Biology subjects

Biswas, B.

Publications and source records attributed to Biswas, B..

14 recordsLinked to original sources

bioRxiv2025

Evolutionary constraints in host shifts: limited adaptation of Plutella xylostella to cardenolide-defended Erysimum cheiranthoides

O_LIPlants and herbivorous insects are engaged in long-term coevolutionary arms races, where gains in novel plant defences and corresponding adaptations in herbivores may drive evolutionary change. One such recent innovation is the gain of cardenolide toxins in the Brassicaceae genus Erysimum, which resulted in the effective deterrence of most herbivores by these plants. Nonetheless, some herbivores continue to attack Erysimum, likely by tolerating cardenolide defences through general detoxification mechanisms that may serve as evolutionary stepping-stones for more specialized resistance. C_LIO_LIWe investigated the interaction between diamondback moth (DBM, Plutella xylostella) and its occasional host plant E. cheiranthoides, by first screening the standing variation in DBM performance, and second by experimentally evolving DBM populations for increased performance on Erysimum. Despite considerable variation among wild DBM populations, larvae consistently avoided Erysimum leaves for feeding, and when constrained to Erysimum, they exhibited reduced growth rate, survival, and lower adult size compared to individuals feeding on control broccoli plants. C_LIO_LISurprisingly, cardenolides could only partly explain the reduced performance of DBM on Erysimum, and experimental evolution failed to improve overall performance. Instead, phenotypes of evolved lines converged on what appears to be a pre-existing, highly plastic phenotype found among wild DBM ancestors and which is characterized by rapid development and high weight gain on control plants, but slow development and low weight gain on Erysimum. C_LIO_LIAlthough DBM failed to evolve improved performance on Erysimum, our results demonstrate that its existing genetic variation and phenotypic plasticity are evidently sufficient to support long-term development on Erysimum, thereby fulfilling a key condition for the future evolution of specialized adaptations. C_LI

evolutionary biology↗

bioRxiv2025

Dissecting the Role of Flagellar Subunits in Clostridioides difficile Mucosal Colonization

Clostridioides difficile is a common cause of acute gastrointestinal (GI) inflammation in mammals, which can have detrimental effects on host health. C. difficile associated disease (CDAD) requires the secretion of high-molecular weight toxins after colonization of the GI tract. The molecular mechanisms of GI colonization by C. difficile, include potential interactions with host cells and the mucus layer formed from secreted mucin glycoproteins. C. difficile associates with the mucus layer in vivo and will associate with both epithelial cells and mucosal surfaces in vitro. Previously, we found a substantial defect in binding to mucosal surfaces for mutants of the major flagellar subunit, fliC, while mutation of the major subunit of type IV pili, pilA1, showed increased adhesion. To elucidate the mechanisms by which C. difficile interacts with ex vivo mucosal surfaces, we have measured swimming motility, mucosal adhesion and levels of flagellation by transmission electron microscopy for mutants of flagellar and T4P genes in C. difficile R20291. We discovered that the pilA1 mutant showed increased flagellation, while decreases in flagellation were found for fliC, fliD, and flg-OFF (a phase-locked mutant with low transcription of the F3 flagellar operon) which were associated with both low swimming motility and low adhesion to mucosal surfaces. However, the reversed flg-ON mutant showed increased flagellation without a significant increase in adhesion. We also found that the fliC mutant was defective in binding to mucus-secreting HT-29 MTX cells, but not HT-29 cells. These results imply that at least two molecular pathways contribute to C. difficile mucosal adhesion. In addition to their direct roles encoding T4P and flagellar subunits, pilA1 and fliC may contribute to regulating other factors relevant to mucosal adhesion.

