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Thiaw MRN, Gantet P. The emerging functions of mini zinc finger (MIF) microproteins in seed plants: A minireview. Biochimie 2024; 218:69-75. [PMID: 37722501 DOI: 10.1016/j.biochi.2023.09.016] [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: 04/18/2023] [Revised: 07/20/2023] [Accepted: 09/14/2023] [Indexed: 09/20/2023]
Abstract
Mini zinc fingers constitute a class of microproteins that appeared early in evolution and expanded in seeds plants. In this review, the phylogenetic history, the functions and the mode of action of Mini zinc fingers in plants are reported and discussed. It appears that mini zinc fingers play an important role in the control of plant development. They are involved in the control of cell division and expansion, in the switch between the determinate/indeterminate state of the meristems and in the regulation of vegetative growth and floral organ development. Their biochemical mode of action seems to be diverse. In some studies, it has been reported that mini zinc fingers can directly bind to DNA and activate target gene expression, whereas other studies have shown that they can interact with and inhibit the activity of specific zinc finger homeodomain transcription factors or act as adaptor proteins necessary to aggregate polymeric protein complexes corresponding to chromatin remodelling factors negatively regulating the expression of specific genes. The diversity of mode of action for mini zinc finger microproteins suggests a wider range of biological functions than what has been that described in the literature thus far, and their involvement in the response to biotic and abiotic stresses should be further investigated in future studies.
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Affiliation(s)
- Marie Rose Ndella Thiaw
- UMR DIADE, Université de Montpellier, IRD, 911 Avenue Agropolis, 34394, cedex 5, Montpellier, France.
| | - Pascal Gantet
- UMR DIADE, Université de Montpellier, IRD, 911 Avenue Agropolis, 34394, cedex 5, Montpellier, France.
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2
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Molinari MDC, Fuganti-Pagliarini R, Yu Y, Florentino LH, Mertz-Henning LM, Lima RN, Bittencourt DMDC, Freire MO, Rech E. Exploring the Proteomic Profile of Soybean Bran: Unlocking the Potential for Improving Protein Quality and Quantity. PLANTS (BASEL, SWITZERLAND) 2023; 12:2704. [PMID: 37514318 PMCID: PMC10383420 DOI: 10.3390/plants12142704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 06/28/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023]
Abstract
Soybean is a rich source of vegetal protein for both animal and human consumption. Despite the high levels of protein in soybean seeds, industrial processing to obtain soybean bran significantly decreases the final protein content of the byproducts. To overcome this problem, cultivars with higher protein contents must be developed. However, selecting the target proteins is difficult because of the lack of information on the proteome profile of soybean bran. Therefore, this study obtained the comparative proteomic profiles of both natural coatless seeds and defatted bran from an elite tropical-soybean cultivar. Thus, their extracts were characterized using LC-MS/MS and a total of 550 proteins were identified. Among these, 526 proteins were detected in coatless seeds and 319 proteins in defatted bran. Moreover, a total of 139 proteins were identified as presenting different levels of content in coatless seeds and defatted bran. Among them, only 46 were retained after the seed processing. These proteins were clustered in several important metabolic pathways, such as amino-acid biosynthesis, sugar biosynthesis, and antioxidant activity, meaning that they could act as targets for bioactive products or genome editing to improve protein quality and quantity in soybean grains. These findings can enhance our understanding regarding protein robustness for both soybean crops and the commercial bran improvement because target proteins must remain intact after processing and must be bioactive when overexpressed. Overall, the soybean bran proteomic profile was explored for the first time, providing a valuable catalogue of target proteins that can tolerate the industrial process.
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Affiliation(s)
| | | | - Yanbao Yu
- J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Lilian Hasegawa Florentino
- Embrapa Genetic Resources and Biotechnology, National Institute of Science and Technology in Synthetic Biology, Distrito Federal 70770-917, Brazil
| | | | - Rayane Nunes Lima
- Embrapa Genetic Resources and Biotechnology, National Institute of Science and Technology in Synthetic Biology, Distrito Federal 70770-917, Brazil
| | | | | | - Elibio Rech
- Embrapa Genetic Resources and Biotechnology, National Institute of Science and Technology in Synthetic Biology, Distrito Federal 70770-917, Brazil
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3
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Yang Z, Qin T, Jin H, Wang J, Li C, Lim KJ, Wang Z. Quantitative Phosphoproteomic Analysis Reveals Potential Regulatory Mechanisms of Early Fruit Enlargement in Pecan ( Carya illinoinensis). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:4901-4914. [PMID: 36938622 DOI: 10.1021/acs.jafc.2c08876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Pecan (Carya illinoinensis) is a popular tree nut. Its fruit development undergoes slow growth, rapid expansion, core hardening, and kernel maturation stages. However, little is known about how pecan initiates fruit development and enlargement after pollination. In this study, we performed the first large-scale identification of potential phosphorylation sites and proteins at early development of pecan fruit by a label-free phosphoproteomic quantification technique. A total of 2155 phosphosites were identified from 1953 phosphopeptides covering 1311 phosphoproteins in unpollinated pistils and fruits at 5 and 9 weeks after pollination. Of these, 699 nonredundant phosphoproteins were differentially phosphorylated (DP). Furthermore, the phosphorylation intensity of DP proteins in brassinolide (BR) and auxin signaling were analyzed, and the function of CiBZR1 was investigated. Ectopic expression of CiBZR1 resulted in BR response phenotypes with curled leaves and fruit, while enlarged seed size in Arabidopsis. Subcellular localization and transcriptional activation activity assay demonstrated that CiBZR1 distributed in both the nucleus and cytoplasm with transcriptional activity. When two phosphosites mutated, CiBZR1S201P,S205G moved to the nucleus completely, while the transcriptional activity remained unchanged. Taken together, our data reveal extensive phosphoproteins and lay a foundation to comprehensively dissect the potential post-translational regulation mechanism of early development of pecan fruit.
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Affiliation(s)
- Zhengfu Yang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an District, 311300 Hangzhou, Zhejiang, China
| | - Tao Qin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an District, 311300 Hangzhou, Zhejiang, China
| | - Hongmiao Jin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an District, 311300 Hangzhou, Zhejiang, China
| | - Jiani Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an District, 311300 Hangzhou, Zhejiang, China
| | - Caiyun Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an District, 311300 Hangzhou, Zhejiang, China
| | - Kean-Jin Lim
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an District, 311300 Hangzhou, Zhejiang, China
| | - Zhengjia Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an District, 311300 Hangzhou, Zhejiang, China
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4
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Recent developments in the engineering of Rubisco activase for enhanced crop yield. Biochem Soc Trans 2023; 51:627-637. [PMID: 36929563 DOI: 10.1042/bst20221281] [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: 12/20/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/18/2023]
Abstract
Rubisco activase (RCA) catalyzes the release of inhibitory sugar phosphates from ribulose-1,6-biphosphate carboxylase/oxygenase (Rubisco) and can play an important role in biochemical limitations of photosynthesis under dynamic light and elevated temperatures. There is interest in increasing RCA activity to improve crop productivity, but a lack of understanding about the regulation of photosynthesis complicates engineering strategies. In this review, we discuss work relevant to improving RCA with a focus on advances in understanding the structural cause of RCA instability under heat stress and the regulatory interactions between RCA and components of photosynthesis. This reveals substantial variation in RCA thermostability that can be influenced by single amino acid substitutions, and that engineered variants can perform better in vitro and in vivo under heat stress. In addition, there are indications RCA activity is controlled by transcriptional, post-transcriptional, post-translational, and spatial regulation, which may be important for balancing between carbon fixation and light capture. Finally, we provide an overview of findings from recent field experiments and consider the requirements for commercial validation as part of efforts to increase crop yields in the face of global climate change.
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Yu L, Dai Z, Zhang Y, Iqbal S, Lu S, Guo L, Yao X. Proteome-wide identification of S-sulfenylated cysteines reveals metabolic response to freezing stress after cold acclimation in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:1014295. [PMID: 36275609 PMCID: PMC9580371 DOI: 10.3389/fpls.2022.1014295] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
Redox regulation plays a wide role in plant growth, development, and adaptation to stresses. Sulfenylation is one of the reversible oxidative post-transcriptional modifications. Here we performed an iodoTMT-based proteomic analysis to identify the redox sensitive proteins in vivo under freezing stress after cold acclimation in Brassica napus. Totally, we obtained 1,372 sulfenylated sites in 714 proteins. The overall sulfenylation level displayed an increased trend under freezing stress after cold acclimation. We identified 171 differentially sulfenylated proteins (DSPs) under freezing stress, which were predicted to be mainly localized in chloroplast and cytoplasm. The up-regulated DSPs were mainly enriched in photosynthesis and glycolytic processes and function of catalytic activity. Enzymes involved in various pathways such as glycolysis and Calvin-Benson-Bassham (CBB) cycle were generally sulfenylated and the metabolite levels in these pathways was significantly reduced under freezing stress after cold acclimation. Furthermore, enzyme activity assay confirmed that the activity of cytosolic pyruvate kinase and malate dehydrogenase 2 was significantly reduced under H2O2 treatment. Our study provides a landscape of redox sensitive proteins in B. napus in response to freezing stress after cold acclimation, which proposes a basis for understanding the redox regulation in plant metabolic response to freezing stress after cold acclimation.
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Affiliation(s)
- Liangqian Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zezhang Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yuting Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Sidra Iqbal
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xuan Yao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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6
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Baudouin E, Puyaubert J, Meimoun P, Blein-Nicolas M, Davanture M, Zivy M, Bailly C. Dynamics of Protein Phosphorylation during Arabidopsis Seed Germination. Int J Mol Sci 2022; 23:ijms23137059. [PMID: 35806063 PMCID: PMC9266807 DOI: 10.3390/ijms23137059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/16/2022] [Accepted: 06/22/2022] [Indexed: 11/16/2022] Open
Abstract
Seed germination is critical for early plantlet development and is tightly controlled by environmental factors. Nevertheless, the signaling networks underlying germination control remain elusive. In this study, the remodeling of Arabidopsis seed phosphoproteome during imbibition was investigated using stable isotope dimethyl labeling and nanoLC-MS/MS analysis. Freshly harvested seeds were imbibed under dark or constant light to restrict or promote germination, respectively. For each light regime, phosphoproteins were extracted and identified from dry and imbibed (6 h, 16 h, and 24 h) seeds. A large repertoire of 10,244 phosphopeptides from 2546 phosphoproteins, including 110 protein kinases and key regulators of seed germination such as Delay Of Germination 1 (DOG1), was established. Most phosphoproteins were only identified in dry seeds. Early imbibition led to a similar massive downregulation in dormant and non-dormant seeds. After 24 h, 411 phosphoproteins were specifically identified in non-dormant seeds. Gene ontology analyses revealed their involvement in RNA and protein metabolism, transport, and signaling. In addition, 489 phosphopeptides were quantified, and 234 exhibited up or downregulation during imbibition. Interaction networks and motif analyses revealed their association with potential signaling modules involved in germination control. Our study provides evidence of a major role of phosphosignaling in the regulation of Arabidopsis seed germination.
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Affiliation(s)
- Emmanuel Baudouin
- Laboratoire de Biologie du Développement, UMR 7622, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, CNRS, F-75005 Paris, France; (J.P.); (P.M.); (C.B.)
- Correspondence: ; Tel.: +33-1-44-27-59-87
| | - Juliette Puyaubert
- Laboratoire de Biologie du Développement, UMR 7622, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, CNRS, F-75005 Paris, France; (J.P.); (P.M.); (C.B.)
| | - Patrice Meimoun
- Laboratoire de Biologie du Développement, UMR 7622, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, CNRS, F-75005 Paris, France; (J.P.); (P.M.); (C.B.)
| | - Mélisande Blein-Nicolas
- PAPPSO, Génétique Quantitative et Evolution (GQE), Université Paris-Saclay, INRAE, CNRS, AgroParisTech, F-91190 Gif-sur-Yvette, France; (M.B.-N.); (M.D.); (M.Z.)
| | - Marlène Davanture
- PAPPSO, Génétique Quantitative et Evolution (GQE), Université Paris-Saclay, INRAE, CNRS, AgroParisTech, F-91190 Gif-sur-Yvette, France; (M.B.-N.); (M.D.); (M.Z.)
| | - Michel Zivy
- PAPPSO, Génétique Quantitative et Evolution (GQE), Université Paris-Saclay, INRAE, CNRS, AgroParisTech, F-91190 Gif-sur-Yvette, France; (M.B.-N.); (M.D.); (M.Z.)
| | - Christophe Bailly
- Laboratoire de Biologie du Développement, UMR 7622, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, CNRS, F-75005 Paris, France; (J.P.); (P.M.); (C.B.)
