National Institute of Plant Genome Research
 
    Dr. Niranjan Chakraborty
    FNASc
    Staff Scientist VI
    Ph. D: Jawaharlal Nehru University, New Delhi
    Tel: 91-11-26735178
    Fax: 91-11-26742658
    E-mail: nchakraborty@nipgr.ac.in, nchakraborty@hotmail.com
 Research
The research in my laboratory is aimed at elucidation of the molecular circuitry used by plants in response to environmental stress. This enables the identification of key components which would help in their targeted manipulation in transgenic plants. Our efforts to address these involve utilization of a repertoire of approaches, which include physiochemical, proteomic and genomic tools. Recent advances in proteomics have created an opportunity for dissecting quantitative and qualitative traits in a more meaningful way. The proteomics approach is ideally suited for fast and sensitive analysis of the functions of the plant genes and gene-products, the proteins. Our research interest can be grouped under two thrust areas: stress proteomics, and gene expression and regulation.

STRESS PROTEOMICS

The application of proteomics technologies to advance our knowledge of stress tolerance in crop species has increased dramatically in the past few years. We are focusing on subcellular proteomics and using a number of proteome mining tools to understand the role of protein modifications and/or their differential expression under stress conditions. We have developed differential proteomes in response to various environmental stresses such as dehydration, high salinity, and low temperature. The major focus is to discover the regulatory genes that control stress tolerance in crop plants, which would not only aid in elucidation of the underlying mechanism(s) of stress tolerance, but also serve as a valuable resource for engineering strategies towards improved stress adaptation.
GENE EXPRESSION AND REGULATION

Stress tolerance is a quantitative trait determined by multiple and complex genetic interactions. Plant response to stress involves changes in the expression of thousands of genes, which in turn are affected by complex interactions with the environment, beyond the stress of interest. To better understand the interdependent action of an array of genes, my group has been working on several crops species, owing to the variable degree of tolerance among cultivars. This approach provides correlative evidence for genes involved in stress adaptation. While our research has shown the involvement of several novel genes in stress physiology, the richness of the candidate genes points to the enormity of the complexity to be deciphered for understanding the stress-responsive network.
 Selected Publications
Kumar R, Kumar A, Subba P, Gayali S, Barua P, Chakraborty S and Chakraborty N (2014) Nuclear phosphoproteome of developing chickpea seedlings (Cicer arietinum L.) and protein-kinase interaction network. J. Proteomics (In Press).
Verma JK, Gayali S, Dass S, Kumar A, Parveen S, Chakraborty S and Chakraborty N (2014) OsAlba1, a dehydration-responsive nuclear protein of rice (Oryza sativa L.), participates in stress adaptatioN Phytochemistry 100: 16-25.
Jaiswal DK, Mishra P, Subba P, Rathi D, Chakraborty S and Chakraborty N (2014) Membrane-associated proteomics of chickpea identifies Sad1/UNC-84 protein (CaSUN1), a novel component of dehydration signaling. Sci.  Rep. 4: 4177.
Chakraborty N, Ghosh R, Ghosh S, Narula K, Tayal R, Datta A and Chakraborty S (2013) Reduction of oxalate levels in tomato fruit and consequent metabolic remodeling following overexpression of a fungal oxalate decarboxylase. Plant Physiol.  162: 364-378.
Agrawal L, Narula K, Basu S, Shekhar S, Ghosh S, Datta A, Chakraborty N and Chakraborty S (2013) Comparative proteomics reveals a role for seed storage protein, AmA1 in cellular growth, development and nutrient accumulation. J. Proteome Res 12: 4904−4930.
Subba P, Barua P, Kumar R, Datta A, Soni K, Chakraborty S and Chakraborty N (2013) Phosphoproteomic dynamics of chickpea (Cicer arietinum L.) reveals shared and distinct components of dehydration response. J. Proteome Res 12: 5025−5047.
