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Paux E, Lafarge S, Balfourier F, Derory J, Charmet G, Alaux M, Perchet G, Bondoux M, Baret F, Barillot R, Ravel C, Sourdille P, Le Gouis J. Breeding for Economically and Environmentally Sustainable Wheat Varieties: An Integrated Approach from Genomics to Selection. BIOLOGY 2022; 11:149. [PMID: 35053148 PMCID: PMC8773325 DOI: 10.3390/biology11010149] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 12/21/2022]
Abstract
There is currently a strong societal demand for sustainability, quality, and safety in bread wheat production. To address these challenges, new and innovative knowledge, resources, tools, and methods to facilitate breeding are needed. This starts with the development of high throughput genomic tools including single nucleotide polymorphism (SNP) arrays, high density molecular marker maps, and full genome sequences. Such powerful tools are essential to perform genome-wide association studies (GWAS), to implement genomic and phenomic selection, and to characterize the worldwide diversity. This is also useful to breeders to broaden the genetic basis of elite varieties through the introduction of novel sources of genetic diversity. Improvement in varieties particularly relies on the detection of genomic regions involved in agronomical traits including tolerance to biotic (diseases and pests) and abiotic (drought, nutrient deficiency, high temperature) stresses. When enough resolution is achieved, this can result in the identification of candidate genes that could further be characterized to identify relevant alleles. Breeding must also now be approached through in silico modeling to simulate plant development, investigate genotype × environment interactions, and introduce marker-trait linkage information in the models to better implement genomic selection. Breeders must be aware of new developments and the information must be made available to the world wheat community to develop new high-yielding varieties that can meet the challenge of higher wheat production in a sustainable and fluctuating agricultural context. In this review, we compiled all knowledge and tools produced during the BREEDWHEAT project to show how they may contribute to face this challenge in the coming years.
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Affiliation(s)
- Etienne Paux
- UMR GDEC Genetics, Diversity & Ecophysiology of Cereals, INRAE—Université Clermont-Auvergne, 5, Chemin de Beaulieu, 63000 Clermont-Ferrand, France; (E.P.); (F.B.); (G.C.); (C.R.); (P.S.)
| | - Stéphane Lafarge
- Limagrain, Chappes Research Center, Route d’Ennezat, 63720 Chappes, France; (S.L.); (J.D.)
| | - François Balfourier
- UMR GDEC Genetics, Diversity & Ecophysiology of Cereals, INRAE—Université Clermont-Auvergne, 5, Chemin de Beaulieu, 63000 Clermont-Ferrand, France; (E.P.); (F.B.); (G.C.); (C.R.); (P.S.)
| | - Jérémy Derory
- Limagrain, Chappes Research Center, Route d’Ennezat, 63720 Chappes, France; (S.L.); (J.D.)
| | - Gilles Charmet
- UMR GDEC Genetics, Diversity & Ecophysiology of Cereals, INRAE—Université Clermont-Auvergne, 5, Chemin de Beaulieu, 63000 Clermont-Ferrand, France; (E.P.); (F.B.); (G.C.); (C.R.); (P.S.)
| | - Michael Alaux
- Université Paris-Saclay—INRAE, URGI, 78026 Versailles, France;
- Université Paris-Saclay—INRAE, BioinfOmics, Plant Bioinformatics Facility, 78026 Versailles, France
| | - Geoffrey Perchet
- Vegepolys Valley, Maison du Végétal, 26 Rue Jean Dixmeras, 49066 Angers, France;
| | - Marion Bondoux
- INRAE—Transfert, 5, Chemin de Beaulieu, 63000 Clermont-Ferrand, France;
| | - Frédéric Baret
- UMR EMMAH, INRAE—Université d’Avignon et des Pays de Vaucluse, 84914 Avignon, France;
| | | | - Catherine Ravel
- UMR GDEC Genetics, Diversity & Ecophysiology of Cereals, INRAE—Université Clermont-Auvergne, 5, Chemin de Beaulieu, 63000 Clermont-Ferrand, France; (E.P.); (F.B.); (G.C.); (C.R.); (P.S.)
| | - Pierre Sourdille
- UMR GDEC Genetics, Diversity & Ecophysiology of Cereals, INRAE—Université Clermont-Auvergne, 5, Chemin de Beaulieu, 63000 Clermont-Ferrand, France; (E.P.); (F.B.); (G.C.); (C.R.); (P.S.)
| | - Jacques Le Gouis
- UMR GDEC Genetics, Diversity & Ecophysiology of Cereals, INRAE—Université Clermont-Auvergne, 5, Chemin de Beaulieu, 63000 Clermont-Ferrand, France; (E.P.); (F.B.); (G.C.); (C.R.); (P.S.)
