1
|
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.
Collapse
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.)
| |
Collapse
|
2
|
Abstract
Proteins are intimately involved in executing and controlling virtually all cellular processes. To understand the molecular mechanisms that underlie plant phenotypes, it is essential to investigate protein expression, interactions, and modifications, to name a few. The proteome is highly dynamic in time and space, and a plethora of protein modifications, protein interactions, and network constellations are at play under specific conditions and developmental stages. Analysis of proteomes aims to characterize the entire protein complement of a particular cell type, tissue, or organism-a challenging task, given the dynamic nature of the proteome. Modern mass spectrometry-based proteomics technology can be used to address this complexity at a system-wide scale by the global identification and quantification of thousands of proteins. In this review, we present current methods and technologies employed in mass spectrometry-based proteomics and provide examples of dynamic changes in the plant proteome elucidated by proteomic approaches.
Collapse
Affiliation(s)
- Julia Mergner
- Bavarian Center for Biomolecular Mass Spectrometry at Klinikum rechts der Isar (BayBioMS@MRI), Technical University of Munich, Munich, Germany;
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany;
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany;
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Butler KJ, Fliege C, Zapotocny R, Diers B, Hudson M, Bent AF. Soybean Cyst Nematode Resistance Quantitative Trait Locus cqSCN-006 Alters the Expression of a γ-SNAP Protein. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1433-1445. [PMID: 34343024 PMCID: PMC8748310 DOI: 10.1094/mpmi-07-21-0163-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Soybean cyst nematode (SCN) is the most economically damaging pathogen of soybean and host resistance is a core management strategy. The SCN resistance quantitative trait locus cqSCN-006, introgressed from the wild relative Glycine soja, provides intermediate resistance against nematode populations, including those with increased virulence on the heavily used rhg1-b resistance locus. cqSCN-006 was previously fine-mapped to a genome interval on chromosome 15. The present study determined that Glyma.15G191200 at cqSCN-006, encoding a γ-SNAP, contributes to SCN resistance. CRISPR/Cas9-mediated disruption of the cqSCN-006 allele reduced SCN resistance in transgenic roots. There are no encoded amino acid polymorphisms between resistant and susceptible alleles. However, other cqSCN-006-specific DNA polymorphisms in the Glyma.15G191200 promoter and gene body were identified, and we observed differing induction of γ-SNAP protein abundance at SCN infection sites between resistant and susceptible roots. We identified alternative RNA splice forms transcribed from the Glyma.15G191200 γ-SNAP gene and observed differential expression of the splice forms 2 days after SCN infection. Heterologous overexpression of γ-SNAPs in plant leaves caused moderate necrosis, suggesting that careful regulation of this protein is required for cellular homeostasis. Apparently, certain G. soja evolved quantitative SCN resistance through altered regulation of γ-SNAP. Previous work has demonstrated SCN resistance impacts of the soybean α-SNAP proteins encoded by Glyma.18G022500 (Rhg1) and Glyma.11G234500. The present study shows that a different type of SNAP protein can also impact SCN resistance. Little is known about γ-SNAPs in any system, but the present work suggests a role for γ-SNAPs during susceptible responses to cyst nematodes.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
Collapse
Affiliation(s)
| | - Christina Fliege
- University of Illinois Urbana-Champaign, Department of Crop Sciences
| | - Ryan Zapotocny
- University of Wisconsin-Madison, Department of Plant Pathology
| | - Brian Diers
- University of Illinois Urbana-Champaign, Department of Crop Sciences
| | - Matthew Hudson
- University of Illinois Urbana-Champaign, Department of Crop Sciences
| | - Andrew F. Bent
- University of Wisconsin-Madison, Department of Plant Pathology
| |
Collapse
|
5
|
Yu K, He Y, Li Y, Li Z, Zhang J, Wang X, Tian E. Quantitative Trait Locus Mapping Combined with RNA Sequencing Reveals the Molecular Basis of Seed Germination in Oilseed Rape. Biomolecules 2021; 11:biom11121780. [PMID: 34944424 PMCID: PMC8698463 DOI: 10.3390/biom11121780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 11/16/2022] Open
Abstract
Rapid and uniform seed germination improves mechanized oilseed rape production in modern agricultural cultivation practices. However, the molecular basis of seed germination is still unclear in Brassica napus. A population of recombined inbred lines of B. napus from a cross between the lower germination rate variety ‘APL01’ and the higher germination rate variety ‘Holly’ was used to study the genetics of seed germination using quantitative trait locus (QTL) mapping. A total of five QTLs for germination energy (GE) and six QTLs for germination percentage (GP) were detected across three seed lots, respectively. In addition, six epistatic interactions between the QTLs for GE and nine epistatic interactions between the QTLs for GP were detected. qGE.C3 for GE and qGP.C3 for GP were co-mapped to the 28.5–30.5 cM interval on C3, which was considered to be a novel major QTL regulating seed germination. Transcriptome analysis revealed that the differences in sugar, protein, lipid, amino acid, and DNA metabolism and the TCA cycle, electron transfer, and signal transduction potentially determined the higher germination rate of ‘Holly’ seeds. These results contribute to our knowledge about the molecular basis of seed germination in rapeseed.
Collapse
Affiliation(s)
- Kunjiang Yu
- Department of Agronomy, College of Agriculture, Guizhou University, Guiyang 550025, China; (K.Y.); (Y.H.); (Y.L.); (Z.L.)
| | - Yuqi He
- Department of Agronomy, College of Agriculture, Guizhou University, Guiyang 550025, China; (K.Y.); (Y.H.); (Y.L.); (Z.L.)
| | - Yuanhong Li
- Department of Agronomy, College of Agriculture, Guizhou University, Guiyang 550025, China; (K.Y.); (Y.H.); (Y.L.); (Z.L.)
| | - Zhenhua Li
- Department of Agronomy, College of Agriculture, Guizhou University, Guiyang 550025, China; (K.Y.); (Y.H.); (Y.L.); (Z.L.)
| | - Jiefu Zhang
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China;
| | - Xiaodong Wang
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China;
- Correspondence: (X.W.); (E.T.)
| | - Entang Tian
- Department of Agronomy, College of Agriculture, Guizhou University, Guiyang 550025, China; (K.Y.); (Y.H.); (Y.L.); (Z.L.)
- Correspondence: (X.W.); (E.T.)
| |
Collapse
|
6
|
Iqbal Z, Iqbal MS, Khan MIR, Ansari MI. Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management. FRONTIERS IN PLANT SCIENCE 2021; 12:741419. [PMID: 34721467 PMCID: PMC8554098 DOI: 10.3389/fpls.2021.741419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/20/2021] [Indexed: 05/04/2023]
Abstract
Rice (Oryza sativa) is an imperative staple crop for nearly half of the world's population. Challenging environmental conditions encompassing abiotic and biotic stresses negatively impact the quality and yield of rice. To assure food supply for the unprecedented ever-growing world population, the improvement of rice as a crop is of utmost importance. In this era, "omics" techniques have been comprehensively utilized to decipher the regulatory mechanisms and cellular intricacies in rice. Advancements in omics technologies have provided a strong platform for the reliable exploration of genetic resources involved in rice trait development. Omics disciplines like genomics, transcriptomics, proteomics, and metabolomics have significantly contributed toward the achievement of desired improvements in rice under optimal and stressful environments. The present review recapitulates the basic and applied multi-omics technologies in providing new orchestration toward the improvement of rice desirable traits. The article also provides a catalog of current scenario of omics applications in comprehending this imperative crop in relation to yield enhancement and various environmental stresses. Further, the appropriate databases in the field of data science to analyze big data, and retrieve relevant information vis-à-vis rice trait improvement and stress management are described.
Collapse
Affiliation(s)
- Zahra Iqbal
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
| | | | | | | |
Collapse
|
7
|
Liang W, Yan F, Wang M, Li X, Zhang Z, Ma X, Hu J, Wang J, Wang L. Comprehensive Phosphoproteomic Analysis of Nostoc flagelliforme in Response to Dehydration Provides Insights into Plant ROS Signaling Transduction. ACS OMEGA 2021; 6:13554-13566. [PMID: 34095650 PMCID: PMC8173544 DOI: 10.1021/acsomega.0c06111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/05/2021] [Indexed: 05/27/2023]
Abstract
Terrestrial cyanobacteria, originated from aquatic cyanobacteria, exhibit a unique mechanism for drought adaptation during long-term evolution. To elucidate this diverse adaptive mechanism exhibited by terrestrial cyanobacteria from the post-translation modification aspect, we performed a global phosphoproteome analysis on the abundance of phosphoproteins in response to dehydration using Nostoc flagelliforme, a kind of terrestrial cyanobacteria having strong ecological adaptability to xeric environments. A total of 329 phosphopeptides from 271 phosphoproteins with 1168 phosphorylation sites were identified. Among these, 76 differentially expressed phosphorylated proteins (DEPPs) were identified for each dehydration treatment (30, 75, and 100% water loss), compared to control. The identified DEPPs were functionally categorized to be mainly involved in a two-component signaling pathway, photosynthesis, energy and carbohydrate metabolism, and an antioxidant system. We concluded that protein phosphorylation modifications related to the reactive oxygen species (ROS) signaling pathway might play an important role in coordinating enzyme activity involved in the antioxidant system in N. flagelliforme to adapt to dehydration stress. This study provides deep insights into the extensive modification of phosphorylation in terrestrial cyanobacteria using a phosphoproteomic approach, which may help to better understand the role of protein phosphorylation in key cellular mechanisms in terrestrial cyanobacteria in response to dehydration.
