Biology subjects

Mandal, S.

Publications and source records attributed to Mandal, S..

6 recordsLinked to original sources

bioRxiv2018

Structural basis of ECF-sigma-factor-dependent transcription initiation.

Extracytoplasmic (ECF) {sigma} factors, the largest class of alternative {sigma} factors, are related to primary {sigma} factors, but have simpler structures, comprising only two of the six conserved functional modules present in primary {sigma} factors: region 2 ({sigma}R2) and region 4 ({sigma}R4). Here, we report crystal structures of transcription initiation complexes containing Mycobacterium tuberculosis RNA polymerase (RNAP), M. tuberculosis ECF {sigma} factor {sigma}L, and promoter DNA. The structures show that {sigma}R2 and {sigma}R4 of the ECF {sigma} factor occupy the same sites on RNAP as in primary {sigma} factors, show that the connector between {sigma}R2 and {sigma}R4 of the ECF {sigma} factor--although unrelated in sequence--follows the same path through RNAP as in primary {sigma} factors, and show that the ECF {sigma} factor uses the same strategy to bind and unwind promoter DNA as primary {sigma} factors. The results define protein-protein and protein-DNA interactions involved in ECF-{sigma}-factor-dependent transcription initiation.

molecular biology↗

bioRxiv2018

Candidate Gene Networks for Acylsugar Metabolism and Plant Defense in Wild Tomato Solanum pennellii

Many plants in the Solanaceae family secrete acylsugars, which are branched-chain and straight-chain fatty acids esterified to glucose or sucrose. These compounds have important roles in plant defense and potential commercial applications. However, several acylsugar metabolic genes remain unidentified, and little is known about regulation of this pathway. We used comparative transcriptomic analysis between low- and high-acylsugar-producing accessions of Solanum pennellii and found that expression levels of most acylsugar metabolic genes, including known acylsucrose biosynthetic genes and novel candidate genes (putatively encoding a ketoacyl-ACP synthase IV/II-like enzyme, peroxisomal acyl-activating enzymes, ABC transporters, and central carbon metabolic enzymes), were positively correlated with acylsugar accumulation, except two acylglucose biosynthetic genes. Genes putatively encoding oxylipin metabolic proteins, subtilisin-like proteases, and other antimicrobial defense proteins were upregulated in low-acylsugar-producing accessions, possibly to compensate for diminished defense activities of acylsugars. Gene co-expression network analysis clustered most differentially expressed genes into two separate modules and identified genetic networks associated with acylsugar production and plant defense. Transcriptome analysis after inhibition of biosynthesis of branched-chain amino acids (precursors to branched-chain fatty acids) further supported the coordinated regulation of most acylsugar candidate genes and identified three putative AP2-family transcription factor genes that form a strong co-expression network with many acylsugar metabolic genes.

plant biology↗

bioRxiv2018

Ontogeny of familiarity with foraging landscape and foraging abilities in the tropical social wasp Ropalidia marginata

Possessing spatial familiarity with their foraging landscape may enable animals to reduce foraging effort without compromising on foraging benefits. For animals inhabiting feature-rich landscapes, spatial familiarity can increase with increasing age/experience. To check whether this holds for individually foraging tropical social wasp Ropalidia marginata, we recorded the number and duration of all foraging trips, the identity of the materials brought to the nest (building material, water or food) and the directions of outbound and inbound flights (respective to their nests) of known-age foragers from three natural colonies, each for three consecutive days. The average trip duration and time spent daily in foraging increased rapidly until about first four weeks of their life, during which they rarely brought food to their nest, although many of them brought building material and water. Thereafter, their average as well as per day duration of foraging trip started decreasing gradually. Nevertheless, their foraging efficiency and success for food kept on increasing monotonically with age. These results suggest that older wasps were more efficient in foraging despite spending less time doing so. With increasing age, wasps developed individual preferences for the direction of their outbound flights, increased directionality of their inbound trips as well as the angular difference between their outbound and subsequent inbound flights, indicating development of spatial memory. We conclude that wasps acquire familiarity with their foraging landscape in their initial foraging phase and gradually develop robust memory for rewarding sites and routes to those sites, which enables them to increase their foraging capabilities.\n\nSUMMARY STATEMENTContrary to insects inhabiting less-featured landscapes, tropical social wasps invest weeks to get familiar with foraging landscapes during their early foraging lives. This eventually enables them to increase foraging gain with reduced effort.

animal behavior and cognition↗

bioRxiv2017

Structural basis of transcription inhibition by fidaxomicin (lipiarmycin A3)