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Li T, Zhu D, Han Z, Zhang J, Zhang M, Yan Y. Label-Free Quantitative Proteome Analysis Reveals the Underlying Mechanisms of Grain Nuclear Proteins Involved in Wheat Water-Deficit Response. FRONTIERS IN PLANT SCIENCE 2021; 12:748487. [PMID: 34759942 PMCID: PMC8572964 DOI: 10.3389/fpls.2021.748487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/05/2021] [Indexed: 06/13/2023]
Abstract
In this study, we performed the first nuclear proteome analysis of wheat developing grains under water deficit by using a label-free based quantitative proteomic approach. In total, we identified 625 unique proteins as differentially accumulated proteins (DAPs), of which 398 DAPs were predicted to be localized in nucleus. Under water deficit, 146 DAPs were up-regulated and mainly involved in the stress response and oxidation-reduction process, while 252 were down-regulated and mainly participated in translation, the cellular amino metabolic process, and the oxidation-reduction process. The cis-acting elements analysis of the key nuclear DAPs encoding genes demonstrated that most of these genes contained the same cis-acting elements in the promoter region, mainly including ABRE involved in abscisic acid response, antioxidant response element, MYB responsive to drought regulation and MYC responsive to early drought. The cis-acting elements related to environmental stress and hormones response were relatively abundant. The transcription expression profiling of the nuclear up-regulated DAPs encoding genes under different organs, developmental stages and abiotic stresses was further detected by RNA-seq and Real-time quantitative polymerase chain reaction, and more than 50% of these genes showed consistency between transcription and translation expression. Finally, we proposed a putative synergistic responsive network of wheat nuclear proteome to water deficit, revealing the underlying mechanisms of wheat grain nuclear proteome in response to water deficit.
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Affiliation(s)
- Tingting Li
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing, China
| | - Dong Zhu
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing, China
| | - Zhisheng Han
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing, China
| | - Junwei Zhang
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing, China
| | - Ming Zhang
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
| | - Yueming Yan
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing, China
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Li S, Luo J, Zhou X, Li X, Wang F, Liu Y. Identification of characteristic proteins of wheat varieties used to commercially produce dried noodles by electrophoresis and proteomics analysis. J Food Compost Anal 2021. [DOI: 10.1016/j.jfca.2020.103685] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Deveshwar P, Sharma S, Prusty A, Sinha N, Zargar SM, Karwal D, Parashar V, Singh S, Tyagi AK. Analysis of rice nuclear-localized seed-expressed proteins and their database (RSNP-DB). Sci Rep 2020; 10:15116. [PMID: 32934280 PMCID: PMC7492263 DOI: 10.1038/s41598-020-70713-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/03/2020] [Indexed: 01/16/2023] Open
Abstract
Nuclear proteins are primarily regulatory factors governing gene expression. Multiple factors determine the localization of a protein in the nucleus. An upright identification of nuclear proteins is way far from accuracy. We have attempted to combine information from subcellular prediction tools, experimental evidence, and nuclear proteome data to identify a reliable list of seed-expressed nuclear proteins in rice. Depending upon the number of prediction tools calling a protein nuclear, we could sort 19,441 seed expressed proteins into five categories. Of which, half of the seed-expressed proteins were called nuclear by at least one out of four prediction tools. Further, gene ontology (GO) enrichment and transcription factor composition analysis showed that 6116 seed-expressed proteins could be called nuclear with a greater assertion. Localization evidence from experimental data was available for 1360 proteins. Their analysis showed that a 92.04% accuracy of a nuclear call is valid for proteins predicted nuclear by at least three tools. Distribution of nuclear localization signals and nuclear export signals showed that the majority of category four members were nuclear resident proteins, whereas other categories have a low fraction of nuclear resident proteins and significantly higher constitution of shuttling proteins. We compiled all the above information for the seed-expressed genes in the form of a searchable database named Rice Seed Nuclear Protein DataBase (RSNP-DB) https://pmb.du.ac.in/rsnpdb. This information will be useful for comprehending the role of seed nuclear proteome in rice.
