Biology subjects

Dutta, S.

Publications and source records attributed to Dutta, S..

At least 91 records · Page 5Linked to original sources

bioRxiv2024

Expansion microscopy reveals unique ultrastructural features of pathogenic budding yeast species

Candida albicans is the most prevalent fungal pathogen isolated from patients with candidemia. As is the case for many other fungi, the complex life cycle of C. albicans has been challenging to study with high-resolution microscopy techniques due to its small size. We employed ultrastructure expansion microscopy (U-ExM) to directly visualise sub-cellular structures at high resolution in the C. albicans yeast and during its transition to hyphal growth. NHS-ester pan-labelling in combination with immunofluorescence (IF) provided the first comprehensive map of nucleolar and mitochondrial dynamics through the C. albicans cell cycle. Analysis of microtubules (MTs) and spindle pole bodies (SPBs) stained with marker proteins suggests that contrary to the pole-to-pole arrangement observed in Saccharomyces cerevisiae, C. albicans yeast cells display a unique side-by-side arrangement of SPBs with a short mitotic spindle and longer astral MTs (aMTs) at the pre-anaphase stage. Modifications to the established U-ExM protocol enabled the expansion of several medically relevant human fungal pathogens, revealing that the side-by-side SPB configuration is a plausible conserved feature shared by many fungal species. We highlight the power of U-ExM to investigate sub-cellular organisation and organellar dynamics at high resolution and low cost in poorly studied, medically relevant microbial pathogens.

cell biology↗

bioRxiv2024

TIAM1 signaling drives prostatic budding and branching phenotypes and is a potential therapeutic target for BPH

Benign prostatic hyperplasia (BPH) is the most prevalent urologic disease in men aged over 50 years. However, the molecular mechanisms that drive BPH pathophysiology remain elusive. In this study, we integrated bioinformatic and experimental analyses of human BPH to identify TIAM1-RAC1 signaling pathway as a promising candidate for a molecular-based approach for BPH therapy. First, elevated TIAM1 expression in a BPH transcriptomic signature that was generated from the analysis of RNA-seq data from three independent BPH patient cohorts was validated at the protein level in a fourth patient cohort. Additional bioinformatic analyses of the BPH transcriptomic signature pointed to TIAM1-RAC1 pathway as the potential lead therapeutic pathway; and NSC23766 - a small molecule inhibitor of TIAM1 signaling - as a developmental lead compound for BPH therapy. Next, a proof-of-concept pharmacological approach of TIAM1-RAC1 inhibition in human prostatic cells using NSC23766 resulted in attenuated organoid budding and branching - a developmental program associated with prostatic nodule formation and BPH pathogenesis. Finally, shRNA-based genetic knock-down of TIAM1 in human prostatic cells led to a reduction in budding and branching phenotypes thereby phenocopying the effects of NSC23766. Together, our observations implicate elevated TIAM1 as a driver of budding and branching in BPH, and our studies pave the way for TIAM1-RAC1 based targeted approach for the treatment of the disease.

cell biology↗

bioRxiv2024

Grasp context-dependent uncertainty alters the relative contribution of anticipatory and feedback-based mechanisms in object manipulation

Predictive control within dexterous object manipulation while allowing for the choice of contact points has been shown to employ a predominantly feedback-based force modulation. Anticipation is thought to be facilitated through the internal representation of the object dynamics being integrated and updated on a trial-to-trial basis with the feedback of contact locations on the object. This is as opposed to the classically studied memory representation-based fingertip force control for grasping with pre-selected contact locations. We designed a study to examine this grasp context-dependent asymmetry in sensorimotor integration by introducing binary uncertainty about the grasp type before movement initiation within the framework of motor planning. An inverted T-shaped instrumented object was presented to 24 participants as the manipulandum, and they were asked to reach, grasp, and lift it while minimising the roll. We dissociated the planning and the execution phases by pseudo-randomly manipulating the availability of visual contact cues on the object after movement onset. Our results suggest that uncertainty about the grasp type during movement preparation anterogradely modulated the differential weighting of feedback and feedforward mechanisms in anticipatory coordination.

neuroscience↗

bioRxiv2024

Artemisinin-resistant Plasmodium falciparum Kelch13 mutant proteins display reduced heme-binding affinity and decreased artemisinin activation

