Decoding survival pathways (antibiotic resistance, stress response, biofilm, and multidrug-resistant) mechanisms in human pathogenic bacteria: A Synergistic research program at the Department of Biosciences and Bioengineering (BSBE), IIT Dharwad
We are interdisciplinary research team aimed at advancing the understanding of bacterial signal transduction and exploiting this knowledge to combat antimicrobial resistance (AMR). We integrate structural biology, microbiology, biochemistry, biophysics, and computational approaches to uncover how bacterial pathogens sense, process, and respond to environmental cues.
A central focus of our research is second-messenger signaling, particularly c-di-GMP, c-di-AMP, and magic spot nucleotides ((p)ppGpp/MSN), which govern critical survival pathways such as biofilm formation, persistence, quorum sensing, virulence, and stress adaptation. We study these mechanisms in clinically relevant pathogens, with an emphasis on ESKAPE pathogens leverage our discoveries to inform the development of next-generation antibiotics (NGAs).
1. Fundamental mechanisms of bacterial signaling
We aim to make foundational discoveries in bacterial signal transduction by identifying and characterizing novel second-messenger effectors and deciphering how they regulate cellular decision-making at the molecular level.
2. Targeting survival pathways such as biofilms, quorum sensing, virulence, and persistence
Our work seeks to exploit second-messenger signaling networks to develop anti-biofilm and anti-c-di-GMP/MSN strategies, with the long-term goal of enabling new classes of antibacterial therapies, particularly against ESKAPE pathogens.
3. Bacterial “Social-IQ” and collective behavior
We investigate the molecular basis of bacterial collective intelligence—referred to as the Bacterial Social-IQ Score—by studying how second messengers control quorum sensing, persistence, and biofilm formation. By correlating Social-IQ scores with the presence and function of second-messenger effectors, we aim to uncover new regulatory principles governing bacterial survival.
4. Translational signaling diagnostics
At BSBE, IIT Dharwad, we also pursue LC-MS-based quantitative profiling of second messengers (including c-di-GMP and related molecules) from patient-derived samples. This approach aims to enable early diagnosis and improved understanding of biofilm-associated chronic infections caused by pathogenic bacteria.
Current projects
Deciphering the molecular mechanisms of signaling in bacteria and their implications in developing next-generation antibiotics
The rapid rise of antibiotic resistance and the slow pace of new antibiotic discovery demand alternative therapeutic strategies. Our research focuses on bacterial survival pathways, rather than classical targets such as DNA replication or cell wall synthesis, as a route to next-generation antibiotics (NGAs).We investigate second messenger–regulated signaling networks, particularly those controlled by (p)ppGpp (magic spot nucleotides), c-di-AMP, and c-di-GMP, which govern key survival processes including biofilm formation, quorum sensing, stress adaptation, and virulence. In major pathogens such as Mycobacterium tuberculosis and Pseudomonas, many effector proteins and signaling mechanisms within these pathways remain unknown.
By systematically identifying and mechanistically characterizing novel second-messenger effector proteins, our work aims to uncover new molecular targets that contribute to antibiotic resistance and pathogenesis, providing a foundation for the development of non-traditional antibacterial strategies.
Novel targets of survival pathways controlled by the second messenger in pathogenic bacteria
Our lab aims to identify novel survival pathway targets regulated by the second messengers c-di-GMP and magic spot nucleotides (MSN) in Mycobacterium tuberculosis and Pseudomonas aeruginosa, using the closely related model organism Pseudomonas fluorescens. We employ state-of-the-art capture compound–based mass spectrometry (CCMS) to perform unbiased, proteome-wide identification of second-messenger effector proteins, followed by detailed biochemical, biophysical, and structural characterization.
By discovering and characterizing new second-messenger targets, our research seeks to elucidate how c-di-GMP and MSN regulate key bacterial survival pathways, including stress adaptation, biofilm formation, antibiotic resistance, virulence, pathogenesis, and host–pathogen interactions. These insights will provide a mechanistic framework for understanding bacterial persistence and open new avenues for targeting survival pathways in the development of next-generation antimicrobial strategies.
Our lab investigates novel scaffold and adaptor proteins that mediate second-messenger signaling in bacteria. We identified HrsB, a previously uncharacterized protein that binds both c-di-GMP and (p)ppGpp with high affinity. Structural studies revealed an unusual, elongated helical-repeat architecture typical of signaling scaffold proteins, with a conserved second-messenger–binding domain.
Bioinformatic and structural analyses indicate that this protein family is widespread across bacteria. We aim to unserstand the this scaffold protein by combining computational prediction, structural biology, and biochemical characterization. Understanding how these scaffold proteins integrate second-messenger signals may uncover new regulatory principles and potential antimicrobial drug targets.
Dissecting the molecular mechanisms of c-di-AMP controlled electrochemical signaling wthin Bacterial Biofilms
This project aims to understand electrochemical communication during bacterial biofilm formation. Biofilm-associated bacteria communicate through ion channel–mediated electrical signaling, particularly via potassium (K⁺) channels, to coordinate collective behavior. Emerging evidence suggests that the second messenger c-di-AMP regulates biofilm formation by directly controlling ion channels and transporters. We seek to define the molecular mechanisms by which c-di-AMP modulates electrochemical signaling within biofilms and how this contributes to biofilm-associated drug resistance. Insights from this work may reveal new strategies to control biofilm-mediated infections and antimicrobial resistance.
PAS (Per-ARNT-Sim) domains are ubiquitous sensory modules that act as signal detectors and interaction hubs in bacterial signaling proteins, including histidine kinases (HKs) that regulate stress responses and antibiotic resistance. Although PAS domains are widespread, their modes of signal sensing and transmission within full-length, multi-domain proteins remain poorly understood.
Our research focuses on elucidating how PAS domains control HK activity through conformational and oligomerization-based mechanisms, particularly in the context of intact proteins embedded in lipid environments. We combine cryo-EM, X-ray crystallography, AlphaFold-guided modeling, and integrated structural biology approaches to determine structures of PAS-containing HKs in physiologically relevant states.
A key objective is to resolve the full-length architecture of the master regulator CckA, both alone and in complex with its signaling partners DivL and DivK-P, to understand how PAS domains switch between kinase and phosphatase states. These studies will provide fundamental insight into PAS-mediated signal transduction and may reveal new targets for antimicrobial intervention.
Integrating artificial intelligence to decode bacterial signaling and accelerate antibiotic discovery
Artificial intelligence (AI) will be integrated into our research plan to analyze bacterial genomes, proteomes, and transcriptomes using machine learning to identify correlations between the Social-IQ Score and second-messenger effectors, predict regulatory networks, and pinpoint vulnerabilities in bacterial signaling pathways. AI-driven virtual screening, drug design, and molecular dynamics simulations will accelerate the discovery and optimization of next-generation antibiotics by predicting drug efficacy, resistance potential, and mechanistic insights into disrupting bacterial survival pathways.
Overall, our long-term vision at the Department of Biosciences and Bioengineering (BSBE), IIT Dharwad, is to elucidate the molecular mechanisms of second-messenger signaling and to provide blueprints for combating bacterial diseases. The knowledge derived will be indispensable for a thorough understanding of antibiotic resistance mechanisms through survival pathways and will open rational avenues for manipulating them to develop NGAs.