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7
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Wang M, Garneau MG, Poudel AN, Lamm D, Koo AJ, Bates PD, Thelen JJ. Overexpression of pea α-carboxyltransferase in Arabidopsis and camelina increases fatty acid synthesis leading to improved seed oil content. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1035-1046. [PMID: 35220631 DOI: 10.1111/tpj.15721] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/11/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
SUMMARYHeteromeric acetyl‐CoA carboxylase (htACCase) catalyzes the committed step of de novo fatty acid biosynthesis in most plant plastids. Plant htACCase is comprised of four subunits: α‐ and β‐carboxyltransferase (α‐ and β‐CT), biotin carboxylase, and biotin carboxyl carrier protein. Based on in vivo absolute quantification of htACCase subunits, α‐CT is 3‐ to 10‐fold less abundant than its partner subunit β‐CT in developing Arabidopsis seeds [Wilson and Thelen, J. Proteome Res., 2018, 17 (5)]. To test the hypothesis that low expression of α‐CT limits htACCase activity and flux through fatty acid synthesis in planta, we overexpressed Pisum sativum α‐CT, either with or without its C‐terminal non‐catalytic domain, in both Arabidopsis thaliana and Camelina sativa. First‐generation Arabidopsis seed of 35S::Ps α‐CT (n = 25) and 35S::Ps α‐CTΔ406‐875 (n = 47) were on average 14% higher in oil content (% dry weight) than wild type co‐cultivated in a growth chamber. First‐generation camelina seed showed an average 8% increase compared to co‐cultivated wild type. Biochemical analyses confirmed the accumulation of Ps α‐CT and Ps α‐CTΔ406‐875 protein and higher htACCase activity in overexpression lines during early seed development. Overexpressed Ps α‐CT co‐migrated with native At β‐CT during anion exchange chromatography, indicating co‐association. By successfully increasing seed oil content upon heterologous overexpression of α‐CT, we demonstrate how absolute quantitation of in vivo protein complex stoichiometry can be used to guide rational metabolic engineering.
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Affiliation(s)
- Minmin Wang
- Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65211, USA
| | - Matthew G Garneau
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, DC, 99164, USA
| | - Arati N Poudel
- Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211, USA
| | - Daniel Lamm
- Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211, USA
| | - Abraham J Koo
- Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211, USA
| | - Philip D Bates
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, DC, 99164, USA
| | - Jay J Thelen
- Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65211, USA
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8
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Islam N, Krishnan HB, Natarajan S. Quantitative proteomic analyses reveal the dynamics of protein and amino acid accumulation during soybean seed development. Proteomics 2022; 22:e2100143. [PMID: 34825757 DOI: 10.1002/pmic.202100143] [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: 06/10/2021] [Revised: 09/28/2021] [Accepted: 10/19/2021] [Indexed: 11/09/2022]
Abstract
Using high throughput tandem mass tag (TMT) based tagging technique, we identified 4172 proteins in three developmental stages: early, mid, and late seed filling. We mapped the identified proteins to metabolic pathways associated with seed filling. The elevated abundance of several kinases was observed from the early to mid-stages of seed filling, indicating that protein phosphorylation was a significant event during this period. The early to late seed filling stages were characterized by an increased abundance of proteins associated with the cell wall, oil, and vacuolar-related processes. Among the seed storage proteins, 7S (β-subunit) and 11S (Gy3, Gy4, Gy5) steadily increased in abundance during early to late stages of seed filling, whereas 2S albumin exhibited a decrease in abundance during the same period. An increased abundance of proteases, senescence-associated proteins, and oil synthesis proteins was observed from the mid to late seed filling stages. The mid to late stages of seed filling was also characterized by a lower abundance of transferases, transporters, Kunitz family trypsin, and protease inhibitors. Two enzymes associated with methionine synthesis exhibited lower abundance from early to late stages. This study unveiled several essential enzymes/proteins related to amino acid and protein synthesis and their accumulation during seed development. All data can be accessed through this link: https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=38784ecbd0854bb3801afc0d89056f84. (Accession MSV000087577).
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Affiliation(s)
- Nazrul Islam
- Soybean Genomics and Improvement Laboratory, USDA Agricultural Research Service, Beltsville, Maryland, USA
| | - Hari B Krishnan
- Plant Genetics Research Unit, USDA Agricultural Research Service, University of Missouri, Columbia, Missouri, USA
| | - Savithiry Natarajan
- Soybean Genomics and Improvement Laboratory, USDA Agricultural Research Service, Beltsville, Maryland, USA
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9
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Farooq A, Bhat KA, Mir RA, Mahajan R, Nazir M, Sharma V, Zargar SM. Emerging trends in developing biosensor techniques to undertake plant phosphoproteomic analysis. J Proteomics 2021; 253:104458. [PMID: 34923172 DOI: 10.1016/j.jprot.2021.104458] [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: 09/21/2021] [Revised: 12/06/2021] [Accepted: 12/08/2021] [Indexed: 11/26/2022]
Abstract
Protein modifications particularly phosphorylation is governed by a complex array of mechanisms to attain a functional conformation and regulate important biological processes in organisms during external environmental stimuli and hormone signaling. Phosphoproteomics is a promising field of proteomics for identification of proteins with phosphate groups and their impact on structure, function and localization of proteins. Techniques that allow quantitative detection of proteins and their post-translational modifications (PTMs) have immensely led to understand the structural and functional dynamics of proteins. Biosensor systems are a relatively new biotechnological approach that works on the principle of transforming the interactions of different biological samples viz proteins, enzymes, aptamers, nucleic acids and so on into the signals such as electrochemical, colorimetric, optical or magnetic which have been effectively useful in the detection and characterization of phosphoproteins. The focus of our review is to provide a comprehensive account of the critical role and utility of novel biosensors such as, fluorescence based, enrichment based, nanobody based biosensors, as promising technical intercessions to identify phosphoproteins and their influence on structural dynamics of proteins. Furthermore, by studying the innovative phosphoprotein biosensors we will be able to identify the aberrant phosphorylation patterns to precisely diagnose diseases.
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Affiliation(s)
- Asmat Farooq
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, Kashmir 190025, India; Division of Biochemistry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu (SKUAST-J), Chatha, Jammu 180009, India
| | - Kaisar Ahmad Bhat
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, Kashmir 190025, India; Department of Biotechnology, School of Biosciences & Biotechnology, BGSB University, Rajouri, India
| | - Rakeeb Ahmad Mir
- Department of Biotechnology, School of Biosciences & Biotechnology, BGSB University, Rajouri, India
| | - Reetika Mahajan
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, Kashmir 190025, India
| | - Muslima Nazir
- CORD, University of Kashmir, Hazratbal, Srinagar, Jammu & Kashmir, India
| | - Vikas Sharma
- Division of Biochemistry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu (SKUAST-J), Chatha, Jammu 180009, India
| | - Sajad Majeed Zargar
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, Kashmir 190025, India.
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10
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Subba P, Prasad TSK. Plant Phosphoproteomics: Known Knowns, Known Unknowns, and Unknown Unknowns of an Emerging Systems Science Frontier. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:750-769. [PMID: 34882020 DOI: 10.1089/omi.2021.0192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Plant systems science research depends on the dynamic functional maps of the biological substrates of plant phenotypes and host/environment interactions in diverse ecologies. In this context, high-resolution mass spectrometry platforms offer comprehensive insights into the molecular pathways regulated by protein phosphorylation. Reversible protein phosphorylation is a ubiquitous reaction in signal transduction mechanisms in biological systems. In contrast to human and animal biology research, a plethora of experimental options for functional mapping and regulation of plant biology are, however, not currently available. Plant phosphoproteomics is an emerging field of research that aims at addressing this gap in systems science and plant omics, and thus has a large scope to empower fundamental discoveries. To date, large-scale data-intensive identification of phosphorylation events in plants remained technically challenging. In this expert review, we present a critical analysis and overview of phosphoproteomic studies performed in the model plant Arabidopsis thaliana. We discuss the technical strategies used for the enrichment of phosphopeptides and methods used for their quantitative assessment. Various types of mass spectrometry data acquisition and fragmentation methods are also discussed. The insights gathered here can allow plant biology and systems science researchers to design high-throughput function-oriented experimental workflows that elucidate the regulatory signaling mechanisms impacting plant physiology and plant diseases.
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Affiliation(s)
- Pratigya Subba
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
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11
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Comparative Phosphoproteomic Analysis Reveals the Response of Starch Metabolism to High-Temperature Stress in Rice Endosperm. Int J Mol Sci 2021; 22:ijms221910546. [PMID: 34638888 PMCID: PMC8508931 DOI: 10.3390/ijms221910546] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 11/30/2022] Open
Abstract
High-temperature stress severely affects rice grain quality. While extensive research has been conducted at the physiological, transcriptional, and protein levels, it is still unknown how protein phosphorylation regulates seed development in high-temperature environments. Here, we explore the impact of high-temperature stress on the phosphoproteome of developing grains from two indica rice varieties, 9311 and Guangluai4 (GLA4), with different starch qualities. A total of 9994 phosphosites from 3216 phosphoproteins were identified in all endosperm samples. We identified several consensus phosphorylation motifs ([sP], [LxRxxs], [Rxxs], [tP]) induced by high-temperature treatment and revealed a core set of protein kinases, splicing factors, and regulatory factors in response to high-temperature stress, especially those involved in starch metabolism. A detailed phosphorylation scenario in the regulation of starch biosynthesis (AGPase, GBSSI, SSIIa, SSIIIa, BEI, BEIIb, ISA1, PUL, PHO1, PTST) in rice endosperm was proposed. Furthermore, the dynamic changes in phosphorylated enzymes related to starch synthesis (SSIIIa-Ser94, BEI-Ser562, BEI-Ser620, BEI-Ser821, BEIIb-Ser685, BEIIb-Ser715) were confirmed by Western blot analysis, which revealed that phosphorylation might play specific roles in amylopectin biosynthesis in response to high-temperature stress. The link between phosphorylation-mediated regulation and starch metabolism will provide new insights into the mechanism underlying grain quality development in response to high-temperature stress.
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12
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Moradi A, Dai S, Wong EOY, Zhu G, Yu F, Lam HM, Wang Z, Burlingame A, Lin C, Afsharifar A, Yu W, Wang T, Li N. Isotopically Dimethyl Labeling-Based Quantitative Proteomic Analysis of Phosphoproteomes of Soybean Cultivars. Biomolecules 2021; 11:1218. [PMID: 34439883 PMCID: PMC8393417 DOI: 10.3390/biom11081218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 12/29/2022] Open
Abstract
Isotopically dimethyl labeling was applied in a quantitative post-translational modification (PTM) proteomic study of phosphoproteomic changes in the drought responses of two contrasting soybean cultivars. A total of 9457 phosphopeptides were identified subsequently, corresponding to 4571 phosphoprotein groups and 3889 leading phosphoproteins, which contained nine kinase families consisting of 279 kinases. These phosphoproteins contained a total of 8087 phosphosites, 6106 of which were newly identified and constituted 54% of the current soybean phosphosite repository. These phosphosites were converted into the highly conserved kinase docking sites by bioinformatics analysis, which predicted six kinase families that matched with those newly found nine kinase families. The overly post-translationally modified proteins (OPP) occupies 2.1% of these leading phosphoproteins. Most of these OPPs are photoreceptors, mRNA-, histone-, and phospholipid-binding proteins, as well as protein kinase/phosphatases. The subgroup population distribution of phosphoproteins over the number of phosphosites of phosphoproteins follows the exponential decay law, Y = 4.13e-0.098X - 0.04. Out of 218 significantly regulated unique phosphopeptide groups, 188 phosphoproteins were regulated by the drought-tolerant cultivar under the water loss condition. These significantly regulated phosphoproteins (SRP) are mainly enriched in the biological functions of water transport and deprivation, methionine metabolic processes, photosynthesis/light reaction, and response to cadmium ion, osmotic stress, and ABA response. Seventeen and 15 SRPs are protein kinases/phosphatases and transcription factors, respectively. Bioinformatics analysis again revealed that three members of the calcium dependent protein kinase family (CAMK family), GmSRK2I, GmCIPK25, and GmAKINβ1 kinases, constitute a phosphor-relay-mediated signal transduction network, regulating ion channel activities and many nuclear events in this drought-tolerant cultivar, which presumably contributes to the development of the soybean drought tolerance under water deprivation process.
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Affiliation(s)
- Atieh Moradi
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China; (A.M.); (E.O.Y.W.); (G.Z.)
- Institute of Biotechnology, School of Agriculture, Shiraz University, Shiraz 71946-84471, Iran
| | - Shuaijian Dai
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, China;
| | - Emily Oi Ying Wong
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China; (A.M.); (E.O.Y.W.); (G.Z.)
| | - Guang Zhu
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China; (A.M.); (E.O.Y.W.); (G.Z.)
| | - Fengchao Yu
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, China;
| | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China;
| | - Zhiyong Wang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA;
| | - Al Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA;
| | - Chengtao Lin
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, CA 90095, USA;
| | - Alireza Afsharifar
- Plant Virology Research Centre, School of Agriculture, Shiraz University, Shiraz 71946-84471, Iran;
| | - Weichuan Yu
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, China;
| | - Tingliang Wang
- Tsinghua-Peking Joint Centre for Life Sciences, Centre for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ning Li
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China; (A.M.); (E.O.Y.W.); (G.Z.)
- The HKUST Shenzhen Research Institut, Shenzhen 518057, China
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13
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Xi L, Zhang Z, Herold S, Kassem S, Wu XN, Schulze WX. Phosphorylation Site Motifs in Plant Protein Kinases and Their Substrates. Methods Mol Biol 2021; 2358:1-16. [PMID: 34270043 DOI: 10.1007/978-1-0716-1625-3_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Protein phosphorylation is an important cellular regulatory mechanism affecting the activity, localization, conformation, and interaction of proteins. Protein phosphorylation is catalyzed by kinases, and thus kinases are the enzymes regulating cellular signaling cascades. In the model plant Arabidopsis, 940 genes encode for kinases. The substrate proteins of kinases are phosphorylated at defined sites, which consist of common patterns around the phosphorylation site, known as phosphorylation motifs. The discovery of kinase specificity with a preference of phosphorylation of certain motifs and application of such motifs in deducing signaling cascades helped to reveal underlying regulation mechanisms, and facilitated the prediction of kinase-target pairs. In this mini-review, we took advantage of retrieved data as examples to present the functions of kinase families along with their commonly found phosphorylation motifs from their substrates.
