1
|
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: 0] [Impact Index Per Article: 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.
Collapse
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.
| |
Collapse
|
2
|
Tiozon RJN, Fettke J, Sreenivasulu N, Fernie AR. More than the main structural genes: Regulation of resistant starch formation in rice endosperm and its potential application. JOURNAL OF PLANT PHYSIOLOGY 2023; 285:153980. [PMID: 37086697 DOI: 10.1016/j.jplph.2023.153980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/07/2023] [Accepted: 04/03/2023] [Indexed: 05/03/2023]
Abstract
In the past decade, research on resistant starch has evoked interest due to the prevention and inhibition of chronic human diseases, such as diabetes, cancer, and obesity. Increasing the amylose content (AC) and resistant starch (RS) has been pivotal in improving the nutritional benefit of rice. However, the exact mechanism of RS formation is complex due to interconnected genetic factors regulating amylose-amylopectin variation. In this review, we discussed the regulatory factors influencing the RS formation centered on the transcription, post-transcriptional, and post-translational processes. Furthermore, we described the developments in RS and AC levels in rice compared with other high RS cereals. Briefly, we enumerated potential applications of high RS mutants in health, medical, and other industries. We contest that the information captured herein can be deployed for marker-assisted breeding and precision breeding techniques through genome editing to improve rice varieties with enhanced RS content.
Collapse
Affiliation(s)
- Rhowell Jr N Tiozon
- Consumer Driven Grain Quality and Nutrition Unit, Rice Breeding and Innovation Platform, International Rice Research Institute, Los Baños, 4030, Philippines; Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Joerg Fettke
- Biopolymer Analytics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Nese Sreenivasulu
- Consumer Driven Grain Quality and Nutrition Unit, Rice Breeding and Innovation Platform, International Rice Research Institute, Los Baños, 4030, Philippines
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
| |
Collapse
|
3
|
Guo X, Meng X, Li Y, Qu C, Liu Y, Cao M, Yao X, Meng F, Wu J, Peng H, Peng D, Xing S, Jiang W. Comparative proteomics reveals biochemical changes in Salvia miltiorrhiza Bunge during sweating processing. JOURNAL OF ETHNOPHARMACOLOGY 2022; 293:115329. [PMID: 35490901 DOI: 10.1016/j.jep.2022.115329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 03/31/2022] [Accepted: 04/25/2022] [Indexed: 06/14/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Salvia miltiorrhiza Bunge is a bulk medicinal material used in traditional Chinese medicine, that can cure cardiovascular diseases, neurasthenia, and other conditions. Sweating is a frequently used method of processing S. miltiorrhiza for medical applications. We previously demonstrated changes to the metabolic profile of linoleic acid, glyoxylate, and dicarboxylate after Sweating. However, this alteration has not been explained at the molecular level. MATERIALS AND METHODS Fresh roots of Salvia miltiorrhiza Bunge were treated by the Sweating processing, and then the tandem mass tag technique was used to compare the proteome difference between Sweating S. miltiorrhiza and non-Sweating S. miltiorrhiza. RESULTS We identified a total of 850 differentially expressed proteins after Sweating treatment in S. miltiorrhiza, including 529 upregulated proteins and 321 downregulated proteins. GO enrichment analysis indicated that these differentially expressed proteins are involved in external encapsulating structure, cell wall, oxidoreductase activity, ligase activity, and others. Further analysis showed that CYP450, the pathogenesis-related protein Bet v 1 family, and the peroxidase domain were the major protein domains. KEGG enrichment identified 18 pathways, of which phenylpropanoid biosynthesis is the most important one related to the metabolite profile and is the principal chemical component of S. miltiorrhiza. CONCLUSION This study addressed potential molecular mechanisms in S. miltiorrhiza after Sweating, and the findings provide reasons for the changes in biochemical properties and metabolites changes which might cause pharmacological variation at the proteome level.
Collapse
Affiliation(s)
- Xiaohu Guo
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Xiaoxi Meng
- Department of Horticultural Science, University of Minnesota, MN, 55108, USA
| | - Yan Li
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region, College of Life Sciences and Environment, Hengyang Normal University, Hengyang, 421008, China
| | - Changqing Qu
- Engineering Technology Research Center of Anti-aging, Chinese Herbal Medicine, Fuyang Normal University, Fuyang, 236037, China
| | - Yingying Liu
- College of Humanities and International Education Exchange, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Mengyang Cao
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Xiaoyan Yao
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Fei Meng
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Jing Wu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Huasheng Peng
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Daiyin Peng
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China; Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, 230012, China; Synergetic Innovation Center of Anhui Authentic Chinese Medicine Quality Improvement, Hefei, 230038, China
| | - Shihai Xing
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China; Synergetic Innovation Center of Anhui Authentic Chinese Medicine Quality Improvement, Hefei, 230038, China; Anhui Province Key Laboratory of Research & Development of Chinese Medicine, Hefei, 230012, China.
| | - Weimin Jiang
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region, College of Life Sciences and Environment, Hengyang Normal University, Hengyang, 421008, China.