Jaiswal D, Ray D, Choudhary M, Subba P, Kumar A, Verma J, Kumar R, Datta A, Chakraborty S and Chakraborty N (2013) Comparative proteomics of dehydration response in the rice nucleus: new insights into the molecular basis of genotype specific adaptation. Proteomics 13: 3478-3497.
Subba P, Kumar R, Gayali S, Shekhar S, Parveen S, Pandey A, Datta A, Chakraborty S and Chakraborty N (2013) Characterization of the nuclear proteome of a dehydration-sensitive cultivar of chickpea and comparative proteomic analysis with a tolerant cultivar. Proteomics 13: 1973-1992.
Ghosh S, Singh UK, Meli VS, Kumar V, Kumar A, Irfan M, Chakraborty N, Chakraborty S and Datta A (2013) Induction of senescence and identification of differentially expressed genes in tomato in response to monoterpene. Plos One 8: e76029.
Jaiswal DK, Ray D, Subba P, Mishra P, Gayali S, Datta A, Chakraborty S and Chakraborty N (2012) Proteomic analysis reveals the diversity and complexity of membrane proteins in chickpea (Cicer arietinum L.). Proteome Sci. 10: 59.
Wardhan V, Jahan K, Gupta S, Chennareddy S, Datta A, Chakraborty S and Chakraborty N (2012) Overexpression of CaTLP1, a putative transcription factor in chickpea (Cicer arietinum L.), promotes stress tolerance. Plant Mol. Biol. 79: 479-493.
Kamthan A, Kamthan M, Azam M, Chakraborty N, Chakraborty S and Datta A (2012) Expression of a fungal sterol desaturase improves tomato drought tolerance, pathogen resistance and nutritional quality. Sci. Rep. 2: 951.
Kamthan M, Mukhopadhyay G, Chakraborty N, Chakraborty S and Datta A (2012) Quantitative proteomics and metabolomics approaches to demonstrate N-acetyl-d-glucosamine inducible amino acid deprivation response as morphological switch in Candida albicans. Fungal Genet. Biol. 49: 369-378.
Gupta S, Wardhan V, Verma S, Gayali S, Rajamani U, Datta A, Chakraborty S and Chakraborty N (2011) Characterization of the secretome of chickpea suspension culture reveals pathway abundance and the expected and unexpected secreted proteins. J. Proteome Res 10: 5006-5015.
Bhushan D, Jaiswal DK, Ray D, Basu D, Datta A, Chakraborty S and Chakraborty N (2011) Dehydration-responsive reversible and irreversible changes in the extracellular matrix: comparative proteomics of chickpea genotypes with contrasting tolerance. J. Proteome ReS 10: 2027-2046.
Ghosh S, Meli VS, Kumar A, Thakur A, Chakraborty N, Chakraborty S and Datta A (2011) The N-glycan processing enzymes α-mannosidase and β-D-N-acetylhexosaminidase are involved in ripening-associated softening in the non-climacteric fruits of capsicum. J. Exp. Bot. 62: 571-582.
Chattopadhyay A, Subba P, Pandey A, Bhushan D, Kumar R, Datta A, Chakraborty S and Chakraborty N (2011) Analysis of the grasspea proteome and identification of stress-responsive proteins upon exposure to high salinity, low temperature and abscisic acid treatment. Phytochemistry 72: 1293-1307.
Chakraborty S, Chakraborty N, Agrawal L, Ghosh S, Narula K, Shekhar S, Naik PS, Pande PC, Chakraborti SK and Datta A (2010) Next-generation protein-rich potato expressing the seed protein gene AmA1 is a result of proteome rebalancing in transgenic tuber. Proc. Natl. Acad. Sci. USA 107: 17533-17538.
Meli VS, Ghosh S, Prabha TN, Chakraborty N, Chakraborty S and Datta A (2010) Enhancement of fruit shelf life by suppressing N-glycan processing enzymes. Proc. Natl. Acad. Sci. USA 107: 2413-2418.