The rapid emergence of artemisinin resistance (ART-R) poses a challenge to global malaria control efforts. ART potency is triggered by ferrous iron- and/or heme-mediated cleavage of the endoperoxide bond to generate reactive heme-ART alkoxy radicals and covalent heme-ART adducts that alkylate parasite targets or inhibit the detoxification of heme into {beta}-hematin crystals; both of which lead to parasite death. Mutations in the P. falciparum Kelch-containing protein Kelch13 (PfKekch13) confer clinical ART-R, in which the resistant parasites exhibit impaired hemoglobin uptake, reduced heme yield, and thus decreased ART activation. However, a more direct involvement of PfKelch13 in heme-mediated ART activation has not been reported. Here, we show that recombinant, purified PfKelch13 wild-type (WT) protein displays measurable binding affinity for both iron and heme, the main effectors for ART activation. Comparative biochemical analyses further indicate weaker heme-binding affinities in the two Southeast Asian ART-R PfKelch13 mutants C580Y and R539T compared to the ART-sensitive WT and A578S mutant proteins, which ultimately translates into reduced yield of heme-ART derivatives. In conclusion, this study provides the first evidence for regulated ART activation via the heme-binding propensity of PfKelch13, which may contribute towards modulating the level of ART-R in malaria parasites with PfKelch13 mutations.

biochemistry↗

bioRxiv2023

Protein search processes mediated by chromatin topology

We investigate the role of compaction of chromatin domains in modulating search kinetics of proteins. Collapsed conformations of chromatin, characterised by long loops which bring distant regions of the genome into contact, and manifested structurally as Topologically Associated Domains (TADs) affect search kinetics of DNA associated transcription factors and other proteins. In this study, we investigate the role of the compactness of chromatin on the dynamics of proteins using a minimal model. Using analytical theory and simulations, we show that an optimal compaction exists for which the residence time of proteins on a chromatin-like polymer backbone is minimum. We show that while bulk diffusion is an advantageous search strategy for extended polymers, for highly folded polymer domains, intersegmental transfers allow optimal search. We extend these results to more detailed polymer models - using the Freely Rotating Chain model, a Lennard-Jones bead-spring polymer model, which approximates chromatin behavior. We show that our results continue to hold for these polymer models, with a minimum residence time at an optimum polymer compaction. Finally, we also analyse the dynamics of proteins on networks generated using experimental chromatin conformation data from 8355 TADs extracted from human chromosomes. Our analysis suggests that TADs exist near this zone of optimality, indicating that chromatin conformations can play a crucial role in modulating protein search strategies.

biophysics↗

bioRxiv2023

Establishment of an intragastric surgical model using C57BL/6 mice to study the vaccine efficacy of OMV-based immunogens against Helicobacter pylori

Chronic gastritis is one of the major symptoms of gastro-duodenal disorders typically induced by Helicobacter pylori (H. pylori). To date, no suitable model is available to study pathophysiology and therapeutic measures accurately. Here, we have presented a successful surgical infection model of H. pylori-induced gastritis in C57BL/6 mice that resembles features similar to human infection. The proposed model does not require any preparatory treatment other than surgical intervention. C57BL/6 mice were injected with wild-type SS1 (Sydney strain 1, reference strain) directly into the stomach. Seven days post infection, infected animals showed alterations in cytokine responses along with inflammatory cell infiltration in the lamina propria, depicting a prominent inflammatory response due to infection. To understand the immunogenicity and protective efficacy, the mice were immunized with outer membrane vesicles (OMVs) isolated from an indigenous strain with putative virulence factors of H. pylori [A61C (1), cag+/vacA s1m1]. In contrast to the nonimmunized cohort, the OMV-immunized cohort showed a gradual increase in serum immunoglobulin(s) levels on the 35th day after the first immunization. This conferred protective immunity against subsequent challenge with the reference strain (SS1). Direct inoculation of H. pylori into the stomach influenced infection in a short time and, more importantly, in a dose-dependent manner, indicating the usefulness of the developed model for pathophysiology, therapeutic and prophylactic studies.

immunology↗

bioRxiv2023

Extremely oligotrophic and complex organic compounds degrading microaerobic bacteria from Arabian Sea oxygen minimum zone sediments