| |
Collapse
|
4
|
Three Diverse Granule Preparation Methods for Proteomic Analysis of Mature Rice (Oryza sativa L.) Starch Grain. Molecules 2022; 27:molecules27103307. [PMID: 35630784 PMCID: PMC9144640 DOI: 10.3390/molecules27103307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 05/09/2022] [Accepted: 05/19/2022] [Indexed: 02/01/2023] Open
Abstract
Starch is the primary form of reserve carbohydrate storage in plants. Rice (Oryza sativa L.) is a monocot whose reserve starch is organized into compounded structures within the amyloplast, rather than a simple starch grain (SG). The mechanism governing the assembly of the compound SG from polyhedral granules in apposition, however, remains unknown. To further characterize the proteome associated with these compounded structures, three distinct methods of starch granule preparation (dispersion, microsieve, and flotation) were performed. Phase separation of peptides (aqueous trypsin-shaving and isopropanol solubilization of residual peptides) isolated starch granule-associated proteins (SGAPs) from the distal proteome of the amyloplast and the proximal ‘amylome’ (the amyloplastic proteome), respectively. The term ‘distal proteome’ refers to SGAPs loosely tethered to the amyloplast, ones that can be rapidly proteolyzed, while proximal SGAPs are those found closer to the remnant amyloplast membrane fragments, perhaps embedded therein—ones that need isopropanol solvent to be removed from the mature organelle surface. These two rice starch-associated peptide samples were analyzed using nano-liquid chromatography–tandem mass spectrometry (Nano-HPLC-MS/MS). Known and novel proteins, as well as septum-like structure (SLS) proteins, in the mature rice SG were found. Data mining and gene ontology software were used to categorize these putative plastoskeletal components as a variety of structural elements, including actins, tubulins, tubulin-like proteins, and cementitious elements such as reticulata related-like (RER) proteins, tegument proteins, and lectins. Delineating the plastoskeletal proteome begins by understanding how each starch granule isolation procedure affects observed cytoplasmic and plastid proteins. The three methods described herein show how the technique used to isolate SGs differentially impacts the subsequent proteomic analysis and results obtained. It can thus be concluded that future investigations must make judicious decisions regarding the methodology used in extracting proteomic information from the compound starch granules being assessed, since different methods are shown to yield contrasting results herein. Data are available via ProteomeXchange with identifier PXD032314.
Collapse
|
5
|
Hooper CM, Castleden IR, Tanz SK, Grasso SV, Millar AH. Subcellular Proteomics as a Unified Approach of Experimental Localizations and Computed Prediction Data for Arabidopsis and Crop Plants. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1346:67-89. [PMID: 35113396 DOI: 10.1007/978-3-030-80352-0_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In eukaryotic organisms, subcellular protein location is critical in defining protein function and understanding sub-functionalization of gene families. Some proteins have defined locations, whereas others have low specificity targeting and complex accumulation patterns. There is no single approach that can be considered entirely adequate for defining the in vivo location of all proteins. By combining evidence from different approaches, the strengths and weaknesses of different technologies can be estimated, and a location consensus can be built. The Subcellular Location of Proteins in Arabidopsis database ( http://suba.live/ ) combines experimental data sets that have been reported in the literature and is analyzing these data to provide useful tools for biologists to interpret their own data. Foremost among these tools is a consensus classifier (SUBAcon) that computes a proposed location for all proteins based on balancing the experimental evidence and predictions. Further tools analyze sets of proteins to define the abundance of cellular structures. Extending these types of resources to plant crop species has been complex due to polyploidy, gene family expansion and contraction, and the movement of pathways and processes within cells across the plant kingdom. The Crop Proteins of Annotated Location database ( http://crop-pal.org/ ) has developed a range of subcellular location resources including a species-specific voting consensus for 12 plant crop species that offers collated evidence and filters for current crop proteomes akin to SUBA. Comprehensive cross-species comparison of these data shows that the sub-cellular proteomes (subcellulomes) depend only to some degree on phylogenetic relationship and are more conserved in major biosynthesis than in metabolic pathways. Together SUBA and cropPAL created reference subcellulomes for plants as well as species-specific subcellulomes for cross-species data mining. These data collections are increasingly used by the research community to provide a subcellular protein location layer, inform models of compartmented cell function and protein-protein interaction network, guide future molecular crop breeding strategies, or simply answer a specific question-where is my protein of interest inside the cell?
Collapse
Affiliation(s)
- Cornelia M Hooper
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - Ian R Castleden
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - Sandra K Tanz
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - Sally V Grasso
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - A Harvey Millar
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia.
| |
Collapse
|
6
|
Gann PJ, Esguerra M, Counce PA, Srivastava V. Genotype-dependent and heat-induced grain chalkiness in rice correlates with the expression patterns of starch biosynthesis genes. PLANT-ENVIRONMENT INTERACTIONS (HOBOKEN, N.J.) 2021; 2:165-176. [PMID: 37283703 PMCID: PMC10168090 DOI: 10.1002/pei3.10054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 05/12/2021] [Accepted: 05/15/2021] [Indexed: 06/08/2023]
Abstract
Starch biosynthesis is a complex process underlying grain chalkiness in rice in a genotype-dependent manner. Coordinated expression of starch biosynthesis genes is important for producing translucent rice grains, while disruption in this process leads to opaque or chalky grains. To better understand the dynamics of starch biosynthesis genes in grain chalkiness, six rice genotypes showing variable chalk levels were subjected to gene expression analysis during reproductive stages. In the chalky genotypes, peak expression of the large subunit genes of ADP-glucose pyrophosphorylase (AGPase), encoding the first key step in starch biosynthesis, occurred in the stages before grain filling commenced, creating a gap with the upregulation of starch synthase genes, granule bound starch synthase I (GBSSI) and starch synthase IIA (SSIIA). Whereas, in low-chalk genotypes, AGPase large subunit genes expressed at later stages, generally following the expression patterns of GBSSI and SSIIA. However, heat treatment altered the expression in a genotype-dependent manner that was accompanied by transformed grain morphology and increased chalkiness. The suppression of AGPase subunit genes during early grain filling stages was observed in the chalky genotypes or upon heat treatment, which could result in a limited pool of ADP-Glucose for synthesizing amylose and amylopectin, the major components of the starch. This suboptimal starch biosynthesis process could subsequently lead to inefficient grain filling and air pockets that contribute to chalkiness. In summary, this study suggests a mechanism of grain chalkiness based on the expression patterns of the starch biosynthesis genes in rice.
