Papers by Santosh C M Kumar
Prokaryotic Multiple Chaperonins: The Mediators of Functional and Evolutionary Diversity
Heat shock proteins, 2017
Chaperonins are a class of molecular chaperones that form large multimeric assemblies for encapsu... more Chaperonins are a class of molecular chaperones that form large multimeric assemblies for encapsulation of substrate proteins. Surprisingly, 30% of newly sequenced bacterial genomes encode multiple copies of the chaperonins. The distribution of these multiple copies appears to follow a phylum-specific pattern. Functional and structural studies on several of these chaperonins have delineated how these extra chaperonins evolved functional diversity and contributed towards the biological adaptation of the hosting organisms. Since several of these bacteria are either pathogenic or economically important, and the chaperonins regulate the pathogenic processes in these organisms, it is important to understand their biology. This chapter is aimed to act as a primer for the subsequent chapters that describe different examples of multiple chaperonins and the plethora of their functional diversity.
Functional Diversity in Mycobacterial Chaperonins: The Generalists and the Specialists
Heat shock proteins, 2017
Chaperonins are a class of molecular chaperones that form cylindrical assemblies and for sequeste... more Chaperonins are a class of molecular chaperones that form cylindrical assemblies and for sequestering the non-native protein and thereby assisting their folding. Genomic annotation studies have identified multiple copies of chaperonin genes in about 30% of the bacteria. Mycobacterium tuberculosis was the first organism where two copies were observed, and similarly other mycobacteria bear two and rarely three copies. Owing to the pathogenic lifestyle, the chaperonins of mycobacteria have been demonstrated to be secretory and possess antigenic properties. Furthermore, biochemical and structural studies have demonstrated that these chaperonins are unusual. One of the chaperonins that exists in operonic arrangement with the co-chaperonin gene has been shown to be required in several pathogenic stages of the bacteria. The other copy that exists independently is essential and thus might be functioning as a general chaperone. Several groups have worked to unravel the functional diversity of these mysterious molecules employing structural, immunochemical, cell-biological, computational and genetic tools. We review the current understanding on the mycobacterial chaperonins and the new paradigms that have arisen.
Materials horizons, 2023
With the increased prevalence of antibiotic-resistant infections, there is an urgent need to deve... more With the increased prevalence of antibiotic-resistant infections, there is an urgent need to develop novel antibacterial materials. In addition, gaining a complete understanding of the structural features that impart activity toward target microorganisms is essential to enable materials optimisation. Here we have reported a rational design to fabricate antibacterial supramolecular nanoparticles with variable shape, size and cationic group density, by exploiting noncovalent interactions between a shape determining template amphiphile and a cationic amphiphile to introduce charge on the nanoparticle surface. We have shown that the monomeric cationic amphiphile alone showed poor antibacterial activity, whereas nanostructures formed by co-assembling the complementary units showed significantly enhanced antibacterial efficiency. Further, the systematic variation of several structural parameters such as shape, spacing between the cationic groups and size of these nanostructures allowed us to elicit the role of each parameter on the overall antibacterial properties. Finally, we investigated the origin of the differing antibacterial activity of these nanoparticles having different shape and size but with the same molecular composition, by comparing the thermodynamic parameters of their binding interactions with a bacterial membrane mimic.
Springer eBooks, 2017
Antibiotics are the chemical or biochemical moieties that specifically and effectively inhibit th... more Antibiotics are the chemical or biochemical moieties that specifically and effectively inhibit the growth of a pathogen but not the host organism and thus are employed in the treatment of the infection by the pathogen. However, the survival pressure in the presence of antimicrobial agents forces a minor fraction of the bacterial population to evolve mechanisms that evade the inhibitory effects of the administered antibiological agent, thereby emerging as a drug-resistant variety and consequently challenging the treatment regime. Additionally, the emergence of multidrug-resistant (MDR) variants of the pathogens that are capable of resisting several structurally dissimilar drugs is becoming very common and resulting in the infections that are difficult or impossible to treat. To counter the vast array of chemically and structurally dissimilar antibiotics within their lifestyle boundaries, different bacteria have developed different antibiotic-and pathogen-specific resistance mechanisms. Although distinct and involving several molecular events, these mechanisms can be broadly classified into two modes, the intrinsic and the acquired modes of resistance, which are further classified into subclasses. This chapter reviews recent advances and current understanding of the molecular details of these mechanisms.