Sediments underlying marine hypoxic zones are huge sinks of unreacted complex organic matter, where despite acute O2-limitation obligately aerobic bacteria thrive, and steady depletion of organic carbon takes place within a few meters below the seafloor. However, little knowledge exists about the sustenance and complex carbon degradation potentials of aerobic chemoorganotrophs in these sulfidic ecosystems. We isolated and characterized a number of aerobic bacterial chemoorganoheterotrophs from across a [~]3 m sediment horizon underlying the perennial hypoxic zone of the eastern Arabian Sea. High levels of sequence correspondence between the isolates genomes and the habitats metagenomes and metatranscriptomes illustrated that the strains were widespread and active across the sediment-cores explored. The isolates catabolized several complex organic compounds of marine and terrestrial origins in the presence of high or low, but not zero, O2. Some of them could also grow anaerobically on yeast extract or acetate by reducing nitrate and/or nitrite. Fermentation did not support growth, but enabled all the strains to maintain a fraction of their cell populations over prolonged anoxia. Under extreme oligotrophy, limited growth followed by protracted stationary phase was observed for all the isolates at low cell density, amid high or low, but not zero, O2 concentration. While population control and maintenance could be particularly useful for the strains survival in the critically carbon-depleted layers below the explored sediment-depths (core-bottom organic carbon: 0.5-1.0 % w/w), metagenomic data suggested that in situ anoxia could be surmounted via potential supplies of cryptic O2 from previously-reported sources such as Nitrosopumilus species.

microbiology↗

bioRxiv2023

PerSEveML: A Web-Based Tool to Identify Persistent Biomarker Structure for Rare Events Using Integrative Machine Learning Approach

Omics datasets often pose a computational challenge due to their high dimensionality, large size, and non-linear structures. Analyzing these datasets becomes especially daunting in the presence of rare events. Machine learning (ML) methods have gained traction for analyzing rare events, yet there remains a limited exploration of bioinformatics tools that integrate ML techniques to comprehend the underlying biology. Expanding upon our previously developed computational framework of an integrative machine learning approach1, we introduce PerSEveML, an interactive web-based that uses crowd-sourced intelligence to predict rare events and determine feature selection structures. PerSEveML provides a comprehensive overview of the integrative approach through evaluation metrics that help users understand the contribution of individual ML methods to the prediction process. Additionally, PerSEveML calculates entropy and rank scores, which visually organize input features into a persistent structure of selected, unselected, and fluctuating categories that help researchers uncover meaningful hypotheses regarding the underlying biology. We have evaluated PerSEveML on three diverse biologically complex data sets with extremely rare events from small to large scale and have demonstrated its ability to generate valid hypotheses. PerSEveML is available at https://biostats-shinyr.kumc.edu/PerSEveML/ and https://github.com/sreejatadutta/PerSEveML.

bioinformatics↗

bioRxiv2023

Bacterial pore-forming toxin pneumolysin drives pathogenicity through shed toxin-loaded host extracellular vesicles

Streptococcus pneumoniae is a global priority respiratory pathogen that kills over a million people annually and produces the pore-forming cytotoxin, pneumolysin (PLY). Host cells expel membrane assembled toxin by shedding microvesicles, but the composition and pathophysiological sequelae of the toxin-induced host extracellular vesicles (EVs) are unknown. Here, we found that EVs shed from PLY-challenged monocytes (PLY-EVs) harbor membrane-bound toxin that induced cytotoxicity upon fusion with recipient cells. EVs from human monocytes challenged with recombinant PLY as well as PLY-expressing pneumococcal strains, but not the isogenic PLY mutant, primed dendritic cells and evoked higher pro-inflammatory cytokines upon infection. Proteomic analysis revealed that PLY-EVs are enriched for key antimicrobial and inflammatory host proteins such as IFI16, NLRC4, PTX3 and MMP9. In vivo, zebrafish and mice administered with PLY-EVs showed mortality, pericardial edema, tissue damage and inflammation. Our findings show that host EVs bearing the cytotoxin PLY constitute a previously unexplored mechanism of pneumococcal pathogenesis.

microbiology↗

bioRxiv2023

Telomeres control regulation of the human Telomerase (hTERT) gene through non-telomeric TRF2 and independent of Telomere looping