Collapse
Affiliation(s)
- Peter James Gann
- Cell and Molecular Biology ProgramUniversity of ArkansasFayettevilleARUSA
- Department of Crop, Soil and Environmental SciencesUniversity of ArkansasFayettevilleARUSA
| | | | - Paul Allen Counce
- Cell and Molecular Biology ProgramUniversity of ArkansasFayettevilleARUSA
- Department of Crop, Soil and Environmental SciencesUniversity of ArkansasFayettevilleARUSA
- Rice Research and Extension CenterStuttgartARUSA
| | - Vibha Srivastava
- Cell and Molecular Biology ProgramUniversity of ArkansasFayettevilleARUSA
- Department of Crop, Soil and Environmental SciencesUniversity of ArkansasFayettevilleARUSA
- Department of HorticultureUniversity of ArkansasFayettevilleARUSA
| |
Collapse
|
7
|
Meng X, Baine JM, Yan T, Wang S. Comprehensive Analysis of Lysine Lactylation in Rice ( Oryza sativa) Grains. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:8287-8297. [PMID: 34264677 DOI: 10.1021/acs.jafc.1c00760] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Protein lysine lactylation is a new post-translational modification (PTM) prevalently found in fungi and mammalian cells that directly stimulates gene transcription and regulates the glycolytic flux. However, lysine lactylation sites and regulations remain largely unexplored, especially in cereal crops. Herein, we report the first global lactylome profile in rice, which effectively identified 638 lysine lactylation sites across 342 proteins in rice grains. Functional annotations demonstrated that lysine lactylation was enriched in proteins associated with central carbon metabolism and protein biosynthesis. We also observed that proteins serving as nutrition reservoirs in rice grains were frequently targeted by lactylation. Homology analyses indicated that lactylation was conserved on both histone and nonhistone proteins across plants, human cells, and fungi. In addition to lactylation, additional types of acylations could co-occur in many proteins at identical lysine residues, indicating potential cross-talks between these modifications. Our study provided a comprehensive profile of protein lysine lactylation in cereal crop grains.
Collapse
Affiliation(s)
- Xiaoxi Meng
- Department of Horticultural Science, University of Minnesota, Saint Paul, Minnesota 55108, United States
| | - Jonathan M Baine
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588, United States
| | - Tingcai Yan
- College of Food Science, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Shu Wang
- College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| |
Collapse
|
8
|
Tappiban P, Ying Y, Xu F, Bao J. Proteomics and Post-Translational Modifications of Starch Biosynthesis-Related Proteins in Developing Seeds of Rice. Int J Mol Sci 2021; 22:5901. [PMID: 34072759 PMCID: PMC8199009 DOI: 10.3390/ijms22115901] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 12/25/2022] Open
Abstract
Rice (Oryza sativa L.) is a foremost staple food for approximately half the world's population. The components of rice starch, amylose, and amylopectin are synthesized by a series of enzymes, which are responsible for rice starch properties and functionality, and then affect rice cooking and eating quality. Recently, proteomics technology has been applied to the establishment of the differentially expressed starch biosynthesis-related proteins and the identification of posttranslational modifications (PTMs) target starch biosynthesis proteins as well. It is necessary to summarize the recent studies in proteomics and PTMs in rice endosperm to deepen our understanding of starch biosynthesis protein expression and regulation, which will provide useful information to rice breeding programs and industrial starch applications. The review provides a comprehensive summary of proteins and PTMs involved in starch biosynthesis based on proteomic studies of rice developing seeds. Starch biosynthesis proteins in rice seeds were differentially expressed in the developing seeds at different developmental stages. All the proteins involving in starch biosynthesis were identified using proteomics methods. Most starch biosynthesis-related proteins are basically increased at 6-20 days after flowering (DAF) and decreased upon the high-temperature conditions. A total of 10, 14, 2, 17, and 7 starch biosynthesis related proteins were identified to be targeted by phosphorylation, lysine acetylation, succinylation, lysine 2-hydroxyisobutyrylation, and malonylation, respectively. The phosphoglucomutase is commonly targeted by five PTMs types. Research on the function of phosphorylation in multiple enzyme complex formation in endosperm starch biosynthesis is underway, while the functions of other PTMs in starch biosynthesis are necessary to be conducted in the near future.
Collapse
Affiliation(s)
- Piengtawan Tappiban
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
| | - Yining Ying
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
| | - Feifei Xu
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
| | - Jinsong Bao
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, China
| |
Collapse
|
9
|
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.
Collapse
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.)
| |
Collapse
|
10
|
Fuentes-Ramírez EO, Vázquez-Acevedo M, Cabrera-Orefice A, Guerrero-Castillo S, González-Halphen D. The plastid proteome of the nonphotosynthetic chlorophycean alga Polytomella parva. Microbiol Res 2020; 243:126649. [PMID: 33285428 DOI: 10.1016/j.micres.2020.126649] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/23/2020] [Accepted: 11/13/2020] [Indexed: 11/19/2022]
Abstract
The unicellular, free-living, nonphotosynthetic chlorophycean alga Polytomella parva, closely related to Chlamydomonas reinhardtii and Volvox carteri, contains colorless, starch-storing plastids. The P. parva plastids lack all light-dependent processes but maintain crucial metabolic pathways. The colorless alga also lacks a plastid genome, meaning no transcription or translation should occur inside the organelle. Here, using an algal fraction enriched in plastids as well as publicly available transcriptome data, we provide a morphological and proteomic characterization of the P. parva plastid, ultimately identifying several plastid proteins, both by mass spectrometry and bioinformatic analyses. Data are available via ProteomeXchange with identifier PXD022051. Altogether these results led us to propose a plastid proteome for P. parva, i.e., a set of proteins that participate in carbohydrate metabolism; in the synthesis and degradation of starch, amino acids and lipids; in the biosynthesis of terpenoids and tetrapyrroles; in solute transport and protein translocation; and in redox homeostasis. This is the first detailed plastid proteome from a unicellular, free-living colorless alga.
