People : Scientific : Faculty & Scientists


Assistant Professor
+91-129-2876326  (1292876326)
atmakrish [at] thsti [dot] res [dot] in
Post doctoral Research Associate, Dept. of Immunology and Infectious Diseases, Harvard School of Public Health, Harvard University, Boston USA.
Post doctoral Research Fellow, Dept. of Microbiology and Molecular Genetics, UT Medical School, University of Texas Health Science Center, Houston USA.
PhD. (Biotechnology), Madurai Kamaraj University Tamilnadu, INDIA

It is fascinating to discern how pathogenic bacteria invade and impose upon their hosts. Delineating the mechanisms employed for onslaught provides fundamental insights into host-pathogen interactions and consequently a handle to prevent, control and possibly eradicate infection and disease spread. Most pathogens deploy a battery of virulent molecules to coerce/modulate host cellular functions for their survival and proliferation. Typically, upon making contact with hosts, they initiate onslaught through their cell surface bound artillery. Once within, they systematically cripple hosts’ cellular pathways by injecting periplasmic and cytosolic arsenal. Generally, these get delivered through specialized protein secretion machines and/or get packed into bacterial-encoded outer membrane-derived vesicles for delivery. To decipher pathogen onslaughts, my laboratory exploits Mycobacterium tuberculosis and Acinetobacter baumannii as model systems.

Mycobacterial pathogenesis: It is predicted that Mycobacterium tuberculosis (Mtb), the causal agent for tuberculosis (TB) might employ similar strategies and/or unidentified mechanisms to hijack and control its host. It encodes at least five specialized type VII secretion systems to help deliver its artillery, redirect host’s cellular machinery and mediate virulence responses. Despite intense research, it remains largely unknown as to how Mtb articulates the macrophage environment. Though several studies indicate that Mtb delivers a combination of proteins, lipids, sugars and small molecules (“virulence effectors”) into macrophages for manipulation, thus far, very few effectors have been identified. Consequently, they fail to explain all cellular modulations that Mtb exerts in its host.

My laboratory is actively involved in (i) Identifying its entire virulence artillery; (ii) Determining their delivery systems/mechanisms; (iii) Delineating their host-specific functions; and (iv) Defining their cognate host molecular targets. This effort will not only aid in identifying novel therapeutic targets among virulence effectors, but also help curtail Mtb’s power to develop drug resistant traits under clinical settings.

Novel genetic, biochemical, proteomic and microscopic approaches/techniques will be employed to quickly identify and delineate the functions of Mtb’s virulent artillery that gain access and manipulate host cellular pathways. Identifying the puppet masters and their functions should significantly impact our understanding of host-pathogen interactions in general and Mtb-mediated pathogenesis in particular.

Acinetobacter pathogenesis: In recent past, Acinetobacter has begun to haunt humans primarily because of their unique skill sets of rapidly acquiring antimicrobial resistant genes from their niche environment. Consequent to this fortifying act, it has evolved to thwart all known antibiotics thus turning into a bane especially for immunocompromised and infants. Surprisingly, its battery of arsenal remains a clear black box. To shed light on and subsequently target its artillery, my laboratory employs diverse molecular strategies. In collaboration with the neonatal group at All India Institute of Medical Sciences, New Delhi and the genomics and smallRNA group at National Centre of Biological Sciences, Bengaluru, we intend to understand and reduce this scourge especially among neonates.

Honour & Awards

  • Ramalingaswami Fellowship, 2012

Scientific Contributions

Pathogenic bacteria deliver virulence effectors into their hosts for subversion. Typically, while the cell surface-associated effectors help establish host contact, the cytosolic- and/or periplasmic-localized effectors engage in post-contact articulations. Intriguingly, cytosolic manipulators employ multi-protein secretion systems for their delivery. Detailed studies on “injectisomes” and their cargo have provided fundamental insights into host-pathogen interactions. Having a similar goal, in my graduate and post doctoral training, I dissected two virulence-mediating translocons, (i) the type IV secretion (T4S) machine of Agrobacterium tumefaciens (Atm; a Gram-negative phytopathogen that causes crowngalls), and (ii) “ESX1” (early secretory antigenic target-6 secretion system 1), a secretion machine of Mycobacterium tuberculosis (Mtb; a Gram-positive human pathogen that causes tuberculosis (TB)).

Atm’s T4S machine: Unlike others, Atm genetically alters its host. It elaborates a T4S needle to inject its DNA and protein effectors into plants. This unique skill of Atm is extensively exploited to genetically engineer plants. In late 1990s, several labs initiated Atm-mediated plant engineering. Interestingly, for reasons unknown, only few Atm strains efficiently transformed plants. Employing translational-reporter fusions to vir genes, and swapping vir components between strains, I dissected out the molecular details that define such varied efficiencies (towards PhD).
Recognising these scientific efforts, Prof. Peter Christie (University of Texas, Houston, USA), an authority in the “secretion biology”, invited me for post-doctoral training. When I joined his lab, it was well established that (i) the injectisome constitutes seven “core” protein partners including three ATPases and (ii) secretion can be inhibited by a 20-kDa oncogenic suppressive activity (OSA) protein. Employing several novel assays, I dissected out the cargo-delivery mechanism and the players involved. While the DNA substrate recruits to the injectisome in a ATPase-dependent manner, effector proteins use their own C-termini signals for recruitment. Post-recruitment, they first dock to the injectisomal dockyard, and then the three injectisomal-ATPases functionally co-ordinate to translocate substrates. While substrates reach the injectisome pore in an ATP-independent manner, their translocation across the pore is ATP dependent. Further, I delineated the mechanism of action of OSA, a T4S inhibitor. This proteins uses its unique fold to binds to one injectisomal-ATPase and prevents both DNA and protein effectors from docking (manuscript in preparation). These remarkable insights paved way for Atm’s T4S system attain a paradigm status.