The function of the human telomerase reverse transcriptase (hTERT) in the synthesis and maintenance of chromosome ends, or telomeres, is widely understood. Whether and how telomeres, on the other hand, influence hTERT regulation is relatively less studied. We found hTERT was transcriptionally altered depending on telomere length (TL). This resulted from TL-dependent binding of TRF2 between telomeres and the hTERT promoter. hTERT promoter-bound TRF2 was non-telomeric and did not involve the looping of telomeres to the hTERT promoter. Cell lines from different tissue types (fibrosarcoma (HT1080), colon cancer (HCT116), and breast cancer (MDA-MB-231), engineered for either telomere elongation/shortening gave increase/decrease in hTERT, respectively. Mechanistically, we show hTERT promoter-bound non-telomeric TRF2 recruits the canonical PRC2-complex inducing repressor histone H3K27-trimethylation in a TL-dependent fashion. This was further supported by TL-dependent promoter activity from an exogenously inserted hTERT reporter. Increase in TL over days followed by gradual decline, resulted in activation followed by repression of hTERT in a concerted manner, further implicating TL as a key factor for hTERT regulation. Notably on reprogramming primary fibroblasts to induced pluripotent stem cells (iPSCs), TRF2 loss from the hTERT promoter was evident along with telomere elongation and hTERT upregulation. Conversely, on telomere shortening in iPSCs, hTERT promoter-bound TRF2 was restored with marked reduction in hTERT further supporting the causal role of TL in hTERT transcription. Mechanisms of tight control of hTERT by TL shown here are likely to have major implications in telomere-related physiologies, particularly, cancer, ageing and pluripotency. TeaserTelomere length controls hTERT expression by modulating TRF2 distribution and PRC2-mediated repression, highlighting a self-regulatory mechanism in cancer.

cancer biology↗

bioRxiv2023

Potential use of Sodium Butyrate (SB) as an anti-virulence agent against Vibrio cholerae targeting ToxT virulence protein.

ABSTRACTCholera, a diarrhoeal disease caused by gram-negative bacterium Vibrio cholerae remains a global health threat in developing countries owing to its high transmissibility and increase in antibiotic resistance. The current issue is to overcome the problem of resistance by antimicrobial therapy. There is a need for alternative strategies with an emphasis on anti-virulent approaches to alter the outcome of bacterial infections. Vibrio cholerae causes cholera by secreting virulence factors in the intestinal epithelial cells. Virulence factors help in cholera toxin production and colonisation during infection. Here, we show that sodium butyrate (SB), a small molecule, had no effect on bacterial viability but was effective in suppressing the virulence attributes of V. cholerae. The production of cholera toxin (CT) was downregulated in a standard V. cholerae El Tor strain and two clinical isolates when grown in presence of sodium butyrate. Analysis of mRNA and protein levels further demonstrated that sodium butyrate reduced the expression of the ToxT-dependent virulence genes like tcpA and ctxAB. DNA-protein interaction assays conducted at cellular (ChIP) and in in vitro conditions (EMSA) indicated that sodium butyrate weakens the binding between ToxT and its downstream promoter DNA, likely by blocking DNA binding. Furthermore, the efficacy of sodium butyrate was confirmed by showing its anti-virulence activity and tissue damage recovery in animal models. Collectively, these findings suggest that sodium butyrate (SB) has the potential to be developed as an anti-virulence agent against V. cholerae in place of conventional antibiotics or as an adjunctive therapy to combat cholera. IMPORTANCEThe world has been facing an upsurge in cholera cases since 2021 with a similar trend continuing into 2022 with over 29 countries reporting cholera outbreaks (World Health Organization 16 December 2022 Disease Outbreak News; Cholera - Global situation). Treatment of cholera involves oral rehydration therapy coupled with antibiotics to reduce the duration of the illness. However, over the last few years, there has been indiscriminate use of antibiotics that contributed largely to the reservoir of antibiotic-resistant strains. In this study, we have addressed the problem of antibiotic resistance by targeting virulence factors. The screening of several compounds led to the identification of a small molecule, sodium butyrate that inhibits the virulence cascade in V. cholerae. We demonstrated that (i) sodium butyrate intervened with ToxT protein-DNA binding and subsequently affected the expression of ToxT-regulated virulence genes (ctxAB and tcpA) (ii) Sodium Butyrate is a potential therapeutic candidate for development of novel antimicrobial agents.