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Affiliation(s)
- Lin Xi
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany.
| | - Zhaoxia Zhang
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Sandra Herold
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Sarah Kassem
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Xu Na Wu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, China
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
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14
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Docking of acetyl-CoA carboxylase to the plastid envelope membrane attenuates fatty acid production in plants. Nat Commun 2020; 11:6191. [PMID: 33273474 PMCID: PMC7712654 DOI: 10.1038/s41467-020-20014-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 11/09/2020] [Indexed: 11/12/2022] Open
Abstract
In plants, light-dependent activation of de novo fatty acid synthesis (FAS) is partially mediated by acetyl-CoA carboxylase (ACCase), the first committed step for this pathway. However, it is not fully understood how plants control light-dependent FAS regulation to meet the cellular demand for acyl chains. We report here the identification of a gene family encoding for three small plastidial proteins of the envelope membrane that interact with the α-carboxyltransferase (α-CT) subunit of ACCase and participate in an original mechanism restraining FAS in the light. Light enhances the interaction between carboxyltransferase interactors (CTIs) and α-CT, which in turn attenuates carbon flux into FAS. Knockouts for CTI exhibit higher rates of FAS and marked increase in absolute triacylglycerol levels in leaves, more than 4-fold higher than in wild-type plants. Furthermore, WRINKLED1, a master transcriptional regulator of FAS, positively regulates CTI1 expression by direct binding to its promoter. This study reveals that in addition to light-dependent activation, “envelope docking” of ACCase permits fine-tuning of fatty acid supply during the plant life cycle. In plants, light-dependent activation fatty acid synthesis (FAS) is mediated in part by acetyl-CoA carboxylase (ACCase). Here the authors identify a family of genes encoding carboxyltransferase interactors that attenuate FAS in the light by docking acetyl-CoA carboxylase to the plastid envelope.
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15
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Smolikova G, Gorbach D, Lukasheva E, Mavropolo-Stolyarenko G, Bilova T, Soboleva A, Tsarev A, Romanovskaya E, Podolskaya E, Zhukov V, Tikhonovich I, Medvedev S, Hoehenwarter W, Frolov A. Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives. Int J Mol Sci 2020; 21:E9162. [PMID: 33271881 PMCID: PMC7729594 DOI: 10.3390/ijms21239162] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/14/2022] Open
Abstract
For centuries, crop plants have represented the basis of the daily human diet. Among them, cereals and legumes, accumulating oils, proteins, and carbohydrates in their seeds, distinctly dominate modern agriculture, thus play an essential role in food industry and fuel production. Therefore, seeds of crop plants are intensively studied by food chemists, biologists, biochemists, and nutritional physiologists. Accordingly, seed development and germination as well as age- and stress-related alterations in seed vigor, longevity, nutritional value, and safety can be addressed by a broad panel of analytical, biochemical, and physiological methods. Currently, functional genomics is one of the most powerful tools, giving direct access to characteristic metabolic changes accompanying plant development, senescence, and response to biotic or abiotic stress. Among individual post-genomic methodological platforms, proteomics represents one of the most effective ones, giving access to cellular metabolism at the level of proteins. During the recent decades, multiple methodological advances were introduced in different branches of life science, although only some of them were established in seed proteomics so far. Therefore, here we discuss main methodological approaches already employed in seed proteomics, as well as those still waiting for implementation in this field of plant research, with a special emphasis on sample preparation, data acquisition, processing, and post-processing. Thereby, the overall goal of this review is to bring new methodologies emerging in different areas of proteomics research (clinical, food, ecological, microbial, and plant proteomics) to the broad society of seed biologists.
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Affiliation(s)
- Galina Smolikova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
| | - Daria Gorbach
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Elena Lukasheva
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Gregory Mavropolo-Stolyarenko
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Tatiana Bilova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Alena Soboleva
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Alexander Tsarev
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Ekaterina Romanovskaya
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Ekaterina Podolskaya
- Institute of Analytical Instrumentation, Russian Academy of Science; 190103 St. Petersburg, Russia;
- Institute of Toxicology, Russian Federal Medical Agency; 192019 St. Petersburg, Russia
| | - Vladimir Zhukov
- All-Russia Research Institute for Agricultural Microbiology; 196608 St. Petersburg, Russia; (V.Z.); (I.T.)
| | - Igor Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology; 196608 St. Petersburg, Russia; (V.Z.); (I.T.)
- Department of Genetics and Biotechnology, St. Petersburg State University; 199034 St. Petersburg, Russia
| | - Sergei Medvedev
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
| | - Wolfgang Hoehenwarter
- Proteome Analytics Research Group, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany;
| | - Andrej Frolov
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
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16
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Møller IM, Rao RSP, Jiang Y, Thelen JJ, Xu D. Proteomic and Bioinformatic Profiling of Transporters in Higher Plant Mitochondria. Biomolecules 2020; 10:biom10081190. [PMID: 32824289 PMCID: PMC7464266 DOI: 10.3390/biom10081190] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 12/17/2022] Open
Abstract
To function as a metabolic hub, plant mitochondria have to exchange a wide variety of metabolic intermediates as well as inorganic ions with the cytosol. As identified by proteomic profiling or as predicted by MU-LOC, a newly developed bioinformatics tool, Arabidopsis thaliana mitochondria contain 128 or 143 different transporters, respectively. The largest group is the mitochondrial carrier family, which consists of symporters and antiporters catalyzing secondary active transport of organic acids, amino acids, and nucleotides across the inner mitochondrial membrane. An impressive 97% (58 out of 60) of all the known mitochondrial carrier family members in Arabidopsis have been experimentally identified in isolated mitochondria. In addition to many other secondary transporters, Arabidopsis mitochondria contain the ATP synthase transporters, the mitochondria protein translocase complexes (responsible for protein uptake across the outer and inner membrane), ATP-binding cassette (ABC) transporters, and a number of transporters and channels responsible for allowing water and inorganic ions to move across the inner membrane driven by their transmembrane electrochemical gradient. A few mitochondrial transporters are tissue-specific, development-specific, or stress-response specific, but this is a relatively unexplored area in proteomics that merits much more attention.
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Affiliation(s)
- Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, DK-4200 Slagelse, Denmark
- Correspondence:
| | - R. Shyama Prasad Rao
- Biostatistics and Bioinformatics Division, Yenepoya Research Center, Yenepoya University, Mangaluru 575018, Karnataka, India;
| | - Yuexu Jiang
- Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; (Y.J.); (D.X.)
| | - Jay J. Thelen
- Department of Biochemistry, University of Missouri, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA;
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; (Y.J.); (D.X.)
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17
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Sinha A, Haider T, Narula K, Ghosh S, Chakraborty N, Chakraborty S. Integrated Seed Proteome and Phosphoproteome Analyses Reveal Interplay of Nutrient Dynamics, Carbon–Nitrogen Partitioning, and Oxidative Signaling in Chickpea. Proteomics 2020; 20:e1900267. [DOI: 10.1002/pmic.201900267] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 02/03/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Arunima Sinha
- National Institute of Plant Genome Research Aruna Asaf Ali Marg New Delhi 110067 India
| | - Toshiba Haider
- National Institute of Plant Genome Research Aruna Asaf Ali Marg New Delhi 110067 India
| | - Kanika Narula
- National Institute of Plant Genome Research Aruna Asaf Ali Marg New Delhi 110067 India
| | - Sudip Ghosh
- National Institute of Plant Genome Research Aruna Asaf Ali Marg New Delhi 110067 India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research Aruna Asaf Ali Marg New Delhi 110067 India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research Aruna Asaf Ali Marg New Delhi 110067 India
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18
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Liu Z, Lv J, Liu Y, Wang J, Zhang Z, Chen W, Song J, Yang B, Tan F, Zou X, Ou L. Comprehensive Phosphoproteomic Analysis of Pepper Fruit Development Provides Insight into Plant Signaling Transduction. Int J Mol Sci 2020; 21:ijms21061962. [PMID: 32183026 PMCID: PMC7139842 DOI: 10.3390/ijms21061962] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 12/29/2022] Open
Abstract
Limited knowledge is available for phosphorylation modifications in pepper (Capsicum annuum L.), especially in pepper fruit development. In this study, we conducted the first comprehensive phosphoproteomic analysis of pepper fruit at four development stage by Tandem Mass Tag proteomic approaches. A total of 2639 unique phosphopeptides spanning 1566 proteins with 4150 nonredundant sites of phosphorylation were identified, among which 2327 peptides in 1413 proteins were accurately quantified at four different stages. Mature Green (MG) to breaker stage showed the largest number of differentially expressed phosphoproteins and the number of downregulated phosphoproteins was significantly higher than that of upregulated after MG stage. Twenty seven phosphorylation motifs, including 22 pSer motifs and five pThr motifs and 85 kinase including 28 serine/threonine kinases, 14 receptor protein kinases, six mitogen-activated protein kinases, seven calcium-dependent protein kinases, two casein kinases, and some other kinases were quantified. Then the dynamic changes of phosphorylated proteins in ethylene and abscisic acid signaling transduction pathways during fruit development were analyzed. Our results provide a cascade of phosphoproteins and a regulatory network of phosphorylation signals, which help to further understand the mechanism of phosphorylation in pepper fruit development.
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Affiliation(s)
- Zhoubin Liu
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Z.L.)
| | - Junheng Lv
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; (J.L.); (Y.L.); (J.W.); (J.S.)
| | - Yuhua Liu
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; (J.L.); (Y.L.); (J.W.); (J.S.)
| | - Jing Wang
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; (J.L.); (Y.L.); (J.W.); (J.S.)
| | - Zhuqing Zhang
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China; (Z.Z.); (W.C.)
| | - Wenchao Chen
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China; (Z.Z.); (W.C.)
| | - Jingshuang Song
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China; (J.L.); (Y.L.); (J.W.); (J.S.)
| | - Bozhi Yang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Z.L.)
| | - Fangjun Tan
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China; (Z.Z.); (W.C.)
| | - Xuexiao Zou
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Z.L.)
- Correspondence: (X.Z.); (L.O.); Tel.: +86-0731-84692619 (L.O.)
| | - Lijun Ou
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Z.L.)
- Correspondence: (X.Z.); (L.O.); Tel.: +86-0731-84692619 (L.O.)
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19
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Ahsan N, Wilson RS, Rao RSP, Salvato F, Sabila M, Ullah H, Miernyk JA. Mass Spectrometry-Based Identification of Phospho-Tyr in Plant Proteomics. J Proteome Res 2020; 19:561-571. [PMID: 31967836 DOI: 10.1021/acs.jproteome.9b00550] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
O-Phosphorylation (phosphorylation of the hydroxyl-group of S, T, and Y residues) is among the first described and most thoroughly studied posttranslational modification (PTM). Y-Phosphorylation, catalyzed by Y-kinases, is a key step in both signal transduction and regulation of enzymatic activity in mammalian systems. Canonical Y-kinase sequences are absent from plant genomes/kinomes, often leading to the assumption that plant cells lack O-phospho-l-tyrosine (pY). However, recent improvements in sample preparation, coupled with advances in instrument sensitivity and accessibility, have led to results that unequivocally disproved this assumption. Identification of hundreds of pY-peptides/proteins, followed by validation using genomic, molecular, and biochemical approaches, implies previously unappreciated roles for this "animal PTM" in plants. Herein, we review extant results from studies of pY in plants and propose a strategy for preparation and analysis of pY-peptides that will allow a depth of coverage of the plant pY-proteome comparable to that achieved in mammalian systems.
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Affiliation(s)
- Nagib Ahsan
- Division of Biology and Medicine , Brown University , Providence , Rhode Island 02903 , United States.,Center for Cancer Research Development, Proteomics Core Facility , Rhode Island Hospital , Providence , Rhode Island 02903 , United States
| | - Rashaun S Wilson
- Keck Mass Spectrometry & Proteomics Resource , Yale University , New Haven , Connecticut 06511 , United States
| | - R Shyama Prasad Rao
- Biostatistics and Bioinformatics Division, Yenepoya Research Center , Yenepoya University , Mangalore 575018 , India
| | - Fernanda Salvato
- Department of Plant and Microbial Biology, College of Agriculture and Life Sciences , North Carolina State University , Raleigh , North Carolina 27695 , United States
| | - Mercy Sabila
- Department of Biology , Howard University , Washington , D.C. 20059 , United States
| | - Hemayet Ullah
- Department of Biology , Howard University , Washington , D.C. 20059 , United States
| | - Ján A Miernyk
- Division of Biochemistry , University of Missouri , Columbia , Missouri 65211 , United States
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20
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Quantitative Phosphoproteomic Analysis of Legume Using TiO 2-Based Enrichment Coupled with Isobaric Labeling. Methods Mol Biol 2020; 2107:395-406. [PMID: 31893461 DOI: 10.1007/978-1-0716-0235-5_22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Phosphorylation of proteins is the most dynamic protein modification, and its analysis aids in determining the functional and regulatory principles of important cellular pathways. The legumes constitute the third largest family of higher plants, Fabaceae, comprising about 20,000 species and are second to cereals in agricultural importance on the basis of global production. Therefore, an understanding of the developmental and adaptive processes of legumes demands identification of their regulatory components. The most crucial signature of the legume family is the symbiotic nitrogen fixation, which makes this fascinating and interesting to investigate phosphorylation events. The research on protein phosphorylation in legumes has been focused primarily on two model species, Medicago truncatula and Lotus japonicus. The development of reciprocal research in other species, particularly the crops, is lagging behind which has limited its beneficial uses in agricultural productivity. In this chapter, we outline the titanium dioxide-based enrichment of phosphopeptides for nuclear proteome analysis of a grain legume, chickpea.
