Biology subjects

Rahman, M. M.

Publications and source records attributed to Rahman, M. M..

At least 19 recordsLinked to original sources

bioRxiv2026

Phage proofing Pseudomonas putida uncovers novel broad-spectrum phage resistance protein Psh

Broad-spectrum phage resistance offers an important layer of protection against bacterial fermenter crashes during biomanufacturing processes, yet the underlying mechanisms are often poorly defined or come at a fitness cost. Using experimental evolution, we generated two Pseudomonas putida strains that were resistant to at least six phage genera. Genome sequencing revealed a single frameshift deletion in each strain that restored functionality of a Type I secretion system (T1SS) ATPase. We also found strong transcriptional upregulation of a nearby protein, PP_1794, which we coin Phage shielding helix rich protein (Psh). Overexpression experiments show that Psh protein is secreted by this restored T1SS to confer complete phage resistance. When compared to wild-type P. putida KT2440, no growth or expression defects were evident, but pyoverdine production was reduced. The Psh gene and T1SS are widely distributed across Gram-negative bacteria. These findings uncover a previously uncharacterized phage defense system in P. putida based on secretion-mediated receptor masking.

microbiology↗

bioRxiv2026

Unraveling Wheat Aphid Diversity in Bangladesh Through Integrative Genetic and Morphological Approaches

Accurate species identification is fundamental for understanding insect pest diversity and developing effective management strategies. Wheat aphids are among the most destructive insect pests worldwide, yet comprehensive molecular confirmation of species diversity in Bangladesh has been lacking. This study employed an integrative taxonomic approach combining DNA barcoding and morphological characterization to identify wheat aphid species collected from major wheat-growing regions of Bangladesh. Aphid specimens were sampled from 11 locations across four districts during the 2024-2025 wheat growing season. A partial fragment of the mitochondrial cytochrome C oxidase subunit I (COI) gene was amplified and sequenced, followed by BLAST analysis, phylogenetic reconstruction using the Maximum Likelihood method, genetic distance estimation, and detailed morphometric analyses. COI sequence analysis identified five wheat aphid species: Sitobion avenae, Rhopalosiphum padi, R. maidis, R. rufiabdominalis, and Hysteroneura setariae. Sitobion avenae was the predominant species, occurring across all surveyed regions. BLAST similarity ranged from 99.68% to 100%, confirming reliable species-level identification. Phylogenetic analysis grouped all specimens into five well-supported species-specific clades with strong bootstrap support (97-100%), corroborating molecular identification. Pairwise genetic distance analysis revealed very low intraspecific divergence (0.0-0.18%) and clear interspecific divergence (4.9-11.9%), indicating strong genetic discrimination among species. Morphological and morphometric analyses further distinguished the five species, with significant interspecific differences (P < 0.0001) observed for body length, antennal length, tubercle width, cauda length, and cornicle length. The concordance between molecular and morphological evidence demonstrates the robustness of the integrative taxonomic framework. This study provides the first comprehensive molecular and morphological characterization of wheat aphid species in Bangladesh, establishing a reliable baseline for biodiversity assessment, pest surveillance, insecticide resistance monitoring, and the development of evidence-based integrated pest management strategies to support sustainable wheat production amid changing agroecological conditions.

zoology↗

bioRxiv2026

Atypical myxomatosis in European rabbits is caused by the recombinant myxoma virus involved in species jumping into hares

