Biology subjects

Mukherjee, A.

Publications and source records attributed to Mukherjee, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

FOXI3 Promotes Migration and Proliferation in Prostate Cancer Bone Metastases, Modulated by FGF8.

Studies have shown that all men who die from prostate cancer exhibit bone involvement, highlighting the clinical significance of bone metastases. Previously, we demonstrated that prostate cancer exhibits elevated expression of FOXI3; a transcription factor critical to bone development. However, its functional role in prostate cancer progression remains unexplored. In this study, we explored FOXI3 expression in human prostate cancer tissues and cell lines. Immunohistochemical analysis revealed a significant association between FOXI3 expression, tumor pathology, and increasing tumor grade. Analysis of publicly available gene expression data from prostate cancer patients showed that that FOXI3 is markedly elevated in bone metastases and strongly correlates with FGF8, suggesting a potential bone-specific regulatory interaction between these factors. Consistent with this, treatment of bone-derived prostate cancer cells with FGF8 increased FOXI3 RNA expression, whereas no such effect was observed in a brain-metastatic cell line. Further, we demonstrated that FGF8-FOXI3 axis regulates bone-derived prostate cancer cell migration and proliferation in a FOXI3 dependent manner. Together, our findings demonstrate a pro-metastatic role of FOXI3 in prostate cancer progression.

cancer biology↗

bioRxiv2025

HMGB1 assists in overcoming cisplatin resistance in chemoresistant human ovarian cancer cells

Cisplatin is one of the most effective chemotherapeutic agents used in the treatment of ovarian cancer. However, the frequent development of cisplatin resistance remains a significant limitation, leading to therapeutic failure and poor patient outcomes. Cisplatin cytotoxicity is attributed to the generation of toxic DNA lesions, which can be recognized and processed by a variety of proteins, including the high mobility group box 1 (HMGB1) protein. HMGB1 is a multifunctional protein, which is involved in chromatin remodeling and multiple DNA damage repair pathways. In this study, we investigated the role of HMGB1 in modulating cisplatin sensitivity in human ovarian cancer cells. Using cisplatin-sensitive and cisplatin-resistant human ovarian cancer cell lines, we employed siRNA-mediated HMGB1 knockdown to assess its impact on the cellular responses to cisplatin treatment. In clonogenic survival assays, HMGB1 depletion resulted in a significant reduction in colony formation in cisplatin-resistant cells upon cisplatin exposure, compared with non-targeting siRNA treated cells. Additionally, HMGB1 inhibition significantly enhanced cisplatin-induced apoptosis in the cisplatin-resistant cells. Mechanistically, HMGB1-depleted cells exhibited altered DNA damage responses via modulation of ATM/CHK2 and ATR/CHK1 activity following cisplatin treatment. Notably, DNA immunoblot and modified alkaline comet assay results demonstrated that HMGB1 depletion stimulated cisplatin-DNA adduct formation and impaired the removal of cisplatin-DNA adducts, particularly in the cisplatin-resistant cells. Collectively, these findings uncover novel functions of HMGB1 in mediating cisplatin sensitivity, emphasizing its potential as a therapeutic target to overcome cisplatin resistance in ovarian cancer.

cancer biology↗

bioRxiv2025

Design, Synthesis, Biological Evaluation and Molecular Docking of New Acid-Functionalized Carbazole Derivatives as Potential Antibiotic Agents

The emergence of antibiotic resistance necessitates the discovery of new scaffolds with improved efficacy and drug-like properties. In this work, a new series of acid-functionalized carbazole derivatives was designed, synthesized, and comprehensively evaluated for their antibacterial potential. The incorporation of acidic functionalities into the carbazole framework enhanced physicochemical properties and biological interactions, yielding distinct strain-specific antibacterial activities. Minimum inhibitory concentration (MIC) studies demonstrated that 3-methyl-1,4-dioxo-4,9-dihydro-1H-carbazole-6-carboxylic acid (2) exhibited broad-spectrum potency, particularly against S. aureus and E. coli, while 6-methyl-9H-carbazole-3-carboxylic acid (3) showed selectivity against B. cereus and (E)-3-methyl-1-(2-tosylhydrazono)-2,3,4,9-tetrahydro-1H-carbazole-6-carboxylic acid (1) displayed strong activity toward S. typhimurium. Molecular docking studies revealed favourable binding affinities of all derivatives toward bacterial dihydrofolate reductase (DHFR), with compound 1 showing the highest docking scores. Molecular dynamics simulations further confirmed the broad conformational adaptability of compound 1, the target-specific stability of compound 3, and protein-dependent binding behaviour of compound 2. Complementary ADMET predictions indicated that all compounds adhered to Lipinskis rules, with compound 3 displaying the most favourable pharmacokinetic profile, including high oral bioavailability and low toxicity risk. Together, these experimental and computational findings establish acid-functionalized carbazole scaffolds as promising antibacterial candidates.

