Hierarchical nanostructured functional materials for flexible supercapacitors A Gowrisankar, K Sureka, T Selvaraju Materials Technology for the Energy and Environmental Nexus, 2023 In this chapter, we focus specifically on the recent advances in the fabrication of flexible supercapacitor devices and their electrochemical performance as supercapacitor materials. The synthesis approaches for HNFMs are categorized, and the electrochemical capacitive performances of various HNFMs are discussed. Finally, the challenges and the promising future of this particular material are discussed.
Spike protein mutational landscape in India during the complete lockdown phase: Could Muller's ratchet be a future game-changer for COVID-19? Rachana Banerjee, Kausik Basak, Anamika Ghosh, Vyshakh Rajachandran, Kamakshi Sureka, Debabani Ganguly, Sujay Chattopadhyay Infection Genetics and Evolution, 2021 The dire need of effective preventive measures and treatment approaches against SARS-CoV-2 virus, causing COVID-19 pandemic, calls for an in-depth understanding of its evolutionary dynamics with attention to specific geographic locations, since lockdown and social distancing to prevent the virus spread could lead to distinct localized dynamics of virus evolution within and between countries owing to different environmental and host-specific selection pressures. To decipher any correlation between SARS-CoV-2 evolution and its epidemiology in India, we studied the mutational diversity of spike glycoprotein, the key player for the attachment, fusion and entry of virus to the host cell. For this, we analyzed the sequences of 630 Indian isolates as available in GISAID database till June 07, 2020 (during the time-period before the start of Unlock 1.0 in India on and from June 08, 2020), and detected the spike protein variants to emerge from two major ancestors – Wuhan-Hu-1/2019 and its D614G variant. Average stability of the docked spike protein – host receptor (S-R) complexes for these variants correlated strongly (R2 = 0.96) with the fatality rates across Indian states. However, while more than half of the variants were found unique to India, 67% of all variants showed lower stability of S-R complex than the respective ancestral variants, indicating a possible fitness loss in recently emerged variants, despite a continuous increase in mutation rate. These results conform to the sharply declining fatality rate countrywide (>7-fold during April 11 – June 28, 2020). Altogether, while we propose the potential of S-R complex stability to track disease severity, we urge an immediate need to explore if SARS-CoV-2 is approaching mutational meltdown in India.
Cyclic di-AMP targets the cystathionine beta-synthase domain of the osmolyte transporter OpuC TuAnh Ngoc Huynh, Philip H. Choi, Kamakshi Sureka, Hannah E. Ledvina, Julian Campillo, Liang Tong, Joshua J. Woodward Molecular Microbiology, 2016 Cellular turgor is of fundamental importance to bacterial growth and survival. Changes in external osmolarity as a consequence of fluctuating environmental conditions and colonization of diverse environments can significantly impact cytoplasmic water content, resulting in cellular lysis or plasmolysis. To ensure maintenance of appropriate cellular turgor, bacteria import ions and small organic osmolytes, deemed compatible solutes, to equilibrate cytoplasmic osmolarity with the extracellular environment. Here, we show that elevated levels of c‐di‐AMP, a ubiquitous second messenger among bacteria, result in significant susceptibility to elevated osmotic stress in the bacterial pathogen Listeria monocytogenes. We found that levels of import of the compatible solute carnitine show an inverse correlation with intracellular c‐di‐AMP content and that c‐di‐AMP directly binds to the CBS domain of the ATPase subunit of the carnitine importer OpuC. Biochemical and structural studies identify conserved residues required for this interaction and transport activity in bacterial cells. Overall, these studies reveal a role for c‐di‐AMP mediated regulation of compatible solute import and provide new insight into the molecular mechanisms by which this essential second messenger impacts bacterial physiology and adaptation to changing environmental conditions.