Myxoma virus (MYXV), a member of the Leporipoxvirus genus (species Leporipoxvirus myxoma; family Poxviridae), causes a highly lethal disease known as myxomatosis in European rabbits. In late 2018, a new natural MYXV isolate, MYXV-Tol (a.k.a. hare MYXV; ha-MYXV), emerged and caused myxomatosis-like disease with high mortality in Iberian hares, European brown hares, and European rabbits. This variant contains an approximately 2.8-kb insertion of a recombination cassette within the M009L gene encoding four additional genes, including the C7-like host range gene, M159L. M159 is essential for replication of MYXV-Tol in hare cells and is likely a key determinant of its pathogenicity in both hares and rabbits. Here, we compared the pathogenicity of wild-type MYXV-Tol (vMyx-Tol), an M159 deletion strain (vMyx-Tol-M159KO), and the classical MYXV-Lau strain (vMyx-Lau) in European rabbits. All three viruses caused systemic disease; however, vMyx-Tol and vMyx-Tol-M159KO produced clinical signs distinct from classical myxomatosis. Infection with vMyx-Tol and vMyx-Tol-M159KO was characterized by the absence of the typical primary and secondary nodular lesions, and caused severe edema, marked fluid accumulation, lymphocyte infection, and significantly reduced or no virus-neutralizing antibody responses. The disease caused by both vMyx-Tol and vMyx-Tol-M159KO progressed rapidly within 9-11 days, resulting in animals reaching humane euthanasia endpoints like vMyx-Lau. Deletion of M159 did not significantly alter MYXV-Tol pathogenicity in rabbits. Collectively, these findings demonstrate that MYXV-Tol has evolved to cause an atypical, amyxomatous-like acute to hyperacute disease in European rabbits and likely in hares. SignificanceNatural evolution enables viruses to cross species barriers and adapt to new hosts. Myxoma virus (MYXV), released in the 1950s in Australia and Europe as a biocontrol agent against European rabbits, became a classic model for real-time monitoring of virus evolution, virulence, and host adaptation. Although MYXV is typically host-restricted, a newly emerged natural isolate, MYXV-Tol, causes lethal disease in both hares and rabbits. Here, we show that MYXV-Tol induces an atypical, amyxomatous-like disease characterized by the absence of nodular lesions, severe edema, lymphocyte infection, and markedly reduced virus-neutralizing antibody responses. These findings reveal previously unrecognized virus-host interactions that shape disease outcome and provide new insight into the mechanisms driving viral adaptation and evolution.

microbiology↗

bioRxiv2026

Quantifying the evolutionary potential for Delta Smelt persistence in a warming habitat

Long-term persistence of managed species will depend, in part, on whether the species harbors the physiological or genetic potential to adjust to warming temperatures, and whether relevant genetic variation is modified by management practices. The critically endangered Delta Smelt (Hypomesus transpacificus) is intensively managed, but little is known about the presence of genetic variation for resistance to elevated temperature, which will be important to maintain for their persistence in a rapidly warming future. Using a pedigree and whole genome sequencing data, we characterized the genetic variation and genomic architecture for CTMax (as a metric of upper thermal tolerance) across control and elevated rearing temperatures, alongside covarying traits (body size, degree of hatchery ancestry). Warmer rearing temperatures increased CTMax through acclimation but also resulted in reduced additive genetic variation for the trait, which could constrain adaptation under thermal stress. We found that larger fish had reduced CTMax, although this effect was diminished at elevated temperatures. We observed modest heritability for CTMax at rearing temperatures of 15{degrees}C and 18{degrees}C (0.26 and 0.16, respectively), but only a limited number of loci were identified that had consistent effects on CTMax across rearing temperatures. Instead, the genomic basis of thermal tolerance was highly dependent on rearing temperature (many loci detected with a GxE effect). The influence of domestication selection was indicated by changes in allele frequency, and divergence in upper thermal tolerance and plasticity, between low and high hatchery ancestry groups. Minimal overlap between loci associated with domestication and CTMax suggests that these traits possess separate genetic underpinnings. Knowledge of genetic variation supporting ecologically relevant physiological variation may be useful for refuge management and may inform supplementation in an ever-warming environment.

evolutionary biology↗

bioRxiv2026

Cross-Cancer Profiling of Cadherin-1 Reveals Context-Dependent Epithelial-Mesenchymal Transition Decoupling, Immune Heterogeneity, and Prognostic Variability in Epithelial Cancers