Agrawal GK, Bourguignon J, Rolland N, Ephritikhine G, Ferro M, Jaquinod M, Alexiou KG, Chardot T, Chakraborty N, Jolivet P, Doonan JH and Rakwal R (2010) Plant organelle proteomics: Collaborating for optimal cell function. Mass Spectrom. Rev. PMID 21038434.
Pandey A, Rajamani U, Verma J, Subba P, Chakraborty N Datta A, Chakraborty S, and Chakraborty N (2010) Identification of extracellular matrix proteins of rice (Oryza sativa L.) involved in dehydration-responsive network: a proteomic approach. J. Proteome ReS 9: 3443-3464.
Choudhary MK, Basu D, Datta A, Chakraborty N and Chakraborty S (2009) Dehydration-responsive nuclear proteome of rice (Oryza sativa L.) illustrates protein network, novel regulators of cellular adaptation and evolutionary perspect. Mol. Cell. Proteomics 8: 1579-1598.
Ashraf N, Ghai D, Barman P, Basu S, Gangisetty N, Mondal MK, Chakraborty N, Datta A and Chakraborty S (2009) Comparative analyses of genotype dependent expressed sequence tags and stress-responsive transcriptome of chickpea wilt illustrates predicted and unexpected genes and novel regulators of plant immunity. BMC Genomics 10: 415.
Pandey A, Chakraborty S, Datta A and Chakraborty N (2008) Proteomics approach to identify dehydration responsive nuclear proteins from chickpea (Cicer arietinum L.). Mol. Cell. Proteomics 7: 88-107.
Agrawal L, Chakraborty S, Jaiswal DK, Gupta S, Datta A and Chakraborty N (2008) Comparative proteomics of tuber induction, development and maturation reveal the complexity of tuberization process in potato (Solanum tuberosum L.) J. Proteome Res 7: 3803-3817.
Chakraborty N, Ohta MO and Zhu JK. (2007) Recognition of a PP2C interaction motif in several plant protein kinases. Methods Mol. Biol. 365: 287-298.
Bhushan D, Pandey A, Choudhary MK, Datta A, Chakraborty S and Chakraborty N (2007) Comparative proteomics analysis of differentially expressed proteins in chickpea extracellular matrix during dehydration stress. Mol. Cell. Proteomics 6: 1868-1884.
Pandey A, Choudhary MK, Bhushan D, Chattopadhyay A, Chakraborty S, Datta A and Chakraborty N (2006) The nuclear proteome of chickpea (Cicer arietinum L.) reveals predicted and unexpected proteins. J. Proteome Res 5: 3301-3311.
Bhushan D, Pandey A, Chattopadhyay A, Choudhary MK, Chakraborty S, Datta A and Chakraborty N (2006) Extracellular matrix proteome of chickpea (Cicer arietinum) illustrates pathway abundance, novel protein functions and evolutionary perspect. J. Proteome Res 5: 1711-1720.
Chakraborty S, Chakraborty N, Jain D, Salunke DM and Datta A (2002) Active site geometry of oxalate decarboxylase from Flammulina velutipes: Role of histidine coordinated manganese in substrate recognition. Protein Sci. 11: 2138-2147.
Chakraborty S, Sarmah B, Chakraborty N and Datta A (2002) Premature termination of RNA polymerase II mediated transcription of a seed protein gene in Schizosaccharomyces pombe. Nucleic Acids Res. 30: 2940-2949.
Sarmah B, Chakraborty N, Chakraborty S and Datta A (2002) Plant pre-mRNA splicing in fission yeast, Schizosaccharomyces pombe. Biochem. Biophy. ReS Commn. 293: 1209-1216.
Chakarborty S, Chakarborty N and Datta A (2000) Increased nutritive value of transgenic potato by expressing a nonallergenic seed albumin gene from Amaranthus hypochondriacus Proc. Natl. Acad. Sci. USA 97:  3724-3729.