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Affiliation(s)
- Priyanka Deveshwar
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, India
| | - Shivam Sharma
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, India
| | - Ankita Prusty
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, India
| | - Neha Sinha
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, India
| | - Sajad Majeed Zargar
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, India.,Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Shalimar, Srinagar, Jammu & Kashmir, India
| | - Divya Karwal
- Institute of Informatics and Communications, University of Delhi, South Campus, New Delhi, India
| | - Vishal Parashar
- Institute of Informatics and Communications, University of Delhi, South Campus, New Delhi, India
| | - Sanjeev Singh
- Institute of Informatics and Communications, University of Delhi, South Campus, New Delhi, India
| | - Akhilesh Kumar Tyagi
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, India.
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Probing early wheat grain development via transcriptomic and proteomic approaches. Funct Integr Genomics 2019; 20:63-74. [DOI: 10.1007/s10142-019-00698-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 06/20/2019] [Accepted: 06/24/2019] [Indexed: 12/20/2022]
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Barua P, Lande NV, Subba P, Gayen D, Pinto S, Keshava Prasad TS, Chakraborty S, Chakraborty N. Dehydration-responsive nuclear proteome landscape of chickpea (Cicer arietinum L.) reveals phosphorylation-mediated regulation of stress response. PLANT, CELL & ENVIRONMENT 2019; 42:230-244. [PMID: 29749054 DOI: 10.1111/pce.13334] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 04/27/2018] [Accepted: 04/30/2018] [Indexed: 06/08/2023]
Abstract
Nonavailability of water or dehydration remains recurring climatic disorder affecting yield of major food crops, legumes in particular. Nuclear proteins (NPs) and phosphoproteins (NPPs) execute crucial cellular functions that form the regulatory hub for coordinated stress response. Phosphoproteins hold enormous influence over cellular signalling. Four-week-old seedlings of a grain legume, chickpea, were subjected to gradual dehydration, and NPs were extracted from unstressed control and from 72- and 144-hr stressed tissues. We identified 4,832 NPs and 478 phosphosites, corresponding to 299 unique NPPs involved in multivariate cellular processes including protein modification and gene expression regulation, among others. The identified proteins included several novel kinases, phosphatases, and transcription factors, besides 660 uncharacterized proteins. Spliceosome complex and splicing related proteins were dominant among differentially regulated NPPs, indicating their dehydration modulated regulation. Phospho-motif analysis revealed stress-induced enrichment of proline-directed serine phosphorylation. Association mapping of NPPs revealed predominance of differential phosphorylation of spliceosome and splicing associated proteins. Also, regulatory proteins of key processes viz., protein degradation, regulation of flowering time, and circadian clock were observed to undergo dehydration-induced dephosphorylation. The characterization of novel regulatory proteins would provide new insights into stress adaptation and enable directed genetic manipulations for developing climate-resilient crops.
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Affiliation(s)
- Pragya Barua
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna, Asaf Ali Marg, New Delhi, 110067, India
| | - Nilesh Vikram Lande
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna, Asaf Ali Marg, New Delhi, 110067, India
| | - Pratigya Subba
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575 018, India
| | - Dipak Gayen
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna, Asaf Ali Marg, New Delhi, 110067, India
| | - Sneha Pinto
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575 018, India
| | - T S Keshava Prasad
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575 018, India
- International Technology Park, Institute of Bioinformatics, Bengaluru, 560066, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna, Asaf Ali Marg, New Delhi, 110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna, Asaf Ali Marg, New Delhi, 110067, India
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Bonnot T, Bancel E, Alvarez D, Davanture M, Boudet J, Pailloux M, Zivy M, Ravel C, Martre P. Grain subproteome responses to nitrogen and sulfur supply in diploid wheat Triticum monococcum ssp. monococcum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017. [PMID: 28628250 DOI: 10.1111/tpj.13615] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Wheat grain storage proteins (GSPs) make up most of the protein content of grain and determine flour end-use value. The synthesis and accumulation of GSPs depend highly on nitrogen (N) and sulfur (S) availability and it is important to understand the underlying control mechanisms. Here we studied how the einkorn (Triticum monococcum ssp. monococcum) grain proteome responds to different amounts of N and S supply during grain development. GSP composition at grain maturity was clearly impacted by nutrition treatments, due to early changes in the rate of GSP accumulation during grain filling. Large-scale analysis of the nuclear and albumin-globulin subproteomes during this key developmental phase revealed that the abundance of 203 proteins was significantly modified by the nutrition treatments. Our results showed that the grain proteome was highly affected by perturbation in the N:S balance. S supply strongly increased the rate of accumulation of S-rich α/β-gliadin and γ-gliadin, and the abundance of several other proteins involved in glutathione metabolism. Post-anthesis N supply resulted in the activation of amino acid metabolism at the expense of carbohydrate metabolism and the activation of transport processes including nucleocytoplasmic transit. Protein accumulation networks were analyzed. Several central actors in the response were identified whose variation in abundance was related to variation in the amounts of many other proteins and are thus potentially important for GSP accumulation. This detailed analysis of grain subproteomes provides information on how wheat GSP composition can possibly be controlled in low-level fertilization condition.