BackgroundCDH1 (E-cadherin) is a key epithelial adhesion molecule traditionally associated with tumor suppression and epithelial-mesenchymal transition (EMT). However, its roles across cancers remain incompletely understood, particularly within multilayer regulatory contexts involving genomic, epigenetic, transcriptional, and immune mechanisms. MethodsCDH1 expression, survival associations, EMT-correlated gene profiles (VIM, SNAI1, ZEB1), immune infiltration patterns, immune checkpoint correlations (PDCD1, CD274, CTLA4), promoter methylation, and genomic alterations were assessed across five epithelial cancers, breast invasive carcinoma (BRCA), colon adenocarcinoma (COAD), lung adenocarcinoma (LUAD), ovarian cancer (OV), and stomach adenocarcinoma (STAD). Cross-platform validation was performed using TCGA/GDC datasets, GEPIA2, UALCAN, TIMER, KM Plotter, cBioPortal, and g:Profiler. ResultsCDH1 was overexpressed but showed variable prognostic significance; higher expression predicted better survival in COAD, LUAD and STAD, worse survival in BRCA and had no impact in OV. Classic inverse relationships between CDH1 and VIM or ZEB1 were evident only in STAD, and SNAI1 showed no consistent association. Immune infiltration patterns were tumor-specific, ranging from cytotoxic T-cell dominance in LUAD to macrophage-rich profiles in OV; immune checkpoint correlations were similarly context-dependent. Co-expressed genes were enriched for endomembrane transport rather than adhesion pathways. Promoter methylation patterns varied by cancer, whereas genomic alterations of CDH1 were rare. ConclusionsCDH1 does not function as a universal epithelial or EMT marker across epithelial cancers. Instead, its associations with EMT, immune contexture, methylation, and prognosis are context-dependent, supporting a model of CDH1 as a heterogeneous regulator of epithelial plasticity. These findings challenge single-function interpretations and support cancer-specific CDH1 evaluation in translational research.

cancer biology↗

bioRxiv2026

First occurrence of Corynespora cassiicola infecting chia plant in Bangladesh and its sensitivity to selected fungicides

Chia (Salvia hispanica L.) is an emerging crop in Bangladesh valued for its medicinal properties and economic significance. In March 2024, target spot-like symptoms were observed in an experimental chia field (24.75{degrees} N, 90.50{degrees} E) at Bangladesh Agricultural University in Mymensingh, Bangladesh with disease incidence ranging from 23% to 47% across approximately 0.25 ha. Initially appearing as brick-red spots, these symptoms developed into target-shaped concentric rings, affecting leaves, stems, and inflorescences. A total of 24 fungal isolates were recovered from infected tissue; two representative isolates (BGECh-3 and BGECh-4) were randomly selected for details characterization. Pathogen identity was established through morphological traits, multilocus phylogenetic analysis of internal transcribed spacer (ITS) and elongation factor 1-alpha (EF-1) genes sequence, and pathogenicity confirmation through Kochs postulates, collectively identifying the causal agent as Corynespora cassiicola. The isolates demonstrated a broad host range, successfully infecting brinjal, chili, bottle gourd, country bean, tomato, and soybean. In vitro fungicide sensitivity assays with seven commercial fungicides showed that both isolates were highly sensitive to Goldzim (50% carbendazim), which completely inhibited mycelial growth at 10 {micro}g mL-{superscript 1}. Conza (10% Hexaconazole) and Amister top (18.2% azoxystrobin + 11.4% difenoconazole) reduced growth by up to 85% and 67%, respectively at equal concentration. Other fungicides showed comparatively lower efficacy even at higher concentrations. This study represents the first report of target spot disease of chia caused by C. cassiicola in Bangladesh and provides insights for effective disease management strategies.

molecular biology↗

bioRxiv2026

Reprogramming of Lipid Metabolism by FLASH Radiotherapy Selectively Protects Radiosensitive Normal Tissues