Molecular basis for the recognition of cyclic-di-AMP by PstA, a PII-like signal transduction protein Philip H. Choi, Kamakshi Sureka, Joshua J. Woodward, Liang Tong Microbiologyopen, 2015 Cyclic‐di‐AMP (c‐di‐AMP) is a broadly conserved bacterial second messenger that is of importance in bacterial physiology. The molecular receptors mediating the cellular responses to the c‐di‐AMP signal are just beginning to be discovered. PstA is a previously uncharacterized PII‐like protein which has been identified as a c‐di‐AMP receptor. PstA is widely distributed and conserved among Gram‐positive bacteria in the phylum Firmicutes. Here, we report the biochemical, structural, and functional characterization of PstA from Listeria monocytogenes. We have determined the crystal structures of PstA in the c‐di‐AMP‐bound and apo forms at 1.6 and 2.9 Å resolution, respectively, which provide the molecular basis for its specific recognition of c‐di‐AMP. PstA forms a homotrimer structure that has overall similarity to the PII protein family which binds ATP. However, PstA is markedly different from PII proteins in the loop regions, and these structural differences mediate the specific recognition of their respective nucleotide ligand. The residues composing the c‐di‐AMP binding pocket are conserved, suggesting that c‐di‐AMP recognition by PstA is of functional importance. Disruption of pstA in L. monocytogenes affected c‐di‐AMP‐mediated alterations in bacterial growth and lysis. Overall, we have defined the PstA family as a conserved and specific c‐di‐AMP receptor in bacteria.
The cyclic dinucleotide c-di-AMP is an allosteric regulator of metabolic enzyme function. Kamakshi Sureka, Philip H. Choi, Mimi Precit, Matthieu Delince, Daniel A. Pensinger, TuAnh Ngoc Huynh, Ashley R. Jurado, Young Ah Goo, Martin Sadilek, Anthony T. Iavarone, John-Demian Sauer, Liang Tong, Joshua J. Woodward Cell, 2014 Cyclic di-adenosine monophosphate (c-di-AMP) is a broadly conserved second messenger required for bacterial growth and infection. However, the molecular mechanisms of c-di-AMP signaling are still poorly understood. Using a chemical proteomics screen for c-di-AMP-interacting proteins in the pathogen Listeria monocytogenes, we identified several broadly conserved protein receptors, including the central metabolic enzyme pyruvate carboxylase (LmPC). Biochemical and crystallographic studies of the LmPC-c-di-AMP interaction revealed a previously unrecognized allosteric regulatory site 25 Å from the active site. Mutations in this site disrupted c-di-AMP binding and affected catalytic activity of LmPC as well as PC from pathogenic Enterococcus faecalis. C-di-AMP depletion resulted in altered metabolic activity in L. monocytogenes. Correction of this metabolic imbalance rescued bacterial growth, reduced bacterial lysis, and resulted in enhanced bacterial burdens during infection. These findings greatly expand the c-di-AMP signaling repertoire and reveal a central metabolic regulatory role for a cyclic dinucleotide.
Phenotypic heterogeneity in mycobacterial stringent response Sayantari Ghosh, Kamakshi Sureka, Bhaswar Ghosh, Indrani Bose, Joyoti Basu, Manikuntala Kundu BMC Systems Biology, 2011 Background A common survival strategy of microorganisms subjected to stress involves the generation of phenotypic heterogeneity in the isogenic microbial population enabling a subset of the population to survive under stress. In a recent study, a mycobacterial population of M. smegmatis was shown to develop phenotypic heterogeneity under nutrient depletion. The observed heterogeneity is in the form of a bimodal distribution of the expression levels of the Green Fluorescent Protein (GFP) as reporter with the gfp fused to the promoter of the rel gene. The stringent response pathway is initiated in the subpopulation with high rel activity. Results In the present study, we characterise quantitatively the single cell promoter activity of the three key genes, namely, mprA, sigE and rel, in the stringent response pathway with gfp as the reporter. The origin of bimodality in the GFP distribution lies in two stable expression states, i.e., bistability. We develop a theoretical model to study the dynamics of the stringent response pathway. The model incorporates a recently proposed mechanism of bistability based on positive feedback and cell growth retardation due to protein synthesis. Based on flow cytometry data, we establish that the distribution of GFP levels in the mycobacterial population at any point of time is a linear superposition of two invariant distributions, one Gaussian and the other lognormal, with only the coefficients in the linear combination depending on time. This allows us to use a binning algorithm and determine the time variation of the mean protein level, the fraction of cells in a subpopulation and also the coefficient of variation, a measure of gene expression noise. Conclusions The results of the theoretical model along with a comprehensive analysis of the flow cytometry data provide definitive evidence for the coexistence of two subpopulations with overlapping protein distributions.
