-415, was identified from an ethyl methanesulfonate-mutagenized population of Chinese tetraploid wheat landrace Jianyangailanmai (LM47). The gene sequence indicated that the mutated Wx-B1 encoded a complete protein; this protein was incompatible with the protein profile obtained using sodium dodecyl sulfate–polyacrylamide gel electrophoresis, which showed the lack of Wx-B1 protein in the mutant line. The prediction of the protein structure showed an amino acid substitution (G470D) at the edge of the ADPG binding pocket, which might affect the binding of Wx-B1 to starch granules. Site-directed mutagenesis was further performed to artificially change the amino acid at the sequence position 469 from alanine (A) to threonine (T) (A469T) downstream of the mutated site in M3-415. Our results indicated that a single amino acid mutation in Wx-B1 reduces its activity by impairing its starch-binding capacity. The present study is the first to report the novel mechanism underlying Wx-1 deletion in wheat; moreover, it provided new insights into the inactivation of the waxy gene and revealed that fine regulation of wheat amylose content is possible by modifying the GBSSI activity.
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Affiliation(s)
- Yulong Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (H.K.); (B.W.); (Q.X.); (Y.Z.); (H.T.); (Y.J.); (P.Q.); (M.D.); (J.M.); (J.L.); (J.W.); (G.C.); (X.L.); (Y.W.); (Y.Z.)
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Hassan Karim
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (H.K.); (B.W.); (Q.X.); (Y.Z.); (H.T.); (Y.J.); (P.Q.); (M.D.); (J.M.); (J.L.); (J.W.); (G.C.); (X.L.); (Y.W.); (Y.Z.)
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Bang Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (H.K.); (B.W.); (Q.X.); (Y.Z.); (H.T.); (Y.J.); (P.Q.); (M.D.); (J.M.); (J.L.); (J.W.); (G.C.); (X.L.); (Y.W.); (Y.Z.)
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Carlos Guzmán
- Departamento de Genética, Escuela Técnica Superior de Ingeniería Agronómica y de Montes, Edificio Gregor Mendel, Campus de Rabanales, Universidad de Córdoba, 14071 Cordoba, Spain;
| | - Wendy Harwood
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK;
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (H.K.); (B.W.); (Q.X.); (Y.Z.); (H.T.); (Y.J.); (P.Q.); (M.D.); (J.M.); (J.L.); (J.W.); (G.C.); (X.L.); (Y.W.); (Y.Z.)
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Yazhou Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (H.K.); (B.W.); (Q.X.); (Y.Z.); (H.T.); (Y.J.); (P.Q.); (M.D.); (J.M.); (J.L.); (J.W.); (G.C.); (X.L.); (Y.W.); (Y.Z.)
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (H.K.); (B.W.); (Q.X.); (Y.Z.); (H.T.); (Y.J.); (P.Q.); (M.D.); (J.M.); (J.L.); (J.W.); (G.C.); (X.L.); (Y.W.); (Y.Z.)
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (H.K.); (B.W.); (Q.X.); (Y.Z.); (H.T.); (Y.J.); (P.Q.); (M.D.); (J.M.); (J.L.); (J.W.); (G.C.); (X.L.); (Y.W.); (Y.Z.)
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (H.K.); (B.W.); (Q.X.); (Y.Z.); (H.T.); (Y.J.); (P.Q.); (M.D.); (J.M.); (J.L.); (J.W.); (G.C.); (X.L.); (Y.W.); (Y.Z.)
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (H.K.); (B.W.); (Q.X.); (Y.Z.); (H.T.); (Y.J.); (P.Q.); (M.D.); (J.M.); (J.L.); (J.W.); (G.C.); (X.L.); (Y.W.); (Y.Z.)
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (H.K.); (B.W.); (Q.X.); (Y.Z.); (H.T.); (Y.J.); (P.Q.); (M.D.); (J.M.); (J.L.); (J.W.); (G.C.); (X.L.); (Y.W.); (Y.Z.)
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Jingyu Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (H.K.); (B.W.); (Q.X.); (Y.Z.); (H.T.); (Y.J.); (P.Q.); (M.D.); (J.M.); (J.L.); (J.W.); (G.C.); (X.L.); (Y.W.); (Y.Z.)
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (H.K.); (B.W.); (Q.X.); (Y.Z.); (H.T.); (Y.J.); (P.Q.); (M.D.); (J.M.); (J.L.); (J.W.); (G.C.); (X.L.); (Y.W.); (Y.Z.)
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (H.K.); (B.W.); (Q.X.); (Y.Z.); (H.T.); (Y.J.); (P.Q.); (M.D.); (J.M.); (J.L.); (J.W.); (G.C.); (X.L.); (Y.W.); (Y.Z.)
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (H.K.); (B.W.); (Q.X.); (Y.Z.); (H.T.); (Y.J.); (P.Q.); (M.D.); (J.M.); (J.L.); (J.W.); (G.C.); (X.L.); (Y.W.); (Y.Z.)
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (H.K.); (B.W.); (Q.X.); (Y.Z.); (H.T.); (Y.J.); (P.Q.); (M.D.); (J.M.); (J.L.); (J.W.); (G.C.); (X.L.); (Y.W.); (Y.Z.)
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (H.K.); (B.W.); (Q.X.); (Y.Z.); (H.T.); (Y.J.); (P.Q.); (M.D.); (J.M.); (J.L.); (J.W.); (G.C.); (X.L.); (Y.W.); (Y.Z.)
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (H.K.); (B.W.); (Q.X.); (Y.Z.); (H.T.); (Y.J.); (P.Q.); (M.D.); (J.M.); (J.L.); (J.W.); (G.C.); (X.L.); (Y.W.); (Y.Z.)
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: ; Tel.: +86-28-8629-0958; Fax: +86-28-8265-0350
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8
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Gao H, Niu J, Zhao W, Zhang D, Li S, Xu Y, Liu Y. The Effect and Regulation Mechanism of Powdery Mildew on Wheat Grain Carbon Metabolism. STARCH-STARKE 2022. [DOI: 10.1002/star.202100239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hongyun Gao
- School of Life Sciences Zhengzhou Normal University Zhengzhou 450044 China
| | - Jishan Niu
- National Centre of Engineering and Technological Research for Wheat Henan Agricultural University Zhengzhou 450046 China
| | - Wanyong Zhao
- College of Food and Bioengineering Zhengzhou University of Light Industry Zhengzhou 450000 China
| | - Dale Zhang
- School of Life Sciences Henan University Kaifeng 475004 China
| | - Suoping Li
- School of Life Sciences Henan University Kaifeng 475004 China
| | - Yanhua Xu
- School of Life Sciences Zhengzhou Normal University Zhengzhou 450044 China
| | - Yumiao Liu
- School of Life Sciences Zhengzhou Normal University Zhengzhou 450044 China
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9
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Zhang S, Li C, Gilbert RG, Malde AK. Understanding the Binding of Starch Fragments to Granule-Bound Starch Synthase. Biomacromolecules 2021; 22:4730-4737. [PMID: 34669391 DOI: 10.1021/acs.biomac.1c01012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Granule-bound starch synthase (GBSS) plays a major role, that of chain elongation, in the biosynthesis of amylose, a starch component with mostly (1 → 4)-α connected long chains of glucose with a few (1 → 6)-α branch points. Chain-length distributions (CLDs) of amylose affect functional properties, which can be controlled by changing appropriate residues on granule-bound starch synthase (GBSS). Knowing the binding of GBSS and amylose at a molecular level can help better determine the key amino acids on GBSS that affect CLDs of amylose for subsequent use in molecular engineering. Atomistic molecular dynamics simulations with explicit solvent and docking approaches were used in this study to build a model of the binding between rice GBSS and amylose. Amylose fragments containing 3-12 linearly linked glucose units were built to represent the starch fragments. The stability of the complexes, interactions between GBSS and sugars, and difference in structure/conformation of bound and free starch fragments were analyzed. The study found that starch/amylose fragments with 5 or 6 glucose units were suitable for modeling starch binding to GBSS. The removal of an interdomain disulfide on GBSS was found to affect both GBSS and starch stability. Key residues that could affect the binding ability were also indicated. This model can help rationalize the design of mutants and suggest ways to make single-point mutations, which could be used to develop plants producing starches with improved functional properties.