FLASH radiotherapy, delivered at ultra-high dose rates exceeding 100 Gy/s, spares normal tissues while maintaining tumor control, yet the molecular mechanisms underlying this differential response remain poorly understood. Here we employed spatial and bulk multi-omics to investigate lipid and protein remodeling in tongue tissue and Mouse oral carcinoma 2 (MOC2) tumors at two weeks post-irradiation with FLASH or conventional dose-rate (CONV) proton radiotherapy. Bulk lipidomics revealed that CONV irradiation induced marked triglyceride (TG) depletion in tongue tissue, whereas FLASH attenuated this depletion. Spatial lipidomics using MALDI-MSI demonstrated that this TG loss was spatially restricted to minor salivary glands, identifying these radiosensitive structures as focal points of radiation-induced lipid damage. Additionally, FLASH irradiation uniquely promoted increases in membrane phospholipids and their lysophospholipid intermediates, consistent with active phospholipid turnover rather than passive damage avoidance. Proteomics revealed divergent metabolic programs: CONV activated a destructive cascade characterized by Ces1d depletion, Acox1-mediated peroxisomal {beta}-oxidation, and Acot7-driven fatty acid overflow, collectively defining a lipid droplet collapse; whereas FLASH engaged a protective program featuring Mgll suppression, Apoe-mediated triglyceride redistribution, and Lypla2-mediated lysophospholipid clearance. We propose a lipid metabolic reprogramming hypothesis in which FLASH not only minimizes acute oxidative damage but actively reprograms lipid metabolism to preserve lipid droplet stores and promote membrane remodeling. These findings provide a putative molecular foundation for the FLASH effect and support published data on the protection of normal tissues.

cancer biology↗

bioRxiv2026

Targeting collagen biosynthesis by small molecules inhibiting the function of the peptide-substrate-binding domain of collagen prolyl 4-hydroxylases

Collagen prolyl 4-hydroxylase (C-P4H) is an essential enzyme in collagen synthesis and known to be a potential target for drugs that prevent excess collagen formation. Currently known C-P4H inhibitors target the catalytic site of C-P4H, being analogues of 2-oxoglutarate (2OG). However, in mammalian cells there are many other 2OG-dependent dioxygenases with a highly similar catalytic domain, which limits the selective specificity of drugs targeting C-P4H activity. The peptide-substrate-binding (PSB) domain is unique for the C-P4H family and known to be important for the catalytic efficiency of C-P4H. Therefore, interfering with peptide binding to the PSB domain might allow more specific inhibition of the hydroxylation activity of C-P4Hs. We developed a robust FRET-based high-throughput screening assay (Z > 0.73) based on PSB-peptide interactions. This assay was used to screen a peptidomimetic library of 15614 compounds with the PSB domains of C-P4H isoforms I and II. A hit compound (OUL-PSBi-001) was identified with IC50s of 40 {micro}M and 62 {micro}M for PSB-I and PSB-II, respectively. We also showed that this compound indeed inhibits the catalytic activity of the full-length CP4H-I and -II. This FRET assay provides a new strategy for finding selective inhibitors for the treatment of fibrotic diseases and cancer.

molecular biology↗

bioRxiv2026

Structural basis of canonical TIR-NLR activation in plant innate immunity

In plants, intracellular NLRs (nucleotide-binding leucine-rich repeat receptors) detect pathogen effector proteins, form oligomeric resistosomes, and activate ETI (effector-triggered immunity). NLRs contain N-terminal signaling, central NB-ARC (nucleotide-binding) and C-terminal LRR (leucine-rich repeat) domains. NLRs with N-terminal TIR (Toll/interleukin-1 receptor) domains (TNLs) hydrolyze NAD+ (nicotinamide adenine dinucleotide) to generate signaling molecules. We determined cryo-EM structures of flax M, a canonical non C-JID (C-terminal jellyroll/Ig-like domain) TNL, in both monomeric autoinhibited conformation, and tetrameric resistosome after activation by its rust fungal effector AvrM-A. AvrM-A homodimers dissociate into monomers to bind directly to the LRR and NB-ARC domains in the M resistosome. The resistosome structure includes a non-hydrolyzable NAD+ analogue, revealing the substrate NAD+ recognition mechanism by the TIR domains. M cleaves NAD+ and generates the same signaling compounds as the related flax TNL, L6. Our findings explain the mechanism of TNL signaling, and provide a basis for rational engineering of disease-resistant crops.