microbiology↗

bioRxiv2023

Transition-based reweighting and neural rational inference analysis of effects of new psychoactive substances on cannabinoid receptors

New psychoactive substances (NPS) targeting cannabinoid receptor 1 pose a significant threat to society as recreational abusive drugs that have pronounced physiological side effects. These greater adverse effects compared to classical cannabinoids have been linked to the higher downstream {beta}-arrestin signaling. Thus, understanding the mechanism of differential signaling will reveal important structure-activity relationship essential for identifying and potentially regulating NPS molecules. In this study, we simulate the slow (un)binding process of NPS MDMB-Fubinaca and classical cannabinoid HU-210 from CB1 using multi-ensemble simulation to decipher the effects of ligand binding dynamics on downstream signaling. The transition-based reweighing method is used for the estimation of transition rates and underlying thermodynamics of (un)binding processes of ligands with nanomolar affinities. Our analyses reveal major interaction differences with transmembrane TM7 between NPS and classical cannabinoids. A variational autoencoder-based approach, neural relational inference (NRI), is applied to assess the allosteric effects on intracellular regions attributable to variations in binding pocket interactions. NRI analysis indicate a heightened level of allosteric control of NPxxY motif for NPS-bound receptors, which contributes to the higher probability of formation of a crucial triad interaction (Y7.53-Y5.58-T3.46) necessary for stronger {beta}-arrestin signaling. Hence, in this work, MD simulation, data-driven statistical methods, and deep learning point out the structural basis for the heightened physiological side effects associated with NPS, contributing to efforts aimed at mitigating their public health impact.

biophysics↗

bioRxiv2023

The Effect of Sunlight Intensity on Flower Opening Time and Exposure Duration in Rice (Oryza sativa ssp. indica) Landraces

Records of sunlight intensity at anthesis of 388 rice landraces (with 32 replicated populations), flowering in the short-day season of 2022, reveal that under cloudy condition, the rice florets tend to open later, or the sunrise-to-anthesis duration (SAD) is longer when rice florets open than at sunny period. This difference in the length of SAD was statistically highly significant (p < 0.0001), confirmed by two sample permutation test with 10,000 iterations. This finding corroborates our general observation previously reported from a larger set of 1114 landraces (including the 388 landraces in this study). However, the intensity of sunlight at the flower opening time (FOT) may not remain uniformly sunny (high illuminance) or cloudy (low illuminance, < 40000 lux) until the flower closing time (FCT). To understand the effect of uniformly low sunlight intensity, we subsequently recorded solar illuminance at FOT of 33 landrace populations (including 8 repeats). Half of each population was kept under artificial shade, compared to the other half exposed to sunlight. This experiment revealed that low illuminance, mimicking overcast days, significantly (p < 0.01) delays FOT and lengthens SAD, corroborating the pattern detected in our earlier findings. Permutation tests with 10,000 iterations decisively confirms (p < 0.0001) the prolongation of SAD under shade and cloudy condition. Experimental shading has an indeterminate effect on FED of the same landraces. We surmise that the delayed FOT during natural cloudy period is an adaptation in rice plants in anticipation of rain, for protection of the pollen from rainwash.

plant biology↗

bioRxiv2023

Contrasting Effects of SARS-CoV-2 Vaccination vs. Infection on Antibody and TCR Repertoires

Antibodies and helper T cells play important roles in SARS-CoV-2 infection and vaccination. We sequenced B- and T-cell receptor repertoires (BCR/TCR) from the blood of 251 infectees, vaccinees, and controls to investigate whether features of these repertoires could predict subjects SARS-CoV-2 neutralizing antibody titer (NAbs), as measured by enzyme-linked immunosorbent assay (ELISA). We sequenced recombined immunoglobulin heavy-chain (IGH), TCR{beta} (TRB), and TCR{delta} (TRD) genes in parallel from all subjects, including select B- and T-cell subsets in most cases, with a focus on their hypervariable CDR3 regions, and correlated this AIRRseq data with demographics and clinical findings from subjects electronic health records. We found that age affected NAb levels in vaccinees but not infectees. Intriguingly, we found that vaccination and infection have an effect on non-productively recombined IGHs, suggesting an effect that precedes clonal selection. We found that repertoires binding capacity to known SARS-CoV-2-specific CD4+ TRBs performs as well as the best hand-tuned approximate or "fuzzy" matching at predicting a protective level of NAbs, while also being more robust to repertoire sample size and not requiring hand-tuning. The overall conclusion from this large, unbiased, clinically well annotated dataset is that B- and T-cell adaptive responses to SARS-CoV-2 infection and vaccination are surprising, subtle, and diffuse. We discuss methodological and statistical challenges faced in attempting to define and quantify such strong-but-diffuse repertoire signatures and present tools and strategies for addressing these challenges.