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Affiliation(s)
- Shaobo Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Joint International Research Laboratory of Agriculture and Agri-Product Safety, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu, Yangzhou University, Yangzhou, Jiangsu 225009, China.,Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Cheng Li
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, Jiangsu, China.,School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Robert G Gilbert
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Joint International Research Laboratory of Agriculture and Agri-Product Safety, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu, Yangzhou University, Yangzhou, Jiangsu 225009, China.,Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Alpeshkumar K Malde
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
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10
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Adegoke TV, Wang Y, Chen L, Wang H, Liu W, Liu X, Cheng YC, Tong X, Ying J, Zhang J. Posttranslational Modification of Waxy to Genetically Improve Starch Quality in Rice Grain. Int J Mol Sci 2021; 22:4845. [PMID: 34063649 PMCID: PMC8124582 DOI: 10.3390/ijms22094845] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 01/07/2023] Open
Abstract
The waxy (Wx) gene, encoding the granule-bound starch synthase (GBSS), is responsible for amylose biosynthesis and plays a crucial role in defining eating and cooking quality. The waxy locus controls both the non-waxy and waxy rice phenotypes. Rice starch can be altered into various forms by either reducing or increasing the amylose content, depending on consumer preference and region. Low-amylose rice is preferred by consumers because of its softness and sticky appearance. A better way of improving crops other than downregulation and overexpression of a gene or genes may be achieved through the posttranslational modification of sites or regulatory enzymes that regulate them because of their significance. The impact of posttranslational GBSSI modifications on extra-long unit chains (ELCs) remains largely unknown. Numerous studies have been reported on different crops, such as wheat, maize, and barley, but the rice starch granule proteome remains largely unknown. There is a need to improve the yield of low-amylose rice by employing posttranslational modification of Wx, since the market demand is increasing every day in order to meet the market demand for low-amylose rice in the regional area that prefers low-amylose rice, particularly in China. In this review, we have conducted an in-depth review of waxy rice, starch properties, starch biosynthesis, and posttranslational modification of waxy protein to genetically improve starch quality in rice grains.
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Affiliation(s)
- Tosin Victor Adegoke
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yifeng Wang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
| | - Lijuan Chen
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
| | - Huimei Wang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
| | - Wanning Liu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
| | - Xingyong Liu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
| | - Yi-Chen Cheng
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
| | - Xiaohong Tong
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
| | - Jiezheng Ying
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
| | - Jian Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
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11
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Identification and molecular characterization of mutant line deficiency in three waxy proteins of common wheat (Triticum aestivum L.). Sci Rep 2021; 11:3510. [PMID: 33568721 PMCID: PMC7876011 DOI: 10.1038/s41598-021-82865-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 07/03/2020] [Indexed: 11/30/2022] Open
Abstract
Starch is the main component of wheat (Triticum aestivum L.) grain and a key factor in determining wheat processing quality. The Wx gene is the gene responsible for amylose synthesis. An ethyl methanesulfonate (EMS) mutagenized population was generated using common wheat cv. Gao 8901, a popular and high-quality cultivar in China. A waxy mutant (Wx-null) was isolated by screening M3 seeds with KI-I2 staining of endosperm starch. No obvious waxy proteins in Wx-null line were detected using Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). DNA sequencing revealed three SNPs and a 3-bp InDel in the first exon, and a 16-bp InDel at the junction region of the first Wx-A1 intron from the Wx-null line. Six SNPs were identified in Wx-B1 gene of Wx-null line compared to the wild-type Gao 8901, including four missense mutations. One nonsense mutation was found at position 857 in the fourth exon, which resulted in a premature stop codon. Expression levels of Wx genes were dramatically reduced in the Wx-null line. There were no detectable differences in granule size and morphology between Wx-null and wild-type, but the Wx-null line contained more B-type starch granules. The amylose content of the Wx-null line (0.22%) was remarkably lower compared to the wild-type Gao 8901 (24.71%). Total starch is also lower in the Wx-null line. The Wx-null line may provide a potential waxy material with high agronomic performance in wheat breeding programs.
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12
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Xu Y, Lin Q, Li X, Wang F, Chen Z, Wang J, Li W, Fan F, Tao Y, Jiang Y, Wei X, Zhang R, Zhu Q, Bu Q, Yang J, Gao C. Fine-tuning the amylose content of rice by precise base editing of the Wx gene. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:11-13. [PMID: 32558105 PMCID: PMC7769246 DOI: 10.1111/pbi.13433] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/04/2020] [Accepted: 05/12/2020] [Indexed: 05/11/2023]
Affiliation(s)
- Yang Xu
- Institute of Food CropsJiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice ImprovementNanjingChina
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhouChina
| | - Qiupeng Lin
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Genome EditingInstitute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijingChina
- College of Advanced Agricultural SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Xiufeng Li
- Northeast Institute of Geography and AgroecologyKey Laboratory of Soybean Molecular Design BreedingChinese Academy of SciencesHarbinChina
| | - Fangquan Wang
- Institute of Food CropsJiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice ImprovementNanjingChina
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhouChina
| | - Zhihui Chen
- Institute of Food CropsJiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice ImprovementNanjingChina
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhouChina
| | - Jun Wang
- Institute of Food CropsJiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice ImprovementNanjingChina
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhouChina
| | - Wenqi Li
- Institute of Food CropsJiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice ImprovementNanjingChina
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhouChina
| | - Fangjun Fan
- Institute of Food CropsJiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice ImprovementNanjingChina
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhouChina
| | - Yajun Tao
- Institute of Food CropsJiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice ImprovementNanjingChina
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhouChina
| | - Yanjie Jiang
- Institute of Food CropsJiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice ImprovementNanjingChina
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhouChina
| | - Xiaodong Wei
- Institute of Food CropsJiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice ImprovementNanjingChina
| | - Rui Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Genome EditingInstitute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | | | - Qingyun Bu
- Northeast Institute of Geography and AgroecologyKey Laboratory of Soybean Molecular Design BreedingChinese Academy of SciencesHarbinChina
| | - Jie Yang
- Institute of Food CropsJiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice ImprovementNanjingChina
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhouChina
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Genome EditingInstitute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijingChina
- College of Advanced Agricultural SciencesUniversity of Chinese Academy of SciencesBeijingChina
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13
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Seung D. Amylose in starch: towards an understanding of biosynthesis, structure and function. THE NEW PHYTOLOGIST 2020; 228:1490-1504. [PMID: 32767769 DOI: 10.1111/nph.16858] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/13/2020] [Indexed: 05/20/2023]
Abstract
Starch granules are composed of two distinct glucose polymers - amylose and amylopectin. Amylose constitutes 5-35% of most natural starches and has a major influence over starch properties in foods. Its synthesis and storage occurs within the semicrystalline amylopectin matrix of starch granules, this poses a great challenge for biochemical and structural analyses. However, the last two decades have seen vast progress in understanding amylose synthesis, including new insights into the action of GRANULE BOUND STARCH SYNTHASE (GBSS), the major glucosyltransferase that synthesises amylose, and the discovery of PROTEIN TARGETING TO STARCH1 (PTST1) that targets GBSS to starch granules. Advances in analytical techniques have resolved the fine structure of amylose, raising new questions on how structure is determined during biosynthesis. Furthermore, the discovery of wild plants that do not produce amylose revives a long-standing question of why starch granules contain amylose, rather than amylopectin alone. Overall, these findings contribute towards a full understanding of amylose biosynthesis, structure and function that will be essential for future approaches to improve starch quality in crops.
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Affiliation(s)
- David Seung
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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14
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Kawamoto Y, Toda H, Inoue H, Kobayashi K, Yamaoka N, Araki T, Yaeno T. Fast and Inexpensive Phenotyping and Genotyping Methods for Evaluation of Barley Mutant Population. PLANTS 2020; 9:plants9091153. [PMID: 32899989 PMCID: PMC7569886 DOI: 10.3390/plants9091153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/19/2020] [Accepted: 09/04/2020] [Indexed: 01/13/2023]
Abstract
To further develop barley breeding and genetics, more information on gene functions based on the analysis of the mutants of each gene is needed. However, the mutant resources are not as well developed as the model plants, such as Arabidopsis and rice. Although genome editing techniques have been able to generate mutants, it is not yet an effective method as it can only be used to transform a limited number of cultivars. Here, we developed a mutant population using ‘Mannenboshi’, which produces good quality grains with high yields but is susceptible to disease, to establish a Targeting Induced Local Lesions IN Genomes (TILLING) system that can isolate mutants in a high-throughput manner. To evaluate the availability of the prepared 8043 M3 lines, we investigated the frequency of mutant occurrence using a rapid, visually detectable waxy phenotype as an indicator. Four mutants were isolated and single nucleotide polymorphisms (SNPs) were identified in the Waxy gene as novel alleles. It was confirmed that the mutations could be easily detected using the mismatch endonuclease CELI, revealing that a sufficient number of mutants could be rapidly isolated from our TILLING population.
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15
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Yu J, Li Y, Qin Z, Guo S, Li Y, Miao Y, Song C, Chen S, Dai S. Plant Chloroplast Stress Response: Insights from Thiol Redox Proteomics. Antioxid Redox Signal 2020; 33:35-57. [PMID: 31989831 DOI: 10.1089/ars.2019.7823] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Significance: Plant chloroplasts generate reactive oxygen species (ROS) during photosynthesis, especially under stresses. The sulfhydryl groups of protein cysteine residues are susceptible to redox modifications, which regulate protein structure and function, and thus different signaling and metabolic processes. The ROS-governed protein thiol redox switches play important roles in chloroplasts. Recent Advances: Various high-throughput thiol redox proteomic approaches have been developed, and they have enabled the improved understanding of redox regulatory mechanisms in chloroplasts. For example, the thioredoxin-modulated antioxidant enzymes help to maintain cellular ROS homeostasis. The light- and dark-dependent redox regulation of photosynthetic electron transport, the Calvin/Benson cycle, and starch biosynthesis ensures metabolic coordination and efficient energy utilization. In addition, redox cascades link the light with the dynamic changes of metabolites in nitrate and sulfur assimilation, shikimate pathway, and biosynthesis of fatty acid hormone as well as purine, pyrimidine, and thiamine. Importantly, redox regulation of tetrapyrrole and chlorophyll biosynthesis is critical to balance the photodynamic tetrapyrrole intermediates and prevent oxidative damage. Moreover, redox regulation of diverse elongation factors, chaperones, and kinases plays an important role in the modulation of gene expression, protein conformation, and posttranslational modification that contribute to photosystem II (PSII) repair, state transition, and signaling in chloroplasts. Critical Issues: This review focuses on recent advances in plant thiol redox proteomics and redox protein networks toward understanding plant chloroplast signaling, metabolism, and stress responses. Future Directions: Using redox proteomics integrated with biochemical and molecular genetic approaches, detailed studies of cysteine residues, their redox states, cross talk with other modifications, and the functional implications will yield a holistic understanding of chloroplast stress responses.