plant biology↗

bioRxiv2025

Stage-specific screening reveals complex resilience pathways to cold stress in rice

Rice cultivation in Bangladeshs northern and northeastern regions face a critical challenge - cold stress during the seedling and reproductive stages, which can drastically reduce yield. As a precursor to generate improved elite lines, a diverse panel of rice germplasm was screened to identify genotypes with resilience to low temperature at both key developmental phases. Seedling-stage tolerance was assessed using an artificial cold-water tank, while reproductive-stage tolerance was evaluated under both natural field conditions and controlled cold screening facilities. Performance was measured through a combination of quantitative traits (plant height, days to heading, panicle length) and qualitative indicators (panicle degeneration, panicle exsertion, spikelet fertility). Two breeding lines - BR8907-B-1-2-CS1-4-CS2-P3-4 and BR8909-B-12-2-CS1-4-CS2-P2-3-2, demonstrated seedling-stage cold tolerance with minimum leaf discoloration and the highest survival rate across three experimental batches. Five genotypes (Bhutan, IR83222-F11-173, Rata Boro, BRRI dhan74, BR11712-4R-227) showed tolerance during the reproductive stage. Three lines (Bhutan, BR11712-4R-227, and BR12266-44-11-32-5-1-1-HR10-B) showed moderately tolerant to tolerant across both stages. Six genotypes, including BR10317-5R-25, IR18A1859, and BRRI dhan28 were consistently vulnerable to cold stress at both stages. Principal Component Analysis (PCA) revealed that under field conditions, both seedling and reproductive traits contributed to shared components - suggesting overlapping physiological mechanisms. However, under controlled environments, the traits separated distinctly, pointing to stage-specific genetic control. These results are consistent with reports of distinct QTLs contributing to cold tolerance at different stages, highlighting the complex nature of cold tolerance and informing breeding strategies for enhanced cold resilience in rice.

plant biology↗

bioRxiv2025

Evolutionary Variation of Poxvirus Genome Architecture

Poxviruses (PXV) are large double-stranded DNA viruses (dsDNA) that infect and cause disease in a wide variety of hosts, including humans.. They are studied as models to understand host-specific disease and they have a wide variety of applications in biotechnology, including vaccines, oncolytic virotherapy, and immunotherapy. Despite a nearly fourfold variation in genome sizes across the Poxviridae family, the basic genome architectural features driving their evolution remain poorly understood. In this study of the summated poxvirus genome sequence database, we report that while only a weak negative correlation exist between viral coding densities and genome sizes, we detected a strong positive correlation between the number of assigned open reading frames (ORF) and genome sizes. We observe an inflection point at a genome size of 229 kb, above or below with the percentage of genes encoding secreted proteins increasing with genome size, and the percentage of predicted cytoplasmic proteins decreasing with genome size. Additionally, we observed a weak positive correlation between the potential of transcript overlap that would be expected to generate dsRNA and genome size. Unexpectedly, we observed a significant positive correlation between coding density and GC-content in mpox virus isolates (R2 = 0.799). Further analysis illustrated a rise in both GC-content and coding density of mpox isolates between 2022 and 2024. Codon usage bias was observed to be clustered by virus families, with tryptophan being the least utilized amino acid across all poxviruses. Protein distribution analysis revealed a right-skewed distribution of poxviral predicted ORFs, with the 150 - 250 amino acid cohort containing the highest number of viral proteins. Finally, we observe a significant positive correlation between ITR sizes and duplicate gene clusters (R2 = 0.679). Together, these architectural findings outline the constraints and adaptive pathways governing poxviral evolution and biology. ImportanceThis study establishes a family genome design rulebook for poxviruses and illustrates how these rules might be linked with their biology and evolution. We demonstrate that genome growth is accompanied by a modest increase in noncoding DNA and an increase in extracellular proteome investment. We further demonstrate that ITR expansions correlate with duplicate gene clusters, rather than genome size, indicating that ITRs serve as hubs of innovation. Our results provide a standard for generating hypotheses and experiments with poxviruses. This work also introduces matrices for within-family viral comparisons.