Collapse
Affiliation(s)
- Wenyu Liang
- School
of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Fengkun Yan
- School
of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Meng Wang
- School
of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Xiaoxu Li
- School
of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Zheng Zhang
- School
of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Xiaorong Ma
- School
of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Jinhong Hu
- School
of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Jun Wang
- College
Education for Nationalities, Ningxia University, Yinchuan 750021, China
| | - Lingxia Wang
- School
of Life Sciences, Ningxia University, Yinchuan 750021, China
| |
Collapse
|
8
|
Tappiban P, Ying Y, Xu F, Bao J. Proteomics and Post-Translational Modifications of Starch Biosynthesis-Related Proteins in Developing Seeds of Rice. Int J Mol Sci 2021; 22:5901. [PMID: 34072759 PMCID: PMC8199009 DOI: 10.3390/ijms22115901] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 12/25/2022] Open
Abstract
Rice (Oryza sativa L.) is a foremost staple food for approximately half the world's population. The components of rice starch, amylose, and amylopectin are synthesized by a series of enzymes, which are responsible for rice starch properties and functionality, and then affect rice cooking and eating quality. Recently, proteomics technology has been applied to the establishment of the differentially expressed starch biosynthesis-related proteins and the identification of posttranslational modifications (PTMs) target starch biosynthesis proteins as well. It is necessary to summarize the recent studies in proteomics and PTMs in rice endosperm to deepen our understanding of starch biosynthesis protein expression and regulation, which will provide useful information to rice breeding programs and industrial starch applications. The review provides a comprehensive summary of proteins and PTMs involved in starch biosynthesis based on proteomic studies of rice developing seeds. Starch biosynthesis proteins in rice seeds were differentially expressed in the developing seeds at different developmental stages. All the proteins involving in starch biosynthesis were identified using proteomics methods. Most starch biosynthesis-related proteins are basically increased at 6-20 days after flowering (DAF) and decreased upon the high-temperature conditions. A total of 10, 14, 2, 17, and 7 starch biosynthesis related proteins were identified to be targeted by phosphorylation, lysine acetylation, succinylation, lysine 2-hydroxyisobutyrylation, and malonylation, respectively. The phosphoglucomutase is commonly targeted by five PTMs types. Research on the function of phosphorylation in multiple enzyme complex formation in endosperm starch biosynthesis is underway, while the functions of other PTMs in starch biosynthesis are necessary to be conducted in the near future.
Collapse
Affiliation(s)
- Piengtawan Tappiban
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
| | - Yining Ying
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
| | - Feifei Xu
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
| | - Jinsong Bao
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, China
| |
Collapse
|
9
|
Arefian M, Bhagya N, Prasad TSK. Phosphorylation-mediated signalling in flowering: prospects and retrospects of phosphoproteomics in crops. Biol Rev Camb Philos Soc 2021; 96:2164-2191. [PMID: 34047006 DOI: 10.1111/brv.12748] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/18/2022]
Abstract
Protein phosphorylation is a major post-translational modification, regulating protein function, stability, and subcellular localization. To date, annotated phosphorylation data are available mainly for model organisms and humans, despite the economic importance of crop species and their large kinomes. Our understanding of the phospho-regulation of flowering in relation to the biology and interaction between the pollen and pistil is still significantly lagging, limiting our knowledge on kinase signalling and its potential applications to crop production. To address this gap, we bring together relevant literature that were previously disconnected to present an overview of the roles of phosphoproteomic signalling pathways in modulating molecular and cellular regulation within specific tissues at different morphological stages of flowering. This review is intended to stimulate research, with the potential to increase crop productivity by providing a platform for novel molecular tools.
Collapse
Affiliation(s)
- Mohammad Arefian
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - N Bhagya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| |
Collapse
|
10
|
Yu F, Li M, He D, Yang P. Advances on Post-translational Modifications Involved in Seed Germination. FRONTIERS IN PLANT SCIENCE 2021; 12:642979. [PMID: 33828574 PMCID: PMC8020409 DOI: 10.3389/fpls.2021.642979] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/16/2021] [Indexed: 05/05/2023]
Abstract
Seed germination and subsequent seedling establishment are important developmental processes that undergo extremely complex changes of physiological status and are precisely regulated at transcriptional and translational levels. Phytohormones including abscisic acid (ABA) and gibberellin (GA) are the critical signaling molecules that modulate the alteration from relative quiescent to a highly active state in seeds. Transcription factors such as ABA insensitive5 (ABI5) and DELLA domain-containing proteins play the central roles in response to ABA and GA, respectively, which antagonize each other during seed germination. Recent investigations have demonstrated that the regulations at translational and post-translational levels, especially post-translational modifications (PTMs), play a decisive role in seed germination. Specifically, phosphorylation and ubiquitination were shown to be involved in regulating the function of ABI5. In this review, we summarized the latest advancement on the function of PTMs involved in the regulation of seed germination, in which the PTMs for ABI5- and DELLA-containing proteins play the key roles. Meanwhile, the studies on PTM-based proteomics during seed germination and the crosstalk of different PTMs are also discussed. Hopefully, it will facilitate in obtaining a comprehensive understanding of the physiological functions of different PTMs in seed germination.
Collapse
|
11
|
Carrera-Castaño G, Calleja-Cabrera J, Pernas M, Gómez L, Oñate-Sánchez L. An Updated Overview on the Regulation of Seed Germination. PLANTS 2020; 9:plants9060703. [PMID: 32492790 PMCID: PMC7356954 DOI: 10.3390/plants9060703] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/22/2020] [Accepted: 05/26/2020] [Indexed: 02/07/2023]
Abstract
The ability of a seed to germinate and establish a plant at the right time of year is of vital importance from an ecological and economical point of view. Due to the fragility of these early growth stages, their swiftness and robustness will impact later developmental stages and crop yield. These traits are modulated by a continuous interaction between the genetic makeup of the plant and the environment from seed production to germination stages. In this review, we have summarized the established knowledge on the control of seed germination from a molecular and a genetic perspective. This serves as a “backbone” to integrate the latest developments in the field. These include the link of germination to events occurring in the mother plant influenced by the environment, the impact of changes in the chromatin landscape, the discovery of new players and new insights related to well-known master regulators. Finally, results from recent studies on hormone transport, signaling, and biophysical and mechanical tissue properties are underscoring the relevance of tissue-specific regulation and the interplay of signals in this crucial developmental process.
Collapse
|
12
|
He D, Li M, Damaris RN, Bu C, Xue J, Yang P. Quantitative ubiquitylomics approach for characterizing the dynamic change and extensive modulation of ubiquitylation in rice seed germination. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1430-1447. [PMID: 31677306 DOI: 10.1111/tpj.14593] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/26/2019] [Accepted: 10/16/2019] [Indexed: 05/22/2023]
Abstract
During seed germination, cells embark on extensive post-transcriptional and post-translational modifications (PTM), providing a perfect platform to study these events in embryo rebooting from relative quiescenct to highly active state. PR-619, a deubiquitylase inhibitor, delayed the rice seed germination and resulted in the accumulation of ubiquitylated proteins, which indicated the protein ubiquitylation is involved in this process. Using the K-Ɛ-GG antibody enrichment method integrated with high-resolution mass spectrometry, a list of 2576 lysine ubiquitylated (Kub) sites in 1171 proteins was compiled for rice embryos at 0, 12 and 24 h after imbibition (HAI). Of these, the abundance of 1419 Kub sites in 777 proteins changed significantly. Most of them substantially increased within the first 12 HAI, which is similar to the dynamic state previously observed for protein phosphorylation, implying that the first 12 HAI are essential for subsequent switch during rice seed germination. We also quantitatively analyzed the embryo proteome in these samples. Generally, a specific protein's abundance in the ubiquitylome was uncorrelated to that in the proteome. The differentially ubiquitinated proteins were greatly enriched in the categories of protein processing, DNA and RNA processing/regulation related, signaling, and transport. The DiGly footprint of the Kub sites was significantly reduced on K48, a linkage typically associated with proteasome-mediated degradation. These observations suggest ubiquitylation may modulate the protein function more than providing 26S degradation signals in the early stage of rice seed germination. Revealing this comprehensive ubiquitylome greatly increases our understanding of this critical PTM during seed germination.
Collapse
Affiliation(s)
- Dongli He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Ming Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Rebecca N Damaris
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Chen Bu
- Jingjie PTM BioLab (Hangzhou) Co. Ltd, Hangzhou, 310018, China
| | - Jianyou Xue
- Jingjie PTM BioLab (Hangzhou) Co. Ltd, Hangzhou, 310018, China
| | - Pingfang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
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.
Collapse
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:
| |
Collapse
|
15
|
Xue C, Liu S, Chen C, Zhu J, Yang X, Zhou Y, Guo R, Liu X, Gong Z. Global Proteome Analysis Links Lysine Acetylation to Diverse Functions in Oryza Sativa. Proteomics 2019; 18. [PMID: 29106068 DOI: 10.1002/pmic.201700036] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 10/11/2017] [Indexed: 01/26/2023]
Abstract
Lysine acetylation (Kac) is an important protein post-translational modification in both eukaryotes and prokaryotes. Herein, we report the results of a global proteome analysis of Kac and its diverse functions in rice (Oryza sativa). We identified 1353 Kac sites in 866 proteins in rice seedlings. A total of 11 Kac motifs are conserved, and 45% of the identified proteins are localized to the chloroplast. Among all acetylated proteins, 38 Kac sites are combined in core histones. Bioinformatics analysis revealed that Kac occurs on a diverse range of proteins involved in a wide variety of biological processes, especially photosynthesis. Protein-protein interaction networks of the identified proteins provided further evidence that Kac contributes to a wide range of regulatory functions. Furthermore, we demonstrated that the acetylation level of histone H3 (lysine 27 and 36) is increased in response to cold stress. In summary, our approach comprehensively profiles the regulatory roles of Kac in the growth and development of rice.