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Affiliation(s)
- Titouan Bonnot
- UMR GDEC, INRA, Université Clermont Auvergne, 5 chemin de Beaulieu, Clermont-Ferrand, 63039, France
| | - Emmanuelle Bancel
- UMR GDEC, INRA, Université Clermont Auvergne, 5 chemin de Beaulieu, Clermont-Ferrand, 63039, France
| | - David Alvarez
- UMR GDEC, INRA, Université Clermont Auvergne, 5 chemin de Beaulieu, Clermont-Ferrand, 63039, France
| | - Marlène Davanture
- UMR GQE, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, 91190, France
| | - Julie Boudet
- UMR GDEC, INRA, Université Clermont Auvergne, 5 chemin de Beaulieu, Clermont-Ferrand, 63039, France
| | - Marie Pailloux
- LIMOS, CNRS, Université Blaise Pascal, Aubière, 63173, France
| | - Michel Zivy
- UMR GQE, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, 91190, France
| | - Catherine Ravel
- UMR GDEC, INRA, Université Clermont Auvergne, 5 chemin de Beaulieu, Clermont-Ferrand, 63039, France
| | - Pierre Martre
- UMR GDEC, INRA, Université Clermont Auvergne, 5 chemin de Beaulieu, Clermont-Ferrand, 63039, France
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A proteomic portrait of dinoflagellate chromatin reveals abundant RNA-binding proteins. Chromosoma 2017; 127:29-43. [PMID: 28852823 DOI: 10.1007/s00412-017-0643-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 08/09/2017] [Accepted: 08/11/2017] [Indexed: 12/20/2022]
Abstract
Dinoflagellate chromatin is unique among eukaryotes, as the chromosomes are permanently condensed in a liquid crystal state instead of being packed in nucleosomes. However, how it is organized is still an unsolved mystery, in part due to the lack of a comprehensive catalog of dinoflagellate nuclear proteins. Here, we report the results of CHromatin Enrichment for Proteomics (CHEP) followed by shotgun mass spectrometry sequencing of the chromatin-associated proteins from the dinoflagellate Lingulodinum polyedra. Our analysis identified proteins involved in DNA replication and repair, transcription, and mRNA splicing, and showed a low level of contamination by proteins from other organelles. A limited number of proteins containing DNA-binding domains were found, consistent with the lack of diversity of these proteins in dinoflagellate transcriptomes. However, the number of proteins containing RNA-binding domains was unexpectedly high supporting a potential role for this type of protein in mediating gene expression and chromatin organization. We also identified a number of proteins involved in chromosome condensation and cell cycle progression as well as a single histone protein (H4). Our results provide the first detailed look at the nuclear proteins associated with the unusual chromatin structure of dinoflagellate nuclei and provide important insights into the biochemical basis of its structure and function.
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Blavet N, Uřinovská J, Jeřábková H, Chamrád I, Vrána J, Lenobel R, Beinhauer J, Šebela M, Doležel J, Petrovská B. UNcleProt (Universal Nuclear Protein database of barley): The first nuclear protein database that distinguishes proteins from different phases of the cell cycle. Nucleus 2016; 8:70-80. [PMID: 27813701 PMCID: PMC5287097 DOI: 10.1080/19491034.2016.1255391] [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] [Indexed: 01/02/2023] Open
Abstract
Proteins are the most abundant component of the cell nucleus, where they perform a plethora of functions, including the assembly of long DNA molecules into condensed chromatin, DNA replication and repair, regulation of gene expression, synthesis of RNA molecules and their modification. Proteins are important components of nuclear bodies and are involved in the maintenance of the nuclear architecture, transport across the nuclear envelope and cell division. Given their importance, the current poor knowledge of plant nuclear proteins and their dynamics during the cell's life and division is striking. Several factors hamper the analysis of the plant nuclear proteome, but the most critical seems to be the contamination of nuclei by cytosolic material during their isolation. With the availability of an efficient protocol for the purification of plant nuclei, based on flow cytometric sorting, contamination by cytoplasmic remnants can be minimized. Moreover, flow cytometry allows the separation of nuclei in different stages of the cell cycle (G1, S, and G2). This strategy has led to the identification of large number of nuclear proteins from barley (Hordeum vulgare), thus triggering the creation of a dedicated database called UNcleProt, http://barley.gambrinus.ueb.cas.cz/.
