National Institute of Plant Genome Research
 
    Dr. Subhra Chakraborty
    Ph. D, FNASc, FNAAS
    Staff Scientist VI (Professor)
    Ph. D, Jawaharlal Nehru University
    Tel: 91-11-26735186
    Fax: 91-11-26742658
    E-mail: schakraborty@nipgr.ac.in, subhrac@hotmail.com
 Career
Staff Scientist VI, National Institute for Plant Genome Research (2011-Present)
Staff Scientist V, National Institute for Plant Genome Research (2007-2011)
Staff Scientist IV, National Institute for Plant Genome Research (2003-2007)
Staff Scientist III, National Institute for Plant Genome Research (2000-2003)
Staff Scientist II, National Institute for Plant Genome Research (1998-2000)
Research Scientist, Jawaharlal Nehru University (1997-1998)
 Awards and Honours
TATA Innovation Award from The Department of Biotechnology, Govt of India (2014)
NASI-Reliance Industries Platinum Jubilee Award (2010)
Visiting Scientist, Yale University, USA (2008)
DBT Overseas Associateship, Govt. of India, India (2007)
Young Women Bioscientist of Promise, ISCA, India (2004)
National Young Women Bioscientist Award, DBT, India (2002)
Professor Hiralal Chakraborty Award, Indian Science Congress (2002)
Technology Development Award, DBT, Govt. of India (2000)
IRRI Core Research Fellowship, IRRI, Philippines (1995)
Young Scientist Award, IUBMB (1994)
Professor Hiralal Chakraborty Award, National Botanical Society (1990)
 
Fellow, National Academy of Sciences
Fellow, National Academy of Agricultural Sciences
Member, Society for Biological Chemists, India
Proteomic Society of India
American Chemical Society, USA
 Research
Our research is focused in three main areas: Nutritional Genomics, Stress Genomics, and delayed fruit softening.

Nutritional Genomics

Our aim is to improve the nutritional quality of important food crops since the nutritional health of humans predominantly depends on pant food. As part of protein quality improvement program, we have cloned a seed albumin gene AmA1 from Amaranthus hypochondriacus and developed protein-rich transgenic potato. Currently, our laboratory is developing transgenic cereals using this novel gene for protein quality improvement. Alternatively, for removal of antinutrient element, we focus on oxalate toxicity as it is the major dietary factor involved in kidney related diseases. Towards this end, an oxalate degrading enzyme, oxalate decarboxylase is being used to develop low-oxalate transgenic plants. Also, we are developing enabling technologies for transforming oxalate-rich fruits and vegetables with oxalate decarboxylase.
Stress Genomics

A second area of our interest is Stress Genomics in plants with specific emphasis to fungal pathogenicity. Plants frequently encounter different biotic stresses that adversely affect growth, development and more importantly the overall productivity. Stress signals perceived by plant cells leads to changes in gene expression profiles that dictate how cells overcome these stresses. Oxalic acid is a potent elicitor in fungal pathogenicity in many crop plants. We have developed fungal resistant transgenic tomato plants that express oxalate decarboxylase. Our current interest is to unravel the role of oxalate decarboxylase in fungal tolerance. In addition, we are identifying resistant gene candidates and defense mechanism of plants in response to fungal wilt. Our laboratory is developing a genome wide transcriptome of legume against Fusarium wilt to study stress perception, differential gene expression and thereby changes in metabolic responses. Our aim is to understand the biological and pathophysiological role of differentially expressed gene/s that control fungal pathogens. The ultimate goal is to use few novel genes for developing transgenic crops with improved fungal tolerance.
A third area of our research is to investigate the regulation of fruit softening using tomato as a model system. We are interested in enhancing shelf-life of fruits and vegetables because delay in fruit softening is the key regulatory mechanism to control their spoilage. Experimental approaches include softening related gene mining and developing knock-out transgenic plants for the candidate genes.
The tools used in our laboratory are molecular biology, biochemistry, Microarray, RNA Seq., Proteomic technology, Computational biology and genetic transformation.
 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, Divya 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 | DOI: 10.1038/srep04177
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
Chakraborty N, Ghosh R, Ghosh S, Narula K, Tayal R, Datta A, 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.
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
Narula K, Datta A, Chakraborty N, and Chakraborty S (2013) Comparative analyses of nuclear proteome: extending its function. Front. Plant Sci. 4: 100.
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: 5025-47
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: 3478-97
Subba P, Kumar R, Gayali S, Shekhar S, Praveen S, Pandey A, Datta A, Chakraborty S, Chakraborty N (2013) Characterisation of the nuclear proteome of a dehydration-sensitive cultivar of chickpea and comparative proteomic analysis with a tolerant cultivar. Proteomics 13: 1973–1992
Shekhar S, Agrawal L, Buragohain AK, Datta A, Chakraborty S and Chakraborty N (2013) Genotype independent regeneration and agrobacterium-mediated genetic transformation of sweet potato (Ipomoea batatas L.). Plant Tissue Cult. Biotech. 23: 87-100.
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.
Kamathan A, Kamthan M, Azam M, Chakraborty N, Chakraborty S, Datta A (2012) Expression of a fungal sterol desaturase improves tomato drought tolerance, pathogen resistance and nutritional quality. Sci. Rep. 2: 951.
Kamthan A, Kamthan M, Chakraborty N, Chakraborty S, Datta A (2012) A simple protocol for extraction, derivatization, and analysis of tomato leaf and fruit lipophilic metabolites using GC-MS. Nature Protocols. Protocol Exchange doi:10.1038 /protex. 2012.061
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 a-mannosidase and b-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.
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 and Datta A, 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.
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 N, Datta A and Chakraborty S (2003) Nutritional genomics: quest for GM crops for better nutrition. Everyman’s Science. 38: 41-43.
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.
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.
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. Nuclei Acids. Res. 30: 2940-2949.
Azam M, Kesarwani M, Chakraborty S, Natarajan K and Datta A (2002) Cloning and characterization of 5’-flanking region of oxalate decarboxylase gene from Flammulina velutipes. Biochem J.367: 66-75.
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.
  
 Patents
US Patents
   
Datta A, Raina A and Biswas S (1998) Method of making seed specific DNA (US Patent No 5,846,736, 1998)
Datta A, Raina A and Biswas S (1997) Seed storage protein with nutritionally balanced amino acid composition (US Patent No.5670635, 1997).
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).
Chakraborty N, Chakraborty S, Datta A and Bhushan D (2012) Extracellular matrix localized ferritin-1 for iron uptake, storage, and stress tolerance [US patent No. 8,163,977].
  
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].
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/2010/004582).
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. WO/2010/004583).
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].
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-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 (Indian Patent Application No. 3671/DEL/2012 dated November 29, 2012).
Datta A, Chakraborty S, Chakraborty N, Ghosh S, Meli, SV (2010) Polynucleotide sequence of fruit softening associated α-mannosidase and its uses for enhancing fruit shelf life [IPA-1647/DEL/2008]. Published by Indian Patent Office on 16.04.2010.
Datta A, Chakraborty S, Chakraborty N, Ghosh S, Meli SV (2010) Polynucleotide sequence of fruit softening associated β-D-N-acetyhexosaminidase and its uses for enhancing fruit shelf life [IPA-1648/DEL/2008]. Published by Indian Patent Office on 23.04.2010.
Chakraborty S, Datta A, Chakraborty N, Asraf N, and Basu S, (2009) Functional genomics and stress responsive polynucloetides from chickpea [IPA-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-1371/DEL/2006]