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Affiliation(s)
- Juanjuan Yu
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China.,Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China.,College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Ying Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
| | - Zhi Qin
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Siyi Guo
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, China
| | - Yongfang Li
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Yuchen Miao
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, China
| | - Chunpeng Song
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, China
| | - Sixue Chen
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
| | - Shaojun Dai
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China.,Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
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16
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Zhang C, Zhu J, Chen S, Fan X, Li Q, Lu Y, Wang M, Yu H, Yi C, Tang S, Gu M, Liu Q. Wx lv, the Ancestral Allele of Rice Waxy Gene. MOLECULAR PLANT 2019; 12:1157-1166. [PMID: 31181338 DOI: 10.1016/j.molp.2019.05.011] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/30/2019] [Accepted: 05/28/2019] [Indexed: 05/07/2023]
Abstract
In rice grains, the Waxy (Wx) gene is responsible for the synthesis of amylose, the most important determinant for eating and cooking quality. The effects of several Wx alleles on amylose content and the taste of cooked rice have been elucidated. However, the relationship between artificial selection and the evolution of various Wx alleles as well as their distribution remain unclear. Here we report the identification of an ancestral allele, Wxlv, which dramatically affects the mouthfeel of rice grains by modulating the size of amylose molecules. We demonstrated that Wxlv originated directly from wild rice, and the three major Wx alleles in cultivated rice (Wxb, Wxa, and Wxin) differentiated after the substitution of one base pair at the functional sites. These data indicate that the Wxlv allele played an important role in artificial selection and domestication. The findings also shed light on the evolution of various Wx alleles, which have greatly contributed to improving the eating and cooking quality of rice.
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Affiliation(s)
- Changquan Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Jihui Zhu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Shengjie Chen
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Xiaolei Fan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Qianfeng Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Yan Lu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Min Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Hengxiu Yu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Chuandeng Yi
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Shuzhu Tang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Minghong Gu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Qiaoquan Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China.
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17
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Pérez L, Soto E, Farré G, Juanos J, Villorbina G, Bassie L, Medina V, Serrato AJ, Sahrawy M, Rojas JA, Romagosa I, Muñoz P, Zhu C, Christou P. CRISPR/Cas9 mutations in the rice Waxy/GBSSI gene induce allele-specific and zygosity-dependent feedback effects on endosperm starch biosynthesis. PLANT CELL REPORTS 2019; 38:417-433. [PMID: 30715580 DOI: 10.1007/s00299-019-02388-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 01/25/2019] [Indexed: 05/07/2023]
Abstract
Induced mutations in the waxy locus in rice endosperm did not abolish GBSS activity completely. Compensatory mechanisms in endosperm and leaves caused a major reprogramming of the starch biosynthetic machinery. The mutation of genes in the starch biosynthesis pathway has a profound effect on starch quality and quantity and is an important target for plant breeders. Mutations in endosperm starch biosynthetic genes may impact starch metabolism in vegetative tissues such as leaves in unexpected ways due to the complex feedback mechanisms regulating the pathway. Surprisingly this aspect of global starch metabolism has received little attention. We used CRISPR/Cas9 to introduce mutations affecting the Waxy (Wx) locus encoding granule-bound starch synthase I (GBSSI) in rice endosperm. Our specific objective was to develop a mechanistic understanding of how the endogenous starch biosynthetic machinery might be affected at the transcriptional level following the targeted knock out of GBSSI in the endosperm. We found that the mutations reduced but did not abolish GBSS activity in seeds due to partial compensation caused by the upregulation of GBSSII. The GBSS activity in the mutants was 61-71% of wild-type levels, similarly to two irradiation mutants, but the amylose content declined to 8-12% in heterozygous seeds and to as low as 5% in homozygous seeds, accompanied by abnormal cellular organization in the aleurone layer and amorphous starch grain structures. Expression of many other starch biosynthetic genes was modulated in seeds and leaves. This modulation of gene expression resulted in changes in AGPase and sucrose synthase activity that explained the corresponding levels of starch and soluble sugars.
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Affiliation(s)
- Lucía Pérez
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure 191, 25198, Lleida, Spain
| | - Erika Soto
- Department of Chemistry, University of Lleida-Agrotecnio Center, Lleida, Spain
| | - Gemma Farré
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure 191, 25198, Lleida, Spain
| | - Julia Juanos
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure 191, 25198, Lleida, Spain
| | - Gemma Villorbina
- Department of Chemistry, University of Lleida-Agrotecnio Center, Lleida, Spain
| | - Ludovic Bassie
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure 191, 25198, Lleida, Spain
| | - Vicente Medina
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure 191, 25198, Lleida, Spain
| | - Antonio Jesús Serrato
- Department of Biochemistry, Molecular and Cellular Plant Biology, Experimental Station of the Zaidín, Superior Council of Scientific Investigations (CSIC), Granada, Spain
| | - Mariam Sahrawy
- Department of Biochemistry, Molecular and Cellular Plant Biology, Experimental Station of the Zaidín, Superior Council of Scientific Investigations (CSIC), Granada, Spain
| | - Jose Antonio Rojas
- Department of Biochemistry, Molecular and Cellular Plant Biology, Experimental Station of the Zaidín, Superior Council of Scientific Investigations (CSIC), Granada, Spain
| | - Ignacio Romagosa
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure 191, 25198, Lleida, Spain
| | - Pilar Muñoz
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure 191, 25198, Lleida, Spain
| | - Changfu Zhu
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure 191, 25198, Lleida, Spain
| | - Paul Christou
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure 191, 25198, Lleida, Spain.
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain.
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18
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Crofts N, Itoh A, Abe M, Miura S, Oitome NF, Bao J, Fujita N. Three Major Nucleotide Polymorphisms in the Waxy Gene Correlated with the Amounts of Extra-long Chains of Amylopectin in Rice Cultivars with S or L-type Amylopectin. J Appl Glycosci (1999) 2019; 66:37-46. [PMID: 34354518 PMCID: PMC8056923 DOI: 10.5458/jag.jag.jag-2018_005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 12/03/2018] [Indexed: 11/19/2022] Open
Abstract
Extra-long chains (ELC) of amylopectin in rice endosperm are synthesized by granule-bound starch synthase I encoded by the Waxy (Wx) gene, which primarily synthesizes amylose. Previous studies showed that single nucleotide polymorphisms (SNP) in intron 1 and exon 6 of the Wx gene influences ELC amount. However, whether these SNPs are conserved among rice cultivars and if any other SNPs are present in the Wx gene remained unknown. Here, we sequenced the Wx gene from 17 rice cultivars with S or L-type amylopectin, including those with known ELC content and those originating in China with unique starch properties, as well as typical japonica and indica cultivars. In addition to the two SNPs described above, an additional SNP correlating with ELC content was found in exon 10. Low ELC cultivars (<3.0 %) had thymine at the splicing donor site of intron 1, Tyr224 in exon 6, and Pro415 in exon 10. Cultivars with moderate ELC content (4.1–6.9 %) had guanine at the splicing donor site of intron 1, Ser224 in exon 6, and Pro415 in exon 10. Cultivars with high ELC content (7.7–13.9 %) had guanine at the splicing donor site of intron 1, Tyr224 in exon 6, and Ser415 in exon 10. The chain length distribution pattern of amylopectin was correlated with the amounts of SSIIa found in starch granules and gelatinization temperature, but not with ELC content. The combinations of SNPs in the Wx gene found in this study may provide useful information for screening specific cultivars with different ELC content.
