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Narula K, Sinha A, Choudhary P, Ghosh S, Elagamey E, Sharma A, Sengupta A, Chakraborty N, Chakraborty S. Combining extracellular matrix proteome and phosphoproteome of chickpea and meta-analysis reveal novel proteoforms and evolutionary significance of clade-specific wall-associated events in plant. PLANT DIRECT 2024; 8:e572. [PMID: 38500675 PMCID: PMC10945595 DOI: 10.1002/pld3.572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/27/2023] [Accepted: 02/10/2024] [Indexed: 03/20/2024]
Abstract
Extracellular matrix (ECM) plays central roles in cell architecture, innate defense and cell wall integrity (CWI) signaling. During transition to multicellularity, modular domain structures of ECM proteins and proteoforms have evolved due to continuous adaptation across taxonomic clades under different ecological niche. Although this incredible diversity has to some extent been investigated at protein level, extracellular phosphorylation events and molecular evolution of ECM proteoform families remains unexplored. We developed matrisome proteoform atlas in a grain legume, chickpea and performed meta-analyses of 74 plant matrisomes. MS/MS analysis identified 1,424 proteins and 315 phosphoproteins involved in diverse functions. Cross-species ECM protein network identified proteoforms associated with CWI maintenance system. Phylogenetic characterization of eighteen matrix protein families highlighted the role of taxon-specific paralogs and orthologs. Novel information was acquired on gene expansion and loss, co-divergence, sub functionalization and neofunctionalization during evolution. Modular networks of matrix protein families and hub proteins showed higher diversity across taxonomic clades than among organs. Furthermore, protein families differ in nonsynonymous to synonymous substitution rates. Our study pointed towards the matrix proteoform functionality, sequence divergence variation, interactions between wall remodelers and molecular evolution using a phylogenetic framework. This is the first report on comprehensive matrisome proteoform network illustrating presence of CWI signaling proteins in land plants.
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Affiliation(s)
- Kanika Narula
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Arunima Sinha
- National Institute of Plant Genome ResearchNew DelhiIndia
| | | | - Sudip Ghosh
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Eman Elagamey
- National Institute of Plant Genome ResearchNew DelhiIndia
- Plant Pathology Research InstituteAgricultural Research Center (ARC)GizaEgypt
| | - Archana Sharma
- National Institute of Plant Genome ResearchNew DelhiIndia
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Resentini F, Orozco-Arroyo G, Cucinotta M, Mendes MA. The impact of heat stress in plant reproduction. FRONTIERS IN PLANT SCIENCE 2023; 14:1271644. [PMID: 38126016 PMCID: PMC10732258 DOI: 10.3389/fpls.2023.1271644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/13/2023] [Indexed: 12/23/2023]
Abstract
The increment in global temperature reduces crop productivity, which in turn threatens food security. Currently, most of our food supply is produced by plants and the human population is estimated to reach 9 billion by 2050. Gaining insights into how plants navigate heat stress in their reproductive phase is essential for effectively overseeing the future of agricultural productivity. The reproductive success of numerous plant species can be jeopardized by just one exceptionally hot day. While the effects of heat stress on seedlings germination and root development have been extensively investigated, studies on reproduction are limited. The intricate processes of gamete development and fertilization unfold within a brief timeframe, largely concealed within the flower. Nonetheless, heat stress is known to have important effects on reproduction. Considering that heat stress typically affects both male and female reproductive structures concurrently, it remains crucial to identify cultivars with thermotolerance. In such cultivars, ovules and pollen can successfully undergo development despite the challenges posed by heat stress, enabling the completion of the fertilization process and resulting in a robust seed yield. Hereby, we review the current understanding of the molecular mechanisms underlying plant resistance to abiotic heat stress, focusing on the reproductive process in the model systems of Arabidopsis and Oryza sativa.
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Affiliation(s)
| | | | | | - Marta A. Mendes
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
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Estimation of genetic diversity using seed storage protein (SSP) profiling in wild and cultivated species of Cicer L. Mol Biol Rep 2023; 50:4175-4185. [PMID: 36894768 DOI: 10.1007/s11033-023-08358-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/23/2023] [Indexed: 03/11/2023]
Abstract
BACKGROUND The narrow genetic diversity of chickpea is a serious impediment to modern cultivar creation. Seed storage proteins (SSPs) are stable and have minimal or no degradation when subjected to isolation and SDS-PAGE. METHODS AND RESULTS We have characterized SSPs of 436 chickpea genotypes, belonging to nine annual Cicer species, originated from 47 countries by SDS-PAGE and determined the extent of genetic diversity in chickpea through clustering. Based on scoring, a total of 44 bands (10 to 170 kDa) were identified, which were all polymorphic. The least appeared protein bands were 11, 160 and 170 kDa where band of 11 and 160 kDa was present exclusively in wild type. Five bands were present in < 10% of genotypes. Bands appeared in 200-300 genotypes were suggested less polymorphic, on contrary bands present in 10-150 genotypes were suggested more polymorphic. Polymorphism of protein bands in context to their potential functions reported in literature were explored and suggested that the glubulins were most and glutelins were least abundant, whereas albumins with their known role in stress tolerance can be used as marker in chickpea breeding. Cluster analysis produced 14 clusters, interestingly three clusters contained only Pakistani genotypes and thus Pakistani genotypes appeared as a separate entity from the rest of the genotypes. CONCLUSION Our results indicate that SDS-PAGE of SSPs is a powerful technique in determining the genetic diversity plus it is easily adaptable, due to its cost effectiveness in comparison to other genomics tools.