An oligopeptide transporter of Mycobacterium tuberculosis regulates cytokine release and apoptosis of infected macrophages Arunava Dasgupta, Kamakshi Sureka, Devrani Mitra, Baisakhee Saha, Sourav Sanyal, Amit K. Das, Parul Chakrabarti, Mary Jackson, Brigitte Gicquel, Manikuntala Kundu, Joyoti Basu Plos One, 2010 Background The Mycobacterium tuberculosis genome encodes two peptide transporters encoded by Rv3665c-Rv3662c and Rv1280c-Rv1283c. Both belong to the family of ABC transporters containing two nucleotide-binding subunits, two integral membrane proteins and one substrate-binding polypeptide. However, little is known about their functions in M. tuberculosis. Here we report functional characterization of the Rv1280c-Rv1283c-encoded transporter and its substrate-binding polypeptide OppAMTB. Methodology/Principal Findings OppAMTB was capable of binding the tripeptide glutathione and the nonapeptide bradykinin, indicative of a somewhat broad substrate specificity. Amino acid residues G109, N110, N230, D494 and F496, situated at the interface between domains I and III of OppA, were required for optimal peptide binding. Complementaton of an oppA knockout mutant of M. smegmatis with OppAMTB confirmed the role of this transporter in importing glutathione and the importance of the aforesaid amino acid residues in peptide transport. Interestingly, this transporter regulated the ability of M. tuberculosis to lower glutathione levels in infected compared to uninfected macrophages. This ability was partly offset by inactivation of oppD. Concomitantly, inactivation of oppD was associated with lowered levels of methyl glyoxal in infected macrophages and reduced apoptosis-inducing ability of the mutant. The ability to induce the production of the cytokines IL-1β, IL-6 and TNF-α was also compromised after inactivation of oppD. Conclusions Taken together, these studies uncover the novel observations that this peptide transporter modulates the innate immune response of macrophages infected with M. tuberculosis.
Cyclic Dinucleotide Signalling in Mycobacteria: Roles of c-di-AMP and c-di-GMP in Physiology and Pathogenesis S Mishra, D Das, K Sureka Tuberculosis, 102764 , 2026 2026
Exploring the evolutionary divergence of cyclic di-nucleotide signaling in diverse mycobacterial species S Mitra, S Paul, K Sureka Archives of Microbiology 208 (2), 92 , 2026 2026 Citations: 1
Nested Multiplex Endpoint Polymerase Chain Reaction: An Alternative Method for Human Papilloma Virus Genotyping in Resource-limited Settings MC SYMEC Research Group (Kamakshi Sureka, Anusha Harishankar, Sudipto Mandal ... Journal of The Academy of Clinical Microbiologists 26 (1) , 2024 2024
Spike protein mutational landscape in India during the complete lockdown phase: Could Muller's ratchet be a future game-changer for COVID-19? R Banerjee, K Basak, A Ghosh, V Rajachandran, K Sureka, D Ganguly, ... Infection, Genetics and Evolution, 104874 , 2021 2021 Citations: 1
Cyclic di‐AMP targets the cystathionine beta‐synthase domain of the osmolyte transporter OpuC TAN Huynh, PH Choi, K Sureka, HE Ledvina, J Campillo, L Tong, ... Molecular Microbiology 102 (2), 233-243 , 2016 2016 Citations: 123
