Shubho Chaudhuri

Shubho Chaudhuri
Professor

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Previous appointments:

2002-2003: Post Doctoral Fellow, Department of Plant Pathology, University of Missouri, Columbia, USA

2003-2005: Post Doctoral fellow, Department of Horticulture, Washington State University, USA

2005-2009: Research coordinator, School of Molecular Biosciences, Washington State University, USA

Research interests:

The highly complex structure of chromatin imparts resistance to several nuclear processes. It is still an unsolved mystery as to how several genes whose sequence might be buried in the complex chromatin structure is accessed by nuclear factors during their expression in response to endogenous and exogenous cues. Post-translation modification of histones (epigenetic mark) as well as active chromatin remodelling guided by either ATP dependent chromatin remodellers or histone chaperones play an important regulatory role in activating or repressing gene expression by generating ‘open’ or ‘closed’ chromatin configuration inside the cell. Such dynamic changes in the chromatin organization are essential for almost all cellular events like transcription, replication, repair and DNA recombination. Stress response in plants have been reported to exhibit similar dynamics at the epigenetic levels which promotes the transcription of plethora of stress responsive genes to mount the response. Further, such stress-induced epigenetic changes in the chromatin can lead to transient response or sustained response where the new chromatin state are maintained as stress memory. It is assumed that the stress memory induced due to epigenetic changes in the chromatin, will provide a “primed state” to plants, for faster and stronger response against subsequent environmental conditions.


Contact:

Address: Biological Sciences
Unified Academic Campus
Bose Institute
EN-80, Sector V
Bidhan Nagar
Kolkata - 700 091, India
E-Mail: shubho[at]jcbose.ac.in
Phone: +91-33-25693247

Research:

Investigating the role of ARID/HMG in modulation of chromatin structure in planta
This project involves the study of a novel class of high mobility group (HMG) protein ARID-HMG known to modulate the chromatin structure during nuclear events. ARID-HMG proteins contain both the AT rich interaction domain (ARID) and the HMG-box domain in a single polypeptide
Recent work has shown that ARID-HMG can bind different DNA topological forms, can bend DNA backbone and can also induce DNA supercoiling to facilitating nuclear processes [Roy et al, (2016) Plant Molecular Biology 92 (3), 371-388]. Identification of genome-wide targets and DNA recognition sequence of the Arabidopsis HMG-box protein during cold stress response using ChIP-on-chip was employed for further study. GO analysis shows genes belonging to abiotic stress response, cold response and root development were AtHMGB15 targets during cold stress. DNA binding and footprinting assays identified A(A/C)--ATA---(A/T)(A/T) as AtHMGB15 binding motif. Further, the expression of cold stress responsive genes decreased in athmgb15 knockout plants compared to wild-type. Taken together, binding enrichment of AtHMGB15 to the promoter and upstream to stress loci suggest an unexplored role of the protein in stress induced transcription regulation. [Mallik  et al, (2020). BBA-Gene Regulatory Mechanisms 1863 (12), 194644]
Ongoing Project:
Investigating the role of ARID-HMG in chromatin remodeling during  plant development.

Explore the different epigenetic changes in plants to understand the transcription regulation of genes that are regulated during abiotic stress response.

Role of rice Trithorax factor, OsULT1, in regulating stress induced gene expression: Co-ordinated interplay between Polycomb group (PcG) and Trithorax group (TrxG) chromatin proteins regulates the spatiotemporal expression of target genes in higher eukaryotes. Rice Trithorax factor ULTRAPETALA 1 (OsULT1) specifically binds to the putative Polycomb response elements “GAGAG” of cold responsive genes, such as, OsDREB1b, to regulate the cold induced transcription. GAGAG is the recognition sequence for GAGA factor (GAF), Pipsqueak (Psq) as well as one of the major sites for PRC2 protein FIE occupancy. OsULT1 physically interacts with SET domain containing methyltransferase, OsTRX1 that methylates H3K4me3. These results collectively suggest that synchronised interaction between PcG and TrxG complex for PRE/TRE element is evolutionarily conserved mechanism throughout the kingdoms to mediated gene regulation [Royet al, 2019. BBA-Gene Regulatory Mechanisms 1862 (5), 582-597].
Low temperature a major abiotic stress, is known to adversely affect the growth and development of rice plants, Oryza sativa. Cellular reprogramming in response to cold stress involves alteration of gene expression. Similar to other plant species originating in tropical and sub-tropical areas, indica rice is highly sensitive to low temperature that adversely affects its growth and grain productivity. A transcriptome profile was generated for cold shock treated seedlings of IR64 variety to identify early responsive transcripts that  includes enrichment of genes involved in altered membrane rigidity and electrolytic leakage, the onset of calcium signaling, ROS generation and activation of stress responsive transcription factors in IR64[Dasgupta, et al, 2020. BMC Genomics 21 (1), 425]. 
Ongoing projects:
Role of rice Trithorax factor, OsULT1, in regulating stress induced gene expression
Comparative epigenome during abiotic stress response  


