Sukhendu Mandal

Bio: Sukhendu Mandal is an academic researcher from University of Calcutta. The author has contributed to research in topics: Medicine & RNA polymerase. The author has an hindex of 20, co-authored 92 publications receiving 1132 citations. Previous affiliations of Sukhendu Mandal include Bose Institute & Rutgers University.

Transcription inhibition by the depsipeptide antibiotic salinamide A

Abstract: We report that bacterial RNA polymerase (RNAP) is the functional cellular target of the depsipeptide antibiotic salinamide A (Sal), and we report that Sal inhibits RNAP through a novel binding site and mechanism. We show that Sal inhibits RNA synthesis in cells and that mutations that confer Sal-resistance map to RNAP genes. We show that Sal interacts with the RNAP active-center ‘bridge-helix cap’ comprising the ‘bridge-helix N-terminal hinge’, ‘F-loop’, and ‘link region’. We show that Sal inhibits nucleotide addition in transcription initiation and elongation. We present a crystal structure that defines interactions between Sal and RNAP and effects of Sal on RNAP conformation. We propose that Sal functions by binding to the RNAP bridge-helix cap and preventing conformational changes of the bridge-helix N-terminal hinge necessary for nucleotide addition. The results provide a target for antibacterial drug discovery and a reagent to probe conformation and function of the bridge-helix N-terminal hinge. DOI: http://dx.doi.org/10.7554/eLife.02451.001

A new selective chromogenic and turn-on fluorogenic probe for copper(II) in solution and vero cells: recognition of sulphide by [CuL]

Abstract: A new coumarin-appended thioimidazole-linked imine conjugate, viz. L has been synthesized and characterized. L has been found to recognize Cu2+ selectively among a wide range of biologically relevant metal ions. The chemosensing behavior of L has been demonstrated through fluorescence, absorption, visual fluorescence color changes, ESI-MS and 1H NMR titrations. The chemosensor L showed selectivity toward Cu2+ by switch on fluorescence among the 18 metal ions studied with a detection limit of 1.53 μM. The complex formed between L and Cu2+ is found to be 1 : 1 on the basis of absorption and fluorescence titrations and was confirmed by ESI-MS. DFT and TDDFT calculations were performed in order to demonstrate the structure of L and [CuL] and the electronic properties of chemosensor L and its copper complex. This highly fluorescent [CuL] complex has been used to recognize sulphide selectively among the other allied anions. Microstructural features of L and its Cu2+ complex have been investigated by SEM imaging (scanning electron microscopy). The biological applications of L were evaluated in Vero cells and it was found to exhibit low cytotoxicity and good membrane permeability for the detection of Cu2+.

Tetrathiobacter kashmirensis gen. nov., sp. nov., a novel mesophilic, neutrophilic, tetrathionate-oxidizing, facultatively chemolithotrophic betaproteobacterium isolated from soil from a temperate orchard in Jammu and Kashmir, India

Abstract: Twelve chemolithotrophic strains were isolated from temperate orchard soil on reduced sulfur compounds as energy and electron sources and characterized on the basis of their physiological properties and ability to oxidize various reduced sulfur compounds. The new isolates could oxidize tetrathionate as well as thiosulfate, and oxidation of the latter involved conversion of thiosulfate to tetrathionate followed by its accumulation and eventual oxidation to sulfate, manifested in the production of acid. The mesophilic, neutrophilic, Gram-negative and coccoid bacteria had a respiratory metabolism. Physiologically and biochemically, all the strains were more or less similar, differing only in their growth rates and ability to utilize a few carbon compounds as single heterotrophic substrates. 16S rRNA gene sequence analysis was performed with five representative strains, which revealed a high degree of similarity (⩾99 %) among them and placed the cluster in the ‘Betaproteobacteria’. The strains showed low levels (93·5–95·3 %) of 16S rRNA gene sequence similarity to Pigmentiphaga kullae, Achromobacter xylosoxidans, Pelistega europaea and species belonging to the genera Alcaligenes, Taylorella and Bordetella. The taxonomic coherence of the new isolates was confirmed by DNA–DNA hybridization. On the basis of their uniformly low 16S rRNA gene sequence similarities to species of all the closest genera, unique fatty acid profile, distinct G+C content (54–55·2 mol%) and phenotypic characteristics that include efficient chemolithotrophic utilization of tetrathionate, the organisms were classified in a new genus, Tetrathiobacter gen. nov. In the absence of any significant discriminatory phenotypic or genotypic characteristics, all the new isolates are considered to constitute a single species, for which the name Tetrathiobacter kashmirensis sp. nov. (type strain WT001T=LMG 22695T=MTCC 7002T) is proposed.