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Affiliation(s)
- Naoko Crofts
- 1 Laboratory of Plant Physiology, Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University
| | - Ayaka Itoh
- 1 Laboratory of Plant Physiology, Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University
| | - Misato Abe
- 1 Laboratory of Plant Physiology, Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University
| | - Satoko Miura
- 1 Laboratory of Plant Physiology, Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University
| | - Naoko F Oitome
- 1 Laboratory of Plant Physiology, Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University
| | - Jinsong Bao
- 2 Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University
| | - Naoko Fujita
- 1 Laboratory of Plant Physiology, Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University
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19
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Qu J, Xu S, Zhang Z, Chen G, Zhong Y, Liu L, Zhang R, Xue J, Guo D. Evolutionary, structural and expression analysis of core genes involved in starch synthesis. Sci Rep 2018; 8:12736. [PMID: 30143668 PMCID: PMC6109180 DOI: 10.1038/s41598-018-30411-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 07/30/2018] [Indexed: 01/29/2023] Open
Abstract
Starch is the main storage carbohydrate in plants and an important natural resource for food, feed and industrial raw materials. However, the details regarding the pathway for starch biosynthesis and the diversity of biosynthetic enzymes involved in this process are poorly understood. This study uses a comprehensive phylogenetic analysis of 74 sequenced plant genomes to revisit the evolutionary history of the genes encoding ADP-glucose pyrophosphorylase (AGPase), starch synthase (SS), starch branching enzyme (SBE) and starch de-branching enzyme (DBE). Additionally, the protein structures and expression patterns of these four core genes in starch biosynthesis were studied to determine their functional differences. The results showed that AGPase, SS, SBE and DBE have undergone complicated evolutionary processes in plants and that gene/genome duplications are responsible for the observed differences in isoform numbers. A structure analysis of these proteins suggested that the deletion/mutation of amino acids in some active sites resulted in not only structural variation but also sub-functionalization or neo-functionalization. Expression profiling indicated that AGPase-, SS-, SBE- and DBE-encoding genes exhibit spatio-temporally divergent expression patterns related to the composition of functional complexes in starch biosynthesis. This study provides a comprehensive atlas of the starch biosynthetic pathway, and these data should support future studies aimed at increasing understanding of starch biosynthesis and the functional evolutionary divergence of AGPase, SS, SBE, and DBE in plants.
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Affiliation(s)
- Jianzhou Qu
- The key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100, Shaanxi, China
| | - Shutu Xu
- The key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100, Shaanxi, China
| | - Zhengquan Zhang
- The key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100, Shaanxi, China
| | - Guangzhou Chen
- The key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100, Shaanxi, China
| | - Yuyue Zhong
- The key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100, Shaanxi, China
| | - Linsan Liu
- The key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100, Shaanxi, China
| | - Renhe Zhang
- The key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100, Shaanxi, China
| | - Jiquan Xue
- The key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100, Shaanxi, China.
| | - Dongwei Guo
- The key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100, Shaanxi, China.
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20
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Okeke UG, Akdemir D, Rabbi I, Kulakow P, Jannink JL. Regional Heritability Mapping Provides Insights into Dry Matter Content in African White and Yellow Cassava Populations. THE PLANT GENOME 2018; 11:10.3835/plantgenome2017.06.0050. [PMID: 29505634 PMCID: PMC7822058 DOI: 10.3835/plantgenome2017.06.0050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 06/20/2017] [Indexed: 05/21/2023]
Abstract
The HarvestPlus program for cassava ( Crantz) fortifies cassava with β-carotene by breeding for carotene-rich tubers (yellow cassava). However, a negative correlation between yellowness and dry matter (DM) content has been identified. We investigated the genetic control of DM in white and yellow cassava. We used regional heritability mapping (RHM) to associate DM with genomic segments in both subpopulations. Significant segments were subjected to candidate gene analysis and candidates were validated with prediction accuracies. The RHM procedure was validated via a simulation approach and revealed significant hits for white cassava on chromosomes 1, 4, 5, 10, 17, and 18, whereas hits for the yellow were on chromosome 1. Candidate gene analysis revealed genes in the carbohydrate biosynthesis pathway including plant serine-threonine protein kinases (SnRKs), UDP (uridine diphosphate)-glycosyltransferases, UDP-sugar transporters, invertases, pectinases, and regulons. Validation using 1252 unique identifiers from the SnRK gene family genome-wide recovered 50% of the predictive accuracy of whole-genome single nucleotide polymorphisms for DM, whereas validation using 53 likely genes (extracted from the literature) from significant segments recovered 32%. Genes including an acid invertase, a neutral or alkaline invertase, and a glucose-6-phosphate isomerase were validated on the basis of an a priori list for the cassava starch pathway, and also a fructose-biphosphate aldolase from the Calvin cycle pathway. The power of the RHM procedure was estimated as 47% when the causal quantitative trait loci generated 10% of the phenotypic variance (sample size = 451). Cassava DM genetics are complex and RHM may be useful for complex traits.
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Affiliation(s)
- Uche Godfrey Okeke
- Section of Plant Breeding and Genetics, School of Integrative
Plant Sci., College of Agriculture and Life Sci., Cornell Univ., 14853, Ithaca,
NY
| | - Deniz Akdemir
- Section of Plant Breeding and Genetics, School of Integrative
Plant Sci., College of Agriculture and Life Sci., Cornell Univ., 14853, Ithaca,
NY
- current address, Statgen Consulting, Ithaca, NY 14850
| | | | | | - Jean-Luc Jannink
- Section of Plant Breeding and Genetics, School of Integrative
Plant Sci., College of Agriculture and Life Sci., Cornell Univ., 14853, Ithaca,
NY
- USDAARS, Robert W. Holley Centre for Agriculture and Health, Tower
Road, Ithaca, NY 14853
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21
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Wambugu P, Ndjiondjop M, Furtado A, Henry R. Sequencing of bulks of segregants allows dissection of genetic control of amylose content in rice. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:100-110. [PMID: 28499072 PMCID: PMC5785344 DOI: 10.1111/pbi.12752] [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: 03/09/2017] [Revised: 04/25/2017] [Accepted: 05/01/2017] [Indexed: 05/03/2023]
Abstract
Amylose content (AC) is a key quality trait in rice. A cross between Oryza glaberrima (African rice) and Oryza sativa (Asian rice) segregating for AC was analysed by sequencing bulks of individuals with high and low AC. SNP associated with the granule bound starch synthase (GBSS1) locus on chromosome 6 were polymorphic between the bulks. In particular, a G/A SNP that would result in an Asp to Asn mutation was identified. This amino acid substitution may be responsible for differences in GBSS activity as it is adjacent to a disulphide linkage conserved in all grass GBSS proteins. Other polymorphisms in genomic regions closely surrounding this variation may be the result of linkage drag. In addition to the variant in the starch biosynthesis gene, SNP on chromosomes 1 and 11 linked to AC was also identified. SNP was found in the genes encoding the NAC and CCAAT-HAP5 transcription factors that have previously been linked to starch biosynthesis. This study has demonstrated that the approach of sequencing bulks was able to identify genes on different chromosomes associated with this complex trait.
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Affiliation(s)
- Peterson Wambugu
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbaneQldAustralia
- Present address:
Kenya Agricultural and Livestock Research Organization (KALRO)Genetic Resources Research InstituteNairobiKenya
| | | | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbaneQldAustralia
| | - Robert Henry
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbaneQldAustralia
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22
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Nielsen MM, Ruzanski C, Krucewicz K, Striebeck A, Cenci U, Ball SG, Palcic MM, Cuesta-Seijo JA. Crystal Structures of the Catalytic Domain of Arabidopsis thaliana Starch Synthase IV, of Granule Bound Starch Synthase From CLg1 and of Granule Bound Starch Synthase I of Cyanophora paradoxa Illustrate Substrate Recognition in Starch Synthases. FRONTIERS IN PLANT SCIENCE 2018; 9:1138. [PMID: 30123236 PMCID: PMC6086201 DOI: 10.3389/fpls.2018.01138] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 07/13/2018] [Indexed: 05/20/2023]
Abstract
Starch synthases (SSs) are responsible for depositing the majority of glucoses in starch. Structural knowledge on these enzymes that is available from the crystal structures of rice granule bound starch synthase (GBSS) and barley SSI provides incomplete information on substrate binding and active site architecture. Here we report the crystal structures of the catalytic domains of SSIV from Arabidopsis thaliana, of GBSS from the cyanobacterium CLg1 and GBSSI from the glaucophyte Cyanophora paradoxa, with all three bound to ADP and the inhibitor acarbose. The SSIV structure illustrates in detail the modes of binding for both donor and acceptor in a plant SS. CLg1GBSS contains, in the same crystal structure, examples of molecules with and without bound acceptor, which illustrates the conformational changes induced upon acceptor binding that presumably precede catalytic activity. With structures available from several isoforms of plant and non-plant SSs, as well as the closely related bacterial glycogen synthases, we analyze, at the structural level, the common elements that define a SS, the elements that are necessary for substrate binding and singularities of the GBSS family that could underlie its processivity. While the phylogeny of the SSIII/IV/V has been recently discussed, we now further report the detailed evolutionary history of the GBSS/SSI/SSII type of SSs enlightening the origin of the GBSS enzymes used in our structural analysis.