Mtb’s translocon: In an interesting parallel to Atm’s injectisome, Mtb encodes five specialized type VII secretion (T7S) systems. Of them ESX-1, -3 and -5 are essential for virulence. Though ESX-1 is predicted to deliver effectors into macrophages, to date, there is no direct demonstration of such a phenomenon. At Harvard School of Public Health, (Harvard University, USA), I set forth and identified ESX-1’s primary function. Contrary to the existing model for substrates delivery into macrophages by ESX-1, detailed genetic, biochemical, microscopic, and proteomic assays on ESX-1 function indicated that it plays a significant role on Mtb’s capsule and cellwall integrity and colony morphology. Consequently, this raised fundamental questions on ESX-1’s functions. Analyses indicate that ESX-1 is required for Mtb’s virulence in vivo, primarily by acting on Mtb’s cell wall integrity and thus loss of ESX-1 functions globally alter Mtb’s interface with the host.
Currently, this model is under detailed investigation. If proven right, it clearly explains why avirulent mycobacterial species also encode fully functional ESX-1. Additionally, all virulent and avirulent mycobacteria with ESX-type loci encode PE and PPE proteins. These proteins are surface-localized and unique to mycobacteria and thus speculated to provide heterogeneity to the bacterial population for survival. Thus, perhaps ESX-type secretion systems secrete “PE/PPE” and “WXG- family” proteins onto bacterial surface to generate a heterogeneous bacterial pool, thus providing a survival edge in the host.

  • Maindola P, Raina R, Goyal P, Atmakuri K, Ojha A, Gupta S, Christie PJ, Iyer LM, Aravind L and Arockiasamy A. (2014) Multiple enzymatic activities of ParB/Srx superfamily mediate sexual conflict between among conjugative plasmids. Nat. Commun. 5:5322. doi: 10.1038/ncomms6322.

  • Cascales E, Atmakuri K, Sarkar M, and Christie P. (2013) DNA Substrate-Induced Activation of the Agrobacterium VirB/VirD4 Type IV Secretion System. J. Bacteriol. 195: 2691-2704.

  • Garces A*, Atmakuri K*, Chase MR, Woodworth JS, Krastins B, Rothchild AC, Ramsdell TL, Lopez MF, Behar SM, Sarracino DA and Fortune SM. (2010) EspA acts as a critical mediator of ESX1-dependent virulence in Mycobacterium tuberculosis by affecting bacterial cell wall integrity. PLoS Pathogens Jun 24 6(6):e1000957 *Co-first author.
  • Atmakuri K, and Fortune SM. (2008). Regulation of protein secretion by…protein secretion Cell Host Microbe4:190-191.
  • Atmakuri K, Cascales E, Burton OT, Banta L, and Christie PJ. (2007) Agrobacterium tumefaciens ParA/MinD-like VirC1 spatially coordinates early conjugative DNA transfer reactions EMBO J. 26:2540-2551.
  • Cascales E, Atmakuri K, Liu Z, Binns AN, and Christie PJ. (2005) Agrobacterium tumefaciens oncogenic suppressors inhibit T-DNA and VirE2 protein substrate binding to the VirD4 coupling protein. Mol. Microbiol. 58:565-579.
  • Christie PJ, Atmakuri K, Krishnamoorthy V, Jakubowski SJ, and Cascales E. (2005) Biogenesis, architecture, and function of bacterial type IV secretion systems. Annu. Rev. Microbiol. 59:451-485.
  • Atmakuri K, Cascales E, and Christie PJ. (2004) Energetic components VirD4, VirB11 and VirB4 mediate early DNA transfer reactions required for bacterial type IV secretion. Mol. Microbiol. 54:1199-1211.
  • Ding Z, Atmakuri K, and Christie PJ. (2003) The outs and ins of bacterial type IV secretion substrates. Trends Microbiol. 11:527-535.
  • Atmakuri K, Ding Z, and Christie PJ. (2003) VirE2, a type IV secretion substrate, interacts with VirD4 transfer protein at cell poles of Agrobacterium tumefaciens. Mol. Microbiol. 49:1699-1713
  • Ding Z, Zhao Z, Jakubowski SJ, Atmakuri K, Margolin W, and Christie PJ. (2002) A novel cytology-based, two-hybrid screen for bacteria applied to protein-protein interaction studies of a type IV secretion system. J. Bacteriol. 184:5572-5582.
  • Atmakuri K, Balaji V, and Veluthambi K. (2001) Efficient vir gene induction in Agrobacterium tumefaciens requires virA, virG, and vir box from the same Ti plasmid. J. Bacteriol. 183:4079-4089.


  • Atmakuri K, and Christie PJ. (2008) Translocation of oncogenic T-DNA and effector proteins to plant cells, 315-364. Book title: Agrobacterium: From Biology to Biotechnology. Publisher: Springer New York.