microbiology↗

bioRxiv2024

Multiomics plasticity in seed traits of pan-genome wheat cultivars

The molecular basis of cultivar-level variations in polyploid wheat that enables environmental adaptation while maintaining yield and quality in polyploid wheat remains poorly understood. We conducted a detailed phenotypic assessment and multiomics analysis of nine pan-genome polyploid wheat cultivars grown under control and drought conditions. We aimed to investigate the subgenome-level variations, cultivar differences and biochemical mechanisms affecting plant fitness under moderate drought stress. Intrinsic water use efficiency, grain yield, and grain protein content and quality differed among cultivars, supporting the plasticity of drought stress responses. Biased proteome and metabolome abundance changes in response to moderate drought stress during the vegetative stage indicate different strategies for the utilization of homeologous protein isoforms assigned to the A, B, and D subgenomes. Drought effects were detected at the protein level, but significant changes were observed in central carbon pathway metabolites and micronutrient profiles. The subgenomic localization of seed storage proteins highlight differences in nutrient reservoir accumulation and emphasizes the enhanced role of S-rich prolamins in the stress response. Subgenomic variations define cultivar phenotypes by producing molecules that accumulate and enable the underlying trade-offs between environmental adaptation and yield- or quality-related traits. These variations can be used to select crops with increased stress resistance without compromising yield.

plant biology↗

bioRxiv2024

Interferon-Induced PARP14-Mediated ADP-Ribosylation in p62 Bodies Requires an Active Ubiquitin-Proteasome System

Biomolecular condensates are cellular compartments without enveloping membranes, enabling them to dynamically adjust their composition in response to environmental changes through post-translational modifications. A recent study has revealed that interferon-induced ADP-ribosylation (ADPr), which can be reversed by a SARS-CoV-2-encoded hydrolase, is enriched within a condensate. However, the identity of the condensate and responsible host ADP-ribosyltransferase remain elusive. Here, we demonstrate that interferon induces ADPr through transcriptional activation of PARP14, requiring both its physical presence and catalytic activity for condensate formation. Interferon-induced ADPr colocalizes with PARP14, and these PARP14/ADPr condensates contain key components of p62 bodies--including the selective autophagy receptor p62 and its binding partner NBR1, along with K48-linked and K63-linked polyubiquitin chains--but lack the autophagosome marker LC3B. Knockdown of p62 disrupts the formation of these ADPr condensates. Importantly, these structures are unaffected by autophagy inhibition but depend on both ubiquitin activation and proteasome activity. Taken together, these findings demonstrate that interferon triggers PARP14-mediated ADP-ribosylation in p62 bodies, which requires an active ubiquitin-proteasome system.

cell biology↗

bioRxiv2024

Socio-ecological context modulates significance of territorial contest competition in Drosophila prolongata

The intensity and direction of sexual selection is intricately linked to the social and ecological context. Both operational sex ratios (OSRs) and population densities can affect the ability of males to monopolize resources and mates, and thus the form and intensity of sexual selection on them. Here, we studied how the mating system of the promiscuous and strongly sexually dimorphic fruit fly Drosophila prolongata responds to changes in the OSR and population density. We recorded groups of flies over five days and quantified territory occupancy, mating success, and competitive fertilization success. Although sexual selection was stronger under male-biased than even OSRs but unrelated to density, realized selection on morphological traits was higher under even OSRs and increased with density. Larger and more territorial males achieved both higher mating success and competitive fertilization success, but only under even OSRs. Our combined results also support a shift in the mating system from territorial contest competition to scramble competition under male-biased OSRs and potentially at low density, where there was no clear contribution of the measured traits to reproductive success. Our study emphasizes the limitations of traditional selection metrics and the role of the socio-ecological context in predicting adaptation to a changing environment. SignificanceMating systems are complex and dynamic, adapting to ongoing ecological change. Studies often assume that changes in the socio-ecological context alter the intensity of sexual selection on traits indicating individual fitness, but our work on Drosophila prolongata challenges this view. By manipulating operational sex ratio and population density, and jointly investigating territorial behavior and both pre- and post-mating reproductive success over several days, we reveal the plastic mating strategies in this fly. This dynamism underscores the limitations of static classifications and the importance of studying selection across diverse socio-ecological contexts. This broader perspective advances our understanding of the tight connections between environmental change, population demographics, and the evolutionary process.

evolutionary biology↗

bioRxiv2024

Essential functions of Inositol hexakisphosphate (IP6) in Murine Leukemia Virus replication