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Affiliation(s)
| | - Christian Ruzanski
- Carlsberg Research Laboratory, Copenhagen, Denmark
- † Present address: Christian Ruzanski, Novo Nordisk A/S, Måløv, Denmark Monica M. Palcic, Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | | | | | - Ugo Cenci
- UMR8576 CNRS-USTL, Unité de Glycobiologie Structurale et Fonctionnelle, Université des Sciences et Technologies de Lille, Villeneuve-d’Ascq, France
| | - Steven G. Ball
- UMR8576 CNRS-USTL, Unité de Glycobiologie Structurale et Fonctionnelle, Université des Sciences et Technologies de Lille, Villeneuve-d’Ascq, France
| | - Monica M. Palcic
- Carlsberg Research Laboratory, Copenhagen, Denmark
- † Present address: Christian Ruzanski, Novo Nordisk A/S, Måløv, Denmark Monica M. Palcic, Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Jose A. Cuesta-Seijo
- Carlsberg Research Laboratory, Copenhagen, Denmark
- *Correspondence: Jose A. Cuesta-Seijo,
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23
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Identification and biochemical characterization of WbwB, a novel UDP-Gal: Neu5Ac-R α1,4-galactosyltransferase from the intestinal pathogen Escherichia coli serotype O104. Glycoconj J 2017; 35:65-76. [PMID: 29063990 DOI: 10.1007/s10719-017-9799-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/11/2017] [Accepted: 09/13/2017] [Indexed: 02/08/2023]
Abstract
The intestinal pathogen Escherichia coli serotype O104:H4 (ECO104) can cause bloody diarrhea and haemolytic uremic syndrome. The ECO104 O antigen has the unique repeating unit structure [4Galα1-4Neu5,7,9Ac3α2-3Galβ1-3GalNAcβ1-], which includes the mammalian sialyl-T antigen as an internal structure. Previously, we identified WbwC from ECO104 as the β3Gal-transferase that synthesizes the T antigen, and showed that α3-sialyl-transferase WbwA transfers sialic acid to the T antigen. Here we identify the wbwB gene product as a unique α1,4-Gal-transferase WbwB that transfers Gal from UDP-Gal to the terminal sialic acid residue of Neu5Acα2-3Galβ1-3GalNAcα-diphosphate-lipid acceptor. NMR analysis of the WbwB enzyme reaction product indicated that Galα1-4Neu5Acα2-3Galβ1-3GalNAcα-diphosphate-lipid was synthesized. WbwB from ECO104 has a unique acceptor specificity for terminal sialic acid as well as the diphosphate group in the acceptor. The characterization studies showed that WbwB does not require divalent metal ion as a cofactor. Mutagenesis identified Lys243 within an RKR motif and both Glu315 and Glu323 of the fourth EX7E motif as essential for the activity. WbwB is the final glycosyltransferase in the biosynthesis pathway of the ECO104 antigen repeating unit. This work contributes to knowledge of the biosynthesis of bacterial virulence factors.
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24
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Nazarian-Firouzabadi F, Visser RGF. Potato starch synthases: Functions and relationships. Biochem Biophys Rep 2017; 10:7-16. [PMID: 29114568 PMCID: PMC5637242 DOI: 10.1016/j.bbrep.2017.02.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 02/01/2017] [Accepted: 02/03/2017] [Indexed: 01/28/2023] Open
Abstract
Starch, a very compact form of glucose units, is the most abundant form of storage polyglucan in nature. The starch synthesis pathway is among the central biochemical pathways, however, our understanding of this important pathway regarding genetic elements controlling this pathway, is still insufficient. Starch biosynthesis requires the action of several enzymes. Soluble starch synthases (SSs) are a group of key players in starch biosynthesis which have proven their impact on different aspects of the starch biosynthesis and functionalities. These enzymes have been studied in different plant species and organs in detail, however, there seem to be key differences among species regarding their contributions to the starch synthesis. In this review, we consider an update on various SSs with an emphasis on potato SSs as a model for storage organs. The genetics and regulatory mechanisms of potato starch synthases will be highlighted. Different aspects of various isoforms of SSs are also discussed.
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Affiliation(s)
- Farhad Nazarian-Firouzabadi
- Agronomy and Plant Breeding Department, Faculty of Agriculture, Lorestan University, P.O.Box 465, Khorramabad, Iran
| | - Richard G F Visser
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
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25
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Hebelstrup KH, Nielsen MM, Carciofi M, Andrzejczak O, Shaik SS, Blennow A, Palcic MM. Waxy and non-waxy barley cultivars exhibit differences in the targeting and catalytic activity of GBSS1a. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:931-941. [PMID: 28199682 PMCID: PMC5441850 DOI: 10.1093/jxb/erw503] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Amylose synthesis is strictly associated with activity of granule-bound starch synthase (GBSS) enzymes. Among several crops there are cultivars containing starch types with either little or no amylose known as near-waxy or waxy. This (near) amylose-free phenotype is associated with a single locus (waxy) which has been mapped to GBSS-type genes in different crops. Most waxy varieties are a result of either low or no expression of a GBSS gene. However, there are some waxy cultivars where the GBSS enzymes are expressed normally. For these types, single nucleotide polymorphisms have been hypothesized to represent amino-acid substitutions leading to loss of catalytic activity. We here confirm that the HvGBSSIa enzyme from one such waxy barley variety, CDC_Alamo, has a 90% reduction in catalytic activity. We also engineered plants with expression of transgenic C-terminal green fluorescent protein-tagged HvGBSSIa of both the non-waxy type and of the CDC_Alamo type to monitor their subcellular localization patterns in grain endosperm. HvGBSSIa from non-waxy cultivars was found to localize in discrete concentric spheres strictly within starch granules. In contrast, HvGBSSIa from waxy CDC_Alamo showed deficient starch targeting mostly into unknown subcellular bodies of 0.5-3 µm in size, indicating that the waxy phenotype of CDC_Alamo is associated with deficient targeting of HvGBSSIa into starch granules.
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Affiliation(s)
- Kim H Hebelstrup
- Department of Molecular Biology and Genetics, Section of Crop Genetics and Biotechnology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
| | | | - Massimiliano Carciofi
- Department of Molecular Biology and Genetics, Section of Crop Genetics and Biotechnology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-1799 København V, Denmark
| | - Olga Andrzejczak
- Department of Molecular Biology and Genetics, Section of Crop Genetics and Biotechnology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
| | - Shahnoor Sultana Shaik
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Andreas Blennow
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Monica M Palcic
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-1799 København V, Denmark
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26
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Larson ME, Falconer DJ, Myers AM, Barb AW. Direct Characterization of the Maize Starch Synthase IIa Product Shows Maltodextrin Elongation Occurs at the Non-reducing End. J Biol Chem 2016; 291:24951-24960. [PMID: 27733678 DOI: 10.1074/jbc.m116.754705] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/06/2016] [Indexed: 11/06/2022] Open
Abstract
A comprehensive description of starch biosynthesis and granule assembly remains undefined despite the central nature of starch as an energy storage molecule in plants and as a fundamental calorie source for many animals. Multiple theories regarding the starch synthase (SS)-catalyzed assembly of (α1-4)-linked d-glucose molecules into maltodextrins generally agree that elongation occurs at the non-reducing terminus based on the degradation of radiolabeled maltodextrins, although recent reports challenge this hypothesis. Surprisingly, a direct analysis of the SS catalytic product has not been reported, to our knowledge. We expressed and characterized recombinant Zea mays SSIIa and prepared pure ADP-[13CU]glucose in a one-pot enzymatic synthesis to address the polarity of maltodextrin chain elongation. We synthesized maltoheptaose (degree of polymerization 7) using ADP-[13CU]glucose, maltohexaose (degree of polymerization 6), and SSIIa. Product analysis by ESI-MS revealed that the [13CU]glucose unit was added to the non-reducing end of the growing chain, and SSIIa demonstrated a >7,850-fold preference for addition to the non-reducing end versus the reducing end. Independent analysis of [13CU]glucose added to maltohexaose by SSIIa using solution NMR spectroscopy confirmed the polarity of maltodextrin chain elongation.
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Affiliation(s)
- Mark E Larson
- From the Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011
| | - Daniel J Falconer
- From the Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011
| | - Alan M Myers
- From the Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011
| | - Adam W Barb
- From the Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011
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27
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Abstract
Starch-rich crops form the basis of our nutrition, but plants have still to yield all their secrets as to how they make this vital substance. Great progress has been made by studying both crop and model systems, and we approach the point of knowing the enzymatic machinery responsible for creating the massive, insoluble starch granules found in plant tissues. Here, we summarize our current understanding of these biosynthetic enzymes, highlighting recent progress in elucidating their specific functions. Yet, in many ways we have only scratched the surface: much uncertainty remains about how these components function together and are controlled. We flag-up recent observations suggesting a significant degree of flexibility during the synthesis of starch and that previously unsuspected non-enzymatic proteins may have a role. We conclude that starch research is not yet a mature subject and that novel experimental and theoretical approaches will be important to advance the field.
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Affiliation(s)
- Barbara Pfister
- Department of Biology, ETH Zurich, 8092, Zurich, Switzerland
| | - Samuel C Zeeman
- Department of Biology, ETH Zurich, 8092, Zurich, Switzerland.
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28
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Raynaud S, Ragel P, Rojas T, Mérida Á. The N-terminal Part of Arabidopsis thaliana Starch Synthase 4 Determines the Localization and Activity of the Enzyme. J Biol Chem 2016; 291:10759-71. [PMID: 26969163 DOI: 10.1074/jbc.m115.698332] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Indexed: 01/22/2023] Open
Abstract
Starch synthase 4 (SS4) plays a specific role in starch synthesis because it controls the number of starch granules synthesized in the chloroplast and is involved in the initiation of the starch granule. We showed previously that SS4 interacts with fibrillins 1 and is associated with plastoglobules, suborganelle compartments physically attached to the thylakoid membrane in chloroplasts. Both SS4 localization and its interaction with fibrillins 1 were mediated by the N-terminal part of SS4. Here we show that the coiled-coil region within the N-terminal portion of SS4 is involved in both processes. Elimination of this region prevents SS4 from binding to fibrillins 1 and alters SS4 localization in the chloroplast. We also show that SS4 forms dimers, which depends on a region located between the coiled-coil region and the glycosyltransferase domain of SS4. This region is highly conserved between all SS4 enzymes sequenced to date. We show that the dimerization seems to be necessary for the activity of the enzyme. Both dimerization and the functionality of the coiled-coil region are conserved among SS4 proteins from phylogenetically distant species, such as Arabidopsis and Brachypodium This finding suggests that the mechanism of action of SS4 is conserved among different plant species.