Molecular basis for the recognition of cyclic‐di‐AMP by PstA, a PII‐like signal transduction protein PH Choi, K Sureka, JJ Woodward, L Tong Microbiologyopen 4 (3), 361-374 , 2015 2015 Citations: 65
The Cyclic Dinucleotide c-di-AMP Is an Allosteric Regulator of Metabolic Enzyme Function K Sureka, PH Choi, M Precit, M Delince, DA Pensinger, TAN Huynh, ... Cell 158 (6), 1389-1401 , 2014 2014 Citations: 266
Phenotypic heterogeneity in mycobacterial stringent response S Ghosh, K Sureka, B Ghosh, I Bose, J Basu, M Kundu BMC systems biology 5 (1), 1-13 , 2011 2011 Citations: 65
An oligopeptide transporter of Mycobacterium tuberculosis regulates cytokine release and apoptosis of infected macrophages A Dasgupta, K Sureka, D Mitra, B Saha, S Sanyal, AK Das, P Chakrabarti, ... PLoS One 5 (8), e12225 , 2010 2010 Citations: 74
RseA, the SigE specific anti‐sigma factor of Mycobacterium tuberculosis, is inactivated by phosphorylation‐dependent ClpC1P2 proteolysis S Barik, K Sureka, P Mukherjee, J Basu, M Kundu Molecular microbiology 75 (3), 592-606 , 2010 2010 Citations: 140
Novel role of phosphorylation-dependent interaction between FtsZ and FipA in mycobacterial cell division K Sureka, T Hossain, P Mukherjee, P Chatterjee, P Datta, M Kundu, ... PLOS one 5 (1), e8590 , 2010 2010 Citations: 111
Polyphosphate kinase 2: a modulator of nucleoside diphosphate kinase activity in mycobacteria K Sureka, S Sanyal, J Basu, M Kundu Molecular microbiology 74 (5), 1187-1197 , 2009 2009 Citations: 79
Novel role of Wag31 in protection of mycobacteria under oxidative stress P Mukherjee, K Sureka, P Datta, T Hossain, S Barik, KP Das, M Kundu, ... Molecular microbiology 73 (1), 103-119 , 2009 2009 Citations: 113
Positive feedback and noise activate the stringent response regulator rel in mycobacteria J Basu, A Dasgupta, I Bose, K Sureka, M Kundu, B Ghosh PUBLIC LIBRARY SCIENCE , 2008 2008
Positive feedback and noise activate the stringent response regulator rel in mycobacteria K Sureka, B Ghosh, A Dasgupta, J Basu, M Kundu, I Bose PLoS One 3 (3), e1771 , 2008 2008 Citations: 139
Polyphosphate kinase is involved in stress‐induced mprAB‐sigE‐rel signalling in mycobacteria K Sureka, S Dey, P Datta, AK Singh, A Dasgupta, S Rodrigue, J Basu, ... Molecular microbiology 65 (2), 261-276 , 2007 2007 Citations: 189
O325 Characterisation of polyphosphate kinase 1 of mycobacteria and its role in persistence K Sureka, S Dey, P Datta, A Singh, A Dasgupta, J Basu, M Kundu International Journal of Antimicrobial Agents, S67-S68 , 2007 2007
MOST CITED SCHOLAR PUBLICATIONS
The Cyclic Dinucleotide c-di-AMP Is an Allosteric Regulator of Metabolic Enzyme Function K Sureka, PH Choi, M Precit, M Delince, DA Pensinger, TAN Huynh, ... Cell 158 (6), 1389-1401 , 2014 2014 Citations: 266
Polyphosphate kinase is involved in stress‐induced mprAB‐sigE‐rel signalling in mycobacteria K Sureka, S Dey, P Datta, AK Singh, A Dasgupta, S Rodrigue, J Basu, ... Molecular microbiology 65 (2), 261-276 , 2007 2007 Citations: 189