Collapse
Affiliation(s)
- Chao Xue
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, P. R. China
| | - Shuai Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, P. R. China
| | - Chen Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, P. R. China
| | - Jun Zhu
- Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou, P. R. China
| | - Xibin Yang
- Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou, P. R. China
| | - Yong Zhou
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, P. R. China
| | - Rui Guo
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, P. R. China
| | - Xiaoyu Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, P. R. China
| | - Zhiyun Gong
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, P. R. China
| |
Collapse
|
16
|
Xia Q, Ponnaiah M, Cueff G, Rajjou L, Prodhomme D, Gibon Y, Bailly C, Corbineau F, Meimoun P, El-Maarouf-Bouteau H. Integrating proteomics and enzymatic profiling to decipher seed metabolism affected by temperature in seed dormancy and germination. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 269:118-125. [PMID: 29606208 DOI: 10.1016/j.plantsci.2018.01.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/24/2018] [Accepted: 01/28/2018] [Indexed: 06/08/2023]
Abstract
Temperature is an important environmental factor affecting seed dormancy and germination. The mechanism by which temperature induces germination in dormant seeds is however still unclear. Proteomic study has been performed in dormant sunflower seeds during imbibition at permissive and non-permissive temperatures for germination, 20 and 10 °C, respectively. Proteome analysis showed an increase of proteins belonging to metabolism and energy from the first hours of imbibition followed by a decrease of proteins involved in protein metabolism and seed storage in germinating compared to non-germinating seeds. Proteomic study was completed by polysome and proteasome activity assessment and enzymatic profiling on several altered proteins involved in metabolism and energy. Results showed that 20 °C treatment induced the activation of both protein synthesis and degradation processes, the latter being related to proteasome activity during the germination sensu stricto, and to other degradation processes such as proteases during the post-germination. Interestingly, enzymatic profiles showed that TCA cycle and glycolysis were more active in non-germinating seeds in the phase I of the germination sensu stricto. This result suggests the regulation of central metabolism activity in germinating seeds. The control of energy production during imbibition seems to be involved in molecular networks controlling seed dormancy and germination.
Collapse
Affiliation(s)
- Qiong Xia
- Sorbonne Université, UMR 7622, 75005 Paris, France; CNRS, UMR 7622, 75005 Paris, France
| | - Maharajah Ponnaiah
- Sorbonne Université, UMR 7622, 75005 Paris, France; CNRS, UMR 7622, 75005 Paris, France
| | - Gwendal Cueff
- Institut Jean-Pierre Bourgin (UMR1318 INRA - AgroParisTech), Institut National de la Recherche Agronomique, Saclay Plant Science, Versailles, France
| | - Loïc Rajjou
- Institut Jean-Pierre Bourgin (UMR1318 INRA - AgroParisTech), Institut National de la Recherche Agronomique, Saclay Plant Science, Versailles, France
| | - Duyen Prodhomme
- UMR1332 Biologie du Fruit et Pathologie, Université de Bordeaux, Institut National de la Recherche Agronomique, Villenave d'Ornon, France; Plateforme Métabolome, Centre Génomique Fonctionnelle Bordeaux, Villenave d'Ornon, France
| | - Yves Gibon
- UMR1332 Biologie du Fruit et Pathologie, Université de Bordeaux, Institut National de la Recherche Agronomique, Villenave d'Ornon, France; Plateforme Métabolome, Centre Génomique Fonctionnelle Bordeaux, Villenave d'Ornon, France
| | - Christophe Bailly
- Sorbonne Université, UMR 7622, 75005 Paris, France; CNRS, UMR 7622, 75005 Paris, France
| | - Françoise Corbineau
- Sorbonne Université, UMR 7622, 75005 Paris, France; CNRS, UMR 7622, 75005 Paris, France
| | - Patrice Meimoun
- Sorbonne Université, UMR 7622, 75005 Paris, France; CNRS, UMR 7622, 75005 Paris, France
| | | |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
Wang Y, Tong X, Qiu J, Li Z, Zhao J, Hou Y, Tang L, Zhang J. A phosphoproteomic landscape of rice (Oryza sativa) tissues. PHYSIOLOGIA PLANTARUM 2017; 160:458-475. [PMID: 28382632 DOI: 10.1111/ppl.12574] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 02/24/2017] [Indexed: 06/07/2023]
Abstract
Protein phosphorylation is an important posttranslational modification that regulates various plant developmental processes. Here, we report a comprehensive, quantitative phosphoproteomic profile of six rice tissues, including callus, leaf, root, shoot meristem, young panicle and mature panicle from Nipponbare by employing a mass spectrometry (MS)-based, label-free approach. A total of 7171 unique phosphorylation sites in 4792 phosphopeptides from 2657 phosphoproteins were identified, of which 4613 peptides were differentially phosphorylated (DP) among the tissues. Motif-X analysis revealed eight significantly enriched motifs, such as [sP], [Rxxs] and [tP] from the rice phosphosites. Hierarchical clustering analysis divided the DP peptides into 63 subgroups, which showed divergent spatial-phosphorylation patterns among tissues. These clustered proteins are functionally related to nutrition uptake in roots, photosynthesis in leaves and tissue differentiation in panicles. Phosphorylations were specific in the tissues where the target proteins execute their functions, suggesting that phosphorylation might be a key mechanism to regulate the protein activity in different tissues. This study greatly expands the rice phosphoproteomic dataset, and also offers insight into the regulatory roles of phosphorylation in tissue development and functions.
Collapse
Affiliation(s)
- Yifeng Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Xiaohong Tong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Jiehua Qiu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Zhiyong Li
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Juan Zhao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yuxuan Hou
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Liqun Tang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Jian Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| |
Collapse
|
19
|
Almadanim MC, Alexandre BM, Rosa MTG, Sapeta H, Leitão AE, Ramalho JC, Lam TT, Negrão S, Abreu IA, Oliveira MM. Rice calcium-dependent protein kinase OsCPK17 targets plasma membrane intrinsic protein and sucrose-phosphate synthase and is required for a proper cold stress response. PLANT, CELL & ENVIRONMENT 2017; 40:1197-1213. [PMID: 28102545 DOI: 10.1111/pce.12916] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/10/2017] [Accepted: 01/15/2017] [Indexed: 05/20/2023]
Abstract
Calcium-dependent protein kinases (CDPKs) are involved in plant tolerance mechanisms to abiotic stresses. Although CDPKs are recognized as key messengers in signal transduction, the specific role of most members of this family remains unknown. Here, we test the hypothesis that OsCPK17 plays a role in rice cold stress response by analysing OsCPK17 knockout, silencing and overexpressing rice lines under low temperature. Altered OsCPK17 gene expression compromises cold tolerance performance, without affecting the expression of key cold stress-inducible genes. A comparative phosphoproteomic approach led to the identification of six potential in vivo OsCPK17 targets, which are associated with sugar and nitrogen metabolism, and with osmotic regulation. To test direct interaction, in vitro kinase assays were performed, showing that the sucrose-phosphate synthase OsSPS4 and the aquaporin OsPIP2;1/OsPIP2;6 are phosphorylated by OsCPK17 in a calcium-dependent manner. Altogether, our data indicates that OsCPK17 is required for a proper cold stress response in rice, likely affecting the activity of membrane channels and sugar metabolism.
Collapse
Affiliation(s)
- M Cecília Almadanim
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
| | - Bruno M Alexandre
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
| | - Margarida T G Rosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
| | - Helena Sapeta
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
| | - António E Leitão
- Plant Stress and Biodiversity, Linking Landscape, Environment, Agriculture and Food (LEAF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia, Universidade de Lisboa, 2784-505, Oeiras, Portugal
| | - José C Ramalho
- Plant Stress and Biodiversity, Linking Landscape, Environment, Agriculture and Food (LEAF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia, Universidade de Lisboa, 2784-505, Oeiras, Portugal
| | - TuKiet T Lam
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520-8024, USA
- MS and Proteomics Resource, WM Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, CT, 06520-8024, USA
| | - Sónia Negrão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Isabel A Abreu
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
| | - M Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
| |
Collapse
|
20
|
Tan BC, Lim YS, Lau SE. Proteomics in commercial crops: An overview. J Proteomics 2017; 169:176-188. [PMID: 28546092 DOI: 10.1016/j.jprot.2017.05.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 04/21/2017] [Accepted: 05/19/2017] [Indexed: 02/06/2023]
Abstract
Proteomics is a rapidly growing area of biological research that is positively affecting plant science. Recent advances in proteomic technology, such as mass spectrometry, can now identify a broad range of proteins and monitor their modulation during plant growth and development, as well as during responses to abiotic and biotic stresses. In this review, we highlight recent proteomic studies of commercial crops and discuss the advances in understanding of the proteomes of these crops. We anticipate that proteomic-based research will continue to expand and contribute to crop improvement. SIGNIFICANCE Plant proteomics study is a rapidly growing area of biological research that is positively impacting plant science. With the recent advances in new technologies, proteomics not only allows us to comprehensively analyses crop proteins, but also help us to understand the functions of the genes. In this review, we highlighted recent proteomic studies in commercial crops and updated the advances in our understanding of the proteomes of these crops. We believe that proteomic-based research will continue to grow and contribute to the improvement of crops.
Collapse
Affiliation(s)
- Boon Chin Tan
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia.
| | - Yin Sze Lim
- School of Biosciences, Faculty of Science, University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor, Malaysia
| | - Su-Ee Lau
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia
| |
Collapse
|
21
|
Ying J, Zhao J, Hou Y, Wang Y, Qiu J, Li Z, Tong X, Shi Z, Zhu J, Zhang J. Mapping the N-linked glycosites of rice (Oryza sativa L.) germinating embryos. PLoS One 2017; 12:e0173853. [PMID: 28328971 PMCID: PMC5362090 DOI: 10.1371/journal.pone.0173853] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/28/2017] [Indexed: 11/19/2022] Open
Abstract
Germination is a key event in the angiosperm life cycle. N-glycosylation of proteins is one of the most common post-translational modifications, and has been recognized to be an important regulator of the proteome of the germinating embryo. Here, we report the first N-linked glycosites mapping of rice embryos during germination by using a hydrophilic interaction chromatography (HILIC) glycopeptides enrichment strategy associated with high accuracy mass spectrometry identification. A total of 242 glycosites from 191 unique proteins was discovered. Inspection of the motifs and sequence structures involved suggested that all the glycosites were concentrated within [NxS/T] motif, while 82.3% of them were in a coil structure. N-glycosylation preferentially occurred on proteins with glycoside hydrolase activities, which were significantly enriched in the starch and sucrose metabolism pathway, suggesting that N-glycosylation is involved in embryo germination by regulating carbohydrate metabolism. Notably, protein-protein interaction analysis revealed a network with several Brassinosteroids signaling proteins, including XIAO and other BR-responsive proteins, implying that glycosylation-mediated Brassinosteroids signaling may be a key mechanism regulating rice embryo germination. In summary, this study expanded our knowledge of protein glycosylation in rice, and provided novel insight into the PTM regulation in rice seed germination.