We have investigated the function of inositol hexakisphosphate (IP6) and inositol pentakisphosphate (IP5) in the replication of murine leukemia virus (MLV). While IP6 is known to be critical for the life cycle of HIV-1, its significance in MLV remains unexplored. We find that IP6 is indeed important for MLV replication. It significantly enhances endogenous reverse transcription (ERT) in MLV. Additionally, a pelleting-based assay reveals that IP6 can stabilize MLV cores, thereby facilitating ERT. We find that IP5 and IP6 are packaged in MLV particles. However, unlike HIV-1, MLV depends upon the presence of IP6 and IP5 in target cells for successful infection. This IP6/5 requirement for infection is reflected in impaired reverse transcription observed in IP6/5-deficient cell lines. In summary, our findings demonstrate the importance of capsid stabilization by IP6/5 in the replication of diverse retroviruses; we suggest possible reasons for the differences from HIV-1 that we observed in MLV.

molecular biology↗

bioRxiv2023

Calcitriol impairs the secretion of IL-4 and IL-13 in Th2 cells via modulating the transcription factors Gata3 and Gfi1

Calcitriol, the bioactive form of vitamin D, exerts its biological functions by binding to its cognate receptor VDR. The indicators of the severity of allergies and asthma have been linked to low vitamin D levels. However, the role of calcitriol in regulating IL-4 and IL-13; two cytokines pivotal to allergic inflammation, remained unclear. Our study observed a decrease in IL-4 and IL-13 secretion in murine and human Th2 cells, treated with calcitriol. In murine Th2 cells, Gata3 expression was attenuated by calcitriol. However, the expression of the transcriptional repressor Gfi1, that prevents Th1 fate of activated CD4+ T cells, too was attenuated in the presence of calcitriol. Ectopic expression of either Gfi1 or VDR impaired the secretion of IL-13 in Th2 cells. Gfi1 significantly impaired Il13 promoter activation; which calcitriol failed to restore. Ecr, a conserved region between the two genes, which enhanced the transactivation of Il4 and Il13 promoters; is essential for calcitriol-mediated suppression of both the genes. In murine Th2 cells, VDR interacted with Gata3 but not Gfi1. Calcitriol augmented the recruitment of VDR to the Il13 promoter and Ecr regions. Gata3 recruitment was significantly impaired at Il13 and Ecr locus in the presence of calcitriol but increased at Il4 promoter. However, in the presence of calcitriol, the overall recruitment of Gfi1 remained unchanged at Il4 but increased at Il13 locus in Th2 cells. Together, our study clearly elucidates that calcitriol modulates VDR, Gata3, and Gfi1 to suppress IL-4 and IL-13 production in Th2 cells. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/569823v3_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@1557aaborg.highwire.dtl.DTLVardef@e8b1dcorg.highwire.dtl.DTLVardef@f505dcorg.highwire.dtl.DTLVardef@53b31c_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2023

Boronic acid derivative inhibits LexA mediated SOS response in Mycobacteria

Antimicrobial resistance (AMR) properties of several pathogens pose as one of the major global concerns demanding continuous innovation in order to be controlled. The bacterial "SOS" response, regulated by LexA and RecA, contributes to AMR through advantageous mutations. Therefore, targeting LexA/RecA system with a novel inhibitor could suppress "SOS" response and may reduce AMR. However, RecA presents a challenge as a therapeutic target due to its conservation across species, including humans. Concurrently, LexA, being absent in eukaryotes, can be potentially targeted, in part, due to its association with "SOS" response and developing AMR. Our studies combining bioinformatic, biochemical, biophysical, and cell-based assays present a unique inhibitor of mycobacterial "SOS" response wherein we show that the inhibitor interacts directly with the catalytic site residues of LexA of Mycobacterium tuberculosis (Mtb), consequently hindering its cleavage, resulting in suppression of "SOS" response. We observed important genes under the "SOS" regulon to be down-regulated in the presence of the inhibitor along with a consequent reduction in the rate of mutation frequency of mycobacterial cells. In essence, this study may facilitate further research on potential LexA inhibitors, reducing mutational rates and offering promise in mitigating AMR.

microbiology↗

bioRxiv2023

Flagellin is essential for initial attachment to mucosal surfaces by Clostridioides difficile