pharmacology and toxicology↗

bioRxiv2025

A programmable genetic platform for engineering noninvasive biosensors

Creating genetic sensors for noninvasive visualization of biological activities in deep, optically opaque tissues holds immense potential for basic research and the development of genetic and cell-based therapies. MRI stands out among deep-tissue imaging methods for its ability to generate high-resolution images without ionizing radiation. However, the adoption of MRI as a mainstream biomolecular technology has been hindered by the lack of adaptable methods to link molecular events with genetically encodable MRI contrast. To address this challenge, we introduce universal reporter circuit-based activatable sensors (URCAS), a highly programmable platform for the systematic creation of genetic sensors for MRI. In developing URCAS, we engineered protease-activatable MRI reporters using two distinct approaches: protein stabilization and subcellular trafficking. We established the applicability of URCAS in five diverse mammalian cell types and showcased its versatility by assembling a toolkit of genetic sensors for viral proteins, small-molecule drugs, logic gates, protein-protein interactions, and calcium, without requiring new customization for each target. Our findings suggest that URCAS provides a modular, programmable platform for streamlining the development of noninvasive, nonionizing, and genetically encoded sensors for biomedical research and in vivo diagnostics.

bioengineering↗

bioRxiv2025

Insilico Investigation of Terpenoid efficacy on Cannabinoid Receptors using QSAR models and fragment-based Pharmacophore modelling

Cannabis Sativa a medical plant rich in phytochemicals have a range of terpenoids and cannabinoids with a wide range of therapeutic uses. The possible interaction of terpenoids with cannabinoid receptors implicated in analgesic pathways has not received enough attention. This work used in silico methods to target Cannabinoid Receptors Type I (CNR1) and II (CNR2) in order to find novel terpenoid compounds from Cannabis sativa that may have pain-relieving properties. QSAR modelling based on known cannabinoid receptor inhibitors was used to build and screen a curated library of 119 terpenoids. The terpenoid library was screened using pharmacophore models that were created. Molecular docking was performed on the top candidates using CNR1 (PDB: 5U09) and CNR2 (PDB: 5ZTY). To evaluate the stability of receptor-ligand complexes over 100 ns, molecular dynamics simulations were run. SwissADME was used for ADMET profiling in order to assess drug-likeness and pharmacokinetic characteristics. Both receptors QSAR models showed strong predictive power (CNR1: r2 = 0.854; CNR2: r2 = 0.798). {gamma}-Eudesmol and Bisabolol were the top hits for CNR1 and CNR2, respectively, according to pharmacophore screening. Strong binding affinities were demonstrated by molecular docking ({gamma}-Eudesmol: -7.9 kcal/mol; Bisabolol: -8.5 kcal/mol), and simulations verified the stable connections. Both compounds were drug-like, according to ADMET analysis, while {gamma}-Eudesmol had better synthetic accessibility and fewer structural alarms. According to the results, bisabolol and {gamma}-Eudesmol show promise as cannabinoid receptor-targeted analgesics. The finding encourages more biological validation and emphasises the potential of terpenoids obtained from Cannabis sativa in medicinal medication discovery. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/674146v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@3e2544org.highwire.dtl.DTLVardef@cefborg.highwire.dtl.DTLVardef@114cf19org.highwire.dtl.DTLVardef@128b069_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Phospholipids that plug the pores of cholesteryl ester transfer protein control its lipid transfer dynamics