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Seed Storage Protein, Functional Diversity and Association with Allergy. ALLERGIES 2023. [DOI: 10.3390/allergies3010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Plants are essential for humans as they serve as a source of food, fuel, medicine, oils, and more. The major elements that are utilized for our needs exist in storage organs, such as seeds. These seeds are rich in proteins, show a broad spectrum of physiological roles, and are classified based on their sequence, structure, and conserved motifs. With the improvements to our knowledge of the basic sequence and our structural understanding, we have acquired better insights into seed proteins and their role. However, we still lack a systematic analysis towards understanding the functional diversity associated within each family and their associations with allergy. This review puts together the information about seed proteins, their classification, and diverse functional roles along with their associations with allergy.
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Awasthi S, Chauhan R, Indoliya Y, Chauhan AS, Mishra SK, Agrawal L, Dwivedi S, Singh SN, Srivastava S, Singh PC, Chauhan PS, Chakrabarty D, Srivastava S, Tripathi RD. Comprehensive illustration of transcriptomic and proteomic dataset for mitigation of arsenic toxicity in rice (Oryza sativa L.) by microbial consortium. Data Brief 2022; 43:108377. [PMID: 35761993 PMCID: PMC9232546 DOI: 10.1016/j.dib.2022.108377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/29/2022] Open
Abstract
The present article represents the data for analysis of microbial consortium (P.putida+C.vulgaris) mediated amelioration of arsenic toxicity in rice plant. In the current study the transcriptome profiling of treated rice root and shoot was performed by illumina sequencing (Platform 2000). To process the reads and to analyse differential gene expression, Fastxtoolkit, NGSQCtoolkit, Bowtie 2 (version 2.1.0), Tophat program (version 2.0.8), Cufflinks and Cuffdiff programs were used. For Proteome profiling, total soluble proteins in shoot of rice plant among different treatments were extracted and separated by 2D poly acrylamide gel electrophoresis (PAGE) and then proteins were identified with the help of MALDI-TOF/TOF. In gel based method of protein identification, the isoelectric focusing machine (IPGphor system,Bio-Rad USA), gel unit (SDS-PAGE) and MALDI-TOF/TOF (4800 proteomic analyzer Applied Biosystem, USA) were used for successful separation and positive identification of proteins. To check the differential abundance of proteins among different treatments, PDQuest software was used for data analysis. For protein identification, Mascot search engine (http://www.matrixscience.com) using NCBIprot/SwissProt databases of rice was used. The analyzed data inferred comprehensive picture of key genes and their respective proteins involved in microbial consortium mediated improved plant growth and amelioration of As induced phyto-toxicity in rice. For the more comprehensive information of data, the related full-length article entitled “Microbial consortium mediated growth promotion and Arsenic reduction in Rice: An integrated transcriptome and proteome profiling” may be accessed.
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Affiliation(s)
- Surabhi Awasthi
- CSIR – National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226 001, India
- Plant Stress Biology Laboratory, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, 221005, India
| | - Reshu Chauhan
- CSIR – National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226 001, India
| | - Yuvraj Indoliya
- CSIR – National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226 001, India
| | - Abhishek Singh Chauhan
- CSIR – National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226 001, India
- Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, 110 001, India
| | - Shashank Kumar Mishra
- CSIR – National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226 001, India
| | - Lalit Agrawal
- Department of Agriculture and Allied Science, Doon Business School, Dehradun, Uttarakhand, India
| | - Sanjay Dwivedi
- CSIR – National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226 001, India
| | - Shiv Naresh Singh
- CSIR – National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226 001, India
| | - Suchi Srivastava
- CSIR – National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226 001, India
| | - Poonam C. Singh
- CSIR – National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226 001, India
| | - Puneet Singh Chauhan
- CSIR – National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226 001, India
| | - Debasis Chakrabarty
- CSIR – National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226 001, India
| | - Sudhakar Srivastava
- Plant Stress Biology Laboratory, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, 221005, India
- Dr. Sudhakar Srivastava, Assistant Professor, Institute of environment & Sustainable Development, Banaras Hindu University, Varanasi, India
| | - Rudra Deo Tripathi
- CSIR – National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226 001, India
- Corresponding author(s). Dr. Rudra Deo Tripathi, NASI Senior Scientist Platinum Jubilee Fellow, CSIR-National Botanical Research Institute, Lucknow, India
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Zhang MJ, Fu Q, Chen MS, He H, Tang M, Ni J, Tao YB, Xu ZF. Characterization of the bark storage protein gene ( JcBSP) family in the perennial woody plant Jatropha curcas and the function of JcBSP1 in Arabidopsis thaliana. PeerJ 2022; 10:e12938. [PMID: 35186503 PMCID: PMC8833228 DOI: 10.7717/peerj.12938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/24/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Bark storage protein (BSP) plays an important role in seasonal nitrogen cycling in perennial deciduous trees. However, there is no report on the function of BSP in the perennial woody oil plant Jatropha curcas. METHODS In this study, we identified six members of JcBSP gene family in J. curcas genome. The patterns, seasonal changes, and responses to nitrogen treatment in gene expression of JcBSPs were detected by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Overexpression of JcBSP1 in transgenic Arabidopsis thaliana was driven by a constitutive cauliflower mosaic virus (CaMV) 35S RNA promoter. RESULTS JcBSP members were found to be expressed in various tissues, except seeds. The seasonal changes in the total protein concentration and JcBSP1 expression in the stems of J. curcas were positively correlated, as both increased in autumn and winter and decreased in spring and summer. In addition, the JcBSP1 expression in J. curcas seedlings treated with different concentrations of an NH4NO3 solution was positively correlated with the NH4NO3 concentration and application duration. Furthermore, JcBSP1 overexpression in Arabidopsis resulted in a phenotype of enlarged rosette leaves, flowers, and seeds, and significantly increased the seed weight and yield in transgenic plants.