Collapse
Affiliation(s)
- Emma O Fuentes-Ramírez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, CDMX, Mexico.
| | - Miriam Vázquez-Acevedo
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, CDMX, Mexico.
| | - Alfredo Cabrera-Orefice
- Radboud Institute for Molecular Life Sciences, Department of Pediatrics, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525, GA, Nijmegen, the Netherlands.
| | - Sergio Guerrero-Castillo
- Radboud Institute for Molecular Life Sciences, Department of Pediatrics, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525, GA, Nijmegen, the Netherlands; University Children's Research@Kinder-UKE, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany.
| | - Diego González-Halphen
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, CDMX, Mexico.
| |
Collapse
|
11
|
Hooper CM, Castleden IR, Aryamanesh N, Black K, Grasso SV, Millar AH. CropPAL for discovering divergence in protein subcellular location in crops to support strategies for molecular crop breeding. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:812-827. [PMID: 32780488 DOI: 10.1111/tpj.14961] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 06/16/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
Agriculture faces increasing demand for yield, higher plant-derived protein content and diversity while facing pressure to achieve sustainability. Although the genomes of many of the important crops have been sequenced, the subcellular locations of most of the encoded proteins remain unknown or are only predicted. Protein subcellular location is crucial in determining protein function and accumulation patterns in plants, and is critical for targeted improvements in yield and resilience. Integrating location data from over 800 studies for 12 major crop species into the cropPAL2020 data collection showed that while >80% of proteins in most species are not localised by experimental data, combining species data or integrating predictions can help bridge gaps at similar accuracy. The collation and integration of over 61 505 experimental localisations and more than 6 million predictions showed that the relative sizes of the protein catalogues located in different subcellular compartments are comparable between crops and Arabidopsis. A comprehensive cross-species comparison showed that between 50% and 80% of the subcellulomes are conserved across species and that conservation only depends to some degree on the phylogenetic relationship of the species. Protein subcellular locations in major biosynthesis pathways are more often conserved than in metabolic pathways. Underlying this conservation is a clear potential for subcellular diversity in protein location between species by means of gene duplication and alternative splicing. Our cropPAL data set and search platform (https://crop-pal.org) provide a comprehensive subcellular proteomics resource to drive compartmentation-based approaches for improving yield, protein composition and resilience in future crop varieties.
Collapse
Affiliation(s)
- Cornelia M Hooper
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Ian R Castleden
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Nader Aryamanesh
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
- Robinson Research Institute and Adelaide Health and Medical Sciences, University of Adelaide, Adelaide, SA, 5000, Australia
| | - Kylie Black
- University Library, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Sally V Grasso
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| |
Collapse
|
12
|
Starch and Glycogen Analyses: Methods and Techniques. Biomolecules 2020; 10:biom10071020. [PMID: 32660096 PMCID: PMC7407607 DOI: 10.3390/biom10071020] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 01/16/2023] Open
Abstract
For complex carbohydrates, such as glycogen and starch, various analytical methods and techniques exist allowing the detailed characterization of these storage carbohydrates. In this article, we give a brief overview of the most frequently used methods, techniques, and results. Furthermore, we give insights in the isolation, purification, and fragmentation of both starch and glycogen. An overview of the different structural levels of the glucans is given and the corresponding analytical techniques are discussed. Moreover, future perspectives of the analytical needs and the challenges of the currently developing scientific questions are included.
Collapse
|
13
|
Optimization of nucleotide sugar supply for polysaccharide formation via thermodynamic buffering. Biochem J 2020; 477:341-356. [PMID: 31967651 DOI: 10.1042/bcj20190807] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/16/2019] [Accepted: 12/18/2019] [Indexed: 02/07/2023]
Abstract
Plant polysaccharides (cellulose, hemicellulose, pectin, starch) are either direct (i.e. leaf starch) or indirect products of photosynthesis, and they belong to the most abundant organic compounds in nature. Although each of these polymers is made by a specific enzymatic machinery, frequently in different cell locations, details of their synthesis share certain common features. Thus, the production of these polysaccharides is preceded by the formation of nucleotide sugars catalyzed by fully reversible reactions of various enzymes, mostly pyrophosphorylases. These 'buffering' enzymes are, generally, quite active and operate close to equilibrium. The nucleotide sugars are then used as substrates for irreversible reactions of various polysaccharide-synthesizing glycosyltransferases ('engine' enzymes), e.g. plastidial starch synthases, or plasma membrane-bound cellulose synthase and callose synthase, or ER/Golgi-located variety of glycosyltransferases forming hemicellulose and pectin backbones. Alternatively, the irreversible step might also be provided by a carrier transporting a given immediate precursor across a membrane. Here, we argue that local equilibria, established within metabolic pathways and cycles resulting in polysaccharide production, bring stability to the system via the arrangement of a flexible supply of nucleotide sugars. This metabolic system is itself under control of adenylate kinase and nucleoside-diphosphate kinase, which determine the availability of nucleotides (adenylates, uridylates, guanylates and cytidylates) and Mg2+, the latter serving as a feedback signal from the nucleotide metabolome. Under these conditions, the supply of nucleotide sugars to engine enzymes is stable and constant, and the metabolic process becomes optimized in its load and consumption, making the system steady and self-regulated.