The mechanism by which cholesteryl ester transfer protein (CETP), a key drug target in cardiovascular disease, moves lipids between lipoproteins, has remained elusive. CETP is the primary protein that regulates plasma circulating levels of lipids (within high, low, and very low-density lipoproteins. The protein, in addition to its terminal openings, has two additional openings, plugged by two phospholipids (PLs). Small molecule inhibitors targeting CETP tunnel displace PL during CETP inhibition. Here, using steered molecular dynamics simulations followed by in-vitro mutagenesis we show that CETP-bound PLs are indispensable in establishing the optimal architecture of CETP tunnel. Our structural and functional analyses revealed that lipid traversal through CETPs central tunnel is facilitated through hydrophobic interaction-mediated diffusion. PLs are critical in synchronizing domain movements of CETP while accelerating triglyceride traversal through the tunnel and their activity regulated through salt-bridge interactions. Most notably, we show for the first time that phospholipids (PLs) bound within CETPs tunnel accelerate lipid movement through a novel "gliding" mechanism, representing the first known example of a lipid regulating the movement of another. We identified conserved phenylalanine (Phe) flaps that act as a regulatory valve, opening and closing concertedly to prevent lipid backflow in the absence of an active motor. This study provides in-depth understanding of the mechanism of lipid exchange by CETP guided, and accentuated by its interaction with PLs. The conservation of these critical structural elements across the BPI/LBP family suggests that this mechanism is broadly applicable, expanding our understanding of lipid transport in this clinically significant protein class. Significance StatementThe mechanism of lipid transport by the cholesteryl ester transfer protein (CETP), a major drug target, has long been a scientific mystery. Neutral lipid exchange through CETP is dependent on the hydrophobic characteristics of the tunnel that has been exploited during inhibitor design. We provide a detailed, molecular-level explanation, showing for the first time that phospholipids (PLs), previously thought to be static plugs, are indispensable for lipid transfer. They actively accelerate lipid movement through a novel gliding mechanism, the first documented instance of a lipid regulating another. This discovery identifies new therapeutic targets for CETP inhibition. Our findings also suggest that this fundamental mechanism is conserved across a large protein family, with broad implications for understanding lipid transport and function.

biophysics↗

bioRxiv2025

Genome-wide overexpression screen reveals a novel transcription termination factor in Trypanosoma brucei

Trypanosoma brucei is a protozoan parasite that causes African trypanosomiasis. Understanding essential cellular processes in T. brucei can provide insights into parasite-specific vulnerabilities. We therefore screened for genes whose overexpression impaired parasite growth. Three top-ranking candidates were confirmed to inhibit T. brucei growth upon overexpression. Among them, TbFOP, a previously uncharacterized protein, exhibited distinct phenotypes beyond growth inhibition. TbFOP overexpression caused severe cell-cycle defects, substantially increasing the proportion of sub-G1 cells lacking nuclear DNA. Transcriptome analysis revealed widespread transcriptional dysregulation following TbFOP overexpression. Specifically, antisense transcript levels substantially increased near transcription termination sites (TTSs) across the genome. TbFOP overexpression also increased the expression of normally silent variant surface glycoprotein (VSG) genes across multiple genomic contexts. These phenotypes resemble those observed in trypanosome mutants lacking TTS-associated chromatin marks, including two histone variants and base J, a kinetoplastid-specific DNA modification. The preferential effects at TTSs and VSG loci raise the possibility that TbFOP overexpression interferes with chromatin-associated transcriptional regulation at specific genomic regions. These findings demonstrate that TbFOP overexpression profoundly affects transcription, cell-cycle progression, and parasite growth.

molecular biology↗

bioRxiv2025

Cleavage of Streptococcus pneumoniae ribosomal protein L27 by the Prp protease

Streptococcus pneumoniae is one of the most important human respiratory pathogens worldwide. The increase in antibiotic resistance in S. pneumoniae and other pathogens is a significant public health concern. The streptococcal 70S ribosome is a prime target for antibiotics. Ribosomal protein L27 reaches into the peptidyl transferase center with its extended N-terminus and may be involved in the translation process. We have shown that L27 in Firmicutes, including staphylococci and streptococci, has an additional 9-12 amino acid N-terminal extension compared to Gram-negative organisms like Escherichia coli. The extension is cleaved by a protease called Prp that is absent from organisms that lack the extension. In S. aureus, Prp and the N-terminal extension of L27 are essential. Here, we have characterized the cleavage of L27 by Prp in S. pneumoniae. Prp forms dimers that efficiently cleave L27 in vitro. An inactive form of Prp (PrpC34S) binds to L27 without cleaving, whereas L27 with a mutation (F12A) of the cleavage site does not bind Prp. Overexpression of PrpC34S in vivo is detrimental to S. pneumoniae growth. Surprisingly, a S. pneumoniae {Delta}prp strain was viable, apparently due to cleavage of L27 by another, unknown protease. Unlike in S. aureus, a mutant strain lacking the N-terminal extension of L27 was viable, but showed impaired growth. Our study sheds light on a process that could be exploited for novel antibiotics, but emphasizes important differences between streptococci and staphylococci. HIGHLIGHTSO_LIRibosomal protein L27 in S. pneumoniae is N-terminally processed by Prp protease C_LIO_LIA S. pneumoniae {Delta}prp mutant is viable, but exhibits impaired growth C_LIO_LICleavage of L27 is required for viability, but the N-terminal extension is not essential C_LIO_LIIn the absence of Prp, L27 is processed by another protease. C_LIO_LIThere are distinct differences in the role of Prp between S. aureus and S. pneumoniae. C_LI