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21
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Aroonluk S, Roytrakul S, Jantasuriyarat C. Identification and Characterization of Phosphoproteins in Somatic Embryogenesis Acquisition during Oil Palm Tissue Culture. PLANTS 2019; 9:plants9010036. [PMID: 31881678 PMCID: PMC7020188 DOI: 10.3390/plants9010036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/08/2019] [Accepted: 12/23/2019] [Indexed: 11/16/2022]
Abstract
Somatic embryogenesis during oil palm tissue culture is a long process. The identification of the proteins that control this process may help to shorten the time of oil palm tissue culture. We collected embryogenic callus and somatic embryos at the globular, torpedo, and cotyledon maturation stages, as well as from plantlets, for total protein extraction. An enrichment column was used to enrich the phosphoproteins, which were subjected to tryptic enzyme digestion. Each sample was analyzed with nano-liquid chromatography-tandem mass spectrometry (nano LC-MS/MS). A total of 460 phosphoproteins were identified and analyzed. The functional characterization of phosphoproteins were observed as highest in the metabolic process, protein/nucleotide/ion binding, and membrane component. The different phosphoproteins are involved in the control of vegetative growth, cellular differentiation, cell morphogenesis, and signaling roles in plants. The Quantitative Real-Time Reverse Transcription-PCR technique (qPCR) was successfully used to verify the expression of genes, and the results were consistent with the level of protein expression from nano-LC-MS/MS. The E3 ubiquitin-protein ligase and sister chromatid cohesion PDS5 were specifically expressed only in the somatic embryo and plantlet, and these could be used as protein biomarkers to determine the oil palm somatic embryo maturation stage. This study sheds light on the protein phosphorylation mechanism that regulates somatic embryogenesis transition during oil palm tissue culture.
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Affiliation(s)
- Suvichark Aroonluk
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
| | - Sittiruk Roytrakul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Klong Luang, Pathumthani 12120, Thailand;
| | - Chatchawan Jantasuriyarat
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart (CASTNAR, NRU-KU), Kasetsart University, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Kasetsart University, Bangkok 10900, Thailand
- Correspondence:
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22
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Ishikawa S, Barrero JM, Takahashi F, Nakagami H, Peck SC, Gubler F, Shinozaki K, Umezawa T. Comparative Phosphoproteomic Analysis Reveals a Decay of ABA Signaling in Barley Embryos during After-Ripening. PLANT & CELL PHYSIOLOGY 2019; 60:2758-2768. [PMID: 31435655 DOI: 10.1093/pcp/pcz163] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/11/2019] [Indexed: 06/10/2023]
Abstract
Abscisic acid (ABA) is a phytohormone and a major determinant of seed dormancy in plants. Seed dormancy is gradually lost during dry storage, a process known as 'after-ripening', and this dormancy decay is related to a decline in ABA content and sensitivity in seeds after imbibition. In this study, we aimed at investigating the effect of after-ripening on ABA signaling in barley, our cereal model species. Phosphosignaling networks in barley grains were investigated by a large-scale analysis of phosphopeptides to examine potential changes in response pathways to after-ripening. We used freshly harvested (FH) and after-ripened (AR) barley grains which showed different ABA sensitivity. A total of 1,730 phosphopeptides were identified in barley embryos isolated from half-cut grains. A comparative analysis showed that 329 and 235 phosphopeptides were upregulated or downregulated, respectively after ABA treatment, and phosphopeptides profiles were quite different between FH and AR embryos. These results were supported by peptide motif analysis which suggested that different sets of protein kinases are active in FH and AR grains. Furthermore, in vitro phosphorylation assays confirmed that some phosphopeptides were phosphorylated by SnRK2s, which are major protein kinases involved in ABA signaling. Taken together, our results revealed very distinctive phosphosignaling networks in FH and AR embryos of barley, and suggested that the after-ripening of barley grains is associated with differential regulation of phosphosignaling pathways leading to a decay of ABA signaling.
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Affiliation(s)
- Shinnosuke Ishikawa
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, 184-8588 Japan
| | - Josï M Barrero
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8538, Japan
| | - Fuminori Takahashi
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Ibaraki, 305-0074 Japan
| | - Hirofumi Nakagami
- Max-Planck-Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Scott C Peck
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8538, Japan
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Frank Gubler
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8538, Japan
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Ibaraki, 305-0074 Japan
| | - Taishi Umezawa
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, 184-8588 Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8538, Japan
- Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8538 Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, 332-0012 Japan
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23
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Kim JY, Jeong S, Kim KH, Lim WJ, Lee HY, Jeong N, Moon JK, Kim N. Dissection of soybean populations according to selection signatures based on whole-genome sequences. Gigascience 2019; 8:giz151. [PMID: 31869408 PMCID: PMC6927394 DOI: 10.1093/gigascience/giz151] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/21/2019] [Accepted: 12/05/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Domestication and improvement processes, accompanied by selections and adaptations, have generated genome-wide divergence and stratification in soybean populations. Simultaneously, soybean populations, which comprise diverse subpopulations, have developed their own adaptive characteristics enhancing fitness, resistance, agronomic traits, and morphological features. The genetic traits underlying these characteristics play a fundamental role in improving other soybean populations. RESULTS This study focused on identifying the selection signatures and adaptive characteristics in soybean populations. A core set of 245 accessions (112 wild-type, 79 landrace, and 54 improvement soybeans) selected from 4,234 soybean accessions was re-sequenced. Their genomic architectures were examined according to the domestication and improvement, and accessions were then classified into 3 wild-type, 2 landrace, and 2 improvement subgroups based on various population analyses. Selection and gene set enrichment analyses revealed that the landrace subgroups have selection signals for soybean-cyst nematode HG type 0 and seed development with germination, and that the improvement subgroups have selection signals for plant development with viability and seed development with embryo development, respectively. The adaptive characteristic for soybean-cyst nematode was partially underpinned by multiple resistance accessions, and the characteristics related to seed development were supported by our phenotypic findings for seed weights. Furthermore, their adaptive characteristics were also confirmed as genome-based evidence, and unique genomic regions that exhibit distinct selection and selective sweep patterns were revealed for 13 candidate genes. CONCLUSIONS Although our findings require further biological validation, they provide valuable information about soybean breeding strategies and present new options for breeders seeking donor lines to improve soybean populations.
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Affiliation(s)
- Jae-Yoon Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro 125, Yuseong-gu, Daejeon 34141, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Gajeong-ro 217, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Seongmun Jeong
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro 125, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Kyoung Hyoun Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro 125, Yuseong-gu, Daejeon 34141, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Gajeong-ro 217, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Won-Jun Lim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro 125, Yuseong-gu, Daejeon 34141, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Gajeong-ro 217, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Ho-Yeon Lee
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro 125, Yuseong-gu, Daejeon 34141, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Gajeong-ro 217, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Namhee Jeong
- National Institute of Crop Science, Rural Development Administration, Nongsaengmyeong-ro 370, Deokjin-gu, Jeon-Ju 54874, Republic of Korea
| | - Jung-Kyung Moon
- National Institute of Crop Science, Rural Development Administration, Nongsaengmyeong-ro 370, Deokjin-gu, Jeon-Ju 54874, Republic of Korea
| | - Namshin Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro 125, Yuseong-gu, Daejeon 34141, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Gajeong-ro 217, Yuseong-gu, Daejeon 34141, Republic of Korea
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24
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Zhang B, Chen J, Zong J, Yan X, Liu J. Unbiased phosphoproteome profiling uncovers novel phosphoproteins and phosphorylation motifs in bermudagrass stolons. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 144:92-99. [PMID: 31561202 DOI: 10.1016/j.plaphy.2019.09.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/06/2019] [Accepted: 09/21/2019] [Indexed: 05/20/2023]
Abstract
As a widely used turfgrass species, bermudagrass (Cynodon dactylon L.) can be easily propagated through colonial growth of stolons. Previous studies collectively revealed that exotic environmental factors and intrinsic hormones and genes are all involved in the differentiation, development, and diageotropical growth of stolons. However, the detailed molecular mechanism how environmental and hormone signals regulate the gene expression and biochemical activities in bermudagrass stolons remains unclear. In this study, we observed that reversible phosphorylation modification plays important roles in normal growth and physiological functions of bermudagrass stolons. LC-MS/MS analyses of the total protein extracts of bermudagrass stolons without preliminary phosphopeptide-enrichment successfully identified 646 nonredundant phosphorylation sites and 485 phosphoproteins. The phosphoproteins were significantly enriched in protein phosphorylation regulation and starch metabolism processes. Motif-X analyses further revealed that phosphoproteins containing novel phosphorylation motifs might be involved in transcription regulation of bermudagrass stolons. These results greatly expanded our understanding of the growth and development of bermudagrass stolons at the post-translational level.
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Affiliation(s)
- Bing Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
| | - Jingbo Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Junqin Zong
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Xuebing Yan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Jianxiu Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
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25
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Geng F, Liu X, Wang J, He R, Zhao J, Xiang D, Zou L, Peng L, Zhao G. In-depth mapping of the seed phosphoproteome and N-glycoproteome of Tartary buckwheat (Fagopyrum tataricum) using off-line high pH RPLC fractionation and nLC-MS/MS. Int J Biol Macromol 2019; 137:688-696. [DOI: 10.1016/j.ijbiomac.2019.07.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/21/2019] [Accepted: 07/03/2019] [Indexed: 12/18/2022]
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26
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Völz R, Rayapuram N, Hirt H. Phosphorylation regulates the activity of INDETERMINATE-DOMAIN (IDD/BIRD) proteins in response to diverse environmental conditions. PLANT SIGNALING & BEHAVIOR 2019; 14:e1642037. [PMID: 31314681 PMCID: PMC6768238 DOI: 10.1080/15592324.2019.1642037] [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: 05/29/2019] [Revised: 07/01/2019] [Accepted: 06/27/2019] [Indexed: 05/29/2023]
Abstract
INDETERMINATE-DOMAIN proteins (IDDs) belong to a diverse plant-specific family of transcriptional regulators that coordinate distinct functions during plant growth and development. The functions of several of these IDD members are transcriptionally regulated, but so far nothing is known about the regulation at the post-translational level in spite of the fact that post-translational modifications of these proteins have been reported in several large-scale proteomics studies. Recently, we showed that IDD4 is a repressor of basal immunity and its characteristic traits are predominantly determined by the phosphorylation at two distinct phosphorylation sites. This finding prompted us to comprehensively review phosphorylation of the various IDD members from the plethora of phosphoproteomics studies demonstrating the post-translational modification of IDDs at highly conserved sites under various experimental conditions. We reckon that the phosphorylation of IDDs is an underrated mechanistic aspect in their regulation and we postulate their importance in IDD/BIRD functioning.
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Affiliation(s)
- Ronny Völz
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources and Plant Immunity Research Center, Seoul National University, Seoul, Korea
| | - Naganand Rayapuram
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Heribert Hirt
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Orsay, France
- University of Vienna, Vienna, Austria
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27
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Bernal J, Mouzo D, López-Pedrouso M, Franco D, García L, Zapata C. The Major Storage Protein in Potato Tuber Is Mobilized by a Mechanism Dependent on Its Phosphorylation Status. Int J Mol Sci 2019; 20:ijms20081889. [PMID: 30999555 PMCID: PMC6514604 DOI: 10.3390/ijms20081889] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/05/2019] [Accepted: 04/13/2019] [Indexed: 12/19/2022] Open
Abstract
The role of the protein phosphorylation mechanism in the mobilization of vegetative storage proteins (VSPs) is totally unknown. Patatin is the major VSP of the potato (Solanum tuberosum L.) tuber that encompasses multiple differentially phosphorylated isoforms. In this study, temporal changes in the phosphorylation status of patatin isoforms and their involvement in patatin mobilization are investigated using phosphoproteomic methods based on targeted two-dimensional electrophoresis (2-DE). High-resolution 2-DE profiles of patatin isoforms were obtained in four sequential tuber life cycle stages of Kennebec cultivar: endodormancy, bud break, sprouting and plant growth. In-gel multiplex identification of phosphorylated isoforms with Pro-Q Diamond phosphoprotein-specific stain revealed an increase in the number of phosphorylated isoforms after the tuber endodormancy stage. In addition, we found that the phosphorylation status of patatin isoforms significantly changed throughout the tuber life cycle (P < 0.05) using the chemical method of protein dephosphorylation with hydrogen fluoride-pyridine (HF-P) coupled to 2-DE. More specifically, patatin phosphorylation increased by 32% from endodormancy to the tuber sprouting stage and subsequently decreased together with patatin degradation. Patatin isoforms were not randomly mobilized because highly phosphorylated Kuras-isoforms were preferably degraded in comparison to less phosphorylated non-Kuras isoforms. These results lead us to conclude that patatin is mobilized by a mechanism dependent on the phosphorylation status of specific isoforms.
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Affiliation(s)
- Javier Bernal
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - Daniel Mouzo
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - María López-Pedrouso
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - Daniel Franco
- Meat Technology Center of Galicia, 32900 San Cibrao das Viñas, Ourense, Spain.
| | - Lucio García
- Meat Technology Center of Galicia, 32900 San Cibrao das Viñas, Ourense, Spain.
| | - Carlos Zapata
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain.