microbiology↗

bioRxiv2025

The centriculum, a membrane that surrounds C. elegans centrosomes, acts as a microtubule filter

Centrosomes are cytoplasmic microtubule-nucleating structures. They are considered membraneless organelles, but in several cell types they are surrounded by ER-derived membrane. In C. elegans early embryos, this membrane forms a dense membrane reticulum, named the centriculum, that affects centrosome structure and microtubule nucleating capacity. The centriculum is adjacent to the centrosomes pericentriolar material (PCM) and to abundant, short peri-centrosomal microtubules. Here we show that when microtubule abundance is reduced, centriculum and PCM size decrease, while the density of the PCM protein SPD-5 increases, suggesting that the PCM can be compacted. We further show that centriculum size is determined by microtubules, and that the centriculum likely limits the length of peri-centrosomal microtubules. Finally, we find that the centriculum is more porous where spindle microtubules pass compared to where astral microtubules pass. These data are consistent with the centriculum serving as a microtubule filter, blocking the extension of most, but not all, centrosome-nucleated microtubules. Finally, if microtubule-centriculum collisions result in microtubule catastrophe, the filter function of the centriculum could also explain the high concentration of soluble tubulin at the C. elegans centrosome. Summary StatementThe centriculum is a centrosome-associated membrane reticulum in C. elegans embryos. This study shows that its size depends on microtubules and that it may act as a filter, limiting microtubule growth.

cell biology↗

bioRxiv2025

Highly and lowly domesticated endangered fish from a conservation hatchery diverge in their thermal physiology, transcriptome, and methylome

Conservation hatcheries aim to produce fish for supplementation of wild populations, but hatchery environments may drive phenotypic divergence from wild fish. These diverged traits may have reduced fitness in the wild, which could compromise wild population sustainability and evolutionary potential, such as in response to climate change. Delta smelt are a critically endangered fish species that are safeguarded against extinction with a hatchery refuge population. We investigated whether elevated rearing temperature through larval development adjusted upper thermal tolerance limits (acclimation) in Delta smelt, whether upper thermal tolerance and plasticity (acclimation ability) differed between fish with old or recent hatchery ancestry (high or low domestication index; DI), and temperature and DI effects on liver transcriptome and methylome patterns. We observed that elevated rearing temperatures induced higher thermal tolerance (acclimation). Individuals with higher DI also had higher upper thermal tolerances, but high DI families had reduced thermal plasticity between rearing temperatures. This is consistent with domestication causing heritable elevation of upper thermal tolerance but at the cost of reduced thermal plasticity. High and low DI fish were differentiated in both genetic variation and methylome variation, suggesting the influence of both during domestication. But methylome differences distinguishing high and low DI fish did not overlap with temperature-induced methylome changes, and do not appear to be stably inherited in the hatchery. We conclude that domestication selection has altered thermal physiology within the refuge hatchery despite careful genetic management, underpinned by shifts in the transcriptome and methylome. These changes could affect Delta smelt fitness upon reintroduction to habitats that continue to warm, and show that physiological traits can diverge even within carefully genetically managed hatchery populations.

evolutionary biology↗

bioRxiv2025

Tomosyn-2 Regulates Postnatal β-Cell Expansion and Insulin Secretion to Maintain Glucose Homeostasis.