Collapse
Affiliation(s)
- Jiezheng Ying
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
| | - Juan Zhao
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
| | - Yuxuan Hou
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
| | - Yifeng Wang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
| | - Jiehua Qiu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
| | - Zhiyong Li
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
| | - Xiaohong Tong
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
| | | | - Jun Zhu
- Jingjie PTM-Biolabs, Hangzhou, P.R. China
| | - Jian Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, P.R. China
- * E-mail:
| |
Collapse
|
22
|
Hou Y, Qiu J, Wang Y, Li Z, Zhao J, Tong X, Lin H, Zhang J. A Quantitative Proteomic Analysis of Brassinosteroid-induced Protein Phosphorylation in Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2017; 8:514. [PMID: 28439285 PMCID: PMC5383725 DOI: 10.3389/fpls.2017.00514] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 03/23/2017] [Indexed: 05/21/2023]
Abstract
The group of polyhydroxysteroid phytohormones referred to as the brassinosteroids (BRs) is known to act on plant development and the stress response. BR signal transduction relies largely on protein phosphorylation. By employing a label-free, MS (Mass Spectrometry)-based phosphoproteomic approach, we report here the largest profiling of 4,034 phosphosites on 1,900 phosphoproteins from rice young seedlings and their dynamic response to BR. 1,821 proteins, including kinases, transcription factors and core components of BR and other hormone signaling pathways, were found to be differentially phosphorylated during the BR treatment. A Western blot analysis verified the differential phosphorylation of five of these proteins, implying that the MS-based phosphoproteomic data were robust. It is proposed that the dephosphorylation of gibberellin (GA) signaling components could represent an important mechanism for the BR-regulated antagonism to GA, and that BR influences the plant architecture of rice by regulating cellulose synthesis via phosphorylation.
Collapse
Affiliation(s)
- Yuxuan Hou
- State Key Lab of Rice Biology, China National Rice Research InstituteHangzhou, China
| | - Jiehua Qiu
- State Key Lab of Rice Biology, China National Rice Research InstituteHangzhou, China
| | - Yifeng Wang
- State Key Lab of Rice Biology, China National Rice Research InstituteHangzhou, China
| | - Zhiyong Li
- State Key Lab of Rice Biology, China National Rice Research InstituteHangzhou, China
| | - Juan Zhao
- State Key Lab of Rice Biology, China National Rice Research InstituteHangzhou, China
| | - Xiaohong Tong
- State Key Lab of Rice Biology, China National Rice Research InstituteHangzhou, China
| | - Haiyan Lin
- State Key Lab of Rice Biology, China National Rice Research InstituteHangzhou, China
- Agricultural Genomes Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhen, China
| | - Jian Zhang
- State Key Lab of Rice Biology, China National Rice Research InstituteHangzhou, China
- *Correspondence: Jian Zhang,
| |
Collapse
|
23
|
Zhao F, Zhang D, Zhao Y, Wang W, Yang H, Tai F, Li C, Hu X. The Difference of Physiological and Proteomic Changes in Maize Leaves Adaptation to Drought, Heat, and Combined Both Stresses. FRONTIERS IN PLANT SCIENCE 2016; 7:1471. [PMID: 27833614 PMCID: PMC5080359 DOI: 10.3389/fpls.2016.01471] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 09/15/2016] [Indexed: 05/18/2023]
Abstract
At the eight-leaf stage, maize is highly sensitive to stresses such as drought, heat, and their combination, which greatly affect its yield. At present, few studies have analyzed maize response to combined drought and heat stress at the eight-leaf stage. In this study, we measured certain physical parameters of maize at the eight-leaf stage when it was exposed to drought, heat, and their combination. The results showed an increase in the content of H2O2 and malondialdehyde (MDA), and in the enzyme activities of superoxide dismutase (SOD), ascorbate peroxidase (APX), and glutathione reductase (GR), but a decrease in the quantum efficiency of photosystem II (ΦPSII). The most obvious increase or decrease in physical parameters was found under the combined stress condition. Moreover, to identify proteins differentially regulated by the three stress conditions at the eight-leaf stage, total proteins from the maize leaves were identified and quantified using multiplex iTRAQ-based quantitative proteomic and LC-MS/MS methods. In summary, the expression levels of 135, 65, and 201 proteins were significantly changed under the heat, drought and combined stress conditions, respectively. Of the 135, 65, and 201 differentially expressed proteins, 61, 28, and 16 responded exclusively to drought stress, heat stress, and combined stress, respectively. Bioinformatics analysis implied that chaperone proteins and proteases play important roles in the adaptive response of maize to heat stress and combined stress, and that the leaf senescence promoted by ethylene-responsive protein and ripening-related protein may play active roles in maize tolerance to combined drought and heat stress. The signaling pathways related to differentially expressed proteins were obviously different under all three stress conditions. Thus, the functional characterization of these differentially expressed proteins will be helpful for discovering new targets to enhance maize tolerance to stress.
Collapse
Affiliation(s)
- Feiyun Zhao
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural UniversityZhengzhou, China
| | - Dayong Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Yulong Zhao
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural UniversityZhengzhou, China
| | - Wei Wang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural UniversityZhengzhou, China
| | - Hao Yang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural UniversityZhengzhou, China
| | - Fuju Tai
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural UniversityZhengzhou, China
| | - Chaohai Li
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural UniversityZhengzhou, China
| | - Xiuli Hu
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural UniversityZhengzhou, China
| |
Collapse
|
24
|
Dissection of brassinosteroid-regulated proteins in rice embryos during germination by quantitative proteomics. Sci Rep 2016; 6:34583. [PMID: 27703189 PMCID: PMC5050409 DOI: 10.1038/srep34583] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/15/2016] [Indexed: 12/11/2022] Open
Abstract
Brassinosteroids (BRs), essential plant-specific steroidal hormones, function in a wide spectrum of plant growth and development events, including seed germination. Rice is not only a monocotyledonous model plant but also one of the most important staple food crops of human beings. Rice seed germination is a decisive event for the next-generation of plant growth and successful seed germination is critical for rice yield. However, little is known about the molecular mechanisms on how BR modulates seed germination in rice. In the present study, we used isobaric tags for relative and absolute quantification (iTRAQ) based proteomic approach to study BR-regulated proteome during the early stage of seed germination. The results showed that more than 800 BR-responsive proteins were identified, including 88 reliable target proteins responsive to stimuli of both BR-deficiency and BR-insensitivity. Moreover, 90% of the 88 target proteins shared a similar expression change pattern. Gene ontology and string analysis indicated that ribosomal structural proteins, as well as proteins involved in protein biosynthesis and carbohydrate metabolisms were highly clustered. These findings not only enrich BR-regulated protein database in rice seeds, but also allow us to gain novel insights into the molecular mechanism of BR regulated seed germination.
Collapse
|
25
|
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.
Collapse
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
| |
Collapse
|
26
|
Zheng W, Komatsu S, Zhu W, Zhang L, Li X, Cui L, Tian J. Response and Defense Mechanisms of Taxus chinensis Leaves Under UV-A Radiation are Revealed Using Comparative Proteomics and Metabolomics Analyses. PLANT & CELL PHYSIOLOGY 2016; 57:1839-1853. [PMID: 27318281 DOI: 10.1093/pcp/pcw106] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 05/22/2016] [Indexed: 06/06/2023]
Abstract
Taxus chinensis var. mairei is a species endemic to south-eastern China and one of the natural sources for the anticancer medicine paclitaxel. To investigate the molecular response and defense mechanisms of T. chinensis leaves to enhanced ultraviolet-A (UV-A) radiation, gel-free/label-free and gel-based proteomics and gas chromatography-mass spectrometry (GC-MS) analyses were performed. The transmission electron microscopy results indicated damage to the chloroplast under UV-A radiation. Proteomics analyses in leaves and chloroplasts showed that photosynthesis-, glycolysis-, secondary metabolism-, stress-, and protein synthesis-, degradation- and activation-related systems were mainly changed under UV-A radiation. Forty-seven PSII proteins and six PSI proteins were identified as being changed in leaves and chloroplasts under UV-A treatment. This indicated that PSII was more sensitive to UV-A than PSI as the target of UV-A light. Enhanced glycolysis, with four glycolysis-related key enzymes increased, provided precursors for secondary metabolism. The 1-deoxy-d-xylulose-5-phosphate reductoisomerase and 4-hydroxy-3-methylbut-2-enyl diphosphate reductase were identified as being significantly increased during UV-A radiation, which resulted in paclitaxel enhancement. Additionally, mRNA expression levels of genes involved in the paclitaxel biosynthetic pathway indicated a down-regulation under UV-A irradiation and up-regulation in dark incubation. These results reveal that a short-term high dose of UV-A radiation could stimulate the plant stress defense system and paclitaxel production.
Collapse
Affiliation(s)
- Wen Zheng
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Setsuko Komatsu
- National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, 305-8518 Japan
| | - Wei Zhu
- Education Ministry Key Laboratory for Biomedical Engineering, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Lin Zhang
- Education Ministry Key Laboratory for Biomedical Engineering, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Ximin Li
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Lei Cui
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Jingkui Tian
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, Zhejiang, 310027, China Education Ministry Key Laboratory for Biomedical Engineering, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| |
Collapse
|
27
|
Mitochondrial Proteome Studies in Seeds during Germination. Proteomes 2016; 4:proteomes4020019. [PMID: 28248229 PMCID: PMC5217346 DOI: 10.3390/proteomes4020019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 06/09/2016] [Accepted: 06/16/2016] [Indexed: 01/25/2023] Open
Abstract
Seed germination is considered to be one of the most critical phases in the plant life cycle, establishing the next generation of a plant species. It is an energy-demanding process that requires functioning mitochondria. One of the earliest events of seed germination is progressive development of structurally simple and metabolically quiescent promitochondria into fully active and cristae-containing mitochondria, known as mitochondrial biogenesis. This is a complex and tightly regulated process, which is accompanied by sequential and dynamic gene expression, protein synthesis, and post-translational modifications. The aim of this review is to give a comprehensive summary of seed mitochondrial proteome studies during germination of various plant model organisms. We describe different gel-based and gel-free proteomic approaches used to characterize mitochondrial proteomes of germinating seeds as well as challenges and limitations of these proteomic studies. Furthermore, the dynamic changes in the abundance of the mitochondrial proteomes of germinating seeds are illustrated, highlighting numerous mitochondrial proteins involved in respiration, tricarboxycylic acid (TCA) cycle, metabolism, import, and stress response as potentially important for seed germination. We then review seed mitochondrial protein carbonylation, phosphorylation, and S-nitrosylation as well as discuss the possible link between these post-translational modifications (PTMs) and the regulation of seed germination.
