Dr. Rajat Banerjee
Ph.D

Lecturer, GCGEB, Calcutta University

Email:rbbcgc@gmail.com

B.Sc Chemistry (Hons) – Barasat Govt. College, Calcutta, Calcutta University

M.Sc (Biophysics and Molecular Biology) – Calcutta University

Ph.D (Biophysics and Molecular Biology) – Bose Institute, Calcutta University

22. An FCS Study of Unfolding and Refolding of CPM-Labeled Human Serum Albumin: Role of Ionic Liquid. Sasmal DK, Mondal T, Sen Mojumdar S, Choudhury A, Banerjee R, Bhattacharyya K. J Phys Chem B. 2011 Oct 13. [Epub ahead of print]

21. Selective extraction of palladium(II) using hydrazone ligand: A novel fluorescent sensor. Mukherjee S, Chowdhury S, Paul AK, Banerjee R. Journal of Luminescence, 131, 2342-2346, 2011.
20. Mitochondrial aminoacyl-tRNA synthetase single-nucleotide polymorphisms that lead to defects in refolding but not aminoacylation. Banerjee R#, Reynolds NM, Yadavalli SS, Rice C, Roy H, Banerjee P, Alexander RW, Ibba M. J Mol Biol. 410,280-93m 2011. # Corresponding Author
19. Redox status affects the catalytic activity of glutamyl-tRNA synthetase. Katz A, Banerjee R, de Armas M, Ibba M, Orellana O. Biochem Biophys Res Commun. 398, 51-5, 2010.
18. Protein Evolution via Amino Acid and Codon Elimination. Goltermann L, Larsen MSY, Banerjee R, Joerger AC,Ibba M and Bentin T. PLoS ONE 5(4): e10104, 2010.
17. Cell-specific differences in the requirements for translation quality control. Reynolds NM, Ling J, Roy H, Banerjee R, Repasky SE, Hamel P, Ibba M. Proc Natl Acad Sci U S A. 107,4063-8m 2010.
16. Enzyme mediated biodegradation of heat treated commercial polyethylene by staphylococcal speices. Chatterjee S, Roy B, Roy D and Banerjee R. Polymer degradation and stability (Accepted)

15. tRNAs: cellular barcodes for amino acids. Banerjee R, Chen S, Dare K, Gilreath M,  Praetorius-Ibba M, Raina M, Reynolds NM, Roy TR, Yadavalli SS, Ibba M. FEBS Lett. 584 (2), 387-95, 2010.  

14. Large-scale movement of functional domains facilitates aminoacylation by human  mitochondrial phenylalanyl-tRNA synthetase. Yadavalli SS, Klipcan L, Zozulya A, Banerjee R, Svergun D, Safro M, Ibba M. FEBS Lett. 583(19): 3204-8, 2009.

 13. The role of the catalytic domain of E. coli GluRS in tRNAGln discrimination. Dasgupta S, Saha R, Dey C, Banerjee R#, Roy S, Basu G#.  FEBS Lett. 583(12):2114-20, 2009. # Corresponding Author

12. Isolation and identification of poly beta hydroxybutyric acid accumulating bacteria of Staphylococcal sp. and characterization of biodegradable polyester. Roy B,
Banerjee R, Chatterjee S. Indian J Exp Biol. 47(4):250-6, 2009.

11. Ghosal A, Bhowmick R, Banerjee R, Ganguly S, Yamasaki S, Ramamurthy T, Hamabata T, Chatterjee NS. “Characterization and studies of the cellular interaction of
native colonization factor CS6 purified from a clinical isolate of enterotoxigenic Escherichia coli.” Infect Immun. 77(5):2125-35 2009.

10. Roy B, Banerjee R, Chatterjee S. “Isolation and identification of poly beta
hydroxybutyric acid accumulating bacteria of Staphylococcal sp. and characterization
of biodegradable polyester.” Indian J Exp Biol. 47(4):250-6. 2009.
               9. Blaise M, Olieric V, Sauter C, Lorber B, Roy B, Karmakar S, Banerjee R, Becker                HD, Kern D. “Crystal structure of glutamyl-queuosine tRNAAsp synthetase complexe                d with L-glutamate: structural elements mediating tRNA-independent activation of gluta               mate and glutamylation of tRNAAsp anticodon.” J Mol Biol., 381(5): 1224-37. 2008.

8. Ataide S. F., Wilson S. N., Dang S., Rogers T. E., Roy B., Banerjee R., Henkin T. M., and Ibba M. “Mechanisms of resistance to an amino acid antibiotic that targets
translation.” ACS Chemical Biology, 2, 819-827. 2007.

7. Basu C., Chowdhury S., Banerjee R., Stoeckli-Evans H. and Mukherjee S. “A novel blue luminescent high-spin iron(III) complex with interlayer O–H_ _ _Cl bridging:
Synthesis, structure and spectroscopic studies.” Polyhedron 26, 3617–3624, 2007.

