Department of
Biology

Saikrishnan Kayarat did his BSc in Physics at the University College, Thiruvananthapuram, followed by an Integrated PhD in Biological Sciences from the Indian Institute of Science, Bangalore, India. He carried out his postdoctoral research work at the Clare Hall Laboratories, Cancer Research UK, and was a visiting scientist at the Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.

Research

Mechanism of macromolecular machines

Multifunctional and multidomain proteins carry out a myriad of cellular processes. These proteins, called macromolecular machines, orchestrate the activities of their functional domains in concert to carry out specific tasks. The principal aim of Dr. Saikrishnan Kayarat's research is to understand how such complex protein molecules work.

As model systems, the group uses the nucleoside triphosphate (NTP) dependent restriction-modification (RM) enzymes, a macromolecular machine involved in bacterial defense against foreign DNA, such as bacteriophage DNA and other mobile genetic elements. The NTP-dependent RM enzymes protect the host by nucleolytically degrading the incoming foreign DNA having specific target sequences. Nucleolytic cleavage occurs when two such enzymes assemble on two target sequences, respectively, and converge on the DNA upon NTP (often ATP) hydrolysis. The same enzyme can also methylate a specific base of the target sequence (modification). Modification prevents DNA cleavage, thus enabling the distinction between foreign and self-DNA. Through the methylation of DNA, the enzyme can also function as a master regulator of gene expression by modulating the epigenetic status of the host genome.

By combining biochemical, biophysical and structural biology techniques, including X-ray crystallography and electron cryo-microscopy, the Kayarat research group has been dissecting the mechanism of DNA cleavage and methylation by the NTP-dependent RM enzymes. Their findings have revealed how the chemical energy released upon NTP hydrolysis is harnessed for DNA cleavage. In the pursuit to understand the working of NTP-dependent RM enzymes, they have discovered new modes of double strand DNA cleavage by enzymes, that may have relevance to bacterial physiology.

Selected Publications

Tumuluri, V.S., Rajgor, V., Xu, S-Y., Chouhan, O. P. & Saikrishnan, K. 2021. Mechanism of DNA cleavage by the endonuclease SauUSI: a major barrier to horizontal gene transfer and antibiotic resistance in Staphylococcus aureus. Nucleic Acids Res., 49, 2161–2178.

Chand, M. K. Carle, V., Anuvind, K. G. & Saikrishnan, K. 2020. DNA-mediated coupling of ATPase, translocase and nuclease activities of a Type ISP restriction-modification enzyme. Nucleic Acids Res. 48, 2594-2603.

Nirwan, N., Itoh, Y., Singh, P., Bandyopadhyay, S., Vinothkumar, K. R., Amunts, A., & Saikrishnan, K. 2019. Structure-based mechanism for activation of the AAA+ GTPase McrB by the endonuclease McrC. Nature Commun. doi.org/10.1038/s41467-019-11084-1.

Nirwan, N., Singh, P., Mishra, G. G., Johnson, C. M., Szczelkun, M. D., Inoue, K., Vinothkumar, K. R. & Saikrishnan, K. 2019. Hexameric assembly of the AAA+ protein McrB is necessary for GTPase activity. Nucleic Acids Res. 47, 868-882.

Ahmad, I., Kulkarni, M., Gopinath, A. & Saikrishnan, K. 2018. Single-site DNA cleavage by Type III restriction endonuclease requires a site-bound enzyme and a trans-acting enzyme that are ATPase-activated. Nucleic Acids Res. 46, 6229 -6237.

Kulkarni, M., Nirwan, N., van Aelst, K., Szczelkun, M. & Saikrishnan, K. 2016. Structural insights into DNA sequence recognition by Type ISP restriction-modification enzymes. Nucleic Acids Res. 44, 4396-4408.

Chand, M. K., Nirwan, N., Diffin, F., van Aelst, K., Kulkarni, M., Pernstich, C., Szczelkun, M. & Saikrishnan, K. 2015. Translocation-coupled DNA cleavage by the Type ISP restriction-modification enzymes. Nature Chemical Biol. 11, 870-877.