The transition from proliferative to functionally mature {beta}-cells is a critical developmental process, yet the molecular mechanisms that coordinate this shift remain poorly understood. Here, we identify Tomosyn-2 as a key regulator of {beta}-cell maturation. Tomosyn-2 expression declines with age in mouse islets, coinciding with enhanced biphasic glucose-stimulated insulin secretion (GSIS) and reduced {beta}-cell proliferation. Genetic deletion of Tomosyn-2 improves glucose tolerance, elevates plasma insulin levels, and augments islet insulin secretion, without altering systemic insulin sensitivity. Mechanistically, Tomosyn-2 interacts with syntaxin-1A (Stx1A) to inhibit insulin granule exocytosis by limiting SNARE complex formation. Transcriptomic and network analyses reveal that Tomosyn-2 loss reprograms gene expression to strengthen the coupling between insulin secretion and proliferative pathways. Its deletion also reduces {beta}-cell proliferation and mass expansion, suppresses cell cycle and Akt1 signaling, and promotes {beta}-cell identity, maturation, and altered islet architecture. These findings identify Tomosyn-2 as a crucial molecular switch that orchestrates the balance between proliferation and functional maturation during postnatal {beta}-cell development.

cell biology↗

bioRxiv2025

Shape-Shifting Conotoxins Reveal Divergent Pore-Targeting Mechanisms in Nicotinic Receptors

The neuronal 7 nicotinic acetylcholine receptor (7-nAChR) and muscle-type nicotinic acetylcholine receptor (mt-nAChR) are pivotal in synaptic signaling within the brain and the neuromuscular junction respectively. Additionally, they are both targets of a wide range of drugs and toxins. Here, we utilize cryoEM to delineate structures of these nAChRs in complex with the conotoxins ImI and ImII from Conus imperialis. Despite nominal sequence divergence, ImI and ImII exhibit discrete binding preferences and adopt drastically different conformational states upon binding. ImI engages the orthosteric sites of the 7-nAChR, while ImII forms distinct pore-bound complexes with both the 7-nAChR and mt-nAChR. Strikingly, ImII adopts a compact globular conformation that binds as a monomer to the 7-nAChR pore and as an oblate dimer to the mt-nAChR pore. These structural characterizations advance our understanding of nAChR-ligand interactions as well as the subtle sequence variations that result in dramatically altered functional outcomes in small peptide toxins. Importantly, these results further elucidate the broad nature of cone snail toxin activities and highlight how targeted molecular evolution can give rise to functionally similar activities with surprisingly diverse mechanisms of action.

neuroscience↗

bioRxiv2025

Poxvirus attack of anti-viral defense pathways unleashes an effector-triggered NF-κB response

Effector-triggered immunity (ETI) is a form of pathogen sensing that involves detection of pathogen-encoded virulence factors or "effectors". To discover novel ETI pathways in mammals, we developed a screening approach in which individual virulence factors are expressed in human monocytes and transcriptional responses are assessed by RNA-seq. Using this approach, we identify a poxvirus effector, myxoma virus M3.1, which elicits an anti-viral NF-{kappa}B response. We find that NF-{kappa}B is unleashed by an ETI pathway that senses M3.1 attack of two anti-viral complexes: ZAP and TBK1. NF-{kappa}B activation occurs because the proteins inhibited by M3.1-- N4BP1, ZC3H12A, and TBK1--are negative regulators of NF-{kappa}B. Our results illustrate how negative regulators can function as pathogen sensors and establish a systematic approach for the discovery of ETI pathways.

immunology↗

bioRxiv2025

Enterococcus faecium MBBL3 Exhibits Promising Probiotic Potential and Antimicrobial Efficacy Against Bovine Mastitis-Associated Escherichia coli and Klebsiella pneumoniae