Collapse
|
28
|
Zhang GL, Zhu Y, Fu WD, Wang P, Zhang RH, Zhang YL, Song Z, Xia GX, Wu JH. iTRAQ Protein Profile Differential Analysis of Dormant and Germinated Grassbur Twin Seeds Reveals that Ribosomal Synthesis and Carbohydrate Metabolism Promote Germination Possibly Through the PI3K Pathway. PLANT & CELL PHYSIOLOGY 2016; 57:1244-1256. [PMID: 27296714 DOI: 10.1093/pcp/pcw074] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 04/03/2016] [Indexed: 06/06/2023]
Abstract
Grassbur is a destructive and invasive weed in pastures, and its burs can cause gastric damage to animals. The strong adaptability and reproductive potential of grassbur are partly due to a unique germination mechanism whereby twin seeds develop in a single bur: one seed germinates, but the other remains dormant. To investigate the molecular mechanism of seed germination in twin seeds, we used isobaric tags for relative and absolute quantitation (iTRAQ) to perform a dynamic proteomic analysis of germination and dormancy. A total of 1,984 proteins were identified, 161 of which were considered to be differentially accumulated. The differentially accumulated proteins comprised 102 up-regulated and 59 down-regulated proteins. These proteins were grouped into seven functional categories, ribosomal proteins being the predominant group. The authenticity and accuracy of the results were confirmed by enzyme-linked immunosorbent assay (ELISA) and quantitative real-time reverse transcription-PCR (qPCR). A dynamic proteomic analysis revealed that ribosome synthesis and carbohydrate metabolism affect seed germination possibly through the phosphoinositide 3-kinase (PI3K) pathway. As the PI3K pathway is generally activated by insulin, analyses of seeds treated with exogenous insulin by qPCR, ELISA and iTRAQ confirmed that the PI3K pathway can be activated, which suppresses dormancy and promotes germination in twin grassbur seeds. Together, these results show that the PI3K pathway may play roles in stimulating seed germination in grassbur by modulating ribosomal synthesis and carbohydrate metabolism.
Collapse
Affiliation(s)
- Guo-Liang Zhang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 10081, China
| | - Yue Zhu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 10081, China The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei-Dong Fu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 10081, China
| | - Peng Wang
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Rui-Hai Zhang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 10081, China
| | - Yan-Lei Zhang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 10081, China
| | - Zhen Song
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 10081, China
| | - Gui-Xian Xia
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jia-He Wu
- The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| |
Collapse
|
29
|
Mustafiz A, Kumari S, Karan R. Ascribing Functions to Genes: Journey Towards Genetic Improvement of Rice Via Functional Genomics. Curr Genomics 2016; 17:155-76. [PMID: 27252584 PMCID: PMC4869004 DOI: 10.2174/1389202917666160202215135] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 07/01/2015] [Accepted: 07/06/2015] [Indexed: 11/22/2022] Open
Abstract
Rice, one of the most important cereal crops for mankind, feeds more than half the world population. Rice has been heralded as a model cereal owing to its small genome size, amenability to easy transformation, high synteny to other cereal crops and availability of complete genome sequence. Moreover, sequence wealth in rice is getting more refined and precise due to resequencing efforts. This humungous resource of sequence data has confronted research fraternity with a herculean challenge as well as an excellent opportunity to functionally validate expressed as well as regulatory portions of the genome. This will not only help us in understanding the genetic basis of plant architecture and physiology but would also steer us towards developing improved cultivars. No single technique can achieve such a mammoth task. Functional genomics through its diverse tools viz. loss and gain of function mutants, multifarious omics strategies like transcriptomics, proteomics, metabolomics and phenomics provide us with the necessary handle. A paradigm shift in technological advances in functional genomics strategies has been instrumental in generating considerable amount of information w.r.t functionality of rice genome. We now have several databases and online resources for functionally validated genes but despite that we are far from reaching the desired milestone of functionally characterizing each and every rice gene. There is an urgent need for a common platform, for information already available in rice, and collaborative efforts between researchers in a concerted manner as well as healthy public-private partnership, for genetic improvement of rice crop better able to handle the pressures of climate change and exponentially increasing population.
Collapse
Affiliation(s)
- Ananda Mustafiz
- South Asian University, Akbar Bhawan, Chanakyapuri, New Delhi
| | - Sumita Kumari
- Sher-e-Kashmir University of Agriculture Sciences and Technology, Jammu 180009, India
| | - Ratna Karan
- Agronomy Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville - 32611, Florida, USA
| |
Collapse
|
30
|
Qiu J, Hou Y, Tong X, Wang Y, Lin H, Liu Q, Zhang W, Li Z, Nallamilli BR, Zhang J. Quantitative phosphoproteomic analysis of early seed development in rice (Oryza sativa L.). PLANT MOLECULAR BIOLOGY 2016; 90:249-265. [PMID: 26613898 DOI: 10.1007/s11103-015-0410-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 11/23/2015] [Indexed: 06/05/2023]
Abstract
Rice (Oryza sativa L.) seed serves as a major food source for over half of the global population. Though it has been long recognized that phosphorylation plays an essential role in rice seed development, the phosphorylation events and dynamics in this process remain largely unknown so far. Here, we report the first large scale identification of rice seed phosphoproteins and phosphosites by using a quantitative phosphoproteomic approach. Thorough proteomic studies in pistils and seeds at 3, 7 days after pollination resulted in the successful identification of 3885, 4313 and 4135 phosphopeptides respectively. A total of 2487 proteins were differentially phosphorylated among the three stages, including Kip related protein 1, Rice basic leucine zipper factor 1, Rice prolamin box binding factor and numerous other master regulators of rice seed development. Moreover, differentially phosphorylated proteins may be extensively involved in the biosynthesis and signaling pathways of phytohormones such as auxin, gibberellin, abscisic acid and brassinosteroid. Our results strongly indicated that protein phosphorylation is a key mechanism regulating cell proliferation and enlargement, phytohormone biosynthesis and signaling, grain filling and grain quality during rice seed development. Overall, the current study enhanced our understanding of the rice phosphoproteome and shed novel insight into the regulatory mechanism of rice seed development.
Collapse
Affiliation(s)
- Jiehua Qiu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Yuxuan Hou
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Xiaohong Tong
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Yifeng Wang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Haiyan Lin
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Qing Liu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Wen Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Zhiyong Li
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China
| | - Babi R Nallamilli
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jian Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People's Republic of China.
| |
Collapse
|
31
|
He D, Wang Q, Li M, Damaris RN, Yi X, Cheng Z, Yang P. Global Proteome Analyses of Lysine Acetylation and Succinylation Reveal the Widespread Involvement of both Modification in Metabolism in the Embryo of Germinating Rice Seed. J Proteome Res 2016; 15:879-90. [PMID: 26767346 DOI: 10.1021/acs.jproteome.5b00805] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Regulation of rice seed germination has been shown to mainly occur at post-transcriptional levels, of which the changes on proteome status is a major one. Lysine acetylation and succinylation are two prevalent protein post-translational modifications (PTMs) involved in multiple biological processes, especially for metabolism regulation. To investigate the potential mechanism controlling metabolism regulation in rice seed germination, we performed the lysine acetylation and succinylation analyses simultaneously. Using high-accuracy nano-LC-MS/MS in combination with the enrichment of lysine acetylated or succinylated peptides from digested embryonic proteins of 24 h after imbibition (HAI) rice seed, a total of 699 acetylated sites from 389 proteins and 665 succinylated sites from 261 proteins were identified. Among these modified lysine sites, 133 sites on 78 proteins were commonly modified by two PTMs. The overlapped PTM sites were more likely to be in polar acidic/basic amino acid regions and exposed on the protein surface. Both of the acetylated and succinylated proteins cover nearly all aspects of cellular functions. Ribosome complex and glycolysis/gluconeogenesis-related proteins were significantly enriched in both acetylated and succinylated protein profiles through KEGG enrichment and protein-protein interaction network analyses. The acetyl-CoA and succinyl-CoA metabolism-related enzymes were found to be extensively modified by both modifications, implying the functional interaction between the two PTMs. This study provides a rich resource to examine the modulation of the two PTMs on the metabolism pathway and other biological processes in germinating rice seed.
Collapse
Affiliation(s)
- Dongli He
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Sino-African Joint Research Center, Chinese Academy of Sciences , Wuhan 430074, China
| | - Qiong Wang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Sino-African Joint Research Center, Chinese Academy of Sciences , Wuhan 430074, China.,University of Chinese Academy of Sciences , Beijing 100049, China
| | - Ming Li
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Sino-African Joint Research Center, Chinese Academy of Sciences , Wuhan 430074, China
| | - Rebecca Njeri Damaris
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Sino-African Joint Research Center, Chinese Academy of Sciences , Wuhan 430074, China.,University of Chinese Academy of Sciences , Beijing 100049, China
| | - Xingling Yi
- Jingjie PTM Biolabs (Hangzhou) Co. Ltd. , Hangzhou 310018, China
| | - Zhongyi Cheng
- Jingjie PTM Biolabs (Hangzhou) Co. Ltd. , Hangzhou 310018, China
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Sino-African Joint Research Center, Chinese Academy of Sciences , Wuhan 430074, China
| |
Collapse
|
32
|
Xu E, Chen M, He H, Zhan C, Cheng Y, Zhang H, Wang Z. Proteomic Analysis Reveals Proteins Involved in Seed Imbibition under Salt Stress in Rice. FRONTIERS IN PLANT SCIENCE 2016; 7:2006. [PMID: 28105039 PMCID: PMC5213780 DOI: 10.3389/fpls.2016.02006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/16/2016] [Indexed: 05/20/2023]
Abstract
Enhancement of salinity tolerance during seed germination is very important for direct seeding in rice. In this study, the salt-tolerant japonica landrace Jiucaiqing was used to determine the regulators that are involved in seed imbibition under salt stress. Briefly, the comparative proteomic analysis was conducted between dry (0 h) and imbibed (24 h) seeds with 150 mM NaCl. Under salt stress, the uptake of water increased rapidly before 24 h imbibition (Phase I), followed by a plateau of seed imbibition from 24 to 96 h imbibition (Phase II). We identified 14 proteins involved in seed imbibition, in which the majority of these proteins were involved in energy supply and storage protein. The early imbibition process was mediated by protein catabolism; the most of proteins were down-regulated after 24 h imbibition. Eleven genes in salt stress treated seeds were expressed early during the seed imbibition in comparison to control seeds. By comparison, 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (BPM), glutelin (GLU2.2 and GLU2.3), glucose-1-phosphate adenylyltransferase large subunit (GAS8), and cupin domain containing protein (CDP3.1 and CDP3.2) were near the regions of quantitative trait loci (QTLs) for seed dormancy, seed reserve utilization, and seed germination in Jiucaiqing. In particular, CDP3.1 was co-located in the region of qIR-3 for imbibition rate, and qGP-3 for germination percentage. The role of CDP3.1 was verified in enhancing seed germination under salt stress using T-DNA mutant. The identified proteins might be applicable for the improvement of seed germination under salt stress in rice.