Collapse
|
14
|
|
15
|
Ultrasonication of Milky Stage Rice Milk with Bioactive Peptides from Rice Bran: Its Bioactivities and Absorption. FOOD BIOPROCESS TECH 2020. [DOI: 10.1007/s11947-019-02371-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
16
|
Meng X, Mujahid H, Zhang Y, Peng X, Redoña ED, Wang C, Peng Z. Comprehensive Analysis of the Lysine Succinylome and Protein Co-modifications in Developing Rice Seeds. Mol Cell Proteomics 2019; 18:2359-2372. [PMID: 31492684 PMCID: PMC6885699 DOI: 10.1074/mcp.ra119.001426] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 08/04/2019] [Indexed: 11/06/2022] Open
Abstract
Lysine succinylation has been recognized as a post-translational modification (PTM) in recent years. It is plausible that succinylation may have a vaster functional impact than acetylation because of bulkier structural changes and more significant charge differences on the modified lysine residue. Currently, however, the quantity and identity of succinylated proteins and their corresponding functions in cereal plants remain largely unknown. In this study, we estimated the native succinylation occupancy on lysine was between 2% to 10% in developing rice seeds. Eight hundred fifty-four lysine succinylation sites on 347 proteins have been identified by a thorough investigation in developing rice seeds. Six motifs were revealed as preferred amino acid sequence arrangements for succinylation sites, and a noteworthy motif preference was identified in proteins associated with different biological processes, molecular functions, pathways, and domains. Remarkably, heavy succinylation was detected on major seed storage proteins, in conjunction with critical enzymes involved in central carbon metabolism and starch biosynthetic pathways for rice seed development. Meanwhile, our results showed that the modification pattern of in vitro nonenzymatically succinylated proteins was different from those of the proteins isolated from cells in Western blots, suggesting that succinylation is not generated via nonenzymatic reaction in the cells, at least not completely. Using the acylation data obtained from the same rice tissue, we mapped many sites harboring lysine succinylation, acetylation, malonylation, crotonylation, and 2-hydroxisobutyrylation in rice seed proteins. A striking number of proteins with multiple modifications were shown to be involved in critical metabolic events. Given that these modification moieties are intermediate products of multiple cellular metabolic pathways, these targeted lysine residues may mediate the crosstalk between different metabolic pathways via modifications by different moieties. Our study exhibits a platform for extensive investigation of molecular networks administrating cereal seed development and metabolism via PTMs.
Collapse
Affiliation(s)
- Xiaoxi Meng
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville MS, 39762
| | - Hana Mujahid
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville MS, 39762
| | - Yadong Zhang
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville MS, 39762; Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of China National Center for Rice Improvement, Nanjing 210014, China
| | - Xiaojun Peng
- Department of Bioinformatics, Jingjie PTM Biolab Co. Ltd, Hangzhou 310018, China
| | - Edilberto D Redoña
- Delta Research and Extension Center, Mississippi State University, Stoneville MS, 38776
| | - Cailin Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of China National Center for Rice Improvement, Nanjing 210014, China.
| | - Zhaohua Peng
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville MS, 39762.
| |
Collapse
|
17
|
Niu L, Ding H, Hao R, Liu H, Wu X, Hu X, Wang W. A rapid and universal method for isolating starch granules in plant tissues. PLANT, CELL & ENVIRONMENT 2019; 42:3355-3371. [PMID: 31429107 DOI: 10.1111/pce.13631] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/23/2019] [Indexed: 06/10/2023]
Abstract
Starch is the major form of carbohydrate storage in plants and exists as discrete starch granules (SGs). Isolation of high-quality SGs in different plant tissues is a prerequisite for studying the roles of SGs during plant growth, development, and responses to abiotic stress. However, it is difficult to isolate transitory SGs from leaves and storage SGs from pollen grains due to their small sizes and low quantities. Herein, we develop a novel method for isolating SGs by using the aqueous two-phase system (ATS) of ethanol/NaH2 PO4 . The ATS method efficiently separated SGs from contaminants based on their differences in density, solubility, and polarity. Using this method, we first isolated and purified three kinds of SGs from maize seeds, pollen, and leaves. The biochemical, microscopic, and proteomic analyses demonstrated the high purity of the isolated SGs. Proteomic analysis revealed distinct differences in SG-bound proteins between seed SGs and pollen SGs. As a simple, rapid, and low-cost method, the ATS-based method exhibits highly universal and reproducible results for starch-containing tissues in various plant species.
Collapse
Affiliation(s)
- Liangjie Niu
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Huiying Ding
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Ruiqi Hao
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hui Liu
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaolin Wu
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiuli Hu
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Wei Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| |
Collapse
|
18
|
Intra-Sample Heterogeneity of Potato Starch Reveals Fluctuation of Starch-Binding Proteins According to Granule Morphology. PLANTS 2019; 8:plants8090324. [PMID: 31487879 PMCID: PMC6784226 DOI: 10.3390/plants8090324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 08/27/2019] [Accepted: 08/29/2019] [Indexed: 11/26/2022]
Abstract
Starch granule morphology is highly variable depending on the botanical origin. Moreover, all investigated plant species display intra-tissular variability of granule size. In potato tubers, the size distribution of starch granules follows a unimodal pattern with diameters ranging from 5 to 100 µm. Several evidences indicate that granule morphology in plants is related to the complex starch metabolic pathway. However, the intra-sample variability of starch-binding metabolic proteins remains unknown. Here, we report on the molecular characterization of size-fractionated potato starch granules with average diameters of 14.2 ± 3.7 µm, 24.5 ± 6.5 µm, 47.7 ± 12.8 µm, and 61.8 ± 17.4 µm. In addition to changes in the phosphate contents as well as small differences in the amylopectin structure, we found that the starch-binding protein stoichiometry varies significantly according to granule size. Label-free quantitative proteomics of each granule fraction revealed that individual proteins can be grouped according to four distinct abundance patterns. This study corroborates that the starch proteome may influence starch granule growth and architecture and opens up new perspectives in understanding the dynamics of starch biosynthesis.