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28
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G protein subunit phosphorylation as a regulatory mechanism in heterotrimeric G protein signaling in mammals, yeast, and plants. Biochem J 2018; 475:3331-3357. [PMID: 30413679 DOI: 10.1042/bcj20160819] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 09/28/2018] [Accepted: 10/02/2018] [Indexed: 12/15/2022]
Abstract
Heterotrimeric G proteins composed of Gα, Gβ, and Gγ subunits are vital eukaryotic signaling elements that convey information from ligand-regulated G protein-coupled receptors (GPCRs) to cellular effectors. Heterotrimeric G protein-based signaling pathways are fundamental to human health [Biochimica et Biophysica Acta (2007) 1768, 994-1005] and are the target of >30% of pharmaceuticals in clinical use [Biotechnology Advances (2013) 31, 1676-1694; Nature Reviews Drug Discovery (2017) 16, 829-842]. This review focuses on phosphorylation of G protein subunits as a regulatory mechanism in mammals, budding yeast, and plants. This is a re-emerging field, as evidence for phosphoregulation of mammalian G protein subunits from biochemical studies in the early 1990s can now be complemented with contemporary phosphoproteomics and genetic approaches applied to a diversity of model systems. In addition, new evidence implicates a family of plant kinases, the receptor-like kinases, which are monophyletic with the interleukin-1 receptor-associated kinase/Pelle kinases of metazoans, as possible GPCRs that signal via subunit phosphorylation. We describe early and modern observations on G protein subunit phosphorylation and its functional consequences in these three classes of organisms, and suggest future research directions.
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29
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Mouzo D, Bernal J, López-Pedrouso M, Franco D, Zapata C. Advances in the Biology of Seed and Vegetative Storage Proteins Based on Two-Dimensional Electrophoresis Coupled to Mass Spectrometry. Molecules 2018; 23:E2462. [PMID: 30261600 PMCID: PMC6222612 DOI: 10.3390/molecules23102462] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/18/2018] [Accepted: 09/21/2018] [Indexed: 12/24/2022] Open
Abstract
Seed storage proteins play a fundamental role in plant reproduction and human nutrition. They accumulate during seed development as reserve material for germination and seedling growth and are a major source of dietary protein for human consumption. Storage proteins encompass multiple isoforms encoded by multi-gene families that undergo abundant glycosylations and phosphorylations. Two-dimensional electrophoresis (2-DE) is a proteomic tool especially suitable for the characterization of storage proteins because of their peculiar characteristics. In particular, storage proteins are soluble multimeric proteins highly represented in the seed proteome that contain polypeptides of molecular mass between 10 and 130 kDa. In addition, high-resolution profiles can be achieved by applying targeted 2-DE protocols. 2-DE coupled with mass spectrometry (MS) has traditionally been the methodology of choice in numerous studies on the biology of storage proteins in a wide diversity of plants. 2-DE-based reference maps have decisively contributed to the current state of our knowledge about storage proteins in multiple key aspects, including identification of isoforms and quantification of their relative abundance, identification of phosphorylated isoforms and assessment of their phosphorylation status, and dynamic changes of isoforms during seed development and germination both qualitatively and quantitatively. These advances have translated into relevant information about meaningful traits in seed breeding such as protein quality, longevity, gluten and allergen content, stress response and antifungal, antibacterial, and insect susceptibility. This review addresses progress on the biology of storage proteins and application areas in seed breeding using 2-DE-based maps.
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Affiliation(s)
- Daniel Mouzo
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - Javier Bernal
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - María López-Pedrouso
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - Daniel Franco
- Meat Technology Center of Galicia, 32900 San Cibrao das Viñas, Ourense, Spain.
| | - Carlos Zapata
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain.
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30
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Patterson JA, Tetlow IJ, Emes MJ. Bioinformatic and in vitro Analyses of Arabidopsis Starch Synthase 2 Reveal Post-translational Regulatory Mechanisms. FRONTIERS IN PLANT SCIENCE 2018; 9:1338. [PMID: 30283470 PMCID: PMC6156364 DOI: 10.3389/fpls.2018.01338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/24/2018] [Indexed: 05/13/2023]
Abstract
Starch synthase 2 (SS2) is an important enzyme in leaf starch synthesis, elongating intermediate-length glucan chains. Loss of SS2 results in a distorted starch granule phenotype and altered physiochemical properties, highlighting its importance in starch biosynthesis, however, the post-translational regulation of SS2 is poorly understood. In this study, a combination of bioinformatic and in vitro analysis of recombinant SS2 was used to identify and characterize SS2 post-translational regulatory mechanisms. The SS2 N-terminal region, comprising the first 185 amino acids of the mature protein sequence, was shown to be highly variable between species, and was predicted to be intrinsically disordered. Intrinsic disorder in proteins is often correlated with protein phosphorylation and protein-protein interactions. Recombinant Arabidopsis thaliana SS2 formed homodimers that required the N-terminal region, but N-terminal peptides could not form stable homodimers alone. Recombinant SS2 was shown to be phosphorylated by chloroplast protein kinases and recombinant casein kinase II at two N-terminal serine residues (S63, S65), but mutation of these phosphorylation sites (Ser>Ala) revealed that they are not required for homo-dimerization. Heteromeric enzyme complex (HEC) formation between SS2 and SBE2.2 was shown to be ATP-dependent. However, SS2 homo-dimerization and protein phosphorylation are not required for its interaction with SBE2.2, as truncation of the SS2 N-terminus did not disrupt ATP-dependent HEC assembly. SS2 phosphorylation had no affect on its catalytic activity. Intriguingly, the removal of the N-terminal region of SS2 resulted in a 47-fold increase in its activity. As N-terminal truncation disrupted dimerization, this suggests that SS2 is more active when monomeric, and that transitions between oligomeric state may be a mechanism for SS2 regulation.
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Affiliation(s)
| | | | - Michael J. Emes
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
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31
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Benlloch R, Lois LM. Sumoylation in plants: mechanistic insights and its role in drought stress. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4539-4554. [PMID: 29931319 DOI: 10.1093/jxb/ery233] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 06/11/2018] [Indexed: 05/20/2023]
Abstract
Post-translational modification by SUMO is an essential process that has a major role in the regulation of plant development and stress responses. Such diverse biological functions are accompanied by functional diversification among the SUMO conjugation machinery components and regulatory mechanisms that has just started to be identified in plants. In this review, we focus on the current knowledge of the SUMO conjugation system in plants in terms of components, substrate specificity, cognate interactions, enzyme activity, and subcellular localization. In addition, we analyze existing data on the role of SUMOylation in plant drought tolerance in model plants and crop species, paying attention to the genetic approaches used to stimulate or inhibit endogenous SUMO conjugation. The role in drought tolerance of potential SUMO targets identified in proteomic analyses is also discussed. Overall, the complexity of SUMOylation and the multiple genetic and environmental factors that are integrated to confer drought tolerance highlight the need for significant efforts to understand the interplay between SUMO and drought.
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Affiliation(s)
- Reyes Benlloch
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - L Maria Lois
- Center for Research in Agricultural Genomics-CRAG, Edifici CRAG-Campus UAB, Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
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32
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Pang Y, Zhou X, Chen Y, Bao J. Comparative Phosphoproteomic Analysis of the Developing Seeds in Two Indica Rice ( Oryza sativa L.) Cultivars with Different Starch Quality. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:3030-3037. [PMID: 29486119 DOI: 10.1021/acs.jafc.8b00074] [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] [Indexed: 05/23/2023]
Abstract
Protein phosphorylation plays important roles in regulation of various molecular events such as plant growth and seed development. However, its involvement in starch biosynthesis is less understood. Here, a comparative phosphoproteomic analysis of two indica rice cultivars during grain development was performed. A total of 2079 and 2434 phosphopeptides from 1273 and 1442 phosphoproteins were identified, covering 2441 and 2808 phosphosites in indica rice 9311 and Guangluai4 (GLA4), respectively. Comparative analysis identified 303 differentially phosphorylated peptides, and 120 and 258 specifically phosphorylated peptides in 9311 and GLA4, respectively. Phosphopeptides in starch biosynthesis related enzymes such as AGPase, SSIIa, SSIIIa, BEI, BEIIb, PUL, and Pho1were identified. GLA4 and 9311 had different amylose content, pasting viscosities, and gelatinization temperature, suggesting subtle difference in starch biosynthesis and regulation between GLA4 and 9311. Our study will give added impetus to further understanding the regulatory mechanism of starch biosynthesis at the phosphorylation level.
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Affiliation(s)
- Yuehan Pang
- Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology , Zhejiang University , Huajiachi Campus, Hangzhou , 310029 , China
| | - Xin Zhou
- Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology , Zhejiang University , Huajiachi Campus, Hangzhou , 310029 , China
| | - Yaling Chen
- College of Life Sciences , Jiangxi Normal University , Nanchang , 330022 , China
| | - Jinsong Bao
- Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology , Zhejiang University , Huajiachi Campus, Hangzhou , 310029 , China
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33
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Ahsan N, Chen M, Salvato F, Wilson RS, Shyama Prasad Rao R, Thelen JJ. Comparative proteomic analysis provides insight into the biological role of protein phosphatase inhibitor-2 from Arabidopsis. J Proteomics 2017; 165:51-60. [DOI: 10.1016/j.jprot.2017.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 05/26/2017] [Accepted: 06/05/2017] [Indexed: 01/21/2023]
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34
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MacNeill GJ, Mehrpouyan S, Minow MAA, Patterson JA, Tetlow IJ, Emes MJ. Starch as a source, starch as a sink: the bifunctional role of starch in carbon allocation. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4433-4453. [PMID: 28981786 DOI: 10.1093/jxb/erx291] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Starch commands a central role in the carbon budget of the majority of plants on earth, and its biological role changes during development and in response to the environment. Throughout the life of a plant, starch plays a dual role in carbon allocation, acting as both a source, releasing carbon reserves in leaves for growth and development, and as a sink, either as a dedicated starch store in its own right (in seeds and tubers), or as a temporary reserve of carbon contributing to sink strength, in organs such as flowers, fruits, and developing non-starchy seeds. The presence of starch in tissues and organs thus has a profound impact on the physiology of the growing plant as its synthesis and degradation governs the availability of free sugars, which in turn control various growth and developmental processes. This review attempts to summarize the large body of information currently available on starch metabolism and its relationship to wider aspects of carbon metabolism and plant nutrition. It highlights gaps in our knowledge and points to research areas that show promise for bioengineering and manipulation of starch metabolism in order to achieve more desirable phenotypes such as increased yield or plant biomass.
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Affiliation(s)
- Gregory J MacNeill
- Department of Molecular and Cellular Biology, College of Biological Science, Summerlee Science Complex, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Sahar Mehrpouyan
- Department of Molecular and Cellular Biology, College of Biological Science, Summerlee Science Complex, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Mark A A Minow
- Department of Molecular and Cellular Biology, College of Biological Science, Summerlee Science Complex, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Jenelle A Patterson
- Department of Molecular and Cellular Biology, College of Biological Science, Summerlee Science Complex, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Ian J Tetlow
- Department of Molecular and Cellular Biology, College of Biological Science, Summerlee Science Complex, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Michael J Emes
- Department of Molecular and Cellular Biology, College of Biological Science, Summerlee Science Complex, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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35
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Gupta M, Bhaskar PB, Sriram S, Wang PH. Integration of omics approaches to understand oil/protein content during seed development in oilseed crops. PLANT CELL REPORTS 2017; 36:637-652. [PMID: 27796489 DOI: 10.1007/s00299-016-2064-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 10/11/2016] [Indexed: 05/23/2023]
Abstract
Oilseed crops, especially soybean (Glycine max) and canola/rapeseed (Brassica napus), produce seeds that are rich in both proteins and oils and that are major sources of energy and nutrition worldwide. Most of the nutritional content in the seed is accumulated in the embryo during the seed filling stages of seed development. Understanding the metabolic pathways that are active during seed filling and how they are regulated are essential prerequisites to crop improvement. In this review, we summarize various omics studies of soybean and canola/rapeseed during seed filling, with emphasis on oil and protein traits, to gain a systems-level understanding of seed development. Currently, most (80-85%) of the soybean and rapeseed reference genomes have been sequenced (950 and 850 megabases, respectively). Parallel to these efforts, extensive omics datasets from different seed filling stages have become available. Transcriptome and proteome studies have detected preponderance of starch metabolism and glycolysis enzymes to be the possible cause of higher oil in B. napus compared to other crops. Small RNAome studies performed during the seed filling stages have revealed miRNA-mediated regulation of transcription factors, with the suggestion that this interaction could be responsible for transitioning the seeds from embryogenesis to maturation. In addition, progress made in dissecting the regulation of de novo fatty acid synthesis and protein storage pathways is described. Advances in high-throughput omics and comprehensive tissue-specific analyses make this an exciting time to attempt knowledge-driven investigation of complex regulatory pathways.
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Affiliation(s)
- Manju Gupta
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN, 46268, USA.
| | - Pudota B Bhaskar
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN, 46268, USA
| | | | - Po-Hao Wang
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN, 46268, USA
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Wang X, Komatsu S. Improvement of Soybean Products Through the Response Mechanism Analysis Using Proteomic Technique. ADVANCES IN FOOD AND NUTRITION RESEARCH 2017; 82:117-148. [PMID: 28427531 DOI: 10.1016/bs.afnr.2016.12.006] [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: 06/07/2023]
Abstract
Soybean is rich in protein/vegetable oil and contains several phytochemicals such as isoflavones and phenolic compounds. Because of the predominated nutritional values, soybean is considered as traditional health benefit food. Soybean is a widely cultivated crop; however, its growth and yield are markedly affected by adverse environmental conditions. Proteomic techniques make it feasible to map protein profiles both during soybean growth and under unfavorable conditions. The stress-responsive mechanisms during soybean growth have been uncovered with the help of proteomic studies. In this review, the history of soybean as food and the morphology/physiology of soybean are described. The utilization of proteomics during soybean germination and development is summarized. In addition, the stress-responsive mechanisms explored using proteomic techniques are reviewed in soybean.