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Affiliation(s)
- Nicolas Blavet
- a Institute of Experimental Botany , Centre of the Region Haná for Biotechnological and Agricultural Research , Olomouc , Czech Republic
| | - Jana Uřinovská
- b Department of Protein Biochemistry and Proteomics , Centre of the Region Haná for Biotechnological and Agricultural Research , Olomouc , Czech Republic
| | - Hana Jeřábková
- a Institute of Experimental Botany , Centre of the Region Haná for Biotechnological and Agricultural Research , Olomouc , Czech Republic
| | - Ivo Chamrád
- b Department of Protein Biochemistry and Proteomics , Centre of the Region Haná for Biotechnological and Agricultural Research , Olomouc , Czech Republic
| | - Jan Vrána
- a Institute of Experimental Botany , Centre of the Region Haná for Biotechnological and Agricultural Research , Olomouc , Czech Republic
| | - René Lenobel
- b Department of Protein Biochemistry and Proteomics , Centre of the Region Haná for Biotechnological and Agricultural Research , Olomouc , Czech Republic
| | - Jana Beinhauer
- b Department of Protein Biochemistry and Proteomics , Centre of the Region Haná for Biotechnological and Agricultural Research , Olomouc , Czech Republic
| | - Marek Šebela
- b Department of Protein Biochemistry and Proteomics , Centre of the Region Haná for Biotechnological and Agricultural Research , Olomouc , Czech Republic
| | - Jaroslav Doležel
- a Institute of Experimental Botany , Centre of the Region Haná for Biotechnological and Agricultural Research , Olomouc , Czech Republic
| | - Beáta Petrovská
- a Institute of Experimental Botany , Centre of the Region Haná for Biotechnological and Agricultural Research , Olomouc , Czech Republic
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Yin X, Komatsu S. Plant nuclear proteomics for unraveling physiological function. N Biotechnol 2016; 33:644-654. [PMID: 27004615 DOI: 10.1016/j.nbt.2016.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 03/09/2016] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
Abstract
The nucleus is the subcellular organelle that functions as the regulatory hub of the cell and is responsible for regulating several critical cellular functions, including cell proliferation, gene expression, and cell survival. Nuclear proteomics is a useful approach for investigating the mechanisms underlying plant responses to abiotic stresses, including protein-protein interactions, enzyme activities, and post-translational modifications. Among abiotic stresses, flooding is a major limiting factor for plant growth and yields, particularly for soybean. In this review, plant nuclei purification methods, modifications of plant nuclear proteins, and recent contributions to the field of plant nuclear proteomics are summarized. In addition, to reveal the upstream regulating mechanisms controlling soybean responses to flooding stress, the functions of flooding-responsive nuclear proteins are reviewed based on the results of nuclear proteomic analysis of soybean in the early stages of flooding stress.
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Affiliation(s)
- Xiaojian Yin
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
| | - Setsuko Komatsu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan.