Mucins are glycoproteins which can be found in host cell membranes and as a gelatinous surface formed from secreted mucins. Mucosal surfaces in mammals form a barrier to invasive microbes, particularly bacteria, but are a point of attachment for others. Clostridioides difficile is anaerobic bacterium which colonizes the mammalian GI tract and is a common cause of acute GI inflammation leading to a variety of negative outcomes. Although C. difficile toxicity stems from secreted toxins, colonization is a prerequisite for C. difficile disease. While C. difficile is known to associate with the mucus layer and underlying epithelium, the mechanisms underlying these interactions that facilitate colonization are less well-understood. To understand the molecular mechanisms by which C. difficile interacts with mucins, we used ex vivo mucosal surfaces to test the ability of C. difficile to bind to mucins from different mammalian tissues. We found significant differences in C. difficile adhesion based upon the source of mucins, with highest levels of binding observed to mucins purified from the human colonic adenocarcinoma line LS174T and lowest levels of binding to porcine gastric mucin. We also observed that defects in adhesion by mutants deficient in flagella, but not type IV pili. These results imply that interactions between host mucins and C. difficile flagella facilitate the initial host attachment of C. difficile to host cells and secreted mucus.

microbiology↗

bioRxiv2022

Uncoupling from transcription protects polyadenylation site cleavage from inhibition by DNA damage

Pre-mRNA 3-end processing by cleavage and polyadenylation (CPA) is a nuclear process in which RNA polymerase II (Pol II) transcripts are cleaved at the polyadenylation site (PAS cleavage) before addition of a poly(A) tail. While PAS cleavage is usually coupled to transcription termination, for some pre-mRNAs it occurs post-transcriptionally, i.e. after pre-mRNA release from chromatin to nucleoplasm through a downstream co-transcriptional cleavage (CoTC) event. DNA-damaging agents such as ultraviolet-C (UV) irradiation trigger rapid shutdown of pre-mRNA 3-end processing. However, specific compensatory mechanisms exist to ensure efficient 3-end processing for some pre-mRNAs encoding proteins involved in the DNA damage response (DDR), such as the p53 tumor suppressor protein. Here, we show that PAS cleavage of the p53 pre-mRNA occurs in part post-transcriptionally, in a PCF11-independent manner, in the nucleoplasm, following a CoTC-type event. Upon UV-irradiation, cells with an engineered deletion of the p53 CoTC site exhibit impaired 3-end processing of the p53 pre-mRNA, decreased mRNA and protein levels of p53 and its transcriptional target, p21, and altered cell cycle progression. Finally, using a transcriptome-wide analysis of PAS cleavage, we identified additional-including DDR related-pre-mRNAs whose PAS cleavage is maintained in response to UV and occurs post-transcriptionally. These findings indicate that CoTC-type cleavage of pre-mRNAs, followed by PAS cleavage in the nucleoplasm, allows specific pre-mRNAs to escape 3-end processing inhibition in response to UV-induced DNA damage.

molecular biology↗

bioRxiv2021

Comparative genomics of Acinetobacter baumannii and therapeutic bacteriophages from a patient undergoing phage therapy

In 2016, a 68-year-old patient with a disseminated multi-drug resistant Acinetobacter baumannii infection was treated using lytic bacteriophages in one of the first modern human clinical uses of phage therapy in the United States. Due to the emergency nature of the treatment there was little time to thoroughly characterize the phages used in this intervention or the pathogen itself. Here we report the genomes of the nine phages used for treatment and three strains of A. baumannii isolated prior to and during treatment. The eight phages used in the initial treatment were found to be a group of closely related T4-like myophages; the ninth phage, AbTP3{Phi}1, was found to be an unrelated Fri1-like podophage. Analysis of 19 A. baumannii isolates collected before and during phage treatment showed that resistance to the T4-like phages appeared as early as two days following the start of treatment. Three A. baumannii strains (TP1, TP2 and TP3) collected before and during treatment were sequenced to closure, and all contained a 3.9 Mb chromosome of sequence type 570 with a KL116 capsule locus and identical 8.7 kb plasmids. Phage-insensitive mutants of A. baumannii strain TP1 were generated in vitro and the majority of identified mutations were located in the bacterial capsule locus. The presence of the same mutation in both the in vitro mutants and in phage-insensitive isolates TP2 and TP3, which evolved in vivo during phage treatment, indicate that in vitro investigations can produce results that are relevant and predictive for the in vivo environment.

microbiology↗

bioRxiv2020

A recombinant fragment of Human surfactant protein D binds Spike protein and inhibits infectivity and replication of SARS-CoV-2 in clinical samples