Publications:

  1.  Identification of genome-wide targets and DNA recognition sequence of the Arabidopsis HMG-box protein AtHMGB15 during cold stress response. R Mallik, P Prasad, A Kundu, S Sachdev, R Biswas, A Dutta, A Roy, J Mukhopadhyay, S K Bag, S Chaudhuri (2020). Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1863 (12), 194644.
  2. Understanding the early cold response mechanism in IR64 indica rice variety through comparative transcriptome analysis. P Dasgupta, A Das, S Datta, I Banerjee, S Tripathy, S Chaudhuri (2020). BMC Genomics 21 (1), 425.
  3. Rice Trithorax factor ULTRAPETALA 1 (OsULT1) specifically binds to “GAGAG” sequence motif present in Polycomb response elements. D Roy, J Chakrabarty, R Mallik, S Chaudhuri (2019). Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1862 (5), 582-597.
  4. High mobility group proteins: the multifaceted regulators of chromatin dynamics. R Mallik, A Kundu, S Chaudhuri (2018). The Nucleus 61 (3), 213-226.
  5. Molecular characterization of the 14-3-3 gene family in rice and its expression studies under abiotic stress. N Yashvardhini, S Bhattacharya, S Chaudhuri, DN Sengupta (2018). Planta 247 (1), 229-253.
  6. Understanding the role of DNA polymerase λ gene in different growth and developmental stages of Oryza sativa L. indica rice cultivars. S Sihi, S Maiti, S Bakshi, A Nayak, S Chaudhuri, DN Sengupta (2018). Plant physiology and biochemistry 120, 156-168.
  7. Molecular and biochemical characterization of a Vigna mungo MAP kinase associated with Mungbean Yellow Mosaic India Virus infection and deciphering its role in restricting the virus multiplication. A Patel, N Dey, S Chaudhuri, A Pal (2017). Plant Science 262, 127-140.
  8. Comparative analysis of Histone modifications and DNA methylation at OsBZ8 locus under salinity stress in IR64 and Nonabokra rice varieties A Paul, P Dasgupta, D Roy, S Chaudhuri (2017). Plant Molecular Biology 95 (1-2), 63-88.
  9. Deciphering the role of the AT-rich interaction domain and the HMG-box domain of ARID-HMG proteins of Arabidopsis thaliana. A Roy, A Dutta, D Roy, P Ganguly, R Ghosh, R K Kar, A Bhunia, J Mukhobadhyay, S Chaudhuri (2016). Plant Molecular biology 92 (3), 371-388.
  10.  Differential acetylation of histone H3 at the regulatory region of OsDREB1b promoter facilitates chromatin remodelling and transcription activation during cold stress. D Roy, A Paul, A Roy, R Ghosh, P Ganguly, S Chaudhuri (2014). PLoS One 9 (6), e100343