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Affiliation(s)
- Ming-Jun Zhang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China,CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, China
| | - Qiantang Fu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, China
| | - Mao-Sheng Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, China
| | - Huiying He
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, China
| | - Mingyong Tang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, China
| | - Jun Ni
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, Guangxi, China
| | - Yan-Bin Tao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, China
| | - Zeng-Fu Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, China,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, Guangxi, China
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CaHSP18.1a, a Small Heat Shock Protein from Pepper (Capsicum annuum L.), Positively Responds to Heat, Drought, and Salt Tolerance. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7050117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Pepper is a thermophilic crop, shallow-rooted plant that is often severely affected by abiotic stresses such as heat, salt, and drought. The growth and development of pepper is seriously affected by adverse stresses, resulting in decreases in the yield and quality of pepper crops. Small heat shock proteins (s HSPs) play a crucial role in protecting plant cells against various stresses. A previous study in our laboratory showed that the expression level of CaHSP18.1a was highly induced by heat stress, but the function and mechanism of CaHSP18.1a responding to abiotic stresses is not clear. In this study, we first analyzed the expression of CaHSP18.1a in the thermo-sensitive B6 line and thermo-tolerant R9 line and demonstrated that the transcription of CaHSP18.1a was strongly induced by heat stress, salt, and drought stress in both R9 and B6, and that the response is more intense and earlier in the R9 line. In the R9 line, the silencing of CaHSP18.1a decreased resistance to heat, drought, and salt stresses. The silencing of CaHSP18.1a resulted in significant increases in relative electrolyte leakage (REL) and malonaldehyde (MDA) contents, while total chlorophyll content decreased under heat, salt, and drought stresses. Overexpression analyses of CaHSP18.1a in transgenic Arabidopsis further confirmed that CaHSP18.1a functions positively in resistance to heat, drought, and salt stresses. The transgenic Arabidopsis had higherchlorophyll content and activities of superoxide dismutase, catalase, and ascorbate peroxidase than the wild type (WT). However, the relative conductivity and MDA content were decreased in transgenic Arabidopsis compared to the wild type (WT). We further showed that the CaHSP18.1a protein is localized to the cell membrane. These results indicate CaHSP18.1a may act as a positive regulator of responses to abiotic stresses.
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Crop Enhancement of Cucumber Plants under Heat Stress by Shungite Carbon. Int J Mol Sci 2020; 21:ijms21144858. [PMID: 32659984 PMCID: PMC7402313 DOI: 10.3390/ijms21144858] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/04/2020] [Accepted: 07/06/2020] [Indexed: 01/10/2023] Open
Abstract
Heat stress negatively impacts plant growth and yield. The effects of carbon materials on plants in response to abiotic stress and antioxidant activity are poorly understood. In this study, we propose a new method for improving heat tolerance in cucumber (Cucumis sativus L.) using a natural carbon material, shungite, which can be easily mixed into any soil. We analyzed the phenotype and physiological changes in cucumber plants maintained at 35 °C or 40 °C for 1 week. Our results show that shungite-treated cucumber plants had a healthier phenotype, exhibiting dark green leaves, compared to the plants in the control soil group. Furthermore, in the shungite-treated plants, the monodehydroascorbate content (a marker of oxidative damage) of the leaf was 34% lower than that in the control group. In addition, scavengers against reactive oxygen species, such as superoxide dismutase, catalase, and peroxidase were significantly upregulated. These results indicate that the successive pre-treatment of soil with a low-cost natural carbon material can improve the tolerance of cucumber plants to heat stress, as well as improve the corresponding antioxidant activity.
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Kumari M, Pandey S, Mishra SK, Giri VP, Agarwal L, Dwivedi S, Pandey AK, Nautiyal CS, Mishra A. Omics-Based Mechanistic Insight Into the Role of Bioengineered Nanoparticles for Biotic Stress Amelioration by Modulating Plant Metabolic Pathways. Front Bioeng Biotechnol 2020; 8:242. [PMID: 32363178 PMCID: PMC7180193 DOI: 10.3389/fbioe.2020.00242] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 03/09/2020] [Indexed: 01/03/2023] Open
Abstract
Bioengineered silver nanoparticles can emerge as a facile approach to combat plant pathogen, reducing the use of pesticides in an eco-friendly manner. The plants' response during tripartite interaction of plant, pathogen, and nanoparticles remains largely unknown. This study demonstrated the use of bioengineered silver nanoparticles in combating black spot disease caused by necrotrophic fungus Alternaria brassicicola in Arabidopsis thaliana via foliar spray. The particles reduced disease severity by 70-80% at 5 μg/ml without showing phytotoxicity. It elicited plant immunity by a significant reduction in reactive oxygen species (ROS), decreases in stress enzymes by 0.6-19.8-fold, and emergence of autophagy. Comparative plant proteomics revealed 599 proteins expressed during the interaction, where 117 differential proteins were identified. Among different categories, proteins involved in bioenergy and metabolism were most abundant (44%), followed by proteins involved in plant defense (20%). Metabolic profiling by gas chromatography-mass spectroscopy yielded 39 metabolite derivatives in non-polar fraction and 25 in the polar fraction of plant extracts. It was observed that proteins involved in protein biogenesis and early plant defense were overexpressed to produce abundant antimicrobial metabolites and minimize ROS production. Bioengineered silver nanoparticles performed dual functions to combat pathogen attack by killing plant pathogen and eliciting immunity by altering plant defense proteome and metabolome.