6. Banerjee R.*, Dubois D. Y.*, Gauthier J., Lin S. X., Roy S. and Lapointe, J. “The
zinc-binding site of a class I aminoacyl-tRNA synthetase is a SWIM domain that
modulates amino acid binding via the tRNA acceptor arm.” Eur J Biochem. 271,
724-33,2004. * Contributed equally

5. Banerjee R., Mandal A. K., Saha R., Guha S., Samaddar A., Bhattacharya A. and Roy S. “Solvation change and ion release during aminoacylation by aminoacyl-tRNA
synthetases.” Nucleic Acids Res. 31, 6035-42, 2003.
   
     4. Mandal A. K., Samaddar S., Banerjee R., Lahiri S., Bhattacharyya A. and Roy
S.   “Glutamate counteracts the denaturing effect of urea through its effect on the denatured  state.” J Biol. Chem. 278, 36077-84, 2003.

     3. Sen P., Mukherjee S., Dutta P., Halder A., Mandal D., Banerjee R., S. Roy S. and Bhattacharyya K. “Solvation Dynamics in the Molten Globule State of a Protein.” J. Phys. Chem. B 107, 14563-568, 2003.

2. Mandal D., Sen S., Sukul D., Bhattacharyya K., Mandal A. K., Banerjee R. and Roy S. “Solvation Dynamics of a Probe Covalently Bound to a Protein and in an AOT
Microemulsion: 4-(N-Bromoacetylamino)-Phthalimide.” J. Phys. Chem. B. 106,
10741-10747, 2002.

1.  Bhattacharyya A., Mandal A.K., Banerjee R. and Roy S. “Dynamics of compact denatured states of glutaminyl-tRNA synthetase probed by bis-ANS binding kinetics.” Biophys Chem., 87, 201-12, 2000 .


 

The maintenance of cellular function is dependent on the fidelity with which information is transmitted from the genes to their gene products. The prevention of amino acid misincorporation into proteins is ensured by the activity of the aminoacyl-tRNA synthetase (aaRS) family of enzymes that play a fundamental role in the translation of the genetic code. AaRSs catalyze the covalent attachment of amino acids to the 3’ end of their cognate transfer RNA (tRNA). The tRNA aminoacylation reaction can be divided into two steps, In the first step amino acid is activated by ATP to form an enzyme-bound aminoacyl-adenylate intermediate (Activation step, equ 1), followed by transfer of the amino acid to the 3’ terminus of the tRNA (Transfer step, equ 2):

       aaRS + ATP:Mg2⁺  + aa →aaRS:aa~AMP +PPi:Mg2⁺          -----------------------------            (1)

       aaRS:aa~AMP +tRNA→aaRS + aa-tRNA +AMP                   -----------------------------            (2)

AaRSs have been studied in exceptional detail and considerable data have accumulated on the mechanism of aa-tRNA formation. In the past decade it has been found that the aaRSs have other crucial cellular functions such as cell signaling, mitochondrial disease, HIV packaging, antibiotic resistance etc. Mutations in genes encoding aaRSs have been reported to be related with neuro degeneration that evoked the question about the role of these enzymes in neural function. These additional activities beyond aminoacylation are far less well understood. Study of structure-function relationship will provide insights into the degree of functional diversity among the aaRSs in general, an emerging family of anti-microbial drug target.

Transcriptional regulation of AlaRS

Alanyl-tRNA synthetase (AlaRS), a class II synthetase, appears to be tetrameric in E. coli. Its N-terminal 461 amino acids are responsible for the catalytic activity whereas the C-terminal domain is responsible for oligomerization and editing. Other than aminoacylation activity it can also repress its own gene expression by binding with a palindromic DNA sequence flanking the gene’s transcription start site.

We will determine the thermodynamical parameters of AlaRS interaction with DNA sequence using biophysical methods and site-directed mutagenesis to pinpoint the elements responsible for its own transcriptional regulation.

Induced conformations and amino acid discrimination during substrates binding of plant arginyl-tRNA synthetases (In collaboration with Professor Gabor Igloi, University of Freiburg, Germany)

The accuracy of aminoacylation as far as the plant systems are concerned, that have been appreciated as a rich source of toxic, non-protein amino acids, provide a rare opportunity of studying how Nature has solved the problem of evolving aminoacyl-tRNA synthetases by the producer plant that discriminates successfully between the proteinogenic amino acid and its nonprotein analogue, thereby avoiding autotoxicity. L-canavanine has been found to occur as a toxic nonprotein amino acid in more than 1500 leguminous plants. One mechanism of its toxicity is its incorporation into proteins, replacing arginine and giving rise to functionally aberrant polypeptides. We have focused our attention on a pair of species specific plant arginyl-tRNA synthetases variants, one of which is said to be evolutionarily adapted to ignore a toxic arginine analogue, while the other lacks this ability. Our main goal of this project is to elucidate the elements present in the tRNA body that are responsible for discrimination between the arginine and canavanine and thus contribute to the fidelity of protein biosynthesis.