Mycobacterial chaperonins in cellular proteostasis: Evidence for chaperone function of Cpn60.1 and Cpn60.2‐mediated protein folding
Molecular Microbiology
Mycobacterium tuberculosis encodes two chaperonin proteins, MtbCpn60.1 and MtbCpn60.2, that share... more Mycobacterium tuberculosis encodes two chaperonin proteins, MtbCpn60.1 and MtbCpn60.2, that share substantial sequence similarity with the Escherichia coli chaperonin, GroEL. However, unlike GroEL, MtbCpn60.1 and MtbCpn60.2 purify as lower‐order oligomers. Previous studies have shown that MtbCpn60.2 can functionally replace GroEL in E. coli, while the function of MtbCpn60.1 remained an enigma. Here, we demonstrate the molecular chaperone function of MtbCpn60.1 and MtbCpn60.2, by probing their ability to assist the folding of obligate chaperonin clients, DapA, FtsE and MetK, in an E. coli strain depleted of endogenous GroEL. We show that both MtbCpn60.1 and MtbCpn60.2 support cell survival and cell division by assisting the folding of DapA and FtsE, but only MtbCpn60.2 completely rescues GroEL‐depleted E. coli cells. We also show that, unlike MtbCpn60.2, MtbCpn60.1 has limited ability to support cell growth and proliferation and assist the folding of MetK. Our findings suggest that t...
Frontiers in Pharmacology
Materials Horizons
Supramolecular cationic nanomaterials of diverse nanostructure prepared by templated assembly. Si... more Supramolecular cationic nanomaterials of diverse nanostructure prepared by templated assembly. Size, shape and cationic group density of the nanomaterials play an important role in antibacterial activity.
Role of Cytoskeletal Protein, Actin in Various Diseases
Dietary Phytochemicals, 2021
Cytoskeletal proteins, which are unique to eukaryotic cells, form a three-dimensional niche filli... more Cytoskeletal proteins, which are unique to eukaryotic cells, form a three-dimensional niche filling the cytoplasm. It is quite essential for a myriad of cellular processes in higher eukaryotes such as cell movement, stability, and cell to cell interaction. There are primarily three major types of cytoskeletal protein, viz microfilaments/actin filaments, microtubules, and intermediate filaments. The polymerization dynamics of these three proteins are in turn regulated by several other accessory proteins depending upon the functional requirement of the cells. These polymerization dynamics of the protein are also responsible for cellular signaling processes that control the cytokine release during various immune responses against foreign particles. It has been widely known that any aberration that occurs during the polymerization dynamics of these three proteins may be responsible for several diseases. These diseases range from various types of cancer, polycystic ovary syndrome, neuropathological disorders, liver cirrhosis, pulmonary fibrosis, and blistering skin diseases. Many microorganisms that infect specialized cell types have been shown to be highly dependent on host cytoskeletal elements.
Drug Resistance in Bacteria, Fungi, Malaria, and Cancer, 2017
Antibiotics are the chemical or biochemical moieties that specifically and effectively inhibit th... more Antibiotics are the chemical or biochemical moieties that specifically and effectively inhibit the growth of a pathogen but not the host organism and thus are employed in the treatment of the infection by the pathogen. However, the survival pressure in the presence of antimicrobial agents forces a minor fraction of the bacterial population to evolve mechanisms that evade the inhibitory effects of the administered antibiological agent, thereby emerging as a drug-resistant variety and consequently challenging the treatment regime. Additionally, the emergence of multidrug-resistant (MDR) variants of the pathogens that are capable of resisting several structurally dissimilar drugs is becoming very common and resulting in the infections that are difficult or impossible to treat. To counter the vast array of chemically and structurally dissimilar antibiotics within their lifestyle boundaries, different bacteria have developed different antibiotic-and pathogen-specific resistance mechanisms. Although distinct and involving several molecular events, these mechanisms can be broadly classified into two modes, the intrinsic and the acquired modes of resistance, which are further classified into subclasses. This chapter reviews recent advances and current understanding of the molecular details of these mechanisms.
Prokaryotic Multiple Chaperonins: The Mediators of Functional and Evolutionary Diversity
Prokaryotic Chaperonins, 2017
Chaperonins are a class of molecular chaperones that form large multimeric assemblies for encapsu... more Chaperonins are a class of molecular chaperones that form large multimeric assemblies for encapsulation of substrate proteins. Surprisingly, 30% of newly sequenced bacterial genomes encode multiple copies of the chaperonins. The distribution of these multiple copies appears to follow a phylum-specific pattern. Functional and structural studies on several of these chaperonins have delineated how these extra chaperonins evolved functional diversity and contributed towards the biological adaptation of the hosting organisms. Since several of these bacteria are either pathogenic or economically important, and the chaperonins regulate the pathogenic processes in these organisms, it is important to understand their biology. This chapter is aimed to act as a primer for the subsequent chapters that describe different examples of multiple chaperonins and the plethora of their functional diversity.