microbiology↗

bioRxiv2025

Exposure to third generation cephalosporin induces L-form transition in Shigella sonnei, potentially acting as a bacterial reservoir for persistent infection

Shigellosis remains a major global health burden, and the increasing prevalence of multidrug-resistant (MDR) Shigella strains is complicating effective antibiotic therapy. Bacteria may survive antibiotics by transitioning into cell wall-deficient L-forms, which are intrinsically resistant to {beta}-lactams and can revert to a virulent state, potentially causing relapsing infections. Here we characterized a clinical MDR isolate Shigella sonnei HK8, a.k.a. PD552A, whose genome contains key resistance (gyrA, PBP3) and virulence (icsA) genes. Exposure to ceftriaxone induced a transition into a viable L-form state that was hyper-adhesive to macrophages in vitro. However, this survival adaptation was linked to a profound loss of pathogenicity. Using murine and guinea pig models, the L-form variant was shown to be profoundly attenuated, failing to cause the keratoconjunctivitis, diarrheal disease, or significant histopathology characteristic of the wild-type strain. These findings reveal a critical virulence-survival trade-off, positioning the L-form as a "stealth" phenotype that enables bacterial persistence at the expense of acute virulence. This offers a potential mechanism for asymptomatic carriage and recurrent infections, highlighting a previously underappreciated mechanism by which antibiotic treatment may resolve acute symptoms while permitting the persistence of a cryptic bacterial reservoir capable of driving recurrent infection. ImportanceOur research provides critical insight into the challenge of antibiotic treatment failure in shigellosis. By integrating experimental validation of reversible L-form transitions with mathematical modelling, we uncover a crucial virulence-survival trade-off. We show that MDR S. sonnei survives ceftriaxone by adopting a "stealth" phenotype, quantified by a high Stealth Index - maintaining bacterial burden while evading host inflammatory detection. These findings imply that standard antibiotics may resolve acute symptoms while inadvertently selecting for a cryptic, persistent reservoir poised for relapse. This work challenges the conventional view of therapeutic success and highlights an urgent need to develop novel diagnostic and therapeutic strategies capable of identifying and eliminating these resilient, "stealth" L-form persisters to achieve true bacterial clearance and prevent chronic infections.

microbiology↗

bioRxiv2025

Transglutaminase mediated crosslinking of pea protein: from rheology to proteomics

Enzymatic crosslinking of pea proteins by transglutaminase (TG) is a promising processing strategy to enhance structure in protein-based systems. Despite its widespread application, detailed insights spanning macro- to molecular-level mechanisms remain limited. This study investigates TG-mediated crosslinking of pea protein by integrating rheological, chemical, and proteomic analyses to establish a comprehensive structure-function relationship. Dispersions of 10% w/v pea protein were treated sing TG dosages of 0-10 U/g protein. Rheological measurements showed a significant increase in storage modulus (G') and altered gelation dynamics, with a clear dose-dependent relationship, indicating enhanced network formation. The content of free primary amino groups, quantified using the o-phthalaldehyde (OPA) method, decreased with higher TG levels, confirming progressive covalent crosslinking. SDS-PAGE further revealed differential participation of pea protein fractions in the crosslinking reaction. To elucidate molecular changes, proteomic profiling via LC-MS/MS was performed. The analysis indicated that glutamine and lysine residues located near glutamic acid or within disordered regions of peptides were preferentially crosslinked. Specific TG-catalyzed adducts were also identified and found to be enriched in disordered protein regions. Together, the findings demonstrate a clear mechanistic link between enzymatic crosslinking at the peptide level and functional alterations in network structure and viscoelastic properties. This integrative approach offers a molecular framework for the rational design of protein-based systems with tuneable mechanical properties, supporting innovation in both plant-based and conventional food applications.