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Affiliation(s)
- Madhuree Kumari
- CSIR-National Botanical Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Shipra Pandey
- CSIR-National Botanical Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Shashank Kumar Mishra
- CSIR-National Botanical Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Ved Prakash Giri
- CSIR-National Botanical Research Institute, Lucknow, India
- Department of Botany, Lucknow University, Lucknow, India
| | - Lalit Agarwal
- CSIR-National Botanical Research Institute, Lucknow, India
- Department of Agriculture and Allied Sciences, Doon Business School, Dehradun, India
| | - Sanjay Dwivedi
- CSIR-National Botanical Research Institute, Lucknow, India
| | | | | | - Aradhana Mishra
- CSIR-National Botanical Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
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Sinha A, Haider T, Narula K, Ghosh S, Chakraborty N, Chakraborty S. Integrated Seed Proteome and Phosphoproteome Analyses Reveal Interplay of Nutrient Dynamics, Carbon–Nitrogen Partitioning, and Oxidative Signaling in Chickpea. Proteomics 2020; 20:e1900267. [DOI: 10.1002/pmic.201900267] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 02/03/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Arunima Sinha
- National Institute of Plant Genome Research Aruna Asaf Ali Marg New Delhi 110067 India
| | - Toshiba Haider
- National Institute of Plant Genome Research Aruna Asaf Ali Marg New Delhi 110067 India
| | - Kanika Narula
- National Institute of Plant Genome Research Aruna Asaf Ali Marg New Delhi 110067 India
| | - Sudip Ghosh
- National Institute of Plant Genome Research Aruna Asaf Ali Marg New Delhi 110067 India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research Aruna Asaf Ali Marg New Delhi 110067 India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research Aruna Asaf Ali Marg New Delhi 110067 India
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ul Haq S, Khan A, Ali M, Khattak AM, Gai WX, Zhang HX, Wei AM, Gong ZH. Heat Shock Proteins: Dynamic Biomolecules to Counter Plant Biotic and Abiotic Stresses. Int J Mol Sci 2019; 20:E5321. [PMID: 31731530 PMCID: PMC6862505 DOI: 10.3390/ijms20215321] [Citation(s) in RCA: 182] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 10/15/2019] [Accepted: 10/23/2019] [Indexed: 12/13/2022] Open
Abstract
Due to the present scenario of climate change, plants have to evolve strategies to survive and perform under a plethora of biotic and abiotic stresses, which restrict plant productivity. Maintenance of plant protein functional conformation and preventing non-native proteins from aggregation, which leads to metabolic disruption, are of prime importance. Plant heat shock proteins (HSPs), as chaperones, play a pivotal role in conferring biotic and abiotic stress tolerance. Moreover, HSP also enhances membrane stability and detoxifies the reactive oxygen species (ROS) by positively regulating the antioxidant enzymes system. Additionally, it uses ROS as a signal to molecules to induce HSP production. HSP also enhances plant immunity by the accumulation and stability of pathogenesis-related (PR) proteins under various biotic stresses. Thus, to unravel the entire plant defense system, the role of HSPs are discussed with a special focus on plant response to biotic and abiotic stresses, which will be helpful in the development of stress tolerance in plant crops.
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Affiliation(s)
- Saeed ul Haq
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (S.u.H.); (A.K.); (M.A.); (W.-X.G.); (H.-X.Z.)
- Department of Horticulture, University of Agriculture Peshawar, Peshawar 25130, Pakistan;
| | - Abid Khan
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (S.u.H.); (A.K.); (M.A.); (W.-X.G.); (H.-X.Z.)
| | - Muhammad Ali
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (S.u.H.); (A.K.); (M.A.); (W.-X.G.); (H.-X.Z.)
| | - Abdul Mateen Khattak
- Department of Horticulture, University of Agriculture Peshawar, Peshawar 25130, Pakistan;
- College of Information and Electrical Engineering, China Agricultural University, Beijing 100083, China
| | - Wen-Xian Gai
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (S.u.H.); (A.K.); (M.A.); (W.-X.G.); (H.-X.Z.)
| | - Huai-Xia Zhang
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (S.u.H.); (A.K.); (M.A.); (W.-X.G.); (H.-X.Z.)
| | - Ai-Min Wei
- Tianjin Vegetable Research Center, Tianjin 300192, China;
| | - Zhen-Hui Gong
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (S.u.H.); (A.K.); (M.A.); (W.-X.G.); (H.-X.Z.)
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin 300384, China
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Narula K, Choudhary P, Ghosh S, Elagamey E, Chakraborty N, Chakraborty S. Comparative Nuclear Proteomics Analysis Provides Insight into the Mechanism of Signaling and Immune Response to Blast Disease Caused byMagnaportheoryzaein Rice. Proteomics 2019; 19:e1800188. [DOI: 10.1002/pmic.201800188] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 10/23/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Kanika Narula
- National Institute of Plant Genome Research New Delhi 110067 India
| | - Pooja Choudhary
- National Institute of Plant Genome Research New Delhi 110067 India
| | - Sudip Ghosh
- National Institute of Plant Genome Research New Delhi 110067 India
| | - Eman Elagamey
- National Institute of Plant Genome Research New Delhi 110067 India
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13
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Elagamey E, Narula K, Sinha A, Ghosh S, Abdellatef MAE, Chakraborty N, Chakraborty S. Quantitative Extracellular Matrix Proteomics Suggests Cell Wall Reprogramming in Host-Specific Immunity During Vascular Wilt Caused by Fusarium oxysporum in Chickpea. Proteomics 2018; 17. [PMID: 29144021 DOI: 10.1002/pmic.201600374] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 10/25/2017] [Indexed: 01/27/2023]
Abstract
Extracellular matrix (ECM) is the unique organelle that perceives stress signals and reprograms molecular events of host cell during patho-stress. However, our understanding of how ECM dictates plant immunity is largely unknown. Vascular wilt caused by the soil borne filamentous fungus Fusarium oxysporum is a major impediment for global crop productivity. To elucidate the role of ECM proteins and molecular mechanism associated with cell wall mediated immunity, the temporal changes of ECM proteome was studied in vascular wilt resistant chickpea cultivar upon F. oxysporum infection. The 2DE protein profiling coupled with mass spectrometric analysis identified 166 immune responsive proteins (IRPs) involved in variety of functions. Our data suggest that wall remodeling; protein translocation, stabilization, and chitin triggered immunity; and extracellular ATP signaling are major players in early, middle, and later phases of ECM signaling during fungal attack. Furthermore, we interrogated the proteome data using network analysis that identified modules enriched in known and novel immunity-related prognostic proteins centered around nascent aminopolypeptide complex (NAC), amine oxidase, thioredoxin, and chaperonin. This study for the first time provides an insight into the complex network operating in the ECM and impinges on the surveillance mechanism of innate immunity during patho-stress in crop plant.