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Affiliation(s)
- Xin Wang
- National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Setsuko Komatsu
- National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.
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Zhen S, Deng X, Zhang M, Zhu G, Lv D, Wang Y, Zhu D, Yan Y. Comparative Phosphoproteomic Analysis under High-Nitrogen Fertilizer Reveals Central Phosphoproteins Promoting Wheat Grain Starch and Protein Synthesis. FRONTIERS IN PLANT SCIENCE 2017; 8:67. [PMID: 28194157 PMCID: PMC5277015 DOI: 10.3389/fpls.2017.00067] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 01/12/2017] [Indexed: 05/20/2023]
Abstract
Nitrogen (N) is a macronutrient important for plant growth and development. It also strongly influences starch and protein synthesis, closely related to grain yield and quality. We performed the first comparative phosphoproteomic analysis of developing wheat grains in response to high-N fertilizer. Physiological and biochemical analyses showed that application of high-N fertilizer resulted in significant increases in leaf length and area, chlorophyll content, the activity of key enzymes in leaves such as nitrate reductase (NR), and in grains such as sucrose phosphate synthase (SPS), sucrose synthase (SuSy), and ADP glucose pyrophosphorylase (AGPase). This enhanced enzyme activity led to significant improvements in starch content, grain yield, and ultimately, bread making quality. Comparative phosphoproteomic analysis of developing grains under the application of high-N fertilizer performed 15 and 25 days post-anthesis identified 2470 phosphosites among 1372 phosphoproteins, of which 411 unique proteins displayed significant changes in phosphorylation level (>2-fold or <0.5-fold). These phosphoproteins are involved mainly in signaling transduction, starch synthesis, energy metabolism. Pro-Q diamond staining and Western blotting confirmed our phosphoproteomic results. We propose a putative pathway to elucidate the important roles of the central phosphoproteins regulating grain starch and protein synthesis. Our results provide new insights into the molecular mechanisms of protein phosphorylation modifications involved in grain development, yield and quality formation.
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Affiliation(s)
- Shoumin Zhen
- College of Life Science, Capital Normal UniversityBeijing, China
| | - Xiong Deng
- College of Life Science, Capital Normal UniversityBeijing, China
| | - Ming Zhang
- College of Life Science, Capital Normal UniversityBeijing, China
- College of Life Science, Heze UniversityShandong, China
| | - Gengrui Zhu
- College of Life Science, Capital Normal UniversityBeijing, China
| | - Dongwen Lv
- College of Life Science, Capital Normal UniversityBeijing, China
| | - Yaping Wang
- College of Life Science, Capital Normal UniversityBeijing, China
| | - Dong Zhu
- College of Life Science, Capital Normal UniversityBeijing, China
| | - Yueming Yan
- College of Life Science, Capital Normal UniversityBeijing, China
- Hubei Collaborative Innovation Center for Grain IndustryJingzhou, China
- *Correspondence: Yueming Yan
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Chen GX, Zhou JW, Liu YL, Lu XB, Han CX, Zhang WY, Xu YH, Yan YM. Biosynthesis and Regulation of Wheat Amylose and Amylopectin from Proteomic and Phosphoproteomic Characterization of Granule-binding Proteins. Sci Rep 2016; 6:33111. [PMID: 27604546 PMCID: PMC5015113 DOI: 10.1038/srep33111] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/14/2016] [Indexed: 11/09/2022] Open
Abstract
Waxy starch has an important influence on the qualities of breads. Generally, grain weight and yield in waxy wheat (Triticum aestivum L.) are significantly lower than in bread wheat. In this study, we performed the first proteomic and phosphoproteomic analyses of starch granule-binding proteins by comparing the waxy wheat cultivar Shannong 119 and the bread wheat cultivar Nongda 5181. These results indicate that reduced amylose content does not affect amylopectin synthesis, but it causes significant reduction of total starch biosynthesis, grain size, weight and grain yield. Two-dimensional differential in-gel electrophoresis identified 40 differentially expressed protein (DEP) spots in waxy and non-waxy wheats, which belonged mainly to starch synthase (SS) I, SS IIa and granule-bound SS I. Most DEPs involved in amylopectin synthesis showed a similar expression pattern during grain development, suggesting relatively independent amylose and amylopectin synthesis pathways. Phosphoproteome analysis of starch granule-binding proteins, using TiO2 microcolumns and LC-MS/MS, showed that the total number of phosphoproteins and their phosphorylation levels in ND5181 were significantly higher than in SN119, but proteins controlling amylopectin synthesis had similar phosphorylation levels. Our results revealed the lack of amylose did not affect the expression and phosphorylation of the starch granule-binding proteins involved in amylopectin biosynthesis.
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Affiliation(s)
- Guan-Xing Chen
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Jian-Wen Zhou
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Yan-Lin Liu
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Xiao-Bing Lu
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Cai-Xia Han
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Wen-Ying Zhang
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, 434025 Jingzhou, China
| | - Yan-Hao Xu
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, 434025 Jingzhou, China
| | - Yue-Ming Yan
- College of Life Science, Capital Normal University, 100048 Beijing, China
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, 434025 Jingzhou, China
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Salie MJ, Zhang N, Lancikova V, Xu D, Thelen JJ. A Family of Negative Regulators Targets the Committed Step of de Novo Fatty Acid Biosynthesis. THE PLANT CELL 2016; 28:2312-2325. [PMID: 27559025 PMCID: PMC5059801 DOI: 10.1105/tpc.16.00317] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 08/12/2016] [Accepted: 08/23/2016] [Indexed: 05/18/2023]
Abstract
Acetyl-CoA carboxylase (ACCase) catalyzes the committed step of de novo fatty acid biosynthesis. In prokaryotes, green algae, and most plants, this enzyme is a heteromeric complex requiring four different subunits for activity. The plant complex is recalcitrant to conventional purification schemes and hence the structure and composition of the full assembly have been unclear. In vivo coimmunoprecipitation using subunit-specific antibodies identified a novel family of proteins in Arabidopsis thaliana annotated as biotin/lipoyl attachment domain containing (BADC) proteins. Results from yeast two-hybrid and coexpression in Escherichia coli confirmed that all three BADC isoforms interact with the two biotin carboxyl carrier protein (BCCP) isoforms of Arabidopsis ACCase. These proteins resemble BCCP subunits but are not biotinylated due to a mutated biotinylation motif. We demonstrate that BADC proteins significantly inhibit ACCase activity in both E. coli and Arabidopsis. Targeted gene silencing of BADC isoform 1 in Arabidopsis significantly increased seed oil content when normalized to either mass or individual seed. We conclude the BADC proteins are ancestral BCCPs that gained a new function as negative regulators of ACCase after initial loss of the biotinylation motif. A functional model is proposed.
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Affiliation(s)
- Matthew J Salie
- Department of Biochemistry, University of Missouri-Columbia, Christopher S. Bond Life Sciences Center, Columbia, Missouri 65211
| | - Ning Zhang
- Informatics Institute and Department of Computer Science, University of Missouri-Columbia, Christopher S. Bond Life Sciences Center, Columbia, Missouri 65211
| | - Veronika Lancikova
- Department of Biochemistry, University of Missouri-Columbia, Christopher S. Bond Life Sciences Center, Columbia, Missouri 65211
| | - Dong Xu
- Informatics Institute and Department of Computer Science, University of Missouri-Columbia, Christopher S. Bond Life Sciences Center, Columbia, Missouri 65211
| | - Jay J Thelen
- Department of Biochemistry, University of Missouri-Columbia, Christopher S. Bond Life Sciences Center, Columbia, Missouri 65211
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Zhu M, Monroe JG, Suhail Y, Villiers F, Mullen J, Pater D, Hauser F, Jeon BW, Bader JS, Kwak JM, Schroeder JI, McKay JK, Assmann SM. Molecular and systems approaches towards drought-tolerant canola crops. THE NEW PHYTOLOGIST 2016; 210:1169-1189. [PMID: 26879345 DOI: 10.1111/nph.13866] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 12/14/2015] [Indexed: 06/05/2023]
Abstract
1169 I. 1170 II. 1170 III. 1172 IV. 1176 V. 1181 VI. 1182 1183 References 1183 SUMMARY: Modern agriculture is facing multiple challenges including the necessity for a substantial increase in production to meet the needs of a burgeoning human population. Water shortage is a deleterious consequence of both population growth and climate change and is one of the most severe factors limiting global crop productivity. Brassica species, particularly canola varieties, are cultivated worldwide for edible oil, animal feed, and biodiesel, and suffer dramatic yield loss upon drought stress. The recent release of the Brassica napus genome supplies essential genetic information to facilitate identification of drought-related genes and provides new information for agricultural improvement in this species. Here we summarize current knowledge regarding drought responses of canola, including physiological and -omics effects of drought. We further discuss knowledge gained through translational biology based on discoveries in the closely related reference species Arabidopsis thaliana and through genetic strategies such as genome-wide association studies and analysis of natural variation. Knowledge of drought tolerance/resistance responses in canola together with research outcomes arising from new technologies and methodologies will inform novel strategies for improvement of drought tolerance and yield in this and other important crop species.
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Affiliation(s)
- Mengmeng Zhu
- Biology Department, Pennsylvania State University, University Park, PA, 16802, USA
| | - J Grey Monroe
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, 80523, USA
| | - Yasir Suhail
- Department of Biomedical Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Florent Villiers
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20740, USA
| | - Jack Mullen
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, 80523, USA
| | - Dianne Pater
- Division of Biological Sciences, Cell and Developmental Biology Section, Food and Fuel for the 21st Century Center, University of California San Diego, La Jolla, CA, 92093-016, USA
| | - Felix Hauser
- Division of Biological Sciences, Cell and Developmental Biology Section, Food and Fuel for the 21st Century Center, University of California San Diego, La Jolla, CA, 92093-016, USA
| | - Byeong Wook Jeon
- Biology Department, Pennsylvania State University, University Park, PA, 16802, USA
| | - Joel S Bader
- Department of Biomedical Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- School of Medicine, The Johns Hopkins University, Baltimore, MD, 21205, USA
| | - June M Kwak
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20740, USA
- Center for Plant Aging Research, Institute for Basic Science, Department of New Biology, DGIST, Daegu, 42988, Korea
| | - Julian I Schroeder
- Division of Biological Sciences, Cell and Developmental Biology Section, Food and Fuel for the 21st Century Center, University of California San Diego, La Jolla, CA, 92093-016, USA
| | - John K McKay
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, 80523, USA
| | - Sarah M Assmann
- Biology Department, Pennsylvania State University, University Park, PA, 16802, USA
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Hafidh S, Fíla J, Honys D. Male gametophyte development and function in angiosperms: a general concept. PLANT REPRODUCTION 2016; 29:31-51. [PMID: 26728623 DOI: 10.1007/s00497-015-0272-4] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 12/19/2015] [Indexed: 05/23/2023]
Abstract
Overview of pollen development. Male gametophyte development of angiosperms is a complex process that requires coordinated activity of different cell types and tissues of both gametophytic and sporophytic origin and the appropriate specific gene expression. Pollen ontogeny is also an excellent model for the dissection of cellular networks that control cell growth, polarity, cellular differentiation and cell signaling. This article describes two sequential phases of angiosperm pollen ontogenesis-developmental phase leading to the formation of mature pollen grains, and a functional or progamic phase, beginning with the impact of the grains on the stigma surface and ending at double fertilization. Here we present an overview of important cellular processes in pollen development and explosive pollen tube growth stressing the importance of reserves accumulation and mobilization and also the mutual activation of pollen tube and pistil tissues, pollen tube guidance and the communication between male and female gametophytes. We further describe the recent advances in regulatory mechanisms involved such as posttranscriptional regulation (including mass transcript storage) and posttranslational modifications to modulate protein function, intracellular metabolic signaling, ionic gradients such as Ca(2+) and H(+) ions, cell wall synthesis, protein secretion and intercellular signaling within the reproductive tissues.
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Affiliation(s)
- Said Hafidh
- Institute of Experimental Botany ASCR, v.v.i., Rozvojová 263, 165 00, Prague 6, Czech Republic
| | - Jan Fíla
- Institute of Experimental Botany ASCR, v.v.i., Rozvojová 263, 165 00, Prague 6, Czech Republic
| | - David Honys
- Institute of Experimental Botany ASCR, v.v.i., Rozvojová 263, 165 00, Prague 6, Czech Republic.
- Department of Experimental Plant Biology, Faculty of Science, Charles University in Prague, Viničná 5, 128 44, Prague 2, Czech Republic.
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Quantitative proteomics and phosphoproteomics of sugar beet monosomic addition line M14 in response to salt stress. J Proteomics 2016; 143:286-297. [PMID: 27233743 DOI: 10.1016/j.jprot.2016.04.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/21/2016] [Accepted: 04/11/2016] [Indexed: 12/18/2022]
Abstract
UNLABELLED Salinity is a major abiotic stress affecting plant growth, development and agriculture productivity. Understanding the molecular mechanisms of salt stress tolerance will provide valuable information for effective crop engineering and breeding. Sugar beet monosomic addition line M14 obtained from the intercross between Beta vulgaris L. and Beta corolliflora Zoss exhibits tolerance to salt stress. In this study, the changes in the M14 proteome and phosphoproteome induced by salt stress were analyzed. We report the characteristics of the M14 plants under 0, 200, and 400mM NaCl using label-free quantitative proteomics approaches. Protein samples were subjected to total proteome profiling using LC-MS/MS and phosphopeptide enrichment to identify phosphopeptides and phosphoproteins. A total of 2182 proteins were identified and 114 proteins showed differential levels under salt stress. Interestingly, 189 phosphoproteins exhibited significant changes at the phosphorylation level under salt stress. Several signaling components associated with salt stress were found, e.g. 14-3-3 and mitogen-activated protein kinases (MAPK). Fifteen differential phosphoproteins and proteins involved in signal transduction were tested at the transcriptional level. The results revealed the short-term salt responsive mechanisms of the special sugar beet M14 line using label-free quantitative phosphoproteomics. BIOLOGICAL SIGNIFICANCE Sugar beet monosomic addition line M14 is a special germplasm with salt stress tolerance. Analysis of the M14 proteome and phosphoproteome under salt stress has provided insight into specific response mechanisms underlying salt stress tolerance. Reversible protein phosphorylation regulates a wide range of cellular processes such as transmembrane signaling, intracellular amplification of signals, and cell-cycle control. This study has identified significantly changed proteins and phosphoproteins, and determined their potential relevance to salt stress response. The knowledge gained can be potentially applied to improving crop salt tolerance.