molecular biology↗

bioRxiv2025

Engineering Escherichia coli FAD synthetase for the biosynthesis of FAD nucleotide analogues results in aminoglycoside antibiotic tolerance

Cofactors such as flavin adenine dinucleotide (FAD), nicotinamide adenine dinucleotide, coenzyme A, and S-adenosylmethionine cofactors share a common adenosine moiety that is generally not considered to contribute directly to catalysis. In FAD biosynthesis, the adenosine group is installed by the flavin mononucleotide adenylyltransferase (FMNAT) domain of the bifunctional FAD synthetase using FMN and ATP. This study explores the nucleotide selectivity of the Escherichia coli FMNAT domain and physiological effects of FAD nucleotide analogues synthesized with cellular nucleotides other than ATP. First, we engineer the FAD synthetase enzyme at an active site loop to produce FAD nucleotide analogues. Chromosomal substitution of the wild-type E. coli FAD synthetase with the mutated version results in the intracellular synthesis of these noncanonical FAD nucleotide analogues and confers tolerance to aminoglycoside antibiotics. Upon investigating their potential downstream metabolic roles, we find that their biosynthesis perturbs cellular metabolism and they could bind to a range of E. coli enzymes. These findings validate the FMNAT domain loop as a viable site for cofactor engineering, with potential for synthetic biology applications. Finally, the observed correlation between FAD analogue production and increased tolerance to aminoglycosides reveals novel metabolic mechanisms underlying antibiotic sensitivity.

microbiology↗

bioRxiv2025

Bio-sintering of Limestone to Produce Pollution Free Cement

Industrial cement is produced by consuming too much energy and emitting very high CO2. Nature too produces cement, but it is pollution-free. This research demonstrates an emulation of natural cement by bio-sintering limestone, a process of successive dissolution and reprecipitation of limestone with the help of bacteria in ambient environmental conditions. When the bacteria Acetobacter aceti were introduced into a mixture of ethanol and limestone powder, the pH came down rapidly, and dissolution of limestone into calcium acetate was observed. After the ethanol was fully consumed, the pH rose gradually, and biocement crystals were reprecipitated. All the reaction rates have been determined, and the products have been characterised. It is observed that the morphology of the biocement could be tailored by controlling the reprecipitation process. The dissolution and reprecipitation took place within the time scale of present construction methods. Thus, this process can potentially manufacture industrial cement from limestone sans the pollution.

bioengineering↗

bioRxiv2025

Signaling and Mechanics influence the number and size of epithelial rosettes in the migrating zebrafish Posterior Lateral Line primordium

A prepattern of Fgf signaling triggers formation of epithelial rosettes as protoneuromasts form periodically in the migrating Posterior Lateral Line primordium. However, the number and size of epithelial rosettes is influenced by the balance of mechanical interactions that promote or oppose their formation. Selective slowing of leading cells in the primordium can result in the fusion of two rosettes to form one larger one, while slowing of trailing cells can result in splitting of a previously formed rosette to form two smaller ones. These observations can be accounted for by mechanics-based models, where local interactions associated with apical constriction and cell adhesion promote formation of rosettes, while tension along the length of the primordium, influenced by the relative efficacy of leading and trailing cell migration, opposes their formation. We describe computational models that illustrate how the relative speed of leading versus trailing cells, as well as changes in cell adhesion and mechanical coupling, can influence the pattern of protoneuromast formation and deposition by the migrating primordium. Our studies illustrate how signaling and mechanics together influence morphogenesis in the migrating primordium.

developmental biology↗

bioRxiv2025

Live-Exudation Assisted Phytobiome Cultromics System (LEAP-CS): A High-Throughput Cultromics System for Studying Plant-Microbiome Interactions through Non-Contact Metabolic Exchange.