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Wang X, Komatsu S. Plant subcellular proteomics: Application for exploring optimal cell function in soybean. J Proteomics 2016; 143:45-56. [PMID: 26808589 DOI: 10.1016/j.jprot.2016.01.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 01/06/2016] [Accepted: 01/13/2016] [Indexed: 01/11/2023]
Abstract
UNLABELLED Plants have evolved complicated responses to developmental changes and stressful environmental conditions. Subcellular proteomics has the potential to elucidate localized cellular responses and investigate communications among subcellular compartments during plant development and in response to biotic and abiotic stresses. Soybean, which is a valuable legume crop rich in protein and vegetable oil, can grow in several climatic zones; however, the growth and yield of soybean are markedly decreased under stresses. To date, numerous proteomic studies have been performed in soybean to examine the specific protein profiles of cell wall, plasma membrane, nucleus, mitochondrion, chloroplast, and endoplasmic reticulum. In this review, methods for the purification and purity assessment of subcellular organelles from soybean are summarized. In addition, the findings from subcellular proteomic analyses of soybean during development and under stresses, particularly flooding stress, are presented and the proteins regulated among subcellular compartments are discussed. Continued advances in subcellular proteomics are expected to greatly contribute to the understanding of the responses and interactions that occur within and among subcellular compartments during development and under stressful environmental conditions. BIOLOGICAL SIGNIFICANCE Subcellular proteomics has the potential to investigate the cellular events and interactions among subcellular compartments in response to development and stresses in plants. Soybean could grow in several climatic zones; however, the growth and yield of soybean are markedly decreased under stresses. Numerous proteomics of cell wall, plasma membrane, nucleus, mitochondrion, chloroplast, and endoplasmic reticulum was carried out to investigate the respecting proteins and their functions in soybean during development or under stresses. In this review, methods of subcellular-organelle enrichment and purity assessment are summarized. In addition, previous findings of subcellular proteomics are presented, and functional proteins regulated among different subcellular are discussed. Subcellular proteomics contributes greatly to uncovering responses and interactions among subcellular compartments during development and under stressful environmental conditions in soybean.
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Affiliation(s)
- Xin Wang
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
| | - Setsuko Komatsu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan.
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Lv DW, Zhu GR, Zhu D, Bian YW, Liang XN, Cheng ZW, Deng X, Yan YM. Proteomic and phosphoproteomic analysis reveals the response and defense mechanism in leaves of diploid wheat T. monococcum under salt stress and recovery. J Proteomics 2016; 143:93-105. [PMID: 27095598 DOI: 10.1016/j.jprot.2016.04.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 04/05/2016] [Accepted: 04/14/2016] [Indexed: 10/21/2022]
Abstract
UNLABELLED Salinity is a major abiotic stress factor affecting crops production and productivity. Triticum monococcum is closely related to Triticum urartu (A(U)A(U)), which is used as a model plant of wheat A genome study. Here, salt stress induced dynamic proteome and phosphoproteome profiling was focused. The T. monococcum seedlings were initially treated with different concentrations of NaCl ranging from 80 to 320mM for 48h followed by a recovery process for 48h prior to proteomic and phosphoproteomic analysis. As a result, a total of 81 spots corresponding to salt stress and recovery were identified by MALDI-TOF/TOF-MS from 2-DE gels. These proteins were mainly involved in regulatory, stress defense, protein folding/assembly/degradation, photosynthesis, carbohydrate metabolism, energy production and transportation, protein metabolism, and cell structure. Pro-Q Diamond staining was used to detect the phosphoproteins. Finally, 20 spots with different phosphorylation levels during salt treatment or recovery compared with controls were identified. A set of potential salt stress response and defense biomarkers was identified, such as cp31BHv, betaine-aldehyde dehydrogenase, leucine aminopeptidase 2, Cu/Zn superoxide dismutase, and 2-Cys peroxiredoxin BAS1, which could lead to a better understanding of the molecular basis of salt response and defense in food crops. BIOLOGICAL SIGNIFICANCE Soil salinity reduces the yield of the major crops, which is one of the severest problems in irrigated agriculture worldwide. However, how crops response and defense during different levels of salt treatment and recovery processes is still unclear, especially at the post-translational modification level. T. monococcum is a useful model for common wheat. Thus, proteomic and phosphoproteomic analyses of T. monococcum leaves were performed in our study, which provided novel insights into the underlying salt response and defense mechanisms in wheat and other crops.
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Affiliation(s)
- Dong-Wen Lv
- College of Life Science, Capital Normal University, 100048 Beijing, China; VCU Philips Institute for Oral Health Research, Virginia Commonwealth University, School of Dentistry, Department of Oral and Craniofacial Molecular Biology, 23298 Richmond, VA, USA
| | - Geng-Rui Zhu
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Dong Zhu
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Yan-Wei Bian
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Xiao-Na Liang
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Zhi-Wei Cheng
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Xiong Deng
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Yue-Ming Yan
- College of Life Science, Capital Normal University, 100048 Beijing, China.