Collapse
Affiliation(s)
- Enshun Xu
- The Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural UniversityNanjing, China
| | - Mingming Chen
- Department of Plant Science, College of Biological Sciences, Henan Agricultural UniversityZhengzhou, China
| | - Hui He
- The Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural UniversityNanjing, China
| | - Chengfang Zhan
- The Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural UniversityNanjing, China
| | - Yanhao Cheng
- The Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural UniversityNanjing, China
| | - Hongsheng Zhang
- The Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural UniversityNanjing, China
- *Correspondence: Hongsheng Zhang
| | - Zhoufei Wang
- The Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural UniversityNanjing, China
- Zhoufei Wang
| |
Collapse
|
33
|
He D, Wang Q, Wang K, Yang P. Genome-Wide Dissection of the MicroRNA Expression Profile in Rice Embryo during Early Stages of Seed Germination. PLoS One 2015; 10:e0145424. [PMID: 26681181 PMCID: PMC4683037 DOI: 10.1371/journal.pone.0145424] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 12/03/2015] [Indexed: 11/19/2022] Open
Abstract
The first 24 hours after imbibition (HAI) is pivotal for rice seed germination, during which embryo cells switch from a quiescent state to a metabolically active state rapidly. MicroRNAs (miRNAs) have increasingly been shown to play important roles in rice development. Nevertheless, limited knowledge about miRNA regulation has been obtained in the early stages of rice seed germination. In this study, the small RNAs (sRNAs) from embryos of 0, 12, and 24 HAI rice seeds were sequenced to investigate the composition and expression patterns of miRNAs. The bioinformatics analysis identified 289 miRNA loci, including 59 known and 230 novel miRNAs, and 35 selected miRNAs were confirmed by stem-loop real-time RT-PCR. Expression analysis revealed that the dry and imbibed seeds have unique miRNA expression patterns compared with other tissues, particularly for the dry seeds. Using three methods, Mireap, psRNATarget and degradome analyses, 1197 potential target genes of identified miRNAs involved in various molecular functions were predicted. Among these target genes, 39 had significantly negative correlations with their corresponding miRNAs as inferred from published transcriptome data, and 6 inversely expressed miRNA-target pairs were confirmed by 5'-RACE assay. Our work provides an inventory of miRNA expression profiles and miRNA-target interactions in rice embryos, and lays a foundation for further studies of miRNA-mediated regulation in initial seed germination.
Collapse
Affiliation(s)
- Dongli He
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Qiong Wang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kun Wang
- College of life science, Wuhan University, Wuhan 430072, China
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| |
Collapse
|
34
|
Gel-free/label-free proteomic analysis of developing rice grains under heat stress. J Proteomics 2015; 133:1-19. [PMID: 26655677 DOI: 10.1016/j.jprot.2015.12.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Revised: 11/21/2015] [Accepted: 12/03/2015] [Indexed: 11/23/2022]
Abstract
UNLABELLED High temperature markedly reduces the yields and quality of rice grains. To identify the mechanisms underlying heat stress-induced responses in rice grains, proteomic technique was used. Developing Khao Dawk Mali 105 rice grains at the milky, dough, and mature stages were treated at 40 °C for 3 days. Aromatic compounds were decreased in rice grains under heat stress. The protein abundance involved in glycolysis and tricarboxylic acid cycle, including glyceraldehyde 3-phosphate dehydrogenase and citrate synthase, was changed in milky and dough grains after heat treatment; however, none changes in mature grains. The abundance involved in amino acid metabolism was increased in dough grains, but decreased in milky grains. In addition, the abundance involved in starch and sucrose metabolism, such as starch synthase, ADP-glucose pyrophosphorylase, granule-bound starch synthase, and alpha amylase, was decreased in milky grains, but increased in dough grains. A number of redox homeostasis-related proteins, such as ascorbate peroxidase and peroxiredoxin, were increased in developing rice grains treated with heat stress. These results suggest that in response to heat stress, the abundance of numerous proteins involved in redox homeostasis and carbohydrate biosynthetic pathways may play a major role in the development of KDML105 rice grains. BIOLOGICAL SIGNIFICANCE Yield of Khao Dawk Mali 105 rice, which is an economical aromatic rice, was disrupted by environmental stress. Rice grains developed under heat stress caused loss of aroma compound. To identify the mechanism of heat response in rice grain, gel-free/label-free proteomic technique was used. The abundance of proteins involved in glycolysis and tricarboxylic acid cycle was disrupted by heat stress. High temperature limited starch biosynthesis; however, it enhanced sugar biosynthesis in developing rice grains. Redox homeostasis related proteins were disrupted by heat stress. These results suggest that proteins involved in redox homeostasis and carbohydrate pathway might play a major role in developing grains in Khao Dawk Mali 105 rice under heat stress.
Collapse
|
35
|
Hou Y, Qiu J, Tong X, Wei X, Nallamilli BR, Wu W, Huang S, Zhang J. A comprehensive quantitative phosphoproteome analysis of rice in response to bacterial blight. BMC PLANT BIOLOGY 2015; 15:163. [PMID: 26112675 PMCID: PMC4482044 DOI: 10.1186/s12870-015-0541-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 06/05/2015] [Indexed: 05/06/2023]
Abstract
BACKGROUND Rice is a major crop worldwide. Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) has become one of the most devastating diseases for rice. It has been clear that phosphorylation plays essential roles in plant disease resistance. However, the role of phosphorylation is poorly understood in rice-Xoo system. Here, we report the first study on large scale enrichment of phosphopeptides and identification of phosphosites in rice before and 24 h after Xoo infection. RESULTS We have successfully identified 2367 and 2223 phosphosites on 1334 and 1297 representative proteins in 0 h and 24 h after Xoo infection, respectively. A total of 762 differentially phosphorylated proteins, including transcription factors, kinases, epi-genetic controlling factors and many well-known disease resistant proteins, are identified after Xoo infection suggesting that they may be functionally relevant to Xoo resistance. In particular, we found that phosphorylation/dephosphorylation might be a key switch turning on/off many epi-genetic controlling factors, including HDT701, in response to Xoo infection, suggesting that phosphorylation switch overriding the epi-genetic regulation may be a very universal model in the plant disease resistance pathway. CONCLUSIONS The phosphosites identified in this study would be a big complementation to our current knowledge in the phosphorylation status and sites of rice proteins. This research represents a substantial advance in understanding the rice phosphoproteome as well as the mechanism of rice bacterial blight resistance.
Collapse
Affiliation(s)
- Yuxuan Hou
- China National Rice Research Institute, Hangzhou, 311400, China.
| | - Jiehua Qiu
- China National Rice Research Institute, Hangzhou, 311400, China.
| | - Xiaohong Tong
- China National Rice Research Institute, Hangzhou, 311400, China.
| | - Xiangjin Wei
- China National Rice Research Institute, Hangzhou, 311400, China.
| | - Babi R Nallamilli
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, U.S.A..
| | - Weihuai Wu
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China.
| | - Shiwen Huang
- China National Rice Research Institute, Hangzhou, 311400, China.
| | - Jian Zhang
- China National Rice Research Institute, Hangzhou, 311400, China.
| |
Collapse
|
36
|
Wei T, He Z, Tan X, Liu X, Yuan X, Luo Y, Hu S. An integrated RNA-Seq and network study reveals a complex regulation process of rice embryo during seed germination. Biochem Biophys Res Commun 2015; 464:176-81. [PMID: 26116530 DOI: 10.1016/j.bbrc.2015.06.110] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Accepted: 06/17/2015] [Indexed: 01/08/2023]
Abstract
Seed germination is a crucial stage for plant development and agricultural production. To investigate its complex regulation process, the RNA-Seq study of rice embryo was conducted at three time points of 0, 12 and 48 h post imbibition (HPI). Dynamic transcriptional alterations were observed, especially in the early stage (0-12 HPI). Seed related genes, especially those encoding desiccation inducible proteins and storage reserves in embryo, decreased drastically after imbibition. The expression profiles of phytohormone related genes indicated distinct roles of abscisic acid (ABA), gibberellin (GA) and brassinosteroid (BR) in germination. Moreover, network analysis revealed the importance of protein phosphorylation in phytohormone interactions. Network and gene ontology (GO) analyses suggested that transcription factors (TFs) played a regulatory role in functional transitions during germination, and the enriched TF families at 0 HPI implied a regulation of epigenetic modification in dry seeds. In addition, 35 germination-specific TF genes in embryo were identified and seven genes were verified by qRT-PCR. Besides, enriched TF binding sites (TFBSs) supported physiological changes in germination. Overall, this study expands our comprehensive knowledge of multiple regulation factors underlying rice seed germination.