Chakraborty N and Tripathy BC (1992) Involvement of singlet oxygen in 5-aminolevulinic acid induced photodynamic damage of cucumber (Cucumis sativus L.) chloroplasts. Plant Physiol. 98: 7-11.
Tripathy BC and Chakraborty N (1991) 5-aminolevulinic acid induced photodynamic damage to the photosynthetic electron transport chain of cucumber (Cucumis sativus L.) cotyledons. Plant Physiol. 96: 761-767.
 PATENTS (NATIONAL AND INTERNATIONAL)
US PATENTS
Chakraborty N, Chakraborty S, Datta A and Bhushan D (2012) Extracellular matrix localized ferritin-1 for iron uptake, storage, and stress tolerance (US patent: 8,163,977).
Chakraborty S, Chakraborty N, Datta A, Asraf N, Basu S, Nag P and Singh M  (2010) Polynucleotides derived from chickpea and uses thereof (US No. 13/393,340). Published by USPTO on 21/06/2012 (Pub. No. US 20120159668 A1).
PCT PATENTS
Chakraborty N, Chakraborty S, Datta A, Wardhan V and Jahan K (2012) Polynucleotide encoding CaTLP1 and uses thereof. [PCT/IN2013/000302]. Published by WIPO on 14/11/2013 [Pub. No. WO2013168181].
Chakraborty S, Chakraborty N, Datta A, Asraf N, Basu S, Nag P, and Singh M  (2010) Polynucleotides derived from chickpea and uses thereof. [PCT/IN2010/000573]. Published by WIPO on 03/11/2011 [Pub. No. WO2011024207A2].
Datta A, Chakraborty S, Chakraborty N, Ghosh S, and Meli SV (2010) Polynucleotide sequence of fruit softening associated α-mannosidase and its uses for enhancing fruit shelf life [PCT/IN2009/000387]. Published by WIPO on 14/01/2010 [Pub. No. WO 2010004582].
Datta A, Chakraborty S, Chakraborty N, Meli SV, and Ghosh S  (2009) Polynucleotide sequence of fruit softening associated β-D-N-acetyhexosaminidase and its uses for enhancing fruit shelf life [PCT/IN2009/000388]. Published by WIPO on 14/01/2010 (Pub. No. WO2010004583).
Chakraborty N, Chakraborty S, Datta A and Bhushan D  (2008) Extracellular matrix localized ferritin-1 for iron uptake, storage, and stress tolerance [PCT/IN2007/000231]. Published by WIPO on 29/05/2008 [Pub. No. WO2007141808A3].
INDIAN PATENTS
Chakraborty N, Chakraborty S, Datta A, Wardhan V and Jahan K (2012) Polynucleotide encoding CaTLP1 and uses thereof. [IPA No.1406/DEL/2012].
Datta A, Chakraborty S, Chakraborty N, Kamthan M and Kamthan A (2012) Polynucleotide sequence of an ergosterol biosynthesis enzyme ?7-sterol-C-5-desaturase and uses thereof. [IPA No. 3671/DEL/2012].
Datta A, Chakraborty S, Chakraborty N, Ghosh S and Meli SV (2010) Polynucleotide sequence of fruit softening associated α-mannosidase and its uses for enhancing fruit shelf life. [IPA No.1647/DEL/2008].
Datta A, Chakraborty S, Chakraborty N, Ghosh S and Meli SV (2010) Polynucleotide sequence of fruit softening associated β-D-N-acetyhexosaminidase and its uses for enhancing fruit shelf life. [IPA No.1648/DEL/2008].
Chakraborty S, Datta A, Chakraborty N, Asraf N and Basu S (2009) Functional genomics and stress responsive polynucloetides from chickpea. [IPA No.1565/DEL/2009].
Chakraborty N, Chakraborty S, Datta A and Bhushan D  (2006) Extracellular matrix localized ferritin-1 for iron uptake, storage, and stress tolerance. [IPA No.1371/DEL/2006].