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Affiliation(s)
- Eman Elagamey
- National Institute of Plant Genome Research, New Delhi, India.,Plant Pathology Research Institute, Agricultural Research Center (ARC), Giza, Egypt
| | - Kanika Narula
- National Institute of Plant Genome Research, New Delhi, India
| | - Arunima Sinha
- National Institute of Plant Genome Research, New Delhi, India
| | - Sudip Ghosh
- National Institute of Plant Genome Research, New Delhi, India
| | - Magdi A E Abdellatef
- National Institute of Plant Genome Research, New Delhi, India.,Plant Pathology Research Institute, Agricultural Research Center (ARC), Giza, Egypt
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14
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Mishra D, Shekhar S, Singh D, Chakraborty S, Chakraborty N. Heat Shock Proteins and Abiotic Stress Tolerance in Plants. REGULATION OF HEAT SHOCK PROTEIN RESPONSES 2018. [DOI: 10.1007/978-3-319-74715-6_3] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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15
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Elagamey E, Sinha A, Narula K, Abdellatef MA, Chakraborty N, Chakraborty S. Molecular Dissection of Extracellular Matrix Proteome Reveals Discrete Mechanism RegulatingVerticillium DahliaeTriggered Vascular Wilt Disease in Potato. Proteomics 2017; 17. [DOI: 10.1002/pmic.201600373] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 08/07/2017] [Indexed: 01/05/2023]
Affiliation(s)
- Eman Elagamey
- National Institute of Plant Genome Research; New Delhi India
- Plant Pathology Research Institute; Agricultural Research Center (ARC); Giza Egypt
| | - Arunima Sinha
- National Institute of Plant Genome Research; New Delhi India
| | - Kanika Narula
- National Institute of Plant Genome Research; New Delhi India
| | - Magdi A.E. Abdellatef
- National Institute of Plant Genome Research; New Delhi India
- Plant Pathology Research Institute; Agricultural Research Center (ARC); Giza Egypt
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16
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Kumari M, Shukla S, Pandey S, Giri VP, Bhatia A, Tripathi T, Kakkar P, Nautiyal CS, Mishra A. Enhanced Cellular Internalization: A Bactericidal Mechanism More Relative to Biogenic Nanoparticles than Chemical Counterparts. ACS APPLIED MATERIALS & INTERFACES 2017; 9:4519-4533. [PMID: 28051856 DOI: 10.1021/acsami.6b15473] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Biogenic synthesis of silver nanoparticles for enhanced antimicrobial activity has gained a lot of momentum making it an urgent need to search for a suitable biocandidate which could be utilized for efficient capping and shaping of silver nanoparticles with enhanced bactericidal activity utilizing its secondary metabolites. Current work illustrates the enhancement of antimicrobial efficacy of silver nanoparticles by reducing and modifying their surface with antimicrobial metabolites of cell free filtrate of Trichoderma viride (MTCC 5661) in comparison to citrate stabilized silver nanoparticles. Nanoparticles were characterized by visual observations, UV-visible spectroscopy, zetasizer, and transmission electron microscopy (TEM). Synthesized particles were monodispersed, spherical in shape and 10-20 nm in size. Presence of metabolites on surface of biosynthesized silver nanoparticles was observed by gas chromatography-mass spectroscopy (GC-MS), energy dispersive X-ray analysis (EDAX), X-ray diffraction (XRD), and Fourier transform infrared spectroscopy (FTIR). The antimicrobial activity of both silver nanoparticles was tested against Shigella sonnei, Pseudomonas aeruginosa (Gram-negative) and Staphylococcus aureus (Gram-positive) by growth inhibition curve analysis and colony formation unit assay. Further, it was noted that internalization of biosynthesized nanoparticles inside the bacterial cell was much higher as compared to citrate stabilized particles which in turn lead to higher production of reactive oxygen species. Increase in oxidative stress caused severe damage to bacterial membrane enhancing further uptake of particles and revoking other pathways for bacterial disintegration resulting in complete and rapid death of pathogens as evidenced by fluorescein diacetate/propidium iodide dual staining and TEM. Thus, study reveals that biologically synthesized silver nanoarchitecture coated with antimicrobial metabolites of T. viride was more potent than their chemical counterpart in killing of pathogenic bacteria.