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Soltis DE, Misra BB, Shan S, Chen S, Soltis PS. Polyploidy and the proteome. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:896-907. [PMID: 26993527 DOI: 10.1016/j.bbapap.2016.03.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 03/06/2016] [Accepted: 03/11/2016] [Indexed: 12/23/2022]
Abstract
Although major advances have been made during the past 20 years in our understanding of the genetic and genomic consequences of polyploidy, our knowledge of polyploidy and the proteome is in its infancy. One of our goals is to stimulate additional study, particularly broad-scale proteomic analyses of polyploids and their progenitors. Although it may be too early to generalize regarding the extent to which transcriptomic data are predictive of the proteome of polyploids, it is clear that the proteome does not always reflect the transcriptome. Despite limited data, important observations on the proteomes of polyploids are emerging. In some cases, proteomic profiles show qualitatively and/or quantitatively non-additive patterns, and proteomic novelty has been observed. Allopolyploids generally combine the parental contributions, but there is evidence of parental dominance of one contributing genome in some allopolyploids. Autopolyploids are typically qualitatively identical to but quantitatively different from their parents. There is also evidence of parental legacy at the proteomic level. Proteomes clearly provide insights into the consequences of genomic merger and doubling beyond what is obtained from genomic and/or transcriptomic data. Translating proteomic changes in polyploids to differences in morphology and physiology remains the holy grail of polyploidy--this daunting task of linking genotype to proteome to phenotype should emerge as a focus of polyploidy research in the next decade. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
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Affiliation(s)
- Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32608, USA; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA.
| | - Biswapriya B Misra
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Shengchen Shan
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA
| | - Sixue Chen
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32608, USA; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA; Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32608, USA; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA.
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14
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Yang M, Dong J, Zhao W, Gao X. Characterization of proteins involved in early stage of wheat grain development by iTRAQ. J Proteomics 2016; 136:157-66. [DOI: 10.1016/j.jprot.2016.01.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 12/02/2015] [Accepted: 01/03/2016] [Indexed: 12/16/2022]
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15
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Bonnot T, Bancel E, Chambon C, Boudet J, Branlard G, Martre P. Changes in the nuclear proteome of developing wheat (Triticum aestivum L.) grain. FRONTIERS IN PLANT SCIENCE 2015; 6:905. [PMID: 26579155 PMCID: PMC4623401 DOI: 10.3389/fpls.2015.00905] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 10/10/2015] [Indexed: 05/24/2023]
Abstract
Wheat grain end-use value is determined by complex molecular interactions that occur during grain development, including those in the cell nucleus. However, our knowledge of how the nuclear proteome changes during grain development is limited. Here, we analyzed nuclear proteins of developing wheat grains collected during the cellularization, effective grain-filling, and maturation phases of development, respectively. Nuclear proteins were extracted and separated by two-dimensional gel electrophoresis. Image analysis revealed 371 and 299 reproducible spots in gels with first dimension separation along pH 4-7 and pH 6-11 isoelectric gradients, respectively. The relative abundance of 464 (67%) protein spots changed during grain development. Abundance profiles of these proteins clustered in six groups associated with the major phases and phase transitions of grain development. Using nano liquid chromatography-tandem mass spectrometry to analyse 387 variant and non-variant protein spots, 114 different proteins were identified that were classified into 16 functional classes. We noted that some proteins involved in the regulation of transcription, like HMG1/2-like protein and histone deacetylase HDAC2, were most abundant before the phase transition from cellularization to grain-filling, suggesting that major transcriptional changes occur during this key developmental phase. The maturation period was characterized by high relative abundance of proteins involved in ribosome biogenesis. Data are available via ProteomeXchange with identifier PXD002999.
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Affiliation(s)
- Titouan Bonnot
- UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Institut National de la Recherche AgronomiqueClermont-Ferrand, France
- UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Blaise Pascal UniversityAubière, France
| | - Emmanuelle Bancel
- UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Institut National de la Recherche AgronomiqueClermont-Ferrand, France
- UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Blaise Pascal UniversityAubière, France
| | - Christophe Chambon
- Metabolism Exploration Platform Proteomic Component, Institut National de la Recherche AgronomiqueSaint-Genès Champanelle, France
| | - Julie Boudet
- UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Institut National de la Recherche AgronomiqueClermont-Ferrand, France
- UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Blaise Pascal UniversityAubière, France
| | - Gérard Branlard
- UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Institut National de la Recherche AgronomiqueClermont-Ferrand, France
- UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Blaise Pascal UniversityAubière, France
| | - Pierre Martre
- UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Institut National de la Recherche AgronomiqueClermont-Ferrand, France
- UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Blaise Pascal UniversityAubière, France
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