This study introduces an innovative methodology for co-cultivating plants and microbes, employing a membrane-based structure to facilitate their physical separation. The Live-Exudation Assisted Phytobiome Cultromics System (LEAP-CS) has the capability to investigate the complex interaction of plant and soil microbiome under in vitro conditions, offering potential benefits. Subsequent validation and testing can be performed through pot, greenhouse, and field trials. The system can efficiently function as a high-throughput screening tool for assessing plant-microbiome interactions and their associated metabolic signatures. Our phytobiome culturing technique harnesses root exudation from live plants, capitalizing on the membranes selective separation to prevent direct physical interaction between plant and microbiome components. Consequently, the interaction is solely through chemical-mediated signalling. By employing this method, we can intricately dissect complex plant-microbiome interactions while faithfully maintaining and emulating the contact independent inherent associations prevalent within these phytobiomes. In conclusion, this user-friendly and reproducible in-vitro model holds immense potential for shedding light on the intricate community and metabolic exchange dynamics of plant-microbiome interactions, thus significantly advancing our understanding in this area.

plant biology↗

bioRxiv2025

A cell-free bacterial signal orchestrates trans-kingdom fitness tradeoff to enhance sulfur deficiency tolerance in plants

Plant-associated microorganisms interact with each other and host plants via intricate chemical signals, offering multiple benefits, including plant nutrition. We report such a mechanism through which the rhizosphere microbiome improves plant growth under sulfur (S) deficiency. Disruption of plant S homeostasis resulted in a coordinated shift in composition and S-metabolism of the rhizosphere microbiome. Using this insight, we developed an 18-membered synthetic rhizosphere bacterial community (SynCom) that rescued growth of Arabidopsis and a leafy Brassicaceae vegetable under S-deficiency. This beneficial trait is taxonomically widespread among SynCom members, with bacterial pairs predominantly providing synergistic benefits to host plants. Notably, stronger competitive interactions among SynCom members conferred greater fitness benefits to the host, suggesting a trans-kingdom fitness tradeoff. Finally, guided chemical screening, deletion knockout mutant, and targeted metabolomics identified and validated microbially released glutathione (GSH) as the necessary bioactive signal that orchestrates plant-microbe (trans-kingdom) fitness tradeoff and improves plant growth under sulfur limitation. HighlightsO_LIAlteration in plant sulfur (S) homeostasis leads to coordinated shifts in the composition and S-metabolism of the rhizosphere microbiome. C_LIO_LITaxonomically divergent bacterial members within the rhizosphere microbiome improve plant growth under S-deficiency. C_LIO_LIStronger competitive interactions within rhizosphere bacterial members provide greater fitness benefit to the host plant under S-deficiency, suggesting a trans-kingdom fitness tradeoff. C_LIO_LIMicrobially released glutathione (GSH) is a necessary bioactive signal that improves plant growth under sulfur limitation and orchestrates plant-microbe (trans-kingdom) fitness tradeoff. C_LI

microbiology↗

bioRxiv2025

Mechanistic Insights into Human Antimicrobial Peptide-Induced Activation of a Broadly Conserved Bacterial Signaling System

Antimicrobial peptides (AMPs) represent a promising class of therapeutics against bacterial pathogens. While their direct bactericidal mechanisms are well-characterized, how bacteria sense and respond to these peptides at sublethal concentrations remains poorly understood. Here, we investigate the activation of the Escherichia coli PhoQ-PhoP signaling system by the human antimicrobial peptide LL-37 and its derivatives (KR-12 and RI-10). We demonstrate that these peptides exhibit variable antimicrobial potency but surprisingly similar abilities to activate the PhoQ-PhoP pathway, indicating that signaling function is separable from bactericidal activity. Notably, sublethal concentrations of these peptides induce significant cell elongation, a phenotype dependent on PhoQ and mediated by the upregulation of QueE, which interferes with bacterial cell division. Contrary to the previous model suggesting peptides activate PhoQ passively by displacing its inhibitor MgrB, we observed enhanced cell elongation in{Delta} mgrB strains across all tested peptides, including RI-10, lacking antibacterial activity. Our findings suggest peptides actively stimulate PhoQ through a mechanism independent of MgrB dissociation, providing a more refined understanding of the peptide signaling through the PhoQ-PhoP system. These insights into bacterial adaptation mechanisms against host-derived peptides may guide the development of peptide therapeutics with enhanced efficacy against drug-resistant pathogens. Significance statementAntimicrobial peptides (AMPs) are promising alternatives to conventional antibiotics, yet how bacteria detect and respond to these host defense molecules remains poorly understood. This study investigates the interaction between bacterial sensing systems and AMPs at the genetic and molecular levels. Unlike other eukaryotes with multiple cathelicidin peptides, humans have only one cathelicidin that produces various active fragments through processing. Rather than creating multiple detectors, E. coli deploys an elegant solution, the PhoQ-PhoP signaling system that recognizes the conserved antimicrobial region shared by all LL-37 fragments. We demonstrate that peptides directly stimulate PhoQ independent of their bactericidal activity, even in the absence of inhibitor MgrB, inducing cell elongation. These insights may inform the development of effective peptide-based therapeutics against drug-resistant pathogens.

