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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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Yin X, Komatsu S. Nuclear Proteomics Reveals the Role of Protein Synthesis and Chromatin Structure in Root Tip of Soybean during the Initial Stage of Flooding Stress. J Proteome Res 2016; 15:2283-98. [PMID: 27291164 DOI: 10.1021/acs.jproteome.6b00330] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
To identify the upstream events controlling the regulation of flooding-responsive proteins in soybean, proteomic analysis of nuclear proteins in root tip was performed. By using nuclear fractions, which were highly enriched, a total of 365 nuclear proteins were changed in soybean root tip at initial stage of flooding stress. Four exon-junction complex-related proteins and NOP1/NOP56, which function in upstream of 60S preribosome biogenesis, were decreased in flooded soybean. Furthermore, proteomic analysis of crude protein extract revealed that the protein translation was suppressed by continuous flooding stress. Seventeen chromatin structure-related nuclear proteins were decreased in response to flooding stress. Out of them, histone H3 was clearly decreased with protein abundance and mRNA expression levels at the initial flooding stress. Additionally, a number of protein synthesis-, RNA-, and DNA-related nuclear proteins were decreased in a time-dependent manner. mRNA expressions of genes encoding the significantly changed flooding-responsive nuclear proteins were inhibited by the transcriptional inhibitor, actinomycin D. These results suggest that protein translation is suppressed through inhibition of preribosome biogenesis- and mRNA processing-related proteins in nuclei of soybean root tip at initial flooding stress. In addition, flooding stress may regulate histone variants with gene expression in root tip.
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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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Gupta DB, Rai Y, Gayali S, Chakraborty S, Chakraborty N. Plant Organellar Proteomics in Response to Dehydration: Turning Protein Repertoire into Insights. FRONTIERS IN PLANT SCIENCE 2016; 7:460. [PMID: 27148291 PMCID: PMC4829595 DOI: 10.3389/fpls.2016.00460] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 03/24/2016] [Indexed: 05/29/2023]
Abstract
Stress adaptation or tolerance in plants is a complex phenomenon involving changes in physiological and metabolic processes. Plants must develop elaborate networks of defense mechanisms, and adapt to and survive for sustainable agriculture. Water-deficit or dehydration is the most critical environmental factor that plants are exposed to during their life cycle, which influences geographical distribution and productivity of many crop species. The cellular responses to dehydration are orchestrated by a series of multidirectional relays of biochemical events at organelle level. The new challenge is to dissect the underlying mechanisms controlling the perception of stress signals and their transmission to cellular machinery for activation of adaptive responses. The completeness of current descriptions of spatial distribution of proteins, the relevance of subcellular locations in diverse functional processes, and the changes of protein abundance in response to dehydration hold the key to understanding how plants cope with such stress conditions. During past decades, organellar proteomics has proved to be useful not only for deciphering reprograming of plant responses to dehydration, but also to dissect stress-responsive pathways. This review summarizes a range of organellar proteomics investigations under dehydration to gain a holistic view of plant responses to water-deficit conditions, which may facilitate future efforts to develop genetically engineered crops for better adaptation.
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Affiliation(s)
- Deepti B. Gupta
- Department of Biotechnology, TERI UniversityNew Delhi, India
| | - Yogita Rai
- Department of Biotechnology, TERI UniversityNew Delhi, India
| | - Saurabh Gayali
- National Institute of Plant Genome Research, Jawaharlal Nehru University CampusNew Delhi, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University CampusNew Delhi, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University CampusNew Delhi, India
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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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Bancel E, Bonnot T, Davanture M, Branlard G, Zivy M, Martre P. Proteomic Approach to Identify Nuclear Proteins in Wheat Grain. J Proteome Res 2015; 14:4432-9. [DOI: 10.1021/acs.jproteome.5b00446] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Emmanuelle Bancel
- INRA, UMR1095
Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, F-63 039 Clermont-Ferrand, France
- Blaise Pascal
University, UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Avenue des Landais, F-63 170 Aubière, France
| | - Titouan Bonnot
- INRA, UMR1095
Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, F-63 039 Clermont-Ferrand, France
- Blaise Pascal
University, UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Avenue des Landais, F-63 170 Aubière, France
| | - Marlène Davanture
- CNRS, PAPPSO, UMR 0320/8120 Génétique
Quantitative et Évolution - Le Moulon, F-91190 Gif-sur-Yvette, France
| | - Gérard Branlard
- INRA, UMR1095
Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, F-63 039 Clermont-Ferrand, France
- Blaise Pascal
University, UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Avenue des Landais, F-63 170 Aubière, France
| | - Michel Zivy
- CNRS, PAPPSO, UMR 0320/8120 Génétique
Quantitative et Évolution - Le Moulon, F-91190 Gif-sur-Yvette, France
| | - Pierre Martre
- INRA, UMR1095
Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, F-63 039 Clermont-Ferrand, France
- Blaise Pascal
University, UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Avenue des Landais, F-63 170 Aubière, France
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Millar AH, Taylor NL. Subcellular proteomics-where cell biology meets protein chemistry. FRONTIERS IN PLANT SCIENCE 2014; 5:55. [PMID: 24616726 PMCID: PMC3935256 DOI: 10.3389/fpls.2014.00055] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 02/04/2014] [Indexed: 05/22/2023]
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Narula K, Datta A, Chakraborty N, Chakraborty S. Comparative analyses of nuclear proteome: extending its function. FRONTIERS IN PLANT SCIENCE 2013; 4:100. [PMID: 23637696 PMCID: PMC3636469 DOI: 10.3389/fpls.2013.00100] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 03/30/2013] [Indexed: 05/20/2023]
Abstract
Organeller proteomics is an emerging technology that is critical in determining the cellular signal transduction pathways. Nucleus, the regulatory hub of the eukaryotic cell is a dynamic system and a repository of various macromolecules that serve as modulators of such signaling that dictate cell fate decisions. Nuclear proteins (NPs) are predicted to comprise about 10-20% of the total cellular proteins, suggesting the involvement of the nucleus in a number of diverse functions. Indeed, NPs constitute a highly organized but complex network that plays diverse roles during development and physiological processes. In plants, relatively little is known about the nature of the molecular components and mechanisms involved in coordinating NP synthesis, their action and function. Proteomic study hold promise to understand the molecular basis of nuclear function using an unbiased comparative and differential approach. We identified a few hundred proteins that include classical and non-canonical nuclear components presumably associated with variety of cellular functions impinging on the complexity of nuclear proteome. Here, we review the nuclear proteome based on our own findings, available literature, and databases focusing on detailed comparative analysis of NPs and their functions in order to understand how plant nucleus works. The review also shed light on the current status of plant nuclear proteome and discusses the future prospect.
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Affiliation(s)
| | | | | | - Subhra Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali MargNew Delhi, India
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