Functional Diversity in Mycobacterial Chaperonins: The Generalists and the Specialists
Prokaryotic Chaperonins, 2017
Chaperonins are a class of molecular chaperones that form cylindrical assemblies and for sequeste... more Chaperonins are a class of molecular chaperones that form cylindrical assemblies and for sequestering the non-native protein and thereby assisting their folding. Genomic annotation studies have identified multiple copies of chaperonin genes in about 30% of the bacteria. Mycobacterium tuberculosis was the first organism where two copies were observed, and similarly other mycobacteria bear two and rarely three copies. Owing to the pathogenic lifestyle, the chaperonins of mycobacteria have been demonstrated to be secretory and possess antigenic properties. Furthermore, biochemical and structural studies have demonstrated that these chaperonins are unusual. One of the chaperonins that exists in operonic arrangement with the co-chaperonin gene has been shown to be required in several pathogenic stages of the bacteria. The other copy that exists independently is essential and thus might be functioning as a general chaperone. Several groups have worked to unravel the functional diversity of these mysterious molecules employing structural, immunochemical, cell-biological, computational and genetic tools. We review the current understanding on the mycobacterial chaperonins and the new paradigms that have arisen.
npj Biofilms and Microbiomes, 2017
PrkC is a conserved Ser/Thr protein kinase encoded in Bacillus anthracis genome. PrkC is shown to... more PrkC is a conserved Ser/Thr protein kinase encoded in Bacillus anthracis genome. PrkC is shown to be important for B. anthracis pathogenesis, but little is known about its other functions and phosphorylated substrates. Systemic analyses indicate the compelling role of PrkC in phosphorylating multiple substrates, including the essential chaperone GroEL. Through mass spectrometry, we identified that PrkC phosphorylates GroEL on six threonine residues that are distributed in three canonical regions. Phosphorylation facilitates the oligomerization of GroEL to the physiologically active tetradecameric state and increases its affinity toward the co-chaperone GroES. Deletion of prkC in B. anthracis abrogates its ability to form biofilm. Overexpression of native GroEL recovers the biofilm-forming ability of prkC deletion strain. Similar overexpression of GroEL phosphorylation site mutants (Thr to Ala) does not augment biofilm formation. Further analyses indicate the phosphorylation of GroEL...
Frontiers in Molecular Biosciences, 2021
The ability of chaperonins to buffer mutations that affect protein folding pathways suggests that... more The ability of chaperonins to buffer mutations that affect protein folding pathways suggests that their abundance should be evolutionarily advantageous. Here, we investigate the effect of chaperonin overproduction on cellular fitness inEscherichia coli. We demonstrate that chaperonin abundance confers 1) an ability to tolerate higher temperatures, 2) improved cellular fitness, and 3) enhanced folding of metabolic enzymes, which is expected to lead to enhanced energy harvesting potential.
Drug Resistance in Malaria
Drug Resistance in Bacteria, Fungi, Malaria, and Cancer, 2017
The ability of chaperonins to buffer mutations that affect protein folding pathways suggests that... more The ability of chaperonins to buffer mutations that affect protein folding pathways suggests that their abundance should be evolutionarily advantageous. Here, we investigate the effect of chaperonin overproduction on cellular fitness in Escherichia coli. We demonstrate that chaperonin abundance confers (a) an ability to tolerate higher temperatures, (b) improved cellular fitness and (c) enhanced folding of metabolic enzymes, which is expected to lead to enhanced energy harvesting potential.
Journal of bacteriology, Jan 9, 2015
Intracellular protein folding is mediated by molecular chaperones, the best studied among which a... more Intracellular protein folding is mediated by molecular chaperones, the best studied among which are the chaperonins, GroEL and GroES. Conformational changes and allosteric transitions between different metastable states are hallmarks of the chaperonin mechanism. These conformational transitions between three structural domains of GroEL are anchored at two hinges. Although hinges are known to be critical for mediating the communication between different domains of GroEL, the relative importance of hinges on GroEL oligomeric assembly, ATPase activity, conformational changes and functional activity are not fully characterized. We have exploited the inability of M. tuberculosis GroEL2 to functionally complement E. coli groEL mutant to address the importance of hinge residues in GroEL mechanism. Various chimeras of M. tuberculosis GroEL2 and E. coli GroEL allowed us to understand the role of hinges, and dissect the consequences of oligomerization and substrate binding capability on confo...
Patterns in Protein Sequences
In vivo Complementation Studies on Mycobacterium tuberculosis groEL Homologues cpn60.1 and cpn60.2
Cloning, Expression and Immunogenic Characterization of r32kDa Protein of BCG as a Vaccine Candidate and the Influence of INF-γ and TNF-α Genotypes in Children
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Papers by Santosh C M Kumar