RationaleCOVID-19 is an acute infectious disease caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Human surfactant protein D (SP-D) is known to interact with spike protein of SARS-CoV, but its immune-surveillance against SARS-CoV-2 is not known. ObjectiveThis study aimed to examine the potential of a recombinant fragment of human SP-D (rfhSP-D) as an inhibitor of replication and infection of SARS-CoV-2. MethodsrfhSP-D interaction with spike protein of SARS-CoV-2 and hACE-2 receptor was predicted via docking analysis. The inhibition of interaction between spike protein and ACE-2 by rfhSP-D was confirmed using direct and indirect ELISA. The effect of rfhSP-D on replication and infectivity of SARS-CoV-2 from clinical samples was studied by measuring the expression of RdRp gene of the virus using qPCR. Measurements and Main ResultsIn-silico interaction studies indicated that three amino acid residues in the RBD of spike of SARS-CoV-2 were commonly involved in interacting with rfhSP-D and ACE-2. Studies using clinical samples of SARS-CoV-2 positive cases (asymptomatic, n=7 and symptomatic, n=8 and negative controls n=15) demonstrated that treatment with 5M rfhSP-D inhibited viral replication by ~5.5 fold and was more efficient than Remdesivir (100 M). Approximately, a 2-fold reduction in viral infectivity was also observed after treatment with 5M rfhSP-D. ConclusionsThese results conclusively demonstrate that the calcium independent rfhSP-D mediated inhibition of binding between the receptor binding domain of the S1 subunit of the SARS-CoV-2 spike protein and human ACE-2, its host cell receptor, and a significant reduction in SARS-CoV-2 infection and replication in-vitro.

immunology↗

bioRxiv2020

Identification and characterisation of the gene encoding an amastine-like surface protein (ALSP) in the Leishmania donovani genome: a putative anti-leishmanial drug target

In the current study, a novel putative protein of Leishmania donovani, amastin-like surface protein (ALSP) has been characterized. The gene was cloned in a bacterial system and the protein was overexpressed. A polyclonal antibody was developed against the protein, which detected a 10 kDa band in the L. donovani amastigote. ALSP mRNA was detected in L. donovani amastigote, which was not expressed in the promastigote. ALSP mRNA was not expressed in either morphological forms of Leishmania major. MALDI-TOF confirmed the molecular weight of ALSP as 10 kDa. I-TASSER predicted the function of ALSP as a lipase, which was confirmed by preliminary in-vitro experiments using amastigotes of L. donovani. ALSP has GAS amino acid sequences, which might act as the active site for its lipase activity. The selective expression of ALSP in amastigotes probably makes it important in virulence mechanisms such as survival in the phagolysosome and modulation of its membrane and other metabolic functions, necessary for parasite survival in the human host. ALSP can act as a peptide vaccine target and maybe detected in the peripheral blood or urine as a molecular biomarker of active disease in visceral leishmaniasis.

molecular biology↗

bioRxiv2020

HIV-1 Gag protein with or without p6 specifically dimerizes on the viral RNA packaging signal

The HIV-1 Gag protein is responsible for genomic RNA (gRNA) packaging and immature viral particle assembly. While the presence of gRNA in virions is required for viral infectivity, in its absence, Gag can assemble around cellular RNAs and form particles resembling gRNA-containing particles. When gRNA is expressed, it is selectively packaged despite the presence of excess host RNA, but how it is selectively packaged is not understood. Specific recognition of a gRNA packaging signal (Psi) has been proposed to stimulate the efficient nucleation of viral assembly. However, the heterogeneity of Gag-RNA interactions renders capturing this transient nucleation complex using traditional structural biology approaches challenging. Here, we used native mass spectrometry to investigate RNA binding of wild-type Gag and Gag lacking the p6 domain (Gag{Delta}p6). Both proteins bind to Psi RNA primarily as dimers, but to a control RNA primarily as monomers. The dimeric complexes on Psi RNA require an intact dimer interface within Gag. Gag{Delta}p6 binds to Psi RNA with high specificity in vitro and also selectively packages gRNA in particles produced in mammalian cells. These studies provide direct support for the idea that Gag binding to Psi specifically nucleates Gag-Gag interactions at the early stages of immature viral particle assembly in a p6-independent manner.

biochemistry↗