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Affiliation(s)
- Sandy Raynaud
- From the Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas, University of Sevilla, Avenida Américo Vespucio 49, 41092 Sevilla, Spain
| | - Paula Ragel
- From the Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas, University of Sevilla, Avenida Américo Vespucio 49, 41092 Sevilla, Spain
| | - Tomás Rojas
- From the Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas, University of Sevilla, Avenida Américo Vespucio 49, 41092 Sevilla, Spain
| | - Ángel Mérida
- From the Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas, University of Sevilla, Avenida Américo Vespucio 49, 41092 Sevilla, Spain
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29
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Chen Y, Bao J. Underlying Mechanisms of Zymographic Diversity in Starch Synthase I and Pullulanase in Rice-Developing Endosperm. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:2030-7. [PMID: 26860852 DOI: 10.1021/acs.jafc.5b06030] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Amylopectin is synthesized by the coordinated actions of many (iso)enzymes, including ADP-glucose pyrophosphorylase (AGPase), starch synthases (SSs), branching enzymes (BEs), and debranching enzymes (DBEs). Here, two polymorphic forms of starch synthase I (SSI) and pullulanase (PUL) in rice-developing seeds, designated as SSI-1/SSI-2 and PUL-1/PUL-2, were discovered for the first time by zymographic analysis. The SSI and PUL polymorphisms were strongly associated with the SSI microsatellite marker (p = 3.6 × 10(-37)) and PUL insertion/deletion (InDel) markers (p < 3.6 × 10(-51)). Western blotting and mass spectrometric analysis confirmed that the polymorphic bands were truly the SSI and PUL enzymes. Only one non-synonymous variation in SSI DNA sequence (the SNP A/G) causing the change of the amino acid K438 to E438 was observed, which coincided well with the polymorphic forms of SSI. Nine non-synonymous variations were found between PUL-1 and PUL-2. Two non-synonymous variations of PUL (F316L and D770E) were identified by mass spectrometric analysis, but all of the variations did not change the structure of PUL. The co-immunoprecipitation results revealed the differences in protein-protein interaction patterns, i.e., strong or weaker signals of SSI-BEI and SSI-BEIIb, between the two forms of SSI. The results will enhance our understanding of SSI and PUL properties and provide helpful information to understand their functions in starch biosynthesis in rice endosperm.
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Affiliation(s)
- Yaling Chen
- Institute of Nuclear Agricultural Science, College of Agriculture and Biotechnology, Zhejiang University , Huajiachi Campus, Hangzhou, Zhejiang 310029, People's Republic of China
| | - Jinsong Bao
- Institute of Nuclear Agricultural Science, College of Agriculture and Biotechnology, Zhejiang University , Huajiachi Campus, Hangzhou, Zhejiang 310029, People's Republic of China
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Cuesta-Seijo JA, Nielsen MM, Ruzanski C, Krucewicz K, Beeren SR, Rydhal MG, Yoshimura Y, Striebeck A, Motawia MS, Willats WGT, Palcic MM. In vitro Biochemical Characterization of All Barley Endosperm Starch Synthases. FRONTIERS IN PLANT SCIENCE 2016; 6:1265. [PMID: 26858729 PMCID: PMC4730117 DOI: 10.3389/fpls.2015.01265] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 12/27/2015] [Indexed: 05/18/2023]
Abstract
Starch is the main storage polysaccharide in cereals and the major source of calories in the human diet. It is synthesized by a panel of enzymes including five classes of starch synthases (SSs). While the overall starch synthase (SS) reaction is known, the functional differences between the five SS classes are poorly understood. Much of our knowledge comes from analyzing mutant plants with altered SS activities, but the resulting data are often difficult to interpret as a result of pleitropic effects, competition between enzymes, overlaps in enzyme activity and disruption of multi-enzyme complexes. Here we provide a detailed biochemical study of the activity of all five classes of SSs in barley endosperm. Each enzyme was produced recombinantly in E. coli and the properties and modes of action in vitro were studied in isolation from other SSs and other substrate modifying activities. Our results define the mode of action of each SS class in unprecedented detail; we analyze their substrate selection, temperature dependence and stability, substrate affinity and temporal abundance during barley development. Our results are at variance with some generally accepted ideas about starch biosynthesis and might lead to the reinterpretation of results obtained in planta. In particular, they indicate that granule bound SS is capable of processive action even in the absence of a starch matrix, that SSI has no elongation limit, and that SSIV, believed to be critical for the initiation of starch granules, has maltoligosaccharides and not polysaccharides as its preferred substrates.
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Affiliation(s)
| | | | | | | | | | - Maja G. Rydhal
- Department of Plant and Environmental Sciences, University of CopenhagenFrederiksberg, Copenhagen, Denmark
| | | | | | - Mohammed S. Motawia
- Department of Plant and Environmental Sciences, University of CopenhagenFrederiksberg, Copenhagen, Denmark
| | - William G. T. Willats
- Department of Plant and Environmental Sciences, University of CopenhagenFrederiksberg, Copenhagen, Denmark
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Skryhan K, Cuesta-Seijo JA, Nielsen MM, Marri L, Mellor SB, Glaring MA, Jensen PE, Palcic MM, Blennow A. The Role of Cysteine Residues in Redox Regulation and Protein Stability of Arabidopsis thaliana Starch Synthase 1. PLoS One 2015; 10:e0136997. [PMID: 26367870 PMCID: PMC4569185 DOI: 10.1371/journal.pone.0136997] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 08/11/2015] [Indexed: 11/23/2022] Open
Abstract
Starch biosynthesis in Arabidopsis thaliana is strictly regulated. In leaf extracts, starch synthase 1 (AtSS1) responds to the redox potential within a physiologically relevant range. This study presents data testing two main hypotheses: 1) that specific thiol-disulfide exchange in AtSS1 influences its catalytic function 2) that each conserved Cys residue has an impact on AtSS1 catalysis. Recombinant AtSS1 versions carrying combinations of cysteine-to-serine substitutions were generated and characterized in vitro. The results demonstrate that AtSS1 is activated and deactivated by the physiological redox transmitters thioredoxin f1 (Trxf1), thioredoxin m4 (Trxm4) and the bifunctional NADPH-dependent thioredoxin reductase C (NTRC). AtSS1 displayed an activity change within the physiologically relevant redox range, with a midpoint potential equal to -306 mV, suggesting that AtSS1 is in the reduced and active form during the day with active photosynthesis. Cys164 and Cys545 were the key cysteine residues involved in regulatory disulfide formation upon oxidation. A C164S_C545S double mutant had considerably decreased redox sensitivity as compared to wild type AtSS1 (30% vs 77%). Michaelis-Menten kinetics and molecular modeling suggest that both cysteines play important roles in enzyme catalysis, namely, Cys545 is involved in ADP-glucose binding and Cys164 is involved in acceptor binding. All the other single mutants had essentially complete redox sensitivity (98–99%). In addition of being part of a redox directed activity “light switch”, reactivation tests and low heterologous expression levels indicate that specific cysteine residues might play additional roles. Specifically, Cys265 in combination with Cys164 can be involved in proper protein folding or/and stabilization of translated protein prior to its transport into the plastid. Cys442 can play an important role in enzyme stability upon oxidation. The physiological and phylogenetic relevance of these findings is discussed.