A new antibiotic kills pathogens without detectable resistance

Abstract: Antibiotic resistance is spreading faster than the introduction of new compounds into clinical practice, causing a public health crisis. Most antibiotics were produced by screening soil microorganisms, but this limited resource of cultivable bacteria was overmined by the 1960s. Synthetic approaches to produce antibiotics have been unable to replace this platform. Uncultured bacteria make up approximately 99% of all species in external environments, and are an untapped source of new antibiotics. We developed several methods to grow uncultured organisms by cultivation in situ or by using specific growth factors. Here we report a new antibiotic that we term teixobactin, discovered in a screen of uncultured bacteria. Teixobactin inhibits cell wall synthesis by binding to a highly conserved motif of lipid II (precursor of peptidoglycan) and lipid III (precursor of cell wall teichoic acid). We did not obtain any mutants of Staphylococcus aureus or Mycobacterium tuberculosis resistant to teixobactin. The properties of this compound suggest a path towards developing antibiotics that are likely to avoid development of resistance.

Excited-state intramolecular proton-transfer (ESIPT) based fluorescence sensors and imaging agents

Abstract: In this review we will explore recent advances in the design and application of excited-state intramolecular proton-transfer (ESIPT) based fluorescent probes. Fluorescence based sensors and imaging agents (probes) are important in biology, physiology, pharmacology, and environmental science for the selective detection of biologically and/or environmentally important species. The development of ESIPT-based fluorescence probes is particularly attractive due to their unique properties, which include a large Stokes shift, environmental sensitivity and potential for ratiometric sensing.

Coordination chemistry of bacterial metal transport and sensing.

Abstract: The transition or d-block metal ions manganese, iron, cobalt, nickel, copper, zinc, and to a more specialized degree, molybdenum, tungsten and vanadium, have been shown to be important for biological systems. These metal ions are ubiquitously found in nature, nearly exclusively as constituents of proteins.1 The unique properties of metal ions have been exploited by nature to perform a wide range of tasks. These include roles as structural components of biomolecules, as signaling molecules, as catalytic cofactors in reversible oxidation-reduction and hydrolytic reactions, and in structural rearrangements of organic molecules and electron transfer chemistry.1 Indeed, metal ions play critical roles in the cell that cannot be performed by any other entity, and are therefore essential for all of life. However, an individual metal ion is capable of performing only one or a few of these functions, but certainly not all; as a result, nature has evolved mechanisms to effectively distinguish one metal from another. The coordination chemistry of metal ion-protein complexes is fundamental to this biological discrimination, and is largely the focus of this review. 1.1. Metal Ion Homeostasis Extensive regulatory and protein-coding machinery is devoted to maintaining the “homeostasis” of biologically required metal ions and underscores the essentiality of this process for cell viability. Homeostasis is defined as the maintenance of an optimal bioavailable concentration, mediated by the balancing of metal uptake and intracellular trafficking with efflux/storage processes so that the needs of the cell for that metal ion is met, i.e., the “right” metal is inserted into the “right” macromolecule at the appropriate time.2,3 Just as a scarcity of a particular metal ion induces a stress response that can lead to reprogramming of cellular metabolism to minimize the consequences of depletion of a particular metal ion, e.g., zinc in ribosome biogenesis4 or Cu vs. Fe in photosynthesis by Synechocystis,5 too much of the same metal ion can also be toxic to a cell or organism. Metal homeostasis is governed by the formation of specific protein-metal coordination complexes used to effect uptake, efflux, intracellular trafficking within compartments, and storage (Figure 1). How metal ions move to and from their target destinations in the active site of a metalloenzyme or as a structural component of biomolecules also contributes to intracellular metal homeostasis (Figure 1). Metal transporters move metal ions or small molecule-metal chelates across otherwise impermeable barriers in a directional fashion, and most of these are integral membrane proteins embedded in the inner or plasma membrane (Figure 1). Specialized protein chelators designated metallochaperones traffic metals within a particular cellular compartment, e.g., the periplasm or the cytosol, and function to “hold” the metal in such a way that it can be readily transferred to an appropriate acceptor protein. This intermolecular transfer is known or is projected to occur through transiently formed, specific protein-protein complexes that mediate coordinated intermolecular metal ligand exchange. Metallochaperones have been described for copper,6-9 nickel10 and iron-sulfur protein biogenesis,11 and recent work suggests that the periplasmic Zn(II) binding protein, YodA, has characteristics consistent with a role as a zinc chaperone in E. coli (Figure 1).12 Salient features of these chaperones are discussed in more detail in the context of acquisition and efflux of individual metal ions (Section 2). Finally, specialized transcriptional regulatory proteins, termed metalloregulatory or metal sensor proteins, control the expression of genes encoding these proteins that establish metal homeostasis in response to either metal deprivation or overload (Section 3). Figure 1 Schematic metal homeostasis models for iron, zinc and manganese, copper, nickel and cobalt, shown specifically in gram-negative bacteria. Homeostasis of molybdate and tungstate oxyanions are not shown, due primarily to a lack of knowledge of these systems, ... A hypothesis that emerges is that in order to effect the cellular homeostasis of a particular metal ion, each component of the homeostasis machinery (Figure 1) must be selective for that metal ion under the prevailing conditions, to the exclusion of all others.13 Furthermore, individual systems must be “tuned” such that the affinity or sensitivity of each component is well-matched, either to coordinate gene expression by pairs of metal sensor proteins that coordinately shut off uptake and up-regulate efflux or detoxification systems, or to facilitate vectorial transport from metal donor to metal acceptor target protein in a metal trafficking pathway in the cell (Figure 1).14-16