immunology↗

bioRxiv2023

Colonization of larval zebrafish (Danio rerio) with adherent-invasive Escherichia coli prevents recovery of the intestinal mucosa from drug-induced colitis

Inflammatory bowel disease (IBD) is a broad term for a range of chronic intestinal disorders, including Crohns disease and ulcerative colitis. The global prevalence of IBD is rising, with over one million patients affected in the US alone. Adherent-invasive E. coli (AIEC) is a pathobiont frequently found in IBD biopsies. AIEC adhere to and invade epithelial cells, and can survive inside phagocytes in vitro. However, how AIEC contribute to IBD in vivo remains unclear. Here, we established a larval zevbrafish (Danio rerio) model to study the interplay between pre-existing intestinal inflammation and AIEC colonization of the gut. We used the pro-inflammatory drug dextran sulfate sodium (DSS) to induce colitis. This was followed by food-borne infection of larvae with AIEC using the protozoan Paramecium caudatum, a natural prey, as a vehicle. We show that AIEC more robustly colonizes the zebrafish gut, and persists for longer, compared to non-pathogenic E. coli. In addition, DSS induced colitis increases both bacterial burden and persistence in the larval gut. We benchmark our model against existing rodent models using two mutants deficient in the known AIEC virulence factors FimH and IbeA, which have virulence defects in both rodent and the larval zebrafish model. Finally, we show that AIEC colonization exacerbates DSS induced colitis and prevents recovery from inflammation. In conclusion, we established a high-throughput, genetically tractable model to study AIEC-host interactions in the context of chronic inflammation. IMPORTANCEAlthough inflammatory bowel diseases are on the rise, a lot remains to be learned about the link between IBD severity and the underlying cause. Although host genetics, microbiome, and environmental factors have all been shown to correlate with the development of IBD, cause and effect are difficult to disentangle in this context. For example, AIEC is a known pathobiont found in IBD patients, but it remains unclear if gut inflammation during IBD facilitates colonization with AIEC, or if AIEC colonization makes the host more susceptible towards pro-inflammatory stimuli. To develop successful therapeutics, it is critical to understand the mechanisms that contribute to AIEC infections in a susceptible host. Here, we show that the larval zebrafish model recapitulates key features of AIEC infections in other animal models, and can be utilized to address these gaps in knowledge.

microbiology↗

bioRxiv2023

An amphipathic helix facilitates direct membrane binding of Mycoplasma FtsZ

Cell division in bacteria is initiated by constriction of the Z-ring comprising two essential proteins FtsZ and FtsA. Despite our knowledge about the crucial function of the Z-ring in bacterial division, the precise roles and mechanism of how FtsZ and FtsA drive cell constriction remain elusive. FtsZ/FtsA in wall-less bacteria like mycoplasmas is an ideal model system for obtaining mechanistic insights into Z-ring constriction in the absence of cell wall machinery. In this study, we have analyzed FtsZ and FtsA sequences of 113 mycoplasma species and compared with the corresponding protein sequences in cell-walled bacteria. We report a phylogenetically distinct group of 12 species that possess FtsZs without the canonical FtsA interacting conserved C-terminal peptide (CCTP) motif. Interestingly, these FtsZs contain a putative membrane-binding amphipathic helix as an N-terminal or C-terminal extension to the globular FtsZ domain. As a proof-of-concept, we experimentally show that the proposed C-terminal amphipathic helix in M. genitalium FtsZ binds liposomes in vitro as well as localizes to E. coli membrane in vivo. Additionally, we identify a putative cholesterol recognition motif within the C-terminal amphipathic helix region of M. genitalium FtsZ. Our study catalogues the functional variations of membrane attachment by the FtsZ and FtsA system in cell wall-less mycoplasmas and provides a new perspective to study novel functions of FtsZ/A system in cell division. ImportanceZ-ring and peptidoglycan synthesis machinery both play crucial roles in bacterial cell division. Currently, our knowledge about how FtsZ and FtsA, the two primary components of the Z-ring, function, is limited to cell-walled bacteria where ring constriction is coupled to peptidoglycan synthesis. Cell wall-less bacterial FtsZ/A system is an excellent model to study the mechanism of Z-ring constriction in the absence of cell wall synthesis machinery. Here, we analysed FtsZ protein sequences across mycoplasma species and identified their characteristic sequence features. Our study reveals a novel group of FtsZs from mycoplasma with an inherent membrane binding and probable cholesterol sensing amphipathic motif, which serves as a new paradigm to explore fundamental roles of FtsZ and FtsA in Z-ring constriction during bacterial division.