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Affiliation(s)
- Madhuree Kumari
- CSIR-National Botanical Research Institute , Rana Pratap Marg, Lucknow, 226 001, India
| | - Shatrunajay Shukla
- CSIR-Indian Institute of Toxicology Research , Vishvigyan Bhawan 31, Mahatma Gandhi Marg, Lucknow, 226 001, India
| | - Shipra Pandey
- CSIR-National Botanical Research Institute , Rana Pratap Marg, Lucknow, 226 001, India
| | - Ved P Giri
- CSIR-National Botanical Research Institute , Rana Pratap Marg, Lucknow, 226 001, India
| | - Anil Bhatia
- CSIR-National Botanical Research Institute , Rana Pratap Marg, Lucknow, 226 001, India
| | - Tusha Tripathi
- CSIR-National Botanical Research Institute , Rana Pratap Marg, Lucknow, 226 001, India
| | - Poonam Kakkar
- CSIR-Indian Institute of Toxicology Research , Vishvigyan Bhawan 31, Mahatma Gandhi Marg, Lucknow, 226 001, India
| | - Chandra S Nautiyal
- CSIR-National Botanical Research Institute , Rana Pratap Marg, Lucknow, 226 001, India
| | - Aradhana Mishra
- CSIR-National Botanical Research Institute , Rana Pratap Marg, Lucknow, 226 001, India
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17
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Wardhan V, Pandey A, Chakraborty S, Chakraborty N. Chickpea transcription factor CaTLP1 interacts with protein kinases, modulates ROS accumulation and promotes ABA-mediated stomatal closure. Sci Rep 2016; 6:38121. [PMID: 27934866 PMCID: PMC5146945 DOI: 10.1038/srep38121] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 11/07/2016] [Indexed: 11/23/2022] Open
Abstract
Tubby and Tubby-like proteins (TLPs), in mammals, play critical roles in neural development, while its function in plants is largely unknown. We previously demonstrated that the chickpea TLP, CaTLP1, participates in osmotic stress response and might be associated with ABA-dependent network. However, how CaTLP1 is connected to ABA signaling remains unclear. The CaTLP1 was found to be engaged in ABA-mediated gene expression and stomatal closure. Complementation of the yeast yap1 mutant with CaTLP1 revealed its role in ROS scavenging. Furthermore, complementation of Arabidopsis attlp2 mutant displayed enhanced stress tolerance, indicating the functional conservation of TLPs across the species. The presence of ABA-responsive element along with other motifs in the proximal promoter regions of TLPs firmly established their involvement in stress signalling pathways. The CaTLP1 promoter driven GUS expression was restricted to the vegetative organs, especially stem and rosette leaves. Global protein expression profiling of wild-type, attlp2 and complemented Arabidopsis plants revealed 95 differentially expressed proteins, presumably involved in maintaining physiological and biological processes under dehydration. Immunoprecipitation assay revealed that protein kinases are most likely to interact with CaTLP1. This study provides the first demonstration that the TLPs act as module for ABA-mediated stomatal closure possibly via interaction with protein kinase.
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Affiliation(s)
- Vijay Wardhan
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Aarti Pandey
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi-110067, 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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18
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Ghosh S, Narula K, Sinha A, Ghosh R, Jawa P, Chakraborty N, Chakraborty S. Proteometabolomic Study of Compatible Interaction in Tomato Fruit Challenged with Sclerotinia rolfsii Illustrates Novel Protein Network during Disease Progression. FRONTIERS IN PLANT SCIENCE 2016; 7:1034. [PMID: 27507973 PMCID: PMC4960257 DOI: 10.3389/fpls.2016.01034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 06/30/2016] [Indexed: 05/27/2023]
Abstract
Fruit is an assimilator of metabolites, nutrients, and signaling molecules, thus considered as potential target for pathogen attack. In response to patho-stress, such as fungal invasion, plants reorganize their proteome, and reconfigure their physiology in the infected organ. This remodeling is coordinated by a poorly understood signal transduction network, hormonal cascades, and metabolite reallocation. The aim of the study was to explore organ-based proteomic alterations in the susceptibility of heterotrophic fruit to necrotrophic fungal attack. We conducted time-series protein profiling of Sclerotinia rolfsii invaded tomato (Solanum lycopersicum) fruit. The differential display of proteome revealed 216 patho-stress responsive proteins (PSRPs) that change their abundance by more than 2.5-fold. Mass spectrometric analyses led to the identification of 56 PSRPs presumably involved in disease progression; regulating diverse functions viz. metabolism, signaling, redox homeostasis, transport, stress-response, protein folding, modification and degradation, development. Metabolome study indicated differential regulation of organic acid, amino acids, and carbohydrates paralleling with the proteomics analysis. Further, we interrogated the proteome data using network analysis that identified two significant functional protein hubs centered around malate dehydrogenase, T-complex protein 1 subunit gamma, and ATP synthase beta. This study reports, for the first-time, kinetically controlled patho-stress responsive protein network during post-harvest storage in a sink tissue, particularly fruit and constitute the basis toward understanding the onset and context of disease signaling and metabolic pathway alterations. The network representation may facilitate the prioritization of candidate proteins for quality improvement in storage organ.
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19
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Comparison of proteomic and metabolomic profiles of two contrasting ecotypes of sweetpotato ( Ipomoea batata L.). J Proteomics 2016; 143:306-317. [DOI: 10.1016/j.jprot.2016.03.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 02/23/2016] [Accepted: 03/16/2016] [Indexed: 11/20/2022]
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20
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Proteometabolomic analysis of transgenic tomato overexpressing oxalate decarboxylase uncovers novel proteins potentially involved in defense mechanism against Sclerotinia. J Proteomics 2016; 143:242-253. [DOI: 10.1016/j.jprot.2016.04.047] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 04/15/2016] [Accepted: 04/28/2016] [Indexed: 11/19/2022]
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21
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Shekhar S, Agrawal L, Mishra D, Buragohain AK, Unnikrishnan M, Mohan C, Chakraborty S, Chakraborty N. Ectopic expression of amaranth seed storage albumin modulates photoassimilate transport and nutrient acquisition in sweetpotato. Sci Rep 2016; 6:25384. [PMID: 27147459 PMCID: PMC4857128 DOI: 10.1038/srep25384] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/18/2016] [Indexed: 11/22/2022] Open
Abstract
Storage proteins in plants, because of high nutrient value, have been a subject of intensive investigation. These proteins are synthesized de novo in the cytoplasm and transported to the storage organelles where they serve as reservoir of energy and supplement of nitrogen during rapid growth and development. Sweetpotato is the seventh most important food crop worldwide, and has a significant contribution to the source of nutrition, albeit with low protein content. To determine the behaviour of seed storage proteins in non-native system, a seed albumin, AmA1, was overexpressed in sweetpotato with an additional aim of improving nutritional quality of tuber proteins. Introduction of AmA1 imparted an increase in protein and amino acid contents as well as the phytophenols. The proteometabolomics analysis revealed a rebalancing of the proteome, with no significant effects on the global metabolome profile of the transgenic tubers. Additionally, the slower degradation of starch and cellulose in transgenic tubers, led to increased post-harvest durability. Present study provides a new insight into the role of a seed storage protein in the modulation of photoassimilate movement and nutrient acquisition.
