Dr. Vinay K. Nandicoori

Research Interest:

Deciphering kinase-mediated signaling networks in Mycobacterium tuberculosis (Mtb). Investigating the role of Mtb protein kinases in regulating cellular events of the pathogen and host-pathogen interactions.

Summary of Research:

Cell-signaling is a consortium of cellular events wherein the transmission of environmental signals to cells sets off a cascade of reactions that ultimately culminate in changes in gene expression and activity.  One of the major mechanisms through which cell signaling pathways operate is the reversible phosphorylation of cellular proteins. Eukaryotic-like serine/threonine protein kinases (STPKs) in Mtb regulate a number of cellular processes including cell division. There are 11 eukaryotic-like STPKs in Mtb, and our lab has been working on analyzing the functional roles of the phosphorylation events mediated by these kinases.

Protein kinases A and B are essential genes that play a role in modulating cell shape, and possibly cell division. Overexpressing of PknA in M. tuberculosis results in a deviation from normal cell morphology with the cells forming an elongated and branched structure, while overexpression of PknB in M. tuberculosis results in the formation of widened and bulging cells. The Mtb protein kinase B (PknB) comprises an intracellular kinase domain, connected through a transmembrane domain to an extracellular region that contains four PASTA domains. We performed comprehensive analysis of different domains of PknB in the context of viability in avirulent and virulent mycobacteria and showed that although the presence of the C-terminal PASTA domain is dispensable in the avirulent M. smegmatis, all four PASTA domains are essential in Mtb.  Work from the lab showed that the stringent regulation of PknB expression is necessary for cell survival, with depletion or overexpression of PknB leading to cell death. Recently we showed that Protein kinase A is essential for in vitro growth as well as for the survival of the pathogen in the host. Although PknA and PknB are expressed as part of the same operon, they appear to be regulating cellular processes through divergent signaling pathways.

Protein kinase G (PknG) has been shown to play a role in the survival of the pathogen in host macrophages by modulating phagosome-lysosome fusion (lysosomal transfer) after macrophages phagocytose mycobacterium, and PknG kinase activity is essential for mediating its effect on lysosomal transfer. We have investigated the role of PknG and PknG mutants in the pathogenesis of mycobacteria in mice, and showed for the first time that the expression of PknG in non-pathogenic mycobacteria allows the continued existence of these bacteria in host tissues. We were the first to characterize PknK and show that PknK modulates the activation of transcription from the promoter of mycobacterial monooxygenase operon, through phosphorylation of the transcriptional regulator VirS.

The identification and characterization of target substrates for kinases is extremely important to decipher the function of the pathway within the cell. We have identified enzymes N-acetylglucosamine-1-phosphate uridyltransferase (GlmU) to be novel substrates of PknA as well as PknB and demonstrated   that   while   PknB   mediated   phosphorylation   of   GlmU   does   not   affect  its uridyltransferase activity, it significantly modulates the protein’s acetyltransferase activity. In collaboration with Dr. Balaji Prakash, we determined the structure of GlmU^Mtb in complex with substrates bound at the acetyltransferase active site, and uncovered unique features in the carboxy terminus of GlmU^Mtb. Recently we have comprehensively dissected the role of GlmU^Mtb in arbitrating the survival of pathogen both in vitro and in vivo. In collaboration with Dr. D. Sriram, we developed a novel oxazolidine derivative targeting the uridyltransferase allosteric site, which specifically inhibited GlmU^Mtb in vitro and ex vivo. Work from our lab showed that phosphorylation of InhA, the primary target of the first-line anti-tuberculosis drug isoniazid and a key enzyme of the Fatty Acid Synthase-II system involved in mycolic acid biosynthesis in Mtb, impacts mycobacterial growth and survival.

Though all the Mtb STPKs have been biochemically characterized and a number of substrates identified, many questions remain to be answered. The role of the extracellular environment on activation/inactivation of kinases has not yet been investigated. Despite the fact that many of the substrates were initially identified to be substrates for one specific kinase or other, most are actually phosphorylated by multiple STPKs. Thus, a key feature amongst all these kinase-substrate interactions is the redundancy of signalling, suggesting a complicated temporal and spatial control over key mycobacterial processes. It is conceivable that many or all of the signalling molecules described here may in fact regulate each other, similar to the cross-talk seen in most eukaryotic signalling pathways.  Our ultimate aim to decipher the signaling pathways in Mtb and determine how these signaling molecules influence the survival in the host upon infection.

Group Members:
Dr. Savita Lochab, Ms. Divya Arora, Ms. Prabhjot Kaur, Ms. Preeti Jain, Ms. Basanti Malakar, Ms. Mehak Zahoor Khan, Mr. Yogesh Chawla, Mr. Vijay Soni, Ms. Saba Naz, Mr. Mahesh Ray, Mr. Babulal Nepali

Awards:
• Fellow, The National Academy of Sciences (India), Allahabad, (2014)
• National Bioscience Award for Career Development (2010)
• Elected Member, Guha Research Conference, India (GRC) (2009)
• NASI-Scopus Young Scientist Award (2009)
• M. Sreenivasaya Award for the Best Thesis, IISc, Bangalore, India (1999)