Collapse
Affiliation(s)
- Ting Wei
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zilong He
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - XinYu Tan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xue Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiao Yuan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingfeng Luo
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Songnian Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| |
Collapse
|
37
|
Li M, Yin X, Sakata K, Yang P, Komatsu S. Proteomic Analysis of Phosphoproteins in the Rice Nucleus During the Early Stage of Seed Germination. J Proteome Res 2015; 14:2884-96. [DOI: 10.1021/acs.jproteome.5b00215] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Ming Li
- Key
Laboratory of Plant Germplasm Enhancement and Specialty Agriculture,
Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- National
Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
| | - Xiaojian Yin
- National
Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
| | - Katsumi Sakata
- Department
of Life Science and Informatics, Maebashi Institute of Technology, Maebashi 371-0816, Japan
| | - Pingfang Yang
- Key
Laboratory of Plant Germplasm Enhancement and Specialty Agriculture,
Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Setsuko Komatsu
- National
Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
| |
Collapse
|
38
|
Chakraborty S, Salekdeh GH, Yang P, Woo SH, Chin CF, Gehring C, Haynes PA, Mirzaei M, Komatsu S. Proteomics of Important Food Crops in the Asia Oceania Region: Current Status and Future Perspectives. J Proteome Res 2015; 14:2723-44. [DOI: 10.1021/acs.jproteome.5b00211] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | | | - Pingfang Yang
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Sun Hee Woo
- Chungbuk National University, Cheongju 362-763, Korea
| | - Chiew Foan Chin
- University of Nottingham Malaysia Campus, 43500 Semenyih, Selangor, Malaysia
| | - Chris Gehring
- King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | | | | | - Setsuko Komatsu
- National Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan
| |
Collapse
|
39
|
Han C, Yang P. Studies on the molecular mechanisms of seed germination. Proteomics 2015; 15:1671-9. [PMID: 25597791 DOI: 10.1002/pmic.201400375] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 12/03/2014] [Accepted: 01/14/2015] [Indexed: 11/07/2022]
Abstract
Seed germination that begins with imbibition and ends with radicle emergence is the first step for plant growth. Successful germination is not only crucial for seedling establishment but also important for crop yield. After being dispersed from mother plant, seed undergoes continuous desiccation in ecosystem and selects proper environment to trigger germination. Owing to the contribution of transcriptomic, proteomic, and molecular biological studies, molecular aspect of seed germination is elucidated well in Arabidopsis. Recently, more and more proteomic and genetic studies concerning cereal seed germination were performed on rice (Oryza sativa) and barley (Hordeum vulgare), which possess completely different seed structure and domestication background with Arabidopsis. In this review, both the common features and the distinct mechanisms of seed germination are compared among different plant species including Arabidopsis, rice, and maize. These features include morphological changes, cell and its related structure recovery, metabolic activation, hormone behavior, and transcription and translation activation. This review will provide more comprehensive insights into the molecular mechanisms of seed germination.
Collapse
Affiliation(s)
- Chao Han
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P. R. China
| |
Collapse
|
40
|
Abstract
The protein content of plant cells is constantly being updated. This process is driven by the opposing actions of protein degradation, which defines the half-life of each polypeptide, and protein synthesis. Our understanding of the processes that regulate protein synthesis and degradation in plants has advanced significantly over the past decade. Post-transcriptional modifications that influence features of the mRNA populations, such as poly(A) tail length and secondary structure, contribute to the regulation of protein synthesis. Post-translational modifications such as phosphorylation, ubiquitination and non-enzymatic processes such as nitrosylation and carbonylation, govern the rate of degradation. Regulators such as the plant TOR kinase, and effectors such as the E3 ligases, allow plants to balance protein synthesis and degradation under developmental and environmental change. Establishing an integrated understanding of the processes that underpin changes in protein abundance under various physiological and developmental scenarios will accelerate our ability to model and rationally engineer plants.
Collapse
Affiliation(s)
- Clark J Nelson
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Hwy, Crawley 6009, Perth, Western Australia, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Hwy, Crawley 6009, Perth, Western Australia, Australia
| |
Collapse
|
41
|
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.
Collapse
Affiliation(s)
- Cecilia Silva-Sanchez
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | | | | |
Collapse
|
42
|
Li J, Silva-Sanchez C, Zhang T, Chen S, Li H. Phosphoproteomics technologies and applications in plant biology research. FRONTIERS IN PLANT SCIENCE 2015; 6:430. [PMID: 26136758 PMCID: PMC4468387 DOI: 10.3389/fpls.2015.00430] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 05/27/2015] [Indexed: 05/20/2023]
Abstract
Protein phosphorylation has long been recognized as an essential mechanism to regulate many important processes of plant life. However, studies on phosphorylation mediated signaling events in plants are challenged with low stoichiometry and dynamic nature of phosphorylated proteins. Significant advances in mass spectrometry based phosphoproteomics have taken place in recent decade, including phosphoprotein/phosphopeptide enrichment, detection and quantification, and phosphorylation site localization. This review describes a variety of separation and enrichment methods for phosphoproteins and phosphopeptides, the applications of technological innovations in plant phosphoproteomics, and highlights significant achievement of phosphoproteomics in the areas of plant signal transduction, growth and development.
Collapse
Affiliation(s)
- Jinna Li
- College of Life Sciences, Heilongjiang UniversityHarbin, China
| | - Cecilia Silva-Sanchez
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of FloridaGainesville, FL, USA
| | - Tong Zhang
- Plant Molecular and Cellular Biology Program, Department of Biology, UF Genetics Institute, University of FloridaGainesville, FL, USA
| | - Sixue Chen
- College of Life Sciences, Heilongjiang UniversityHarbin, China
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of FloridaGainesville, FL, USA
- Plant Molecular and Cellular Biology Program, Department of Biology, UF Genetics Institute, University of FloridaGainesville, FL, USA
| | - Haiying Li
- College of Life Sciences, Heilongjiang UniversityHarbin, China
- *Correspondence: Haiying Li, College of Life Sciences, Heilongjiang University, 74 Xuefu Rd, Harbin 150080, China
| |
Collapse
|
43
|
Abstract
Cereals are the most important crop plant supplying staple food throughout the world. The economic importance and continued breeding of crop plants such as rice, maize, wheat, or barley require a detailed scientific understanding of adaptive and developmental processes. Protein phosphorylation is one of the most important regulatory posttranslational modifications and its analysis allows deriving functional and regulatory principles in plants. This minireview summarizes the current knowledge of phosphoproteomic studies in cereals.
Collapse
Affiliation(s)
- Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuchang Moshan, Wuhan, 430074, China,
| |
Collapse
|
44
|
Kamal AHM, Rashid H, Sakata K, Komatsu S. Gel-free quantitative proteomic approach to identify cotyledon proteins in soybean under flooding stress. J Proteomics 2015; 112:1-13. [PMID: 25201076 DOI: 10.1016/j.jprot.2014.08.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Revised: 08/22/2014] [Accepted: 08/27/2014] [Indexed: 01/10/2023]
Abstract
Flooding stress causes growth inhibition and ultimately death in most crop species by limiting of energy production. To better understand plant responses to flooding stress, here, flooding-responsive proteins in the cotyledons of soybean were identified using a gel-free quantitative proteomic approach. One hundred forty six proteins were commonly observed in both control and flooding-stressed plants, and 19 were identified under only flooding stress conditions. The main functional categories were protein and development-related proteins. Protein-protein interaction analysis revealed that zincin-like metalloprotease and cupin family proteins were found to highly interact with other proteins under flooding stress. Plant stearoyl acyl-carrier protein, ascorbate peroxidase 1, and secretion-associated RAS superfamily 2 were down-regulated, whereas ferretin 1 was up-regulated at the transcription level. Notably, the levels of all corresponding proteins were decreased, indicating that mRNA translation to proteins is impaired under flooding conditions. Decreased levels of ferritin may lead to a strong deregulation of the expression of several metal transporter genes and over-accumulation of iron, which led to increased levels of reactive oxygen species, resulting to detoxification of these reactive species. Taken together, these results suggest that ferritin might have an essential role in protecting plant cells against oxidative damage under flooding conditions. BIOLOGICAL SIGNIFICANCE This study reported the comparative proteomic analysis of cotyledon of soybean plants between non-flooding and flooding conditions using the gel-free quantitative techniques. Mass spectrometry analysis of the proteins from cotyledon resulted in the identification of a total of 165 proteins under flooding stress. These proteins were assigned to different functional categories, such as protein, development, stress, redox, and glycolysis. Therefore, this study provides not only the comparative proteomic analysis but also the molecular mechanism underlying the flooding responsive protein functions in the cotyledon.
Collapse
Affiliation(s)
| | - Hamid Rashid
- Mohammad Ali Jinnah University, Islamabad, Pakistan
| | - Katsumi Sakata
- Maebashi Institute of Technology, Maebashi 371-0816, Japan
| | - Setsuko Komatsu
- National Institute of Crop Science, NARO, Tsukuba 305-8518, Japan.
| |
Collapse
|
45
|
Hu X, Wu L, Zhao F, Zhang D, Li N, Zhu G, Li C, Wang W. Phosphoproteomic analysis of the response of maize leaves to drought, heat and their combination stress. FRONTIERS IN PLANT SCIENCE 2015. [PMID: 25999967 DOI: 10.3389/flps.2015.00298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Drought and heat stress, especially their combination, greatly affect crop production. Many studies have described transcriptome, proteome and phosphoproteome changes in response of plants to drought or heat stress. However, the study about the phosphoproteomic changes in response of crops to the combination stress is scare. To understand the mechanism of maize responses to the drought and heat combination stress, phosphoproteomic analysis was performed on maize leaves by using multiplex iTRAQ-based quantitative proteomic and LC-MS/MS methods. Five-leaf-stage maize was subjected to drought, heat or their combination, and the leaves were collected. Globally, heat, drought and the combined stress significantly changed the phosphorylation levels of 172, 149, and 144 phosphopeptides, respectively. These phosphopeptides corresponded to 282 proteins. Among them, 23 only responded to the combined stress and could not be predicted from their responses to single stressors; 30 and 75 only responded to drought and heat, respectively. Notably, 19 proteins were phosphorylated on different sites in response to the single and combination stresses. Of the seven significantly enriched phosphorylation motifs identified, two were common for all stresses, two were common for heat and the combined stress, and one was specific to the combined stress. The signaling pathways in which the phosphoproteins were involved clearly differed among the three stresses. Functional characterization of the phosphoproteins and the pathways identified here could lead to new targets for the enhancement of crop stress tolerance, which will be particularly important in the face of climate change and the increasing prevalence of abiotic stressors.