Fidaxomicin is an antibacterial drug in clinical use in treatment of Clostridium difficile diarrhea1-2. The active pharmaceutical ingredient of fidaxomicin, lipiarmycin A3 (Lpm)1-4, is a macrocyclic antibiotic with bactericidal activity against Gram-positive bacteria and efflux-deficient strains of Gram-negative bacteria1-2, 5. Lpm functions by inhibiting bacterial RNA polymerase (RNAP)6-8. Lpm exhibits no cross-resistance with the classic RNAP inhibitor rifampin (Rif)7, 9 and inhibits transcription initiation at an earlier step than Rif8-11, suggesting that the binding site and mechanism of Lpm differ from those of Rif. Efforts spanning a decade to obtain a crystal structure of RNAP in complex with Lpm have been unsuccessful. Here, we report a cryo-EM12-13 structure of Mycobacterium tuberculosis RNAP holoenzyme in complex with Lpm at 3.5 [A] resolution. The structure shows that Lpm binds at the base of the RNAP \"clamp,\" interacting with the RNAP switch region and the RNAP RNA exit channel. The binding site on RNAP for Lpm does not overlap the binding sites for other RNAP inhibitors, accounting for the absence of cross-resistance of Lpm with other RNAP inhibitors. The structure exhibits an open conformation of the RNAP clamp, with the RNAP clamp swung outward by ~17{degrees} relative to its position in catalytically competent RNAP-promoter transcription initiation complexes, suggesting that Lpm traps an open-clamp conformational state. Single-molecule fluorescence resonance energy transfer14 experiments confirm that Lpm traps an open-clamp conformational state and define effects of Lpm on clamp opening and closing dynamics. We propose that Lpm inhibits transcription initiation by trapping an open-clamp conformational state, thereby preventing simultaneous engagement of transcription initiation factor {sigma} regions 2 and 4 with promoter -10 and -35 elements. The results provide information essential to understanding the mode of action of Lpm, account for structure-activity relationships of known Lpm analogs, and suggest modifications to Lpm that could yield new, improved Lpm analogs.

molecular biology↗

bioRxiv2017

Distribution of Sigma factors delineates segregation of virulent and avirulent Mycobacterium

Sigma factors, in combination with RNA polymerase and several transcription factors play specific role in expression of housekeeping as well as various stress responsive genes in mycobacterial species. The genus Mycobacterium includes a wide range of species under major pathogens, opportunists and non-pathogens. The number and combination of sigma factors is extremely diversified among Mycobacterium. We have performed comparative genome analysis among 40 different species of Mycobacterium whose whole genome sequence is available, in order to identify the distribution of sigma factors. The study illustrate that SigC, SigD, SigG, SigH, SigK and SigI are dominant among the true pathogens. Moreover, 16S rDNA based phylogenetic analyses distinctly differentiate the slow growing Mycobacterium from the fast growers, and clusters the true pathogens from the opportunists and non-pathogens. While evaluating the similarity coefficient upon the allotment of sigma factors of different Mycobacterium species through UPGMA dendrogram analysis, it is apparent that the true pathogens are grouped separately following the similar trend observed from evolutionary approach. Sigma factors playing dominant role in pathogenicity are found stable in nature with high aliphatic index thereby remain flexible at a wide range of temperature. The comparative distribution of six well known virulence factors of Mycobacterium - PhoP, PcaA, FbpA, Mce1B, KatG and PE_PGRS and various sigma factors justify the allotment pattern of mycobacterial sigma factors among pathogenic species. The pathogenicity responsible sigma factors elicit close resemblance with few notable characters of the known virulence factors. Thus the analysis renders that the distribution of sigma factors of different species of Mycobacterium can be a potential tool to predict the pathogenicity index of this genus.

microbiology↗

bioRxiv2017

Structural basis of Mycobacterium tuberculosis transcription and transcription inhibition

One Sentence SummaryStructures of Mycobacterium tuberculosis RNA polymerase reveal taxon-specific properties and binding sites of known and new antituberculosis agents\n\nAbstractMycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, which kills 1.8 million annually. Mtb RNA polymerase (RNAP) is the target of the first-line antituberculosis drug rifampin (Rif). We report crystal structures of Mtb RNAP, alone and in complex with Rif. The results identify an Mtb-specific structural module of Mtb RNAP and establish that Rif functions by a steric-occlusion mechanism that prevents extension of RNA. We also report novel non-Rif-related compounds-N-aroyl-N-aryl-phenylalaninamides (AAPs)-that potently and selectively inhibit Mtb RNAP and Mtb growth, and we report crystal structures of Mtb RNAP in complex with AAPs. AAPs bind to a different site on Mtb RNAP than Rif, exhibit no cross-resistance with Rif, function additively when co-administered with Rif, and suppress resistance emergence when co-administered with Rif.

molecular biology↗