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Affiliation(s)
- Katsiaryna Skryhan
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | | | - Morten M. Nielsen
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, 1799 Copenhagen V, Denmark
| | - Lucia Marri
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, 1799 Copenhagen V, Denmark
| | - Silas B. Mellor
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Mikkel A. Glaring
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Poul E. Jensen
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Monica M. Palcic
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, 1799 Copenhagen V, Denmark
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Andreas Blennow
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
- * E-mail:
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Seung D, Soyk S, Coiro M, Maier BA, Eicke S, Zeeman SC. PROTEIN TARGETING TO STARCH is required for localising GRANULE-BOUND STARCH SYNTHASE to starch granules and for normal amylose synthesis in Arabidopsis. PLoS Biol 2015; 13:e1002080. [PMID: 25710501 PMCID: PMC4339375 DOI: 10.1371/journal.pbio.1002080] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 01/14/2015] [Indexed: 02/03/2023] Open
Abstract
The domestication of starch crops underpinned the development of human civilisation, yet we still do not fully understand how plants make starch. Starch is composed of glucose polymers that are branched (amylopectin) or linear (amylose). The amount of amylose strongly influences the physico-chemical behaviour of starchy foods during cooking and of starch mixtures in non-food manufacturing processes. The GRANULE-BOUND STARCH SYNTHASE (GBSS) is the glucosyltransferase specifically responsible for elongating amylose polymers and was the only protein known to be required for its biosynthesis. Here, we demonstrate that PROTEIN TARGETING TO STARCH (PTST) is also specifically required for amylose synthesis in Arabidopsis. PTST is a plastidial protein possessing an N-terminal coiled coil domain and a C-terminal carbohydrate binding module (CBM). We discovered that Arabidopsis ptst mutants synthesise amylose-free starch and are phenotypically similar to mutants lacking GBSS. Analysis of granule-bound proteins showed a dramatic reduction of GBSS protein in ptst mutant starch granules. Pull-down assays with recombinant proteins in vitro, as well as immunoprecipitation assays in planta, revealed that GBSS physically interacts with PTST via a coiled coil. Furthermore, we show that the CBM domain of PTST, which mediates its interaction with starch granules, is also required for correct GBSS localisation. Fluorescently tagged Arabidopsis GBSS, expressed either in tobacco or Arabidopsis leaves, required the presence of Arabidopsis PTST to localise to starch granules. Mutation of the CBM of PTST caused GBSS to remain in the plastid stroma. PTST fulfils a previously unknown function in targeting GBSS to starch. This sheds new light on the importance of targeting biosynthetic enzymes to sub-cellular sites where their action is required. Importantly, PTST represents a promising new gene target for the biotechnological modification of starch composition, as it is exclusively involved in amylose synthesis. The biosynthesis of starch in plant chloroplasts depends on a novel protein that targets starch synthase to the growing starch granules; this represents a potential target for the biotechnological modification of starch. Read the Synopsis. Starch plays a vital role in our everyday lives. It is not only a major dietary carbohydrate, but is also used to manufacture household products such as pharmaceuticals, paper, and textiles. Plants produce starch as a means of storing energy; it is composed of two glucose polymers—amylopectin and amylose. While amylose is present in a smaller quantity than amylopectin, it has a major impact on starch processing. Being able to control the amount of amylose is therefore a goal for biotechnology. Amylose is made by the enzyme GRANULE BOUND STARCH SYNTHASE (GBSS), which was for decades believed to be the only protein required for amylose production. We now report here that a second protein, PROTEIN TARGETING TO STARCH (PTST), is involved in the process. Mutants lacking the PTST protein in the model plant Arabidopsis thaliana fail to make any amylose in starch. This is because the GBSS protein, which normally binds to starch, cannot bind in the absence of PTST. This discovery sheds new light on a previously unknown protein targeting process by which enzymes are delivered to the starch. Furthermore, our discovery highlights PTST an ideal target gene for biotechnology.
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Affiliation(s)
- David Seung
- Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Sebastian Soyk
- Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Mario Coiro
- Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | | | - Simona Eicke
- Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Samuel C. Zeeman
- Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
- * E-mail:
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Liu H, Yu G, Wei B, Wang Y, Zhang J, Hu Y, Liu Y, Yu G, Zhang H, Huang Y. Identification and Phylogenetic Analysis of a Novel Starch Synthase in Maize. FRONTIERS IN PLANT SCIENCE 2015; 6:1013. [PMID: 26635839 PMCID: PMC4653816 DOI: 10.3389/fpls.2015.01013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 11/02/2015] [Indexed: 05/02/2023]
Abstract
Starch is an important reserve of carbon and energy in plants, providing the majority of calories in the human diet and animal feed. Its synthesis is orchestrated by several key enzymes, and the amount and structure of starch, affecting crop yield and quality, are determined mainly by starch synthase (SS) activity. To date, five SS isoforms, including SSI-IV and Granule Bound Starch Synthase (GBSS) have been identified and their physiological functions have been well characterized. Here, we report the identification of a new SS isoform in maize, designated SSV. By searching sequenced genomes, SSV has been found in all green plants with conserved sequences and gene structures. Our phylogenetic analysis based on 780 base pairs has suggested that SSIV and SSV resulted from a gene duplication event, which may have occurred before the algae formation. An expression profile analysis of SSV in maize has indicated that ZmSSV is mainly transcribed in the kernel and ear leaf during the grain filling stage, which is partly similar to other SS isoforms. Therefore, it is likely that SSV may play an important role in starch biosynthesis. Subsequent analysis of SSV function may facilitate understanding the mechanism of starch granules formation, number and structure.
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Affiliation(s)
- Hanmei Liu
- College of Life Science, Sichuan Agricultural UniversityYa’an, China
| | - Guiling Yu
- College of Life Science, Sichuan Agricultural UniversityYa’an, China
| | - Bin Wei
- Maize Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Yongbin Wang
- Maize Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Junjie Zhang
- College of Life Science, Sichuan Agricultural UniversityYa’an, China
| | - Yufeng Hu
- College of Agronomy, Sichuan Agricultural UniversityChengdu, China
| | - Yinghong Liu
- Maize Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Guowu Yu
- College of Agronomy, Sichuan Agricultural UniversityChengdu, China
| | - Huaiyu Zhang
- College of Life Science, Sichuan Agricultural UniversityYa’an, China
| | - Yubi Huang
- Maize Research Institute, Sichuan Agricultural UniversityChengdu, China
- College of Agronomy, Sichuan Agricultural UniversityChengdu, China
- *Correspondence: Yubi Huang,
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Liang DM, Liu JH, Wu H, Wang BB, Zhu HJ, Qiao JJ. Glycosyltransferases: mechanisms and applications in natural product development. Chem Soc Rev 2015; 44:8350-74. [DOI: 10.1039/c5cs00600g] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Glycosylation reactions mainly catalyzed by glycosyltransferases (Gts) occur almost everywhere in the biosphere, and always play crucial roles in vital processes.
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Affiliation(s)
- Dong-Mei Liang
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Jia-Heng Liu
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Hao Wu
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Bin-Bin Wang
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Hong-Ji Zhu
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Jian-Jun Qiao
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
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Liu D, Wang W, Cai X. Modulation of amylose content by structure-based modification of OsGBSS1 activity in rice (Oryza sativa L.). PLANT BIOTECHNOLOGY JOURNAL 2014; 12:1297-307. [PMID: 25052102 DOI: 10.1111/pbi.12228] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 05/21/2014] [Accepted: 06/12/2014] [Indexed: 05/23/2023]
Abstract
The rice Waxy (Wx) gene encodes granule-bound starch synthase 1 (EC 2.4.1.242), OsGBSS1, which is responsible for amylose synthesis in rice seed endosperm. In this study, we determined the functional contribution of eight amino acids on the activity of OsGBSS1 by introducing site-directed mutated Wx gene constructs into the wx mutant glutinous rice. The eight amino acid residues are suspected to play roles in OsGBSS1 structure maintenance or function based on homologous enzyme sequence alignment and homology modelling. Both OsGBSS1 activity and amylose content were analysed in homozygous transgenic lines carrying the mutated OsGBSS1 (Wx) genes. Our results indicate that mutations at diverse sites in OsGBSS1 reduces its activity by affecting its starch-binding capacity, its ADP-glucose-binding capability or its protein stability. Our results shed new light on the structural basis of OsGBSS1 activity and the mechanisms of OsGBSS1 activity on amylose synthesis in vivo. This study also demonstrates that it is feasible to finely modulate amylose content in rice grains by modifying the OsGBSS1 activity.
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Affiliation(s)
- Derui Liu
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; Graduate School of the Chinese Academy of Sciences, Beijing, China
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Sparla F, Falini G, Botticella E, Pirone C, Talamè V, Bovina R, Salvi S, Tuberosa R, Sestili F, Trost P. New starch phenotypes produced by TILLING in barley. PLoS One 2014; 9:e107779. [PMID: 25271438 PMCID: PMC4182681 DOI: 10.1371/journal.pone.0107779] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 08/15/2014] [Indexed: 01/08/2023] Open
Abstract
Barley grain starch is formed by amylose and amylopectin in a 1∶3 ratio, and is packed into granules of different dimensions. The distribution of granule dimension is bimodal, with a majority of small spherical B-granules and a smaller amount of large discoidal A-granules containing the majority of the starch. Starch granules are semi-crystalline structures with characteristic X-ray diffraction patterns. Distinct features of starch granules are controlled by different enzymes and are relevant for nutritional value or industrial applications. Here, the Targeting-Induced Local Lesions IN Genomes (TILLING) approach was applied on the barley TILLMore TILLING population to identify 29 new alleles in five genes related to starch metabolism known to be expressed in the endosperm during grain filling: BMY1 (Beta-amylase 1), GBSSI (Granule Bound Starch Synthase I), LDA1 (Limit Dextrinase 1), SSI (Starch Synthase I), SSIIa (Starch Synthase IIa). Reserve starch of nine M3 mutant lines carrying missense or nonsense mutations was analysed for granule size, crystallinity and amylose/amylopectin content. Seven mutant lines presented starches with different features in respect to the wild-type: (i) a mutant line with a missense mutation in GBSSI showed a 4-fold reduced amylose/amylopectin ratio; (ii) a missense mutations in SSI resulted in 2-fold increase in A:B granule ratio; (iii) a nonsense mutation in SSIIa was associated with shrunken seeds with a 2-fold increased amylose/amylopectin ratio and different type of crystal packing in the granule; (iv) the remaining four missense mutations suggested a role of LDA1 in granule initiation, and of SSIIa in determining the size of A-granules. We demonstrate the feasibility of the TILLING approach to identify new alleles in genes related to starch metabolism in barley. Based on their novel physicochemical properties, some of the identified new mutations may have nutritional and/or industrial applications.