  11. Functional characterization of a serine-threonine protein kinase of Bambusabalcooa that implicates in cellulose overproduction and superior quality fiber formation. JS Ghosh, S Chaudhuri, NrisinghaDey and Amita Pal (2013). BMC Plant Biology, 13: 128 DOI:10.1186/1471-2229-13-128
  12. TLR signaling-mediated differential histone modification at IL-10 and IL-12 promoter region leads to functional impairments in tumor-associated macrophages. S Banerjee, K Halder, A Bose, P Bhattacharya, G Gupta, S Karmahapatra, S Das, S Chaudhuri, SB Majumdar, S Majumdar (2011). Carcinogenesis 32 (12), 1789-1797
  13. Arabinosylated lipoarabinomannan skews Th2 phenotype towards Th1 during Leishmania infection by chromatin modification: involvement of MAPK signaling. Bhattacharya P, Gupta G, Majumder S, Adhikari A, Banerjee S, Halder K, Majumdar SB, Ghosh M, Chaudhuri S, Roy S, Majumdar S (2011).PLoS One. 2011;6(9):e24141 DOI: 10.1371/journal.pone.0024141
  14. A calcium/calmodulin-regulated member of the receptor-like kinase confers cold tolerance in Plants.  T Yang, S Chaudhuri, L Yang, L Du and B.W. Poovaiah (2010).J. Biol. Chem 285(10):7119-26.
  15.  Histone H3 Lys79 Methylation is Required for Efficient Nucleotide Excision Repair in a Silenced Locus of Saccharomyces cerevisiae. S Chaudhuri, JJ. Wyrick, and M J. Smerdon. (2009).Nucleic acids research 37(5): 1690-1700
  16. Nodulation independent of rhizobia is induced by a calcium activated kinase lacking autoinhibition. C Gleason, S Chaudhuri, T Yang, A Munoz-Gutierrez , B. W.  Poovaiah, G Oldroyd. (2006). Nature 441 (7097): 1149–1152
  17. Domain analysis of a groundnut calcium-dependent protein kinase: nuclear localization sequence in the junction domain is coupled with nonconsensus calcium binding domains. Raichaudhuri A, Bhattacharyya R, Chaudhuri S, Chakrabarti P, Dasgupta M. (2006). J. Biol. Chem., 281:10399-409.
  18. Calcium/calmodulin up-regulates a cytoplasmic receptor-like kinase in plants. T Yang, S Chaudhuri, L Yang, Y Chen, and   B. W. Poovaiah. (2004). J. Biol. Chem., 279: 42552-42559
  19.  Identification of regulators of hrp/hop genes of Erwiniacarotovora ssp. carotovora and characterization of HrpLEcc(sigma LEcc), an alternative sigma factor.  A Chatterjee, Y Cui, S Chaudhuri and A Chatterjee (2002).Molecular Plant Pathology 3(5), 359-370
  20. Exogenous auxin depletion renders Arachis hypogea suspension culture sensitive to water loss without affecting cell growth. Seal, A., Hazra A., Nag, R., Chaudhuri, S. and DasGupta, M (2001).Plant Cell Reports. 20(6): 567 – 573
  21.  Autophosphorylation Dependent Activation of a Calcium Dependent Protein Kinase from Arachis hypogea Plant.  S Chaudhuri, A Seal & M DasGupta (1999). Plant Physiology 120: 859-866