Evolution of Glutamyl-Q- tRNA^Asp Synthetase (In collaboration with Professor Daniel Kern, University of Strasbourg, France)

Glutamyl-Q-tRNA Synthetase (GluQRS), a paralog of Glutamyl-tRNA Synthetase (GluRS), lacks C terminal anticodon binding domain. GluQRS displays 34% identity with N-terminal sequence of E. coli GluRS and the crystal structure showed striking similarity with N-terminal of catalytic binding domain of GluRS. GluQRS is present in the genome of > 40 species of proteobacteria, cyanobacteria and actinobacteria. Unlike GluRS that requires the presence of cognate tRNA in the activation step to form glutamyl-AMP before being transfer the L-glutamate to the 3’ end of tRNA^Glu, GluQRS forms glutamyl-adenynate in a tRNA independent fashion but transfer the activated L-glutamate to Queuosine, the modified nucleoside occupying the first anticodon position of tRNA^Asp. It was proposed that  paralogs of aminoacyl tRNA synthetase lacked of an anticodon binding domain are either remnants of primitive aminoacyl tRNA synthetase  that did not acquired the anticodon  binding domain or modern aminoacyl tRNA synthetase which lost the anticodon binding domain.

The objective of this project is to search evolutionary origin of Glutamyl-Q-tRNA Synthetase.

Mechanism of substrate recognition by truncated glutamyl-tRNA synthetase (In collaboration with Professor Gautam Basu, Bose Institute, Kolkata, funded by Council for Scientific and Industrial research, Govt of India)

Based on crystal structure of T. thermophilus GluRS, we cloned two truncated versions of E. coli GluRS, namely the N-terminal 1-314 residues and the C-terminal 318-471 residues, to investigate the functional and structural roles of each domain in isolation and when added in trans. To complement the experimental data detailed Bioinformatics work also has been undertaken.

Structure-function studies of tyrosyl-tRNA synthetase (TyrRS) from   Mimi virus        (Acanthomoeba polyphega)

Tyrosyl-tRNA synthetases are dimeric, belong to class I and have some special properties such as half-a-site reactivity. The crystal structure of Mimivirus TyrRS (TyrRSapm) has been solved recently and found to be structurally and functionally more closely related to eukaryotes rather than prokaryotes. TyrRSapm has some idiosyncratic features and is unique having altered motif structure (α6-α7).

Our overall objective of this project is to study the structure-function relationship of Mimivirus TyrRS to understand the role of different domains and/or motifs in substrate recognition and evolution.

Secret Sharing Scheme Using DNA Cryptography (In collaboration with Dr. Avishek Adhikari, department of Pure Mathematics, University of Calcutta; funded by Ministry of Information Technology, Govt. of India.)

The broader objective of our project is to find a strong connection between the three emerging subjects, namely cryptography from computer science; molecular biology and DNA computing to develop a perfectly secured DNA secret sharing scheme for threshold as well as for general access structure by using mathematics and statistics. Due to the recent development of computers and computer networks, huge amount of digital data can easily be transmitted or stored. But the transmitted data in networks or stored in computers may easily be destroyed or substituted by enemies if the data are not enciphered by some cryptographic tools. Three major reasons, namely very small size, huge storage capacity and massive parallel processing in DNA computing drive us think about “DNA” as a medium for secret sharing.

Isolation, identification and characterization of biodegradable polyester from bacterial sp. (In collaboration with Dr. Sumana Chatterjee, Department of Chemistry, Basanti Devi College, Kolkata)

At present there is a great need for the development of an alternative to the non–biodegradable, synthetic plastics based on petrochemicals. The biodegradable polyhydroxyalkonates obtainable from bacteria and fungi that mimic the properties of thermoplastics, could not yet reach the common people due to the prohibitively high price. Scientists throughout the world are in a desperate hunt for an economically viable process of getting better plastics from nature. Many microorganisms in nature synthesize polyhydroxyalkanoates (PHAs) as an energy storage material, in much the same way animals store fat. These microorganisms can be used in fermentation to produce significant quantities of PHAs, but often they exhibit slow growth, instability, low yields, or difficulties in downstream isolation of PHAs. Metabolic engineering has allowed the creation of microbes with better fermentation characteristics. Our main objective is to optimize the PHA production to bring the cost down and tuned the microbes for better product yields, while maintaining the viability of the microbial "biofactory".

Lab Members

	Bappaditya Roy Project Scientist bappaditya_2004@yahoo.com
	Sutapa Ray PhD student (Junior research fellow) sutapaaray@gmail.com
	Arparajita Choudhury PhD student (Junior research fellow) apr.choudh@gmail.com
	Baisakhi Banerjee PhD student (Junior research fellow) baisakhirimi@gmail.com