Biology subjects

Gonen, S.

Publications and source records attributed to Gonen, S..

13 recordsLinked to original sources

bioRxiv2026

Capsular Polysaccharide Safeguards a Prophage-Bacterium Symbiosis by Preventing Collateral Attack and Promoting Viral Transmission

Many symbioses exist along a continuum from cooperation to conflict. Latent bacterial viruses known as prophages embody this duality. Acting as both partner and predator, they can enhance bacterial fitness while retaining the capacity to kill their hosts through lytic replication. Yet what determines the balance between cooperation and conflict in prophage-bacterium symbioses, and how these associations avoid collapse, remains poorly characterized. To identify mechanisms that stabilize prophag-bacterium partnerships, we used experimental evolution to perturb a natural association through repeated cycles of transmission and reinfection. This perturbation consistently selected mutant hosts lacking capsular polysaccharide production and exposed a hidden conflict that proved detrimental to both partners. During lytic outbreaks, host cells suffered lethal collateral prophage attack while dispersing virions became entrapped on neighboring cells and lysis debris, severely restricting transmission. Genetic and imaging-based studies revealed that capsular polysaccharides suppress these maladaptive interactions by limiting phage readsorption at the cell surface. We term this host-mediated safeguard the Hyperion effect, after the Greek Titan of light. Hyperion interactions enable phages to radiate outward from host populations, thereby averting collateral attack and promoting viral transmission. Our findings demonstrate that conflicts between prophages and their hosts can extend beyond individual cells to whole populations, with consequences that scale to shape patterns of prophage spread and microbial community assembly. More broadly, our work illustrates how mutually beneficial prophage-bacterium interactions can arise not only through cooperation, but also through the suppression of mutually detrimental conflicts.

microbiology↗

bioRxiv2025

Optimization of reference population for imputation of low-density SNPs panel for genomic prediction in Atlantic salmon.

In recent years many advances have been made towards developing cost-efficient low-density genomic tools for a wider implementation of genomic selection in aquaculture breeding programmes. Genotype imputation from very low-density (LD) SNP panels of just a few hundred markers to high-density (HD) SNP panels has become a promising strategy to reduce the cost of genotyping while maintaining accurate genomic prediction. The objective of this study is to assess the impact of the makeup of HD-genotyped reference populations on i) the accuracy of imputation for LD-genotyped individuals and ii) the accuracy of genomic prediction for three traits of importance in Atlantic salmon production: growth, resistance to cardiomyopathy syndrome and resistance to pancreas disease. An Atlantic salmon population genotyped with a 47K SNP array was used for the study, along with an in silico LD panel of 554 SNPs. Five reference population scenarios for imputation were tested, which could include only the parents of the candidates for selection, a combination of parents and candidates, or just candidates. All scenarios resulted in highly accurate imputation rates (over 80%) except when the HD reference population was only composed of selection candidates. Nonetheless, the accuracy of imputation barely had an impact on the accuracy of genomic prediction, as the imputed datasets performed very similarly to the HD-panel. Adding a proportion of the offspring to the reference population, in addition to the parents, did not result in any benefit in terms of genomic prediction. Imputation is a cost-effective and robust option for genomic selection in aquaculture.

genetics↗

bioRxiv2025

Bacteria deliver a microtubule-binding protein into mammalian cells to promote colonization

Pathogenic Bordetella bacteria infect the ciliated respiratory epithelia of mammalian and avian hosts. Several bacterial proteins mediate host cell adhesion, but filamentous hemagglutinin (FhaB) is a principal adhesin because mutants lacking this protein exhibit profound colonization defects. Here, we show that FhaB carries a C-terminal microtubule-binding domain (FhaB-CT), which is translocated into the host-cell cytoplasm to promote bacterial colonization. Cryogenic electron microscopy of microtubule-bound FhaB-CT shows that the domain binds primarily to -tubulin through a network of polar interactions. Live-cell microscopy of infected tracheal explants reveals that FhaB-CT delivery is required for Bordetella to occupy a niche at the base of cilia on airway epithelia. Finally, we demonstrate that the microtubule-binding domain is required for long-term colonization of the mouse nasal cavity by B. pertussis. These observations suggest that the FhaB-CT domain is delivered into motile cilia, where it interacts with axonemal microtubules. We propose that Bordetella initially adhere to the tips of cilia, then deploy multiple FhaB adhesin molecules to migrate to the base of the cilial forest. This mechanism enables Bordetella to resist removal by the mucociliary escalator that clears the respiratory tract of microbes and debris.

microbiology↗

bioRxiv2024

Structural basis of inhibition of human NaV1.8 by the tarantula venom peptide Protoxin-I

Voltage-gated sodium channels (NaVs) selectively permit diffusion of sodium ions across the cell membrane and