I have been always interested in understanding the fundamental cellular processes at the molecular level. Groups of interacting proteins form the basis for the molecular machines that carry out fundamental processes such as DNA replication , transcription, translation etc. An initial understanding of how most biological processes work, therefore, can be gained by knowing how the various proteins interact with each other. I am particularly interested in understanding the molecular architechture of the eukaryotic replisome, how is the replisome assembly regulated, what is the mode of action of the eukaryotic replicative helicase? I would be taking a combinatorial approach involving biochemical, biophysical and cell biology techniques to address these questions.
B.Sc: Zoology (Hons.), Chemistry, Physiology (Presidency College, University of Calcutta, 1999)
M.Sc : Biophysics, Molecular Biology and Genetics (University of Calcutta, 2001)
Ph.D: Microbiology and Molecular Biology (Indian Institute of Science, Bangalore, 2008)
Post doctoral training at Paterson Institute for Cancer Research, University of Manchester (2008-2012)
My doctoral thesis work involved identification and characterization of three endogenous inhibitors of an essential bacterial enzyme, DNA gyrase. My studies revealed that all these endogenous inhibitors essentially influence the enzyme activity by sequestering the enzyme away from DNA. None of them cause any cytotoxicity, which usually arises as a result of DNA damage caused by accumulation of gyrase-DNA covalent intermediate. On the contrary they provide protection against such gyrase poisons. Based on these studies, it was proposed that these endogenous proteins exist to serve as cellular defense strategies against external abuse and also modulate the intracellular activity of DNA gyrase as and when required, for accurate division, functioning and survival of the cell. After getting my degree in 2008, I joined Paterson Institute for Cancer Research, University of Manchester, England, for my post doctoral studies. During my tenure (2008-2012), I was trying to understand the molecular composition of the eukaryotic replisome, using budding yeast as a model system. My studies were directed towards understanding how the processivity is achieved in the eukaryotic repisome. I have specifically focussed on illustrating the the molecular link between the DNA polymerase epsilon and the replicative helicase. I have also investigated the importance of certain unique structural features of MCM helicase. My studies have shown several novel aspects of the eukaryotic replisome which makes it quite distinct and complex from its bacterial counterpart.
The process of DNA replication is central to cell survival and the maintenance of genome integrity. The faithful duplication of the genetic information is an absolute requirement in proliferating cells and this process is known to be defective in many human cancers, explaining the efficacy of traditional cancer treatments that damage DNA or impede dNTP synthesis. Thus a better understanding of this process is a key part of cancer research, as future cancer therapies could exploit better the inherent replication defects of cancer cells, without being as toxic as traditional treatments. Many important questions in this field still remain unanswered, as the eukaryotic chromosome replication machinery is still poorly characterised. I would like to focus on understanding this complex machinery in greater details. Two probable projects in this area are described here. In my postdoctoral research, I have been studying the structure and function of the eukaryotic ‘replisome’ using budding yeast as the model system, as all replisome components have been very highly conserved during evolution. Replisome structure is poorly understood and my postdoctoral work has shown how the leading strand DNA polymerase is associated with the replicative DNA helicase at eukaryotic replication forks. I have identified a unique domain of DNA polymerase epsilon that associates with other replisome components including the ‘GINS’ component of the active DNA helicase. My future work will be based on a detailed structure-function analysis of this interaction, using purified recombinant proteins corresponding to the yeast and human orthologues (the orthologues from other species will also be studied if necessary).
Unlike the bacterial replicative helicase, studies from several groups now suggest the MCM complex alone may not be sufficient to act as replicative helicase in eukaryotes, and there is an absolute requirement for the assembly of active CMG complex (Cdc45-MCM-GINS) for the helicase activity. Although it is quite evident that MCM forms the helicase motor, but functional roles of Cdc45 and GINS is not very clear at present. It would be an interesting endeavor to carry out biochemical studies of the helicase complex in order to understand its mode of action. Site directed mutagenesis studies with Cdc45 and GINS would help elucidating their function in greater details.
In all these planned experiments, Escherichia coli and Saccharomyces cerevisiae would serve as the model organisms and I have already gained extensive experience in expressing and purifying proteins in these two systems, as well as the in vivo analysis of chromosome replication in budding yeast.
My preferred areas of teaching would include understanding of the fundamental cellular processes like DNA replication, transcription, translation, DNA repair mechanisms and DNA recombination. Based on my research experience, I am also interested in teaching the fundamental principles of cell cycle regulation with special focus on checkpoint controls that exist in order to ensure genome integrity.
1. Vos SM, Lyubimov AY, Hershey DM, Schoeffler AJ, Sengupta S, Nagaraja V, Berger JM. (2014) Direct control of type IIA topoisomerase activity by a chromosomally encoded regulatory protein. Genes Dev. 28:1485-1497
2. Sengupta S, van Deursen F, De Piccoli G, Labib K.(2013) Dpb2 Integrates the Leading-Strand DNA Polymerase into the Eukaryotic Replisome. Curr. Biol 23: 543-552
3. van Deursen F, Sengupta S, De Piccoli G, Sanchez-Diaz A, Labib K.(2012) Mcm10 associates with the loaded DNA helicase at replication origin and defines a novel step in its activation EMBO J. 31:2195-2206
4. Sengupta S, Ghosh S and Nagaraja V. (2008) Moonlighting function of glutamate racemase from Mycobacterium tuberculosis: racemization and DNA gyrase inhibition are two independent activities of the enzyme. Microbiology. 154: 2796-2803
5. Sengupta S and Nagaraja V. (2008) YacG from Escherichia coli is a specific endogenous inhibitor of DNA gyrase. Nucleic Acids Res. 36: 4310-4316
6. Sengupta S and Nagaraja V. (2008) Inhibition of DNA gyrase activity by Mycobacterium smegmatis MurI. FEMS Microbiol Lett. 279: 40-47
7. Sengupta S, Shah M and Nagaraja V. (2006) Glutamate racemase from Mycobacterium tuberculosis inhibits DNA gyrase by affecting its DNA-binding. Nucleic Acids Res. 34: 5567-5576
8. Chatterji M, Sengupta S and Nagaraja V. (2003) Chromosomally encoded gyrase inhibitor GyrI protects Escherichia coli against DNA-damaging agents. Arch. Microbiol. 180: 339-346
Presidency University Students Corner