Collapse
|
19
|
Crofts N, Iizuka Y, Abe N, Miura S, Kikuchi K, Matsushima R, Fujita N. Rice Mutants Lacking Starch Synthase I or Branching Enzyme IIb Activity Altered Starch Biosynthetic Protein Complexes. FRONTIERS IN PLANT SCIENCE 2018; 9:1817. [PMID: 30581451 PMCID: PMC6292963 DOI: 10.3389/fpls.2018.01817] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/22/2018] [Indexed: 05/21/2023]
Abstract
Amylopectin, the major component of starch, is synthesized by synergistic activity of multiple isozymes of starch synthases (SSs) and branching enzymes (BEs). The frequency and length of amylopectin branches determine the functionality of starch. In the rice endosperm, BEIIb generates short side chains of amylopectin and SSI elongates those branches, which can be further elongated by SSIIa. Absence of these enzymes greatly affects amylopectin structure. SSI, SSIIa, and BEIIb associate with each other and with other starch biosynthetic enzymes although SSIIa is low activity in japonica rice. The aim of the current study was to understand how the activity of starch biosynthetic enzyme complexes is compensated in the absence of SSI or BEIIb, and whether the compensatory effects are different in the absence of BEIIb or in the presence of inactive BEIIb. Interactions between starch biosynthetic enzymes were analyzed using one ss1 null mutant and two be2b japonica rice mutants (a mutant producing inactive BEIIb and a mutant that did not produce BEIIb). Soluble proteins extracted from the developing rice seeds were separated by gel filtration chromatography. In the absence of BEIIb activity, BEIIa was eluted in a broad molecular weight range (60-700 kDa). BEIIa in the wild-type was eluted with a mass below 300 kDa. Further, majority of inactive BEIIb co-eluted with SSI, SSIIa, and BEI, in a mass fraction over 700 kDa, whereas only small amounts of these isozymes were found in the wild-type. Compared with the be2b lines, the ss1 mutant showed subtle differences in protein profiles, but the amounts of SSIIa, SSIVb, and BEI in the over-700-kDa fraction were elevated. Immunoprecipitation revealed reduced association of SSIIa and BEIIb in the ss1 mutant, while the association of BEIIb with SSI, SSIIa, SSIVb, BEI, and BEIIa were more pronounced in the be2b mutant that produced inactive BEIIb enzyme. Mass spectrometry and western blotting revealed that SSI, SSIIa, SSIIIa, BEI, BEIIa, starch phosphorylase 1, and pullulanase were bound to the starch granules in the be2b mutants, but not in the wild-type and ss1 mutant. These results will aid the understanding of the mechanism of amylopectin biosynthesis.
Collapse
Affiliation(s)
- Naoko Crofts
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, Akita, Japan
| | - Yuriko Iizuka
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, Akita, Japan
| | - Natsuko Abe
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, Akita, Japan
| | - Satoko Miura
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, Akita, Japan
| | - Kana Kikuchi
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, Akita, Japan
| | - Ryo Matsushima
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Naoko Fujita
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, Akita, Japan
| |
Collapse
|
20
|
Ye X, Zhang Y, Qiu C, Corke H, Sui Z. Extraction and characterization of starch granule-associated proteins from rice that affect in vitro starch digestibility. Food Chem 2018; 276:754-760. [PMID: 30409658 DOI: 10.1016/j.foodchem.2018.10.042] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 10/06/2018] [Accepted: 10/08/2018] [Indexed: 10/28/2022]
Abstract
Starch granule-associated proteins (SGAPs) including granule-surface proteins and granule-channel proteins in waxy, low- and high-amylose rice starch were extracted and identified. The in vitro digestibility of starch was investigated before and after the extraction of granule-channel proteins or total SGAPs. The results showed that 10 types of major differentially expressed proteins (DEPs) including 14-3-3-like protein and ribosomal protein were found among starches. In addition, the lack of only granule-channel proteins or total SGAPs led to significant and different changes in the levels of rapidly digestible starch, slowly digestible starch and resistant starch. Possible mechanisms are related to the accessibility of amylase into starch granules and structural properties of SGAPs. This study provides more information about DEPs in rice starch with different amylose content and supports further study on the relationship between SGAPs and in vitro starch digestibility.