Collapse
Affiliation(s)
- Xiuli Hu
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural University Zhengzhou, China
| | - Liuji Wu
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural University Zhengzhou, China
| | - Feiyun Zhao
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural University Zhengzhou, China
| | - Dayong Zhang
- Jiangsu Academy of Agricultural Sciences Institute of Biotechnology Nanjing, China
| | - Nana Li
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural University Zhengzhou, China
| | - Guohui Zhu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University Guangzhou, China
| | - Chaohao Li
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural University Zhengzhou, China
| | - Wei Wang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural University Zhengzhou, China
| |
Collapse
|
46
|
Hu X, Wu L, Zhao F, Zhang D, Li N, Zhu G, Li C, Wang W. Phosphoproteomic analysis of the response of maize leaves to drought, heat and their combination stress. FRONTIERS IN PLANT SCIENCE 2015; 6:298. [PMID: 25999967 PMCID: PMC4419667 DOI: 10.3389/fpls.2015.00298] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 04/14/2015] [Indexed: 05/18/2023]
Abstract
Drought and heat stress, especially their combination, greatly affect crop production. Many studies have described transcriptome, proteome and phosphoproteome changes in response of plants to drought or heat stress. However, the study about the phosphoproteomic changes in response of crops to the combination stress is scare. To understand the mechanism of maize responses to the drought and heat combination stress, phosphoproteomic analysis was performed on maize leaves by using multiplex iTRAQ-based quantitative proteomic and LC-MS/MS methods. Five-leaf-stage maize was subjected to drought, heat or their combination, and the leaves were collected. Globally, heat, drought and the combined stress significantly changed the phosphorylation levels of 172, 149, and 144 phosphopeptides, respectively. These phosphopeptides corresponded to 282 proteins. Among them, 23 only responded to the combined stress and could not be predicted from their responses to single stressors; 30 and 75 only responded to drought and heat, respectively. Notably, 19 proteins were phosphorylated on different sites in response to the single and combination stresses. Of the seven significantly enriched phosphorylation motifs identified, two were common for all stresses, two were common for heat and the combined stress, and one was specific to the combined stress. The signaling pathways in which the phosphoproteins were involved clearly differed among the three stresses. Functional characterization of the phosphoproteins and the pathways identified here could lead to new targets for the enhancement of crop stress tolerance, which will be particularly important in the face of climate change and the increasing prevalence of abiotic stressors.
Collapse
Affiliation(s)
- Xiuli Hu
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural UniversityZhengzhou, China
| | - Liuji Wu
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural UniversityZhengzhou, China
| | - Feiyun Zhao
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural UniversityZhengzhou, China
| | - Dayong Zhang
- Jiangsu Academy of Agricultural Sciences Institute of BiotechnologyNanjing, China
| | - Nana Li
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural UniversityZhengzhou, China
| | - Guohui Zhu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural UniversityGuangzhou, China
| | - Chaohao Li
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural UniversityZhengzhou, China
| | - Wei Wang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural UniversityZhengzhou, China
- *Correspondence: Wei Wang, State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural University, 63 Nongye Road, Zhengzhou 450002, China
| |
Collapse
|
47
|
Wang WQ, Liu SJ, Song SQ, Møller IM. Proteomics of seed development, desiccation tolerance, germination and vigor. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 86:1-15. [PMID: 25461695 DOI: 10.1016/j.plaphy.2014.11.003] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 11/03/2014] [Indexed: 05/19/2023]
Abstract
Proteomics, the large-scale study of the total complement of proteins in a given sample, has been applied to all aspects of seed biology mainly using model species such as Arabidopsis or important agricultural crops such as corn and rice. Proteins extracted from the sample have typically been separated and quantified by 2-dimensional polyacrylamide gel electrophoresis followed by liquid chromatography and mass spectrometry to identify the proteins in the gel spots. In this way, qualitative and quantitative changes in the proteome during seed development, desiccation tolerance, germination, dormancy release, vigor alteration and responses to environmental factors have all been studied. Many proteins or biological processes potentially important for each seed process have been highlighted by these studies, which greatly expands our knowledge of seed biology. Proteins that have been identified to be particularly important for at least two of the seed processes are involved in detoxification of reactive oxygen species, the cytoskeleton, glycolysis, protein biosynthesis, post-translational modifications, methionine metabolism, and late embryogenesis-abundant (LEA) proteins. It will be useful for molecular biologists and molecular plant breeders to identify and study genes encoding particularly interesting target proteins with the aim to improve the yield, stress tolerance or other critical properties of our crop species.
Collapse
Affiliation(s)
- Wei-Qing Wang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
| | - Shu-Jun Liu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
| | - Song-Quan Song
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China.
| | - Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Flakkebjerg, DK-4200 Slagelse, Denmark.
| |
Collapse
|
48
|
Zhang M, Ma CY, Lv DW, Zhen SM, Li XH, Yan YM. Comparative phosphoproteome analysis of the developing grains in bread wheat (Triticum aestivum L.) under well-watered and water-deficit conditions. J Proteome Res 2014; 13:4281-97. [PMID: 25145454 DOI: 10.1021/pr500400t] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Wheat (Triticum aestivum), one of the most important cereal crops, is often threatened by drought. In this study, water deficit significantly reduced the height of plants and yield of grains. To explore further the effect of drought stress on the development and yield of grains, we first performed a large scale phosphoproteome analysis of developing grains in wheat. A total of 590 unique phosphopeptides, representing 471 phosphoproteins, were identified under well-watered conditions. Motif-X analysis showed that four motifs were enriched, including [sP], [Rxxs], [sDxE], and [sxD]. Through comparative phosphoproteome analysis between well-watered and water-deficit conditions, we found that 63 unique phosphopeptides, corresponding to 61 phosphoproteins, showed significant changes in phosphorylation level (≥2-fold intensities). Functional analysis suggested that some of these proteins may be involved in signal transduction, embryo and endosperm development of grains, and drought response and defense under water-deficit conditions. Moreover, we also found that some chaperones may play important roles in protein refolding or degradation when the plant is subjected to water stress. These results provide a detailed insight into the stress response and defense mechanisms of developmental grains at the phosphoproteome level. They also suggested some potential candidates for further study of transgenosis and drought stress as well as incorporation into molecular breeding for drought resistance.
Collapse
Affiliation(s)
- Ming Zhang
- College of Life Science, Capital Normal University , 100048 Beijing, China
| | | | | | | | | | | |
Collapse
|
49
|
The mitochondrion-located protein OsB12D1 enhances flooding tolerance during seed germination and early seedling growth in rice. Int J Mol Sci 2014; 15:13461-81. [PMID: 25089878 PMCID: PMC4159805 DOI: 10.3390/ijms150813461] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Revised: 06/22/2014] [Accepted: 07/21/2014] [Indexed: 11/17/2022] Open
Abstract
B12D belongs to a function unknown subgroup of the Balem (Barley aleurone and embryo) proteins. In our previous work on rice seed germination, we identified a B12D-like protein encoded by LOC_Os7g41350 (named OsB12D1). OsB12D1 pertains to an ancient protein family with an amino acid sequence highly conserved from moss to angiosperms. Among the six OsB12Ds, OsB12D1 is one of the major transcripts and is primarily expressed in germinating seed and root. Bioinformatics analyses indicated that OsB12D1 is an anoxic or submergence resistance-related gene. RT-PCR results showed OsB12D1 is induced remarkably in the coleoptiles or roots by flooding during seed germination and early seedling growth. The OsB12D1-overexpressed rice seeds could protrude radicles in 8 cm deep water, further exhibiting significant flooding tolerance compared to the wild type. Moreover, this tolerance was not affected by the gibberellin biosynthesis inhibitor paclobutrazol. OsB12D1 was identified in the mitochondrion by subcellular localization analysis and possibly enhances electron transport through mediating Fe and oxygen availability under flooded conditions. This work indicated that OsB12D1 is a promising gene that can help to enhance rice seedling establishment in farming practices, especially for direct seeding.
Collapse
|
50
|
Lv DW, Ge P, Zhang M, Cheng ZW, Li XH, Yan YM. Integrative network analysis of the signaling cascades in seedling leaves of bread wheat by large-scale phosphoproteomic profiling. J Proteome Res 2014; 13:2381-95. [PMID: 24679076 DOI: 10.1021/pr401184v] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Here, we conducted the first large-scale leaf phosphoproteome analysis of two bread wheat cultivars by liquid chromatography-tandem mass spectrometry. Altogether, 1802 unambiguous phosphorylation sites representing 1175 phosphoproteins implicated in various molecular functions and cellular processes were identified by gene ontology enrichment analysis. Among the 1175 phosphoproteins, 141 contained 3-10 phosphorylation sites. The phosphorylation sites were located more frequently in the N- and C-terminal regions than in internal regions, and ∼70% were located outside the conserved regions. Conservation analysis showed that 90.5% of the phosphoproteins had phosphorylated orthologs in other plant species. Eighteen significantly enriched phosphorylation motifs, of which six were new wheat phosphorylation motifs, were identified. In particular, 52 phosphorylated transcription factors (TFs), 85 protein kinases (PKs), and 16 protein phosphatases (PPs) were classified and analyzed in depth. All the Tyr phosphorylation sites were in PKs such as mitogen-activated PKs (MAPKs) and SHAGGY-like kinases. A complicated cross-talk phosphorylation regulatory network based on PKs such as Snf1-related kinases (SnRKs), calcium-dependent PKs (CDPKs), and glycogen synthase kinase 3 (GSK3) and PPs including PP2C, PP2A, and BRI1 suppressor 1 (BSU1)-like protein (BSL) was constructed and was found to be potentially involved in rapid leaf growth. Our results provide a series of phosphoproteins and phosphorylation sites in addition to a potential network of phosphorylation signaling cascades in wheat seedling leaves.
Collapse
Affiliation(s)
- Dong-Wen Lv
- College of Life Science, Capital Normal University , 100048 Beijing, China
| | | | | | | | | | | |
Collapse
|