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Affiliation(s)
- Francesca Sparla
- Department of Pharmacy and Biotechnology FABIT, University of Bologna, Bologna, Italy
| | - Giuseppe Falini
- Department of Chemistry “G. Ciamician”, University of Bologna, Bologna, Italy
| | - Ermelinda Botticella
- Department of Agriculture, Forestry, Nature & Energy, University of Tuscia, Viterbo, Italy
| | - Claudia Pirone
- Department of Pharmacy and Biotechnology FABIT, University of Bologna, Bologna, Italy
| | - Valentina Talamè
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Riccardo Bovina
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Silvio Salvi
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Roberto Tuberosa
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Francesco Sestili
- Department of Agriculture, Forestry, Nature & Energy, University of Tuscia, Viterbo, Italy
| | - Paolo Trost
- Department of Pharmacy and Biotechnology FABIT, University of Bologna, Bologna, Italy
- * E-mail:
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Busi MV, Gomez-Casati DF, Martín M, Barchiesi J, Grisolía MJ, Hedín N, Carrillo JB. Starch Metabolism in Green Plants. POLYSACCHARIDES 2014. [DOI: 10.1007/978-3-319-03751-6_78-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Wang X, Feng B, Xu Z, Sestili F, Zhao G, Xiang C, Lafiandra D, Wang T. Identification and characterization of granule bound starch synthase I (GBSSI) gene of tartary buckwheat (Fagopyrum tataricum Gaertn.). Gene 2013; 534:229-35. [PMID: 24211386 DOI: 10.1016/j.gene.2013.10.053] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 10/08/2013] [Accepted: 10/24/2013] [Indexed: 10/26/2022]
Abstract
Tartary buckwheat (Fagopyrum tataricum Gaertn.) is increasingly considered as an important functional food material because of its rich nutraceutical compounds. Reserve starch is the major component of tartary buckwheat seed. However, the gene sequences and the molecular mechanism of tartary buckwheat starch synthesis are unknown so far. In this study, the complete genomic sequence and full-size cDNA coding tartary buckwheat granule-bound starch synthase I (FtGBSSI), which is responsible for amylose synthesis, were isolated and analyzed. The genomic sequence of the FtGBSSI contained 3947 nucleotides and was composed of 14 exons and 13 introns. The cDNA coding sequence of FtGBSSI shared 63.3%-75.1% identities with those of dicots and 56.6%-57.5% identities with monocots (Poaceae). In deduced amino acid sequence of FtGBSSI, eight motifs conserved among plant starch synthases were identified. A cleavage at the site IVC↓G of FtGBSSI protein produces the chloroplast transit sequence of 78 amino acids and the mature protein of 527 amino acids. The FtGBSSI mature protein showed an identity of 73.4%-77.8% with dicot plants, and 67.6%-70.4% with monocot plants (Poaceae). The mature protein was composed of 20 α-helixes and 16 β-strands, and folds into two main domains, N- and C-terminal domains. The critical residues which are involved in ADP and sugar binding were predicted. These results will be useful to modulate starch composition of buckwheat kernels with the aim to produce novel improved varieties in future breeding programs.
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Affiliation(s)
- Xun Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Bo Feng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Zhibin Xu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Francesco Sestili
- Department of Agriculture, Forestry, Nature & Energy, University of Tuscia, Viterbo, Italy
| | - Guojun Zhao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Chao Xiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Domenico Lafiandra
- Department of Agriculture, Forestry, Nature & Energy, University of Tuscia, Viterbo, Italy
| | - Tao Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
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Liu DR, Huang WX, Cai XL. Oligomerization of rice granule-bound starch synthase 1 modulates its activity regulation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 210:141-50. [PMID: 23849121 DOI: 10.1016/j.plantsci.2013.05.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 05/16/2013] [Accepted: 05/17/2013] [Indexed: 05/23/2023]
Abstract
Granule-bound starch synthase 1 (GBSS1) is responsible for amylose synthesis in cereals, and this enzyme is regulated at the transcriptional and post-transcriptional levels. In this study, we show that GBSS1 from Oryza sativa L. (OsGBSS1) can form oligomers in rice endosperm, and oligomerized OsGBSS1 exhibits much higher specific enzymatic activity than the monomer. A monomer-oligomer transition equilibrium for OsGBSS1 occurs in the endosperm during development. Redox potential is a key factor affecting the oligomer percentage as well as the enzymatic activity of OsGBSS1. Adenosine diphosphate glucose, the direct donor of glucose, also impacts OsGBSS1 oligomerization in a concentration-dependent manner. OsGBSS1 oligomerization is influenced by phosphorylation status, which was strongly enhanced by Mitogen-activated protein kinase (MAPK) and ATP treatment and was sharply weakened by protein phosphatase (PPase) treatment. The activity of OsGBSS1 affects the ratio of amylose to amylopectin and therefore the eating quality of rice. Understanding the regulation of OsGBSS1 activity may lead to the improvement of rice eating quality.
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Affiliation(s)
- De-Rui Liu
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.
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Blennow A, Jensen SL, Shaik SS, Skryhan K, Carciofi M, Holm PB, Hebelstrup KH, Tanackovic V. Future Cereal Starch Bioengineering: Cereal Ancestors Encounter Gene Technology and Designer Enzymes. Cereal Chem 2013. [DOI: 10.1094/cchem-01-13-0010-fi] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Andreas Blennow
- Department of Plant and Environmental Sciences, University of Copenhagen, Denmark
- Corresponding author. Phone: +45 35333304. Fax: +45 35333333. E-mail:
| | - Susanne L. Jensen
- Department of Plant and Environmental Sciences, University of Copenhagen, Denmark
| | - Shahnoor S. Shaik
- Department of Plant and Environmental Sciences, University of Copenhagen, Denmark
| | - Katsiaryna Skryhan
- Department of Plant and Environmental Sciences, University of Copenhagen, Denmark
| | - Massimiliano Carciofi
- Department of Molecular Biology and Genetics, Section of Crop Genetics and Biotechnology, Aarhus University, Denmark
| | - Preben B. Holm
- Department of Molecular Biology and Genetics, Section of Crop Genetics and Biotechnology, Aarhus University, Denmark
| | - Kim H. Hebelstrup
- Department of Molecular Biology and Genetics, Section of Crop Genetics and Biotechnology, Aarhus University, Denmark
| | - Vanja Tanackovic
- Department of Plant and Environmental Sciences, University of Copenhagen, Denmark
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Krishnan HB, Chen MH. Identification of an abundant 56 kDa protein implicated in food allergy as granule-bound starch synthase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:5404-5409. [PMID: 23675783 DOI: 10.1021/jf4014372] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Rice, the staple food of south and east Asian counties, is considered to be hypoallergenic. However, several clinical studies have documented rice-induced allergy in sensitive patients. Rice proteins with molecular weights of 14-16, 26, 33, and 56 kDa have been identified as allergens. Recently, it was documented that the 56 kDa rice allergen was responsible for rice-induced anaphylaxis. The 14-16 kDa allergens have been identified as α-amylase inhibitors; the 26 kDa protein has been identified as α-globulin; and the 33 kDa protein has been identified as glyoxalase I. However, the identity of the 56 kDa rice allergen has not yet been determined. In this study, we demonstrate that serum from patients allergic to maize shows IgE binding to a 56 kDa protein that was present in both maize and rice but not in the oil seeds soybean and peanut. The 56 kDa IgE-binding protein was abundant in the rice endosperm. We have purified this protein from rice endosperm and demonstrated its reactivity to IgE antibodies from the serum of maize-allergic patients. The purified protein was subjected to matrix-assisted laser desorption ionization-time of flight-tandem mass spectrometry analysis, resulting in identification of this rice allergen as granule-bound starch synthase, a product of the Waxy gene. Immunoblot analysis using protein extracts from a waxy mutant of rice revealed the absence of the 56 kDa IgE-binding protein. Our results demonstrate that the 56 kDa rice allergen is granule-bound starch synthase and raise the possibility of using waxy mutants of rice as a potential source of the hypoallergenic diet for patients sensitized to the 56 kDa rice allergen.
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Affiliation(s)
- Hari B Krishnan
- Plant Genetics Research Unit, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), University of Missouri , Columbia, Missouri 65211, United States
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Cuesta-Seijo JA, Nielsen MM, Marri L, Tanaka H, Beeren SR, Palcic MM. Structure of starch synthase I from barley: insight into regulatory mechanisms of starch synthase activity. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1013-25. [DOI: 10.1107/s090744491300440x] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 02/14/2013] [Indexed: 11/11/2022]
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Kawagoe Y. The Characteristic Polyhedral, Sharp-edged Shape of Compound-type Starch Granules in Rice Endosperm is Achieved via the Septum-like Structure of the Amyloplast. J Appl Glycosci (1999) 2013. [DOI: 10.5458/jag.jag.jag-2012_013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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