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Affiliation(s)
- Shubhendu Shekhar
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi-110067, India.,Department of Molecular Biology and Biotechnology, Tezpur University, Assam, India
| | - Lalit Agrawal
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Divya Mishra
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi-110067, India
| | | | | | - Chokkappan Mohan
- Central Tuber Crops Research Institute, Thiruvananthapuram, Kerala, 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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22
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Jain A, Kumar A, Salunke DM. Crystal structure of the vicilin from Solanum melongena reveals existence of different anionic ligands in structurally similar pockets. Sci Rep 2016; 6:23600. [PMID: 27004988 PMCID: PMC4804240 DOI: 10.1038/srep23600] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 03/07/2016] [Indexed: 11/09/2022] Open
Abstract
Crystal structure of a vicilin, SM80.1, was determined towards exploring its possible physiological functions. The protein was purified from Solanum melongena by combination of ammonium sulphate fractionation and size exclusion chromatography. Structure was determined ab initio at resolution of 1.5 Å by X-ray crystallography showing the three-dimensional topology of the trimeric protein. Each monomer of SM80.1 consists of two similar domains with hydrophobic binding pocket and each accommodating different ligands, i.e. acetate and pyroglutamate. The relatively high stability of these independent anionic ligands in similar pockets indicated a strict requirement of stabilization by hydrogen bonds with the charged residues, suggesting a degree of plasticity within the binding pocket. Comparison of SM80.1 structure with those of other 7S vicilins indicated conservation of putative binding pocket for anionic ligands. Here we propose the possibility of trapping of these ligands in the protein for their requirement in the metabolic processes.
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Affiliation(s)
- Abha Jain
- Regional Centre for Biotechnology, Faridabad-121001, India.,Manipal University, Manipal, Karnataka-576104, India
| | - Ashish Kumar
- Regional Centre for Biotechnology, Faridabad-121001, India.,National Institute of Immunology, New Delhi-110067, India
| | - Dinakar M Salunke
- Regional Centre for Biotechnology, Faridabad-121001, India.,International Centre for Genetic Engineering and Biotechnology, New Delhi-110067, India
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23
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Agrawal L, Gupta S, Mishra SK, Pandey G, Kumar S, Chauhan PS, Chakrabarty D, Nautiyal CS. Elucidation of Complex Nature of PEG Induced Drought-Stress Response in Rice Root Using Comparative Proteomics Approach. FRONTIERS IN PLANT SCIENCE 2016; 7:1466. [PMID: 27746797 PMCID: PMC5040710 DOI: 10.3389/fpls.2016.01466] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 09/14/2016] [Indexed: 05/22/2023]
Abstract
Along with many adaptive strategies, dynamic changes in protein abundance seem to be the common strategy to cope up with abiotic stresses which can be best explored through proteomics. Understanding of drought response is the key to decipher regulatory mechanism of better adaptation. Rice (Oryza sativa L.) proteome represents a phenomenal source of proteins that govern traits of agronomic importance, such as drought tolerance. In this study, a comparison of root cytoplasmic proteome was done for a drought tolerant rice (Heena) cultivar in PEG induced drought conditions. A total of 510 protein spots were observed by PDQuest analysis and 125 differentially regulated spots were subjected for MALDI-TOF MS-MS analysis out of which 102 protein spots identified which further led to identification of 78 proteins with a significant score. These 78 differentially expressed proteins appeared to be involved in different biological pathways. The largest percentage of identified proteins was involved in bioenergy and metabolism (29%) and mainly consists of malate dehydrogenase, succinyl-CoA, putative acetyl-CoA synthetase, and pyruvate dehydrogenase etc. This was followed by proteins related to cell defense and rescue (22%) such as monodehydroascorbate reductase and stress-induced protein sti1, then by protein biogenesis and storage class (21%) e.g. putative thiamine biosynthesis protein, putative beta-alanine synthase, and cysteine synthase. Further, cell signaling (9%) proteins like actin and prolyl endopeptidase, and proteins with miscellaneous function (19%) like Sgt1 and some hypothetical proteins were also represented a large contribution toward drought regulatory mechanism in rice. We propose that protein biogenesis, cell defense, and superior homeostasis may render better drought-adaptation. These findings might expedite the functional determination of the drought-responsive proteins and their prioritization as potential molecular targets for perfect adaptation.