microbiology↗

bioRxiv2025

SoxB1 family members inhibit Wnt signaling to promote maturation and deposition of stable neuromasts by the zebrafish Posterior Lateral Line primordium

Periodic formation of protoneuromasts within the migrating zebrafish Posterior Lateral Line primordium serves as a model for understanding steps that determine the self-organization of organ systems in development. Protoneuromast formation is initiated by Fgf signaling at the trailing zone of the migrating primordium in response to Fgfs produced by Wnt active cells in a leading zone. Progressive restriction of an initially broad Wnt signaling domain to a smaller leading zone allows new Fgf signaling-dependent protoneuromasts to form in the wake of the shrinking Wnt system. We show Sox2 and Sox3 are expressed in nascent and maturing protoneuromasts in a trailing part of the primordium in a pattern that is complementary to Wnt activity in a leading domain, where Sox1a, is expressed. Together, these SoxB1 factors help inhibit Wnt signaling to determine effective maturation of trailing protoneuromasts and the timely deposition of stable neuromasts. Using dkk1b and atoh1b to monitor initiation and subsequent maturation of protoneuromasts, respectively, we show how Wnt signaling regulates the pace of protoneuromast maturation in the migrating primordium, and how its inhibition by SoxB1 family members ensures maturation and deposition of stable neuromasts. Together, our observations define three steps in the periodic formation of neuromasts: first, polarization of Wnt activity in the primordium; second, pattern forming step that determines periodic formation of protoneuromasts in the context of polarized Wnt activity; and third, inhibition of Wnt signaling, which is essential for stabilizing nascent neuromasts formed in the earlier pattern forming stage.

developmental biology↗

bioRxiv2025

Globally prevalent Kelch13 mutations increase partial artemisinin resistance and fitness in Bangladeshi Plasmodium falciparum parasites

Artemisinin partial resistance (ArtR), mediated by Kelch13 (K13) gene mutations in Plasmodium falciparum, has caused delayed parasite clearance and, together with partner drug resistance, treatment failures in the Greater Mekong Subregion (GMS). The Chittagong Hill Tracts (CHTs), located in southeastern Bangladesh and bordering Myanmar and India, regions with prevalent K13 mutations, account for approximately 90% of the countrys malaria infections but have not yet reported ArtR-causing K13 mutations. Importantly, however, some isolates from the CHTs have demonstrated moderate in vitro ArtR in the absence of K13 mutations. To assess the potential threat of K13-mediated ArtR in Bangladesh, we proactively evaluated the impact of three prevalent neighboring K13 mutations (F446I, R561H, and C580Y) on ArtR and parasite fitness in parasites isolated from the CHTs. We edited these mutations into two distinct genetic backgrounds: an artemisinin-sensitive strain (CHT-S) and a K13-independent, moderately resistant strain (CHT-R). In these edited lines, we then evaluated ArtR levels and fitness using ring-stage survival assays (RSA), post-drug treatment recovery assays, and competitive fitness assays against isogenic control strains. Prior to genome editing, both isolates were characterized for baseline drug susceptibility, resistance-associated mutations, and population structure. We found that C580Y and R561H mutations, but not F446I, confer increased in vitro ArtR in the CHT-R background already exhibiting K13-independent moderate resistance. All three mutations incurred minimal or no fitness costs in both genetic backgrounds. Notably, R561H, the dominant allele at the Thai-Myanmar border and currently expanding in Rwanda, mediates extreme resistance in the CHT-R background, with mean RSA survival rates of 30.9{+/-}1.9%, an unprecedented resistance level among K13-engineered lines. R561H also showed fitness advantages (0.5% per generation) and the highest growth recovery post-treatment. This represents the first experimental study modeling this K13 mediated ArtR risk in Bangladeshi parasites. In conclusion, we found that indigenous P. falciparum isolates in the CHTs possess inherent genetic potential to sustain high-level ArtR and fitness advantages if K13 mutations emerge, raising urgent concerns for containment and surveillance strategies during Bangladeshs malaria elimination phase.

microbiology↗