Enterococcus faecium, a promising probiotic, combats pathogens, supports gut health, strengthens immunity, and provides a natural approach to address the escalating global challenge of antimicrobial resistance. This study aimed to investigate the genome of E. faecium MBBL3, isolated from healthy cow milk, to assess its probiotic potential and antimicrobial activity against pathogens causing bovine mastitis. The strain was analyzed through whole genome sequencing, along with in-vitro and in-silico assessments were conducted to determine its antimicrobial efficacy against bovine mastitis pathogens, Klebsiella pneumoniae MBBL2 (Kp MBBL2) and Escherichia coli MBBL4 (Ec MBBL4). The genome assembly and functional annotations uncovered many important probiotic traits in MBBL3, where genome comparison revealed its high genetic similarity with other Enterococcus strains. MBBL3 demonstrated the ability to ferment a wide range of carbohydrates and possessed 76 carbohydrate-active enzyme-related genes, including five key CAZy families namely GH73, GH18, CBM50, CE4, and AA10. It also possessed importance genes for bile salt and acid tolerance, stress resistance, and surface adhesion. Additionally, MBBL3 contained metabolite regions involved in the biosynthesis of antimicrobial compounds such as 2,4-DAPG, aborycin, enterocin NKR-5-3B, and sodorifen, and bacteriocin gene clusters for sactipeptides, Enterolysin_A, and UviB. Safety assessments indicated low pathogenic potential, while in-vitro assays demonstrated antibiotic susceptibility and suppressed the growth of Kp MBBL2 and Ec MBBL4, respectively. Its bacteriocin compound Enterolysin_A exhibited strong molecular interactions with virulence proteins of these mastitis pathogens. Therefore, the promising probiotic potential and antimicrobial efficacy of E. faecium MBBL3, especially against mastitis pathogens combined with its safety, position it as a valuable candidate for therapeutic applications. Key pointsO_LIE. faecium MBBL3 genosme showed high similarity with other species of this genera. C_LIO_LIGenetic makeup of MBBL3 revealed its ability to survival and adaptation in different niches including hosts gut. C_LIO_LIIn-vitro and in-silico study results, along with several genes linked to antimicrobials demonstrated its ability to combat against mastitis pathogens. C_LI

microbiology↗

bioRxiv2024

Divergence in poxvirus-encoded E3-like proteins can dictate poxvirus activation of cellular necroptosis

Poxviruses encode a plethora of proteins to modulate diverse cellular responses against viruses. Poxvirus-encoded E3-like proteins are multifunctional, regulating diverse cellular antiviral responses. The canonical Vaccinia E3-like proteins have two domains: an N-terminal Z-form nucleic acid binding domain (Z-BD) and a C-terminal double-stranded RNA binding domain (dsRNA-BD)-.Using protein sequence and structural homology modeling, we identified the presence of dsRNA- BD-containing proteins in all the poxviruses except Avipoxviruses, Salmon poxvirus and Entemopoxviruses. However, the acquisition of these proteins likely happened under three distinct events. Using structural homology modeling and FATCAT score, we can classify E3-like proteins in three distinct categories: i) the E3-like proteins with highly conserved dsRNA-BD but with or without the N-terminal domain, present in most poxviruses; ii) unconventional E3-like proteins with highly diverged dsRNA-BD, present in Macropoxvirus and Molluscipoxvirus and iii) E3-like protein with dsRNA-BD that may have different origin present in Crocodilepoxvirus.12-52-6 Members of Leporipoxvirus, Waddenpoxvirus, Cetaceanpoxvirus, and selected members of Orthopoxvirus contain E3-like proteins missing the N-terminal Z-BD required for necroptosis inhibition. Additionally, using Alphafold, we show that the Z-BD of Chordopoxviruses E3-like proteins is structurally more variable than the ds-RNA binding domain. Compared to members of Orthopoxviruses-Vaccinia virus (VACV) and Cowpox virus (CPXV) that have been shown to inhibit necroptosis and contain an N-terminus Z-BD of the canonical E3 protein, our results show that members of leporipoxviruses induce necroptosis in human and mouse necroptosis competent cell lines. Furthermore, myxoma virus (MYXV) infection activates RIP1 and RIP3-mediated necroptosis in both human and mouse necroptosis-competent cells. These data suggest that Leporipoxviruses lack countermeasures to necroptosis compared to Orthopoxviruses that encode multiple key regulators of necroptosis, possibly due to a lack of selective pressure within the viral host species (Lagomorphs). Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/627069v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@132ce9borg.highwire.dtl.DTLVardef@9a459borg.highwire.dtl.DTLVardef@4fc88dorg.highwire.dtl.DTLVardef@1f7ac6c_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