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Salie MJ, Thelen JJ. Regulation and structure of the heteromeric acetyl-CoA carboxylase. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1861:1207-1213. [PMID: 27091637 DOI: 10.1016/j.bbalip.2016.04.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/31/2016] [Accepted: 04/01/2016] [Indexed: 11/16/2022]
Abstract
The enzyme acetyl-CoA carboxylase (ACCase) catalyzes the committed step of the de novo fatty acid biosynthesis (FAS) pathway by converting acetyl-CoA to malonyl-CoA. Two forms of ACCase exist in nature, a homomeric and heteromic form. The heteromeric form of this enzyme requires four different subunits for activity: biotin carboxylase; biotin carboxyl carrier protein; and α- and β-carboxyltransferases. Heteromeric ACCases (htACCase) can be found in prokaryotes and the plastids of most plants. The plant htACCase is regulated by diverse mechanisms reflected by the biochemical and genetic complexity of this multienzyme complex and the plastid stroma where it resides. In this review we summarize the regulation of the plant htACCase and also describe the structural characteristics of this complex from both prokaryotes and plants. This article is part of a Special Issue entitled: Plant Lipid Biology edited by Kent D. Chapman and Ivo Feussner.
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Affiliation(s)
- Matthew J Salie
- Department of Biochemistry, University of Missouri-Columbia, Christopher S. Bond Life Sciences Center, 1201 E. Rollins, Columbia, MO 65201, USA.
| | - Jay J Thelen
- Department of Biochemistry, University of Missouri-Columbia, Christopher S. Bond Life Sciences Center, 1201 E. Rollins, Columbia, MO 65201, USA.
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Ning DL, Liu KH, Liu CC, Liu JW, Qian CR, Yu Y, Wang YF, Wang YC, Wang BC. Large-scale comparative phosphoprotein analysis of maize seedling leaves during greening. PLANTA 2016; 243:501-517. [PMID: 26497871 DOI: 10.1007/s00425-015-2420-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Accepted: 10/06/2015] [Indexed: 06/05/2023]
Abstract
MAIN CONCLUSION : Large-scale comparative phosphoprotein analysis in maize seedlings reveals a complicated molecular regulation mechanism at the phosphoproteomic level during de-etiolation. In the present study we report a phosphoproteomic study conducted on Zea mays etiolated leaves harvested at three time points during greening (etiolated seedlings and seedlings exposed to light for 6 or 12 h). We identified a total of 2483 phosphopeptides containing 2389 unambiguous phosphosites from 1339 proteins. The abundance of nearly 692 phosphorylated peptides containing 783 phosphosites was reproducible and profiled with high confidence among treatments. Comparisons with other large-scale phosphoproteomic studies revealed that 473 of the phosphosites are novel to this study. Of the 783 phosphosites identified, 171, 79, and 138 were identified in 0, 6, and 12 h samples, respectively, which suggest that regulation of phosphorylation plays important roles during maize seedling de-etiolation. Our experimental methods included enrichment of phosphoproteins, allowing the identification of a great number of low abundance proteins, such as transcription factors, protein kinases, and photoreceptors. Most of the identified phosphoproteins were involved in gene transcription, post-transcriptional regulation, or signal transduction, and only a few were involved in photosynthesis and carbon metabolism. It is noteworthy that tyrosine phosphorylation and calcium signaling pathways might play important roles during maize seedling de-etiolation. Taken together, we have elucidated a new level of complexity in light-induced reversible protein phosphorylation during maize seedling de-etiolation.
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45
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Kim SY, Bender KW, Walker BJ, Zielinski RE, Spalding MH, Ort DR, Huber SC. The Plastid Casein Kinase 2 Phosphorylates Rubisco Activase at the Thr-78 Site but Is Not Essential for Regulation of Rubisco Activation State. FRONTIERS IN PLANT SCIENCE 2016; 7:404. [PMID: 27064346 PMCID: PMC4814456 DOI: 10.3389/fpls.2016.00404] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/16/2016] [Indexed: 05/05/2023]
Abstract
Rubisco activase (RCA) is essential for the activation of Rubisco, the carboxylating enzyme of photosynthesis. In Arabidopsis, RCA is composed of a large RCAα and small RCAβ isoform that are formed by alternative splicing of a single gene (At2g39730). The activity of Rubisco is controlled in response to changes in irradiance by regulation of RCA activity, which is known to involve a redox-sensitive disulfide bond located in the carboxy-terminal extension of the RCAα subunit. Additionally, phosphorylation of RCA threonine-78 (Thr-78) has been reported to occur in the dark suggesting that phosphorylation may also be associated with dark-inactivation of RCA and deactivation of Rubisco. In the present study, we developed site-specific antibodies to monitor phosphorylation of RCA at the Thr-78 site and used non-reducing SDS-PAGE to monitor the redox status of the RCAα subunit. By immunoblotting, phosphorylation of both RCA isoforms occurred at low light and in the dark and feeding peroxide or DTT to leaf segments indicated that redox status of the chloroplast stroma was a critical factor controlling RCA phosphorylation. Use of a knockout mutant identified the plastid-targeted casein kinase 2 (cpCK2α) as the major protein kinase involved in RCA phosphorylation. Studies with recombinant cpCK2α and synthetic peptide substrates identified acidic residues at the -1, +2, and +3 positions surrounding Thr-78 as strong positive recognition elements. The cpck2 knockout mutant had strongly reduced phosphorylation at the Thr-78 site but was similar to wild type plants in terms of induction kinetics of photosynthesis following transfer from darkness or low light to high light, suggesting that if phosphorylation of RCA Thr-78 plays a direct role it would be redundant to redox regulation for control of Rubisco activation state under normal conditions.
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Affiliation(s)
- Sang Y. Kim
- Global Change and Photosynthesis Research Unit, United States Department of Agriculture – Agricultural Research Service, UrbanaIL, USA
- Plant Biology, University of Illinois at Champaign–Urbana, UrbanaIL, USA
| | - Kyle W. Bender
- Plant Biology, University of Illinois at Champaign–Urbana, UrbanaIL, USA
| | - Berkley J. Walker
- Global Change and Photosynthesis Research Unit, United States Department of Agriculture – Agricultural Research Service, UrbanaIL, USA
- Carl R. Woese Institute for Genomic Biology, UrbanaIL, USA
| | | | - Martin H. Spalding
- Genetics, Development and Cell Biology, Iowa State University, AmesIA, USA
| | - Donald R. Ort
- Global Change and Photosynthesis Research Unit, United States Department of Agriculture – Agricultural Research Service, UrbanaIL, USA
- Plant Biology, University of Illinois at Champaign–Urbana, UrbanaIL, USA
- Carl R. Woese Institute for Genomic Biology, UrbanaIL, USA
| | - Steven C. Huber
- Global Change and Photosynthesis Research Unit, United States Department of Agriculture – Agricultural Research Service, UrbanaIL, USA
- Plant Biology, University of Illinois at Champaign–Urbana, UrbanaIL, USA
- *Correspondence: Steven C. Huber,
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Schwender J, Hebbelmann I, Heinzel N, Hildebrandt T, Rogers A, Naik D, Klapperstück M, Braun HP, Schreiber F, Denolf P, Borisjuk L, Rolletschek H. Quantitative Multilevel Analysis of Central Metabolism in Developing Oilseeds of Oilseed Rape during in Vitro Culture. PLANT PHYSIOLOGY 2015; 168:828-48. [PMID: 25944824 PMCID: PMC4741336 DOI: 10.1104/pp.15.00385] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 05/04/2015] [Indexed: 05/05/2023]
Abstract
Seeds provide the basis for many food, feed, and fuel products. Continued increases in seed yield, composition, and quality require an improved understanding of how the developing seed converts carbon and nitrogen supplies into storage. Current knowledge of this process is often based on the premise that transcriptional regulation directly translates via enzyme concentration into flux. In an attempt to highlight metabolic control, we explore genotypic differences in carbon partitioning for in vitro cultured developing embryos of oilseed rape (Brassica napus). We determined biomass composition as well as 79 net fluxes, the levels of 77 metabolites, and 26 enzyme activities with specific focus on central metabolism in nine selected germplasm accessions. Overall, we observed a tradeoff between the biomass component fractions of lipid and starch. With increasing lipid content over the spectrum of genotypes, plastidic fatty acid synthesis and glycolytic flux increased concomitantly, while glycolytic intermediates decreased. The lipid/starch tradeoff was not reflected at the proteome level, pointing to the significance of (posttranslational) metabolic control. Enzyme activity/flux and metabolite/flux correlations suggest that plastidic pyruvate kinase exerts flux control and that the lipid/starch tradeoff is most likely mediated by allosteric feedback regulation of phosphofructokinase and ADP-glucose pyrophosphorylase. Quantitative data were also used to calculate in vivo mass action ratios, reaction equilibria, and metabolite turnover times. Compounds like cyclic 3',5'-AMP and sucrose-6-phosphate were identified to potentially be involved in so far unknown mechanisms of metabolic control. This study provides a rich source of quantitative data for those studying central metabolism.
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Affiliation(s)
- Jörg Schwender
- Brookhaven National Laboratory, Biological, Environmental, and Climate Sciences Department, Upton, New York 11973 (J.S., I.H., A.R., D.N.);Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (N.H., L.B., H.R.);Institut für Pflanzengenetik, Universität Hannover, 30419 Hannover, Germany (T.H., H.-P.B.);Department of Environmental Science, Indian Institute of Advanced Research, Koba, Gandhinagar 382007, Gujarat, India (D.N.);Clayton School of Information Technology, Monash University, Melbourne, Victoria 3800, Australia (M.K., F.S.);Institute of Computer Science, University Halle-Wittenberg, 06120 Halle, Germany (F.S.); andBayer CropScience, 9052 Zwijnaarde, Belgium (P.D.)
| | - Inga Hebbelmann
- Brookhaven National Laboratory, Biological, Environmental, and Climate Sciences Department, Upton, New York 11973 (J.S., I.H., A.R., D.N.);Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (N.H., L.B., H.R.);Institut für Pflanzengenetik, Universität Hannover, 30419 Hannover, Germany (T.H., H.-P.B.);Department of Environmental Science, Indian Institute of Advanced Research, Koba, Gandhinagar 382007, Gujarat, India (D.N.);Clayton School of Information Technology, Monash University, Melbourne, Victoria 3800, Australia (M.K., F.S.);Institute of Computer Science, University Halle-Wittenberg, 06120 Halle, Germany (F.S.); andBayer CropScience, 9052 Zwijnaarde, Belgium (P.D.)
| | - Nicolas Heinzel
- Brookhaven National Laboratory, Biological, Environmental, and Climate Sciences Department, Upton, New York 11973 (J.S., I.H., A.R., D.N.);Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (N.H., L.B., H.R.);Institut für Pflanzengenetik, Universität Hannover, 30419 Hannover, Germany (T.H., H.-P.B.);Department of Environmental Science, Indian Institute of Advanced Research, Koba, Gandhinagar 382007, Gujarat, India (D.N.);Clayton School of Information Technology, Monash University, Melbourne, Victoria 3800, Australia (M.K., F.S.);Institute of Computer Science, University Halle-Wittenberg, 06120 Halle, Germany (F.S.); andBayer CropScience, 9052 Zwijnaarde, Belgium (P.D.)
| | - Tatjana Hildebrandt
- Brookhaven National Laboratory, Biological, Environmental, and Climate Sciences Department, Upton, New York 11973 (J.S., I.H., A.R., D.N.);Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (N.H., L.B., H.R.);Institut für Pflanzengenetik, Universität Hannover, 30419 Hannover, Germany (T.H., H.-P.B.);Department of Environmental Science, Indian Institute of Advanced Research, Koba, Gandhinagar 382007, Gujarat, India (D.N.);Clayton School of Information Technology, Monash University, Melbourne, Victoria 3800, Australia (M.K., F.S.);Institute of Computer Science, University Halle-Wittenberg, 06120 Halle, Germany (F.S.); andBayer CropScience, 9052 Zwijnaarde, Belgium (P.D.)
| | - Alistair Rogers
- Brookhaven National Laboratory, Biological, Environmental, and Climate Sciences Department, Upton, New York 11973 (J.S., I.H., A.R., D.N.);Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (N.H., L.B., H.R.);Institut für Pflanzengenetik, Universität Hannover, 30419 Hannover, Germany (T.H., H.-P.B.);Department of Environmental Science, Indian Institute of Advanced Research, Koba, Gandhinagar 382007, Gujarat, India (D.N.);Clayton School of Information Technology, Monash University, Melbourne, Victoria 3800, Australia (M.K., F.S.);Institute of Computer Science, University Halle-Wittenberg, 06120 Halle, Germany (F.S.); andBayer CropScience, 9052 Zwijnaarde, Belgium (P.D.)