 

BOOK CHAPTERS:

  1.  Analysis of DNA Methylation Profile in Plants by Chop-PCR. P Dasgupta, S Chaudhuri (2019). Plant Innate Immunity, Methods in Molecular Biology, Springer Protocols, Humana Press, 79-90.
  2. Change in Nucleosome Dynamics During Stress Responses in Plants A Paul, S Chaudhuri (2019). Plant Innate Immunity, Methods in Molecular Biology, Springer Protocols, Humana Press, 91-100.
  3. CDPKS in plant signaling networks- Progress in research on Groundnut CDPK.  In “Signal transduction in plants” (S.K. Sopory; R. Oelmuller and S. C. Maheshwari, Eds.). M DasGupta and S Chaudhuri (2001). Kluwer academic Press, Page 145-156.

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Recognition:

    Teaching:

     TEACHING

     

    1.      Involved in teaching of Cell Biology, Plant biology Course of Integrated M.Sc. PhD Course in Life Science (Bose Institute).

    2.      Involved in taking Pre-Ph.D course work classes for research scholars in Bose Institute.

    Students:

    Image Name Designation Department Campus Contact number Email
    profile image Ayantika Nandi Junior Research Fellow Division of Plant Biology Unified ayantikanandi1234@gmail.com
    profile image Pratyay Ghosh Project Associate - I Biological Sciences Unified pratyay828@gmail.com
    profile image Ruby Biswas Junior Research Fellow Division of Plant Biology Centenary rubybsws@gmail.com
    profile image Rukshar Parveen Junior Research Fellow Division of Plant Biology Unified rukshar1209@gmail.com
    profile image Shabini Basu Junior Research Fellow Division of Plant Biology Unified sabinabasu@yahoo.com
    profile image Sonal Sachdev Junior Research Fellow Division of Plant Biology Centenary sonalsachdev@jcbose.ac.in
    profile image Vishal Roy Junior Research Fellow Division of Plant Biology Unified roy23032@gmail.com

    Former:

    PhD students

    Ms. Pratiti Dasgupta                     pratiti2509@gmail.com

    Ms. Jinia Chakrabarty                   jiniachakrabarty@gmail.com 

    Ms Sonal Sachdev                       sonal.sachdev511@gmail.com  

    Ms Ruby Biswas                          rubybsws@gmail.com


    Former Students

    STUDENTS

    FORMER POSITION

    CONTACT

    CURRENT POSITION

    Dr. Sudip Saha

    Research Associate

    saha4sudip@gmail.com

    Assistant professor at Techno India University, West Bengal

    Dr.Anindya Kundu

    Research Associate

    anindya.kundu65@gmail.com

    Joined NIAB-Cambridge, UK

    Dr.Dipan Roy

    PhD Scholar

    roydipan1286@gmail.com

    Post-doctoral Fellow at Durham University, UK

    Dr.Adrita Roy

    PhD Scholar

    adritaroy_2007@yahoo.co.in

    Joined Industry

    Dr. Amit Paul

    PhD Scholar

    amitpaul2710@gmail.com

    Post-doctoral Fellow at UCLA, USA

    Dr. Rwitie Mallik

    PhD student

    rwitie@gmail.com

     

    Group News:

     GROUP NEWS

    2019: Dr Shubho Chaudhuri received the SERB-ITS grant for poster presentation at Plant Biology 2019 (hosted by ASPB) in San Jose, California, USA in August, 2019.

    2018: Ms. Pratiti Dasgupta received the SERB-ITS grant for poster presentation at Keystone Symposia meeting on Chromatin Architecture and Chromosome Organization held at Whistler Conference Centre, BC, Canada in March, 2018.

    2017: Ms Adrita Roy received the best poster award  [International symposium on Insights to Plant Biology,]



    Call for PhD position enrollment

    Positions available: Four position available (JRF)


    RA: Interested candidates can directly contact shubho@jcbose.ac.in


    Our group at Bose Institute, Kolkata is seeking for highly motivated doctoral research candidates, who are interested to work in understanding the molecular events instrumental in plant development and plant response to external cues at genetic and epigenetic levels. The group is currently involved in understanding the regulation in Arabidopsis thaliana and rice (Oryza sativa) plant species.


    Our work has the following focus areas:


    1.     To explore the different epigenetic changes in plants to understand the transcription regulation of genes that are regulated during abiotic stress response.


    2.     To identify the chromatin state (modifications) that can be transferred to the offspring as stress memory for better stress perception and adaptability, in cases of repeated stress cycles.


    3.     Study the mechanism of chromatin remodelling in plants (with emphasis on HMG superfamily) to understand the transcription regulation of genes that are regulated by endogenous and exogenous cues.


    We are looking for prospective candidates for filling up four vacancies in the above-mentioned areas of research.


    Essential Qualification:

    • Master Degree or equivalent degree in either of the following: Biotechnology, Biochemistry, Botany, Genetics, Microbiology, Life Sciences.
    • Candidates must have an award of a valid JRF (CSIR-UGC JRF/ DBT-JRF/ DST-INSPIRE/ DBT-BINC or equivalent). Candidates, currently in their final year of their Master’s degree and in possession of an award of a JRF can apply. If selected, they will be asked to submit their final degree certificate at the time of joining.


    Interested candidates are encouraged to apply.

    Application related query and submissions (application letter along with Curriculum Vitae) may be directly addressed to the lab supervisor


    Dr Shubho Chaudhuri at shubho@jcbose.ac.in