RseA, the SigE specific anti‐sigma factor of Mycobacterium tuberculosis, is inactivated by phosphorylation‐dependent ClpC1P2 proteolysis S Barik, K Sureka, P Mukherjee, J Basu, M Kundu Molecular microbiology 75 (3), 592-606 , 2010 2010 Citations: 140
Positive feedback and noise activate the stringent response regulator rel in mycobacteria K Sureka, B Ghosh, A Dasgupta, J Basu, M Kundu, I Bose PLoS One 3 (3), e1771 , 2008 2008 Citations: 139
Cyclic di‐AMP targets the cystathionine beta‐synthase domain of the osmolyte transporter OpuC TAN Huynh, PH Choi, K Sureka, HE Ledvina, J Campillo, L Tong, ... Molecular Microbiology 102 (2), 233-243 , 2016 2016 Citations: 123
Novel role of Wag31 in protection of mycobacteria under oxidative stress P Mukherjee, K Sureka, P Datta, T Hossain, S Barik, KP Das, M Kundu, ... Molecular microbiology 73 (1), 103-119 , 2009 2009 Citations: 113
Novel role of phosphorylation-dependent interaction between FtsZ and FipA in mycobacterial cell division K Sureka, T Hossain, P Mukherjee, P Chatterjee, P Datta, M Kundu, ... PLOS one 5 (1), e8590 , 2010 2010 Citations: 111
Polyphosphate kinase 2: a modulator of nucleoside diphosphate kinase activity in mycobacteria K Sureka, S Sanyal, J Basu, M Kundu Molecular microbiology 74 (5), 1187-1197 , 2009 2009 Citations: 79
An oligopeptide transporter of Mycobacterium tuberculosis regulates cytokine release and apoptosis of infected macrophages A Dasgupta, K Sureka, D Mitra, B Saha, S Sanyal, AK Das, P Chakrabarti, ... PLoS One 5 (8), e12225 , 2010 2010 Citations: 74
Molecular basis for the recognition of cyclic‐di‐AMP by PstA, a PII‐like signal transduction protein PH Choi, K Sureka, JJ Woodward, L Tong Microbiologyopen 4 (3), 361-374 , 2015 2015 Citations: 65
Phenotypic heterogeneity in mycobacterial stringent response S Ghosh, K Sureka, B Ghosh, I Bose, J Basu, M Kundu BMC systems biology 5 (1), 1-13 , 2011 2011 Citations: 65
Exploring the evolutionary divergence of cyclic di-nucleotide signaling in diverse mycobacterial species S Mitra, S Paul, K Sureka Archives of Microbiology 208 (2), 92 , 2026 2026 Citations: 1
Spike protein mutational landscape in India during the complete lockdown phase: Could Muller's ratchet be a future game-changer for COVID-19? R Banerjee, K Basak, A Ghosh, V Rajachandran, K Sureka, D Ganguly, ... Infection, Genetics and Evolution, 104874 , 2021 2021 Citations: 1
Cyclic Dinucleotide Signalling in Mycobacteria: Roles of c-di-AMP and c-di-GMP in Physiology and Pathogenesis S Mishra, D Das, K Sureka Tuberculosis, 102764 , 2026 2026
Nested Multiplex Endpoint Polymerase Chain Reaction: An Alternative Method for Human Papilloma Virus Genotyping in Resource-limited Settings MC SYMEC Research Group (Kamakshi Sureka, Anusha Harishankar, Sudipto Mandal ... Journal of The Academy of Clinical Microbiologists 26 (1) , 2024 2024
Positive feedback and noise activate the stringent response regulator rel in mycobacteria J Basu, A Dasgupta, I Bose, K Sureka, M Kundu, B Ghosh PUBLIC LIBRARY SCIENCE , 2008 2008
O325 Characterisation of polyphosphate kinase 1 of mycobacteria and its role in persistence K Sureka, S Dey, P Datta, A Singh, A Dasgupta, J Basu, M Kundu International Journal of Antimicrobial Agents, S67-S68 , 2007 2007