| | - Dhiraj Naik
- Brookhaven National Laboratory, Biological, Environmental, and Climate Sciences Department, Upton, New York 11973 (J.S., I.H., A.R., D.N.);Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (N.H., L.B., H.R.);Institut für Pflanzengenetik, Universität Hannover, 30419 Hannover, Germany (T.H., H.-P.B.);Department of Environmental Science, Indian Institute of Advanced Research, Koba, Gandhinagar 382007, Gujarat, India (D.N.);Clayton School of Information Technology, Monash University, Melbourne, Victoria 3800, Australia (M.K., F.S.);Institute of Computer Science, University Halle-Wittenberg, 06120 Halle, Germany (F.S.); andBayer CropScience, 9052 Zwijnaarde, Belgium (P.D.)
| | - Matthias Klapperstück
- Brookhaven National Laboratory, Biological, Environmental, and Climate Sciences Department, Upton, New York 11973 (J.S., I.H., A.R., D.N.);Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (N.H., L.B., H.R.);Institut für Pflanzengenetik, Universität Hannover, 30419 Hannover, Germany (T.H., H.-P.B.);Department of Environmental Science, Indian Institute of Advanced Research, Koba, Gandhinagar 382007, Gujarat, India (D.N.);Clayton School of Information Technology, Monash University, Melbourne, Victoria 3800, Australia (M.K., F.S.);Institute of Computer Science, University Halle-Wittenberg, 06120 Halle, Germany (F.S.); andBayer CropScience, 9052 Zwijnaarde, Belgium (P.D.)
| | - Hans-Peter Braun
- Brookhaven National Laboratory, Biological, Environmental, and Climate Sciences Department, Upton, New York 11973 (J.S., I.H., A.R., D.N.);Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (N.H., L.B., H.R.);Institut für Pflanzengenetik, Universität Hannover, 30419 Hannover, Germany (T.H., H.-P.B.);Department of Environmental Science, Indian Institute of Advanced Research, Koba, Gandhinagar 382007, Gujarat, India (D.N.);Clayton School of Information Technology, Monash University, Melbourne, Victoria 3800, Australia (M.K., F.S.);Institute of Computer Science, University Halle-Wittenberg, 06120 Halle, Germany (F.S.); andBayer CropScience, 9052 Zwijnaarde, Belgium (P.D.)
| | - Falk Schreiber
- Brookhaven National Laboratory, Biological, Environmental, and Climate Sciences Department, Upton, New York 11973 (J.S., I.H., A.R., D.N.);Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (N.H., L.B., H.R.);Institut für Pflanzengenetik, Universität Hannover, 30419 Hannover, Germany (T.H., H.-P.B.);Department of Environmental Science, Indian Institute of Advanced Research, Koba, Gandhinagar 382007, Gujarat, India (D.N.);Clayton School of Information Technology, Monash University, Melbourne, Victoria 3800, Australia (M.K., F.S.);Institute of Computer Science, University Halle-Wittenberg, 06120 Halle, Germany (F.S.); andBayer CropScience, 9052 Zwijnaarde, Belgium (P.D.)
| | - Peter Denolf
- Brookhaven National Laboratory, Biological, Environmental, and Climate Sciences Department, Upton, New York 11973 (J.S., I.H., A.R., D.N.);Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (N.H., L.B., H.R.);Institut für Pflanzengenetik, Universität Hannover, 30419 Hannover, Germany (T.H., H.-P.B.);Department of Environmental Science, Indian Institute of Advanced Research, Koba, Gandhinagar 382007, Gujarat, India (D.N.);Clayton School of Information Technology, Monash University, Melbourne, Victoria 3800, Australia (M.K., F.S.);Institute of Computer Science, University Halle-Wittenberg, 06120 Halle, Germany (F.S.); andBayer CropScience, 9052 Zwijnaarde, Belgium (P.D.)
| | - Ljudmilla Borisjuk
- Brookhaven National Laboratory, Biological, Environmental, and Climate Sciences Department, Upton, New York 11973 (J.S., I.H., A.R., D.N.);Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (N.H., L.B., H.R.);Institut für Pflanzengenetik, Universität Hannover, 30419 Hannover, Germany (T.H., H.-P.B.);Department of Environmental Science, Indian Institute of Advanced Research, Koba, Gandhinagar 382007, Gujarat, India (D.N.);Clayton School of Information Technology, Monash University, Melbourne, Victoria 3800, Australia (M.K., F.S.);Institute of Computer Science, University Halle-Wittenberg, 06120 Halle, Germany (F.S.); andBayer CropScience, 9052 Zwijnaarde, Belgium (P.D.)
| | - Hardy Rolletschek
- Brookhaven National Laboratory, Biological, Environmental, and Climate Sciences Department, Upton, New York 11973 (J.S., I.H., A.R., D.N.);Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (N.H., L.B., H.R.);Institut für Pflanzengenetik, Universität Hannover, 30419 Hannover, Germany (T.H., H.-P.B.);Department of Environmental Science, Indian Institute of Advanced Research, Koba, Gandhinagar 382007, Gujarat, India (D.N.);Clayton School of Information Technology, Monash University, Melbourne, Victoria 3800, Australia (M.K., F.S.);Institute of Computer Science, University Halle-Wittenberg, 06120 Halle, Germany (F.S.); andBayer CropScience, 9052 Zwijnaarde, Belgium (P.D.)
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47
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Zhang C, Hou Y, Hao Q, Chen H, Chen L, Yuan S, Shan Z, Zhang X, Yang Z, Qiu D, Zhou X, Huang W. Genome-wide survey of the soybean GATA transcription factor gene family and expression analysis under low nitrogen stress. PLoS One 2015; 10:e0125174. [PMID: 25886477 PMCID: PMC4401516 DOI: 10.1371/journal.pone.0125174] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 03/21/2015] [Indexed: 01/03/2023] Open
Abstract
GATA transcription factors are transcriptional regulatory proteins that contain a characteristic type-IV zinc finger DNA-binding domain and recognize the conserved GATA motif in the promoter sequence of target genes. Previous studies demonstrated that plant GATA factors possess critical functions in developmental control and responses to the environment. To date, the GATA factors in soybean (Glycine max) have yet to be characterized. Thus, this study identified 64 putative GATA factors from the entire soybean genomic sequence. The chromosomal distributions, gene structures, duplication patterns, phylogenetic tree, tissue expression patterns, and response to low nitrogen stress of the 64 GATA factors in soybean were analyzed to further investigate the functions of these factors. Results indicated that segmental duplication predominantly contributed to the expansion of the GATA factor gene family in soybean. These GATA proteins were phylogenetically clustered into four distinct subfamilies, wherein their gene structure and motif compositions were considerably conserved. A comparative phylogenetic analysis of the GATA factor zinc finger domain sequences in soybean, Arabidopsis (Arabidopsis thaliana), and rice (Oryza sativa) revealed four major classes. The GATA factors in soybean exhibited expression diversity among different tissues; some of these factors showed tissue-specific expression patterns. Numerous GATA factors displayed upregulation or downregulation in soybean leaf in response to low nitrogen stress, and two GATA factors GATA44 and GATA58 were likely to be involved in the regulation of nitrogen metabolism in soybean. Overexpression of GmGATA44 complemented the reduced chlorophyll phenotype of the Arabidopsis ortholog AtGATA21 mutant, implying that GmGATA44 played an important role in modulating chlorophyll biosynthesis. Overall, our study provides useful information for the further analysis of the biological functions of GATA factors in soybean and other crops.
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Affiliation(s)
- Chanjuan Zhang
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yuqing Hou
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Qingnan Hao
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Haifeng Chen
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Limiao Chen
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Songli Yuan
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Zhihui Shan
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaojuan Zhang
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Zhonglu Yang
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Dezhen Qiu
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xinan Zhou
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Wenjun Huang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
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48
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Silva-Sanchez C, Li H, Chen S. Recent advances and challenges in plant phosphoproteomics. Proteomics 2015; 15:1127-41. [PMID: 25429768 DOI: 10.1002/pmic.201400410] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 09/29/2014] [Accepted: 11/24/2014] [Indexed: 12/13/2022]
Abstract
Plants are sessile organisms that need to respond to environmental changes quickly and efficiently. They can accomplish this by triggering specialized signaling pathways often mediated by protein phosphorylation and dephosphorylation. Phosphorylation is a fast response that can switch on or off a myriad of biological pathways and processes. Proteomics and MS are the main tools employed in the study of protein phosphorylation. Advances in the technologies allow simultaneous identification and quantification of thousands of phosphopeptides and proteins that are essential to understanding the sophisticated biological systems and regulations. In this review, we summarize the advances in phosphopeptide enrichment and quantitation, MS for phosphorylation site mapping and new data acquisition methods, databases and informatics, interpretation of biological insights and crosstalk with other PTMs, as well as future directions and challenges in the field of phosphoproteomics.
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Affiliation(s)
- Cecilia Silva-Sanchez
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
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49
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Roitinger E, Hofer M, Köcher T, Pichler P, Novatchkova M, Yang J, Schlögelhofer P, Mechtler K. Quantitative phosphoproteomics of the ataxia telangiectasia-mutated (ATM) and ataxia telangiectasia-mutated and rad3-related (ATR) dependent DNA damage response in Arabidopsis thaliana. Mol Cell Proteomics 2015; 14:556-71. [PMID: 25561503 PMCID: PMC4349977 DOI: 10.1074/mcp.m114.040352] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The reversible phosphorylation of proteins on serine, threonine, and tyrosine residues is an important biological regulatory mechanism. In the context of genome integrity, signaling cascades driven by phosphorylation are crucial for the coordination and regulation of DNA repair. The two serine/threonine protein kinases ataxia telangiectasia-mutated (ATM) and Ataxia telangiectasia-mutated and Rad3-related (ATR) are key factors in this process, each specific for different kinds of DNA lesions. They are conserved across eukaryotes, mediating the activation of cell-cycle checkpoints, chromatin modifications, and regulation of DNA repair proteins. We designed a novel mass spectrometry-based phosphoproteomics approach to study DNA damage repair in Arabidopsis thaliana. The protocol combines filter aided sample preparation, immobilized metal affinity chromatography, metal oxide affinity chromatography, and strong cation exchange chromatography for phosphopeptide generation, enrichment, and separation. Isobaric labeling employing iTRAQ (isobaric tags for relative and absolute quantitation) was used for profiling the phosphoproteome of atm atr double mutants and wild type plants under either regular growth conditions or challenged by irradiation. A total of 10,831 proteins were identified and 15,445 unique phosphopeptides were quantified, containing 134 up- and 38 down-regulated ATM/ATR dependent phosphopeptides. We identified known and novel ATM/ATR targets such as LIG4 and MRE11 (needed for resistance against ionizing radiation), PIE1 and SDG26 (implicated in chromatin remodeling), PCNA1, WAPL, and PDS5 (implicated in DNA replication), and ASK1 and HTA10 (involved in meiosis).
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Affiliation(s)
- Elisabeth Roitinger
- From the ‡Institute of Molecular Pathology (IMP), Vienna, Austria; ¶Institute of Molecular Biotechnology (IMBA), Vienna, Austria
| | - Manuel Hofer
- §Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Thomas Köcher
- From the ‡Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Peter Pichler
- From the ‡Institute of Molecular Pathology (IMP), Vienna, Austria; ¶Institute of Molecular Biotechnology (IMBA), Vienna, Austria
| | - Maria Novatchkova
- From the ‡Institute of Molecular Pathology (IMP), Vienna, Austria; ¶Institute of Molecular Biotechnology (IMBA), Vienna, Austria
| | - Jianhua Yang
- ‖School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Peter Schlögelhofer
- §Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria;
| | - Karl Mechtler
- From the ‡Institute of Molecular Pathology (IMP), Vienna, Austria; ¶Institute of Molecular Biotechnology (IMBA), Vienna, Austria;
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50
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Chaudhary J, Patil GB, Sonah H, Deshmukh RK, Vuong TD, Valliyodan B, Nguyen HT. Expanding Omics Resources for Improvement of Soybean Seed Composition Traits. FRONTIERS IN PLANT SCIENCE 2015; 6:1021. [PMID: 26635846 PMCID: PMC4657443 DOI: 10.3389/fpls.2015.01021] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 11/05/2015] [Indexed: 05/19/2023]
Abstract
Food resources of the modern world are strained due to the increasing population. There is an urgent need for innovative methods and approaches to augment food production. Legume seeds are major resources of human food and animal feed with their unique nutrient compositions including oil, protein, carbohydrates, and other beneficial nutrients. Recent advances in next-generation sequencing (NGS) together with "omics" technologies have considerably strengthened soybean research. The availability of well annotated soybean genome sequence along with hundreds of identified quantitative trait loci (QTL) associated with different seed traits can be used for gene discovery and molecular marker development for breeding applications. Despite the remarkable progress in these technologies, the analysis and mining of existing seed genomics data are still challenging due to the complexity of genetic inheritance, metabolic partitioning, and developmental regulations. Integration of "omics tools" is an effective strategy to discover key regulators of various seed traits. In this review, recent advances in "omics" approaches and their use in soybean seed trait investigations are presented along with the available databases and technological platforms and their applicability in the improvement of soybean. This article also highlights the use of modern breeding approaches, such as genome-wide association studies (GWAS), genomic selection (GS), and marker-assisted recurrent selection (MARS) for developing superior cultivars. A catalog of available important resources for major seed composition traits, such as seed oil, protein, carbohydrates, and yield traits are provided to improve the knowledge base and future utilization of this information in the soybean crop improvement programs.
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