Collapse
Affiliation(s)
- Xiaoting Ye
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; International Institute for Professional Education, Shanghai University of Finance and Economics, Shanghai 200083, China
| | - Yu Zhang
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chen Qiu
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Harold Corke
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Zhongquan Sui
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
| |
Collapse
|
21
|
Helle S, Bray F, Verbeke J, Devassine S, Courseaux A, Facon M, Tokarski C, Rolando C, Szydlowski N. Proteome Analysis of Potato Starch Reveals the Presence of New Starch Metabolic Proteins as Well as Multiple Protease Inhibitors. FRONTIERS IN PLANT SCIENCE 2018; 9:746. [PMID: 29963063 PMCID: PMC6013586 DOI: 10.3389/fpls.2018.00746] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 05/15/2018] [Indexed: 05/20/2023]
Abstract
Starch bound proteins mainly include enzymes from the starch biosynthesis pathway. Recently, new functions in starch molecular assembly or active protein targeting were also proposed for starch associated proteins. The potato genome sequence reveals 77 loci encoding starch metabolizing enzymes with the identification of previously unknown putative isoforms. Here we show by bottom-up proteomics that most of the starch biosynthetic enzymes in potato remain associated with starch even after washing with SDS or protease treatment of the granule surface. Moreover, our study confirmed the presence of PTST1 (Protein Targeting to Starch), ESV1 (Early StarVation1) and LESV (Like ESV), that have recently been identified in Arabidopsis. In addition, we report on the presence of a new isoform of starch synthase, SS6, containing both K-X-G-G-L catalytic motifs. Furthermore, multiple protease inhibitors were also identified that are cleared away from starch by SDS and thermolysin treatments. Our results indicate that SS6 may play a yet uncharacterized function in starch biosynthesis and open new perspectives both in understanding storage starch metabolism as well as breeding improved potato lines.
Collapse
Affiliation(s)
- Stanislas Helle
- Univ. Lille, CNRS, UMR8576 – UGSF – Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
- Univ. Lille, CNRS, USR 3290 – MSAP – Miniaturisation pour la Synthèse, l’Analyse et la Protéomique, Lille, France
| | - Fabrice Bray
- Univ. Lille, CNRS, USR 3290 – MSAP – Miniaturisation pour la Synthèse, l’Analyse et la Protéomique, Lille, France
| | - Jérémy Verbeke
- Univ. Lille, CNRS, USR 3290 – MSAP – Miniaturisation pour la Synthèse, l’Analyse et la Protéomique, Lille, France
| | - Stéphanie Devassine
- Univ. Lille, CNRS, USR 3290 – MSAP – Miniaturisation pour la Synthèse, l’Analyse et la Protéomique, Lille, France
| | - Adeline Courseaux
- Univ. Lille, CNRS, UMR8576 – UGSF – Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Maud Facon
- Univ. Lille, CNRS, UMR8576 – UGSF – Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
- Univ. Lille, CNRS, USR 3290 – MSAP – Miniaturisation pour la Synthèse, l’Analyse et la Protéomique, Lille, France
| | - Caroline Tokarski
- Univ. Lille, CNRS, USR 3290 – MSAP – Miniaturisation pour la Synthèse, l’Analyse et la Protéomique, Lille, France
| | - Christian Rolando
- Univ. Lille, CNRS, USR 3290 – MSAP – Miniaturisation pour la Synthèse, l’Analyse et la Protéomique, Lille, France
| | - Nicolas Szydlowski
- Univ. Lille, CNRS, UMR8576 – UGSF – Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
- Univ. Lille, CNRS, USR 3290 – MSAP – Miniaturisation pour la Synthèse, l’Analyse et la Protéomique, Lille, France
| |
Collapse
|
22
|
Niu L, Yuan H, Gong F, Wu X, Wang W. Protein Extraction Methods Shape Much of the Extracted Proteomes. FRONTIERS IN PLANT SCIENCE 2018; 9:802. [PMID: 29946336 PMCID: PMC6005817 DOI: 10.3389/fpls.2018.00802] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/25/2018] [Indexed: 05/05/2023]
Affiliation(s)
| | | | | | | | - Wei Wang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| |
Collapse
|
23
|
Meng X, Xing S, Perez LM, Peng X, Zhao Q, Redoña ED, Wang C, Peng Z. Proteome-wide Analysis of Lysine 2-hydroxyisobutyrylation in Developing Rice (Oryza sativa) Seeds. Sci Rep 2017; 7:17486. [PMID: 29235492 PMCID: PMC5727541 DOI: 10.1038/s41598-017-17756-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 11/28/2017] [Indexed: 11/26/2022] Open
Abstract
Lysine 2-hydroxyisobutyrylation is a recently identified protein post-translational modification that is known to affect the association between histone and DNA. However, non-histone protein lysine 2-hydroxyisobutyrylation remains largely unexplored. Utilizing antibody-based affinity enrichment and nano-HPLC/MS/MS analyses of 2-hydroxyisobutyrylation peptides, we efficaciously identified 9,916 2-hydroxyisobutyryl lysine sites on 2,512 proteins in developing rice seeds, representing the first lysine 2-hydroxyisobutyrylome dataset in plants. Functional annotation analyses indicated that a wide variety of vital biological processes were preferably targeted by lysine 2-hydroxyisobutyrylation, including glycolysis/gluconeogenesis, TCA cycle, starch biosynthesis, lipid metabolism, protein biosynthesis and processing. Our finding showed that 2-hydroxyisobutyrylated histone sites were conserved across plants, human, and mouse. A number of 2-hydroxyisobutyryl sites were shared with other lysine acylations in both histone and non-histone proteins. Comprehensive analysis of the lysine 2-hydroxyisobutyrylation sites illustrated that the modification sites were highly sequence specific with distinct motifs, and they had less surface accessibility than other lysine residues in the protein. Overall, our study provides the first systematic analysis of lysine 2-hydroxyisobutyrylation proteome in plants, and it serves as an important resource for future investigations of the regulatory mechanisms and functions of lysine 2-hydroxyisobutyrylation.