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24
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Narula K, Pandey A, Gayali S, Chakraborty N, Chakraborty S. Birth of plant proteomics in India: a new horizon. J Proteomics 2015; 127:34-43. [PMID: 25920368 DOI: 10.1016/j.jprot.2015.04.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/20/2015] [Accepted: 04/21/2015] [Indexed: 01/02/2023]
Abstract
UNLABELLED In the post-genomic era, proteomics is acknowledged as the next frontier for biological research. Although India has a long and distinguished tradition in protein research, the initiation of proteomics studies was a new horizon. Protein research witnessed enormous progress in protein separation, high-resolution refinements, biochemical identification of the proteins, protein-protein interaction, and structure-function analysis. Plant proteomics research, in India, began its journey on investigation of the proteome profiling, complexity analysis, protein trafficking, and biochemical modeling. The research article by Bhushan et al. in 2006 marked the birth of the plant proteomics research in India. Since then plant proteomics studies expanded progressively and are now being carried out in various institutions spread across the country. The compilation presented here seeks to trace the history of development in the area during the past decade based on publications till date. In this review, we emphasize on outcomes of the field providing prospects on proteomic pathway analyses. Finally, we discuss the connotation of strategies and the potential that would provide the framework of plant proteome research. BIOLOGICAL SIGNIFICANCE The past decades have seen rapidly growing number of sequenced plant genomes and associated genomic resources. To keep pace with this increasing body of data, India is in the provisional phase of proteomics research to develop a comparative hub for plant proteomes and protein families, but it requires a strong impetus from intellectuals, entrepreneurs, and government agencies. Here, we aim to provide an overview of past, present and future of Indian plant proteomics, which would serve as an evaluation platform for those seeking to incorporate proteomics into their research programs. This article is part of a Special Issue entitled: Proteomics in India.
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Affiliation(s)
- Kanika Narula
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Aarti Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Saurabh Gayali
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
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25
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Shekhar S, Mishra D, Buragohain AK, Chakraborty S, Chakraborty N. Comparative analysis of phytochemicals and nutrient availability in two contrasting cultivars of sweet potato (Ipomoea batatas L.). Food Chem 2014; 173:957-65. [PMID: 25466112 DOI: 10.1016/j.foodchem.2014.09.172] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 09/11/2014] [Accepted: 09/19/2014] [Indexed: 11/12/2022]
Abstract
Sweet potato ranks as the world's seventh most important food crop, and has major contribution to energy and phytochemical source of nutrition. To unravel the molecular basis for differential nutrient availability, and to exploit the natural genetic variation(s) of sweet potato, a series of physiochemical and proteomics experiment was conducted using two contrasting cultivars, an orange-fleshed sweet potato (OFSP) and a white-fleshed sweet potato (WFSP). Phytochemical screening revealed high percentage of carbohydrate, reducing sugar and phenolics in WFSP, whereas OFSP showed increased levels of total protein, flavonoids, anthocyanins, and carotenoids. The rate of starch and cellulose degradation was found to be less in OFSP during storage, indicating tight regulation of gene(s) responsible for starch-degradation. Comparative proteomics displayed a cultivar-dependent expression of proteins along with evolutionarily conserved proteins. These results suggest that cultivar-specific expression of proteins and/or their interacting partners might play a crucial role for nutrient acquisition in sweet potato.
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Affiliation(s)
- Shubhendu Shekhar
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India; Department of Molecular Biology and Biotechnology, Tezpur University, Assam, India
| | - Divya Mishra
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, 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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26
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Silva RDC, Carmo LST, Luis ZG, Silva LP, Scherwinski-Pereira JE, Mehta A. Proteomic identification of differentially expressed proteins during the acquisition of somatic embryogenesis in oil palm (Elaeis guineensis Jacq.). J Proteomics 2014; 104:112-27. [PMID: 24675181 DOI: 10.1016/j.jprot.2014.03.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 02/24/2014] [Accepted: 03/12/2014] [Indexed: 01/03/2023]
Abstract
UNLABELLED In the present study we have identified and characterized the proteins expressed during different developmental stages of Elaeis guineensis calli obtained from zygotic embryos. We were interested in the possible proteomic changes that would occur during the acquisition of somatic embryogenesis and therefore samples were collected from zygotic embryos (E1), swollen explants 14days (E2) in induction medium, primary callus (E3), and pro-embryogenic callus (E4). The samples were grinded in liquid nitrogen, followed by total protein extraction using phenol and extraction buffer. Proteins were analyzed by two-dimensional electrophoresis (2-DE) and the differentially expressed protein spots were analyzed by MALDI-TOF mass spectrometry (MS and MS/MS). Interestingly, we have identified proteins, which can be used as potential candidates for future studies aiming at the development of biomarkers for embryogenesis acquisition and for the different stages leading to pro-embryogenic callus formation such as type IIIa membrane protein cp-wap13, fructokinase and PR proteins. The results obtained shed some light on the biochemical events involved in the process of somatic embryogenesis of E. guineensis obtained from zygotic embryos. The use of stage-specific protein markers can help monitor cell differentiation and contribute to improve the protocols for successfully cloning the species. BIOLOGICAL SIGNIFICANCE Understanding the fate and dynamics of cells and tissues during callus formation is essential to understand totipotency and the mechanisms involved during acquisition of somatic embryogenesis (SE). In this study we have investigated the early stages of somatic embryogenesis induction in oil palm and have identified potential markers as well as proteins potentially involved in embryogenic competence acquisition. The use of these proteins can help improve tissue culture protocols in order to increase regeneration rates. This article is part of a Special Issue entitled: Environmental and structural proteomics.
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Affiliation(s)
- Rafael de Carvalho Silva
- PPGBIOTEC, Departamento de Biologia, Universidade Federal do Amazonas, CEP 69077-000, Manaus, AM, Brazil
| | | | - Zanderluce Gomes Luis
- PPGBOT, Departamento de Botanica, Instituto de Biologia, Universidade de Brasilia, CEP 70910-900, Brasília, DF, Brazil
| | - Luciano Paulino Silva
- Embrapa Recursos Genéticos e Biotecnologia, Av. W5 Norte Final, CEP 70770-917, Brasília, DF, Brazil
| | - Jonny Everson Scherwinski-Pereira
- Embrapa Recursos Genéticos e Biotecnologia, Av. W5 Norte Final, CEP 70770-917, Brasília, DF, Brazil; PPGBOT, Departamento de Botanica, Instituto de Biologia, Universidade de Brasilia, CEP 70910-900, Brasília, DF, Brazil.
| | - Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia, Av. W5 Norte Final, CEP 70770-917, Brasília, DF, Brazil.
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