microbiology↗

bioRxiv2023

Comparative metagenomic analysis of diarrheal and non-diarrheal gut microbiome delineating the prospective development of prognostic markers and probiotics to protect from diarrhea

A cross-sectional gut microbiome analysis of 23 non-diarrheal and 5 diarrheal fecal samples was conducted by employing 16s rRNA amplicon sequencing and subsequent analysis for taxonomic profiling of OTUs and abundance interpretation of reads. Significant differences in the structural composition of the two groups were observed. In both Firmicutes was the most abundant phylum in majority of the samples. B/F ratio was consistently <1 in all diarrheal samples. Significant difference in mean B/F ratio of the two groups was found. Proteobacteria was significantly more abundant in the diarrheal group. Prevotellaceae was the most abundant family in non-diarrheal samples and was suppressed significantly in diarrheal samples. Streptococcaceae was the most abundant family in 60% diarrheal samples and where Streptococcaceae was suppressed, Bacteroideaceae and Nocardeaceae were the most abundant. In non-diarrheal samples where Streptococcaceae was almost completely suppressed Bifidobacteriaceae was the most abundant and suppressed other families significantly. A negative correlation was observed between Prevotellaceae and Bacteroideaceae in the non-diarrheal group. Prevotella copri was the most abundant species in 70% non-diarrheal samples and was significantly suppressed in diarrheal samples. Proteus mirabilis was identified in all the non-diarrheal samples while they were absent in diarrheal samples. The OTUs associated with diarrheal dysbiosis can serve as prognostic markers. This is the first report on the comparative analysis of diarrheal and non-diarrheal microbiome, to our knowledge, and distinctly addressing the gut microbiome dysbiosis from the context that can lead to the development of prognostic markers and probiotics for protecting the endemic population from diarrhea.

microbiology↗

bioRxiv2023

The gut microbiome of the healthy population in Kolkata, India, is a reservoir of antimicrobial resistance genes emphasizing the need of enforcing antimicrobial stewardship

Antimicrobial resistance (AMR) alleviation warrants antimicrobial stewardship (AS) entailing indispensability of epidemiological surveillance. We undertook a small-scale surveillance in Kolkata to detect the presence of antimicrobial resistance genes (ARGs) in the healthy gut microbiome. We found that it was a reservoir of ARGs against common antibiotics. A targeted PCR and sequencing-based ARGs detection against tetracyclines, macrolides, trimethoprim, sulfamethoxazole, aminoglycosides, amphenicol and mobile genetic element (MGE) markers was deployed in twenty-five fecal samples. Relative abundance and frequency of ARGs was calculated. We detected markers against all these classes of antibiotics. 100% samples carried aminoglycoside resistance marker and int1U. A comparison with our previously published diarrheal resistome from the same spatial and temporal frame revealed that a higher diversity of ARGs were detected in the community and a higher rate of isolation of tetC, msrA, tmp and sul-2 was found. The presence of common markers in the two cohorts proves that the gut microbiome has been contaminated with ARGs and which are being disseminated among different ecosystems. This is an issue of discerning concern for public health. The study raises an alarming picture of the AMR crisis in low-middle and emergent economies. It emphasizes the strict enforcement of AS in the community.

microbiology↗