Collapse
Affiliation(s)
- Xiaoxi Meng
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, Mississippi, 39762, USA
| | - Shihai Xing
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, Mississippi, 39762, USA
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, Anhui, 230000, China
| | - Loida M Perez
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, Mississippi, 39762, USA
| | - Xiaojun Peng
- Department of Bioinformatics, Jingjie PTM Biolab Co. Ltd, Hangzhou, 310018, China
| | - Qingyong Zhao
- Institute of Crop Sciences, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Edilberto D Redoña
- Delta Research and Extension Center, Stoneville, P.O. Box 197, Mississippi, 38776, USA
| | - Cailin Wang
- Institute of Crop Sciences, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| | - Zhaohua Peng
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, Mississippi, 39762, USA.
| |
Collapse
|
24
|
Meng X, Lv Y, Mujahid H, Edelmann MJ, Zhao H, Peng X, Peng Z. Proteome-wide lysine acetylation identification in developing rice (Oryza sativa) seeds and protein co-modification by acetylation, succinylation, ubiquitination, and phosphorylation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1866:451-463. [PMID: 29313810 DOI: 10.1016/j.bbapap.2017.12.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 11/20/2017] [Accepted: 12/03/2017] [Indexed: 12/31/2022]
Abstract
Protein lysine acetylation is a highly conserved post-translational modification with various biological functions. However, only a limited number of acetylation sites have been reported in plants, especially in cereals, and the function of non-histone protein acetylation is still largely unknown. In this report, we identified 1003 lysine acetylation sites in 692 proteins of developing rice seeds, which greatly extended the number of known acetylated sites in plants. Seven distinguished motifs were detected flanking acetylated lysines. Functional annotation analyses indicated diverse biological processes and pathways engaged in lysine acetylation. Remarkably, we found that several key enzymes in storage starch synthesis pathway and the main storage proteins were heavily acetylated. A comprehensive comparison of the rice acetylome, succinylome, ubiquitome and phosphorylome with available published data was conducted. A large number of proteins carrying multiple kinds of modifications were identified and many of these proteins are known to be key enzymes of vital metabolic pathways. Our study provides extending knowledge of protein acetylation. It will have critical reference value for understanding the mechanisms underlying PTM mediated multiple signal integration in the regulation of metabolism and development in plants.
Collapse
Affiliation(s)
- Xiaoxi Meng
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS, United States
| | - Yuanda Lv
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS, United States; Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Hana Mujahid
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS, United States
| | - Mariola J Edelmann
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| | - Han Zhao
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Xiaojun Peng
- Department of Bioinformatics, Jingjie PTM Biolab Co. Ltd, Hangzhou, Zhejiang, China
| | - Zhaohua Peng
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS, United States.
| |
Collapse
|
25
|
Mujahid H, Meng X, Xing S, Peng X, Wang C, Peng Z. Malonylome analysis in developing rice (Oryza sativa) seeds suggesting that protein lysine malonylation is well-conserved and overlaps with acetylation and succinylation substantially. J Proteomics 2017; 170:88-98. [PMID: 28882676 DOI: 10.1016/j.jprot.2017.08.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/29/2017] [Accepted: 08/31/2017] [Indexed: 12/13/2022]
Abstract
In recent years, lysine malonylation has garnered wide spread interest due to its potential regulatory roles. While studies have been performed in bacteria, mouse, and human, the involvement and the biological function of this modification in plant are still largely unknown. We examined the global proteome profile of lysine malonylation in developing rice seeds using affinity enrichment followed by LC-MS/MS analysis. We identified 421 malonylated lysine sites across 247 proteins. Functional analyses showed predominant presence of malonylated proteins in metabolic processes, including carbon metabolism, glycolysis/gluconeogenesis, TCA cycle, as well as photosynthesis. Malonylation was also detected on enzymes in starch biosynthesis pathway in developing rice seeds. In addition, we found a remarkable overlap among the malonylated, succinylated and acetylated sites identified in rice. Furthermore, malonylation at conserved sites of homologous proteins was observed across organisms of different kingdoms, including mouse, human, and bacteria. Finally, distinct motifs were identified when the rice malonylation sites were analyzed and conserved motifs were observed from bacterium to human and rice. Our results provide an initial understanding of the lysine malonylome in plants. The study has critical reference value for future understanding of the biological function of protein lysine malonylation in plants. BIOLOGICAL SIGNIFICANCE Lysine malonylation is a newly discovered acylation with functional potential in regulating cellular metabolisms and activities. However, the malonylation status has not been reported in plants. Grain yield and quality, mainly determined during cereal seed development, are closely related to food security, human health and economic value. To evaluate malonylation level in plants and the possible regulatory functions of malonylation in seed development, we conducted comprehensive analyses of malonylome in developing rice seeds. A total of 421 malonylated lysine sites from 247 proteins were identified, which involved in multiple critical metabolic processes, including central carbon metabolism, lipid metabolism, photosynthesis, and starch biosynthesis. We found that charged amino acids, lysine and arginine, were the preferred residues in positions flanking the modified lysines. Highly conserved modification sites on both histone and non-histone proteins were observed among different organisms through sequence alignment analysis. More interestingly, a large number of modification sites shared by malonylation, acetylation and succinylation were identified in rice. The study presents a comprehensive understanding of malonylome in plants, which will serve as an initial platform for further investigation of the functions of lysine malonylation, especially in cereal seeds development.
Collapse
Affiliation(s)
- Hana Mujahid
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS 39762, USA
| | - Xiaoxi Meng
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS 39762, USA
| | - Shihai Xing
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS 39762, USA
| | - Xiaojun Peng
- Department of Bioinformatics, Jingjie PTM Biolab Co. Ltd, Hangzhou, Zhejiang 310018, China
| | - Cailin Wang
- Institute of Crop Sciences, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China.
| | - Zhaohua Peng
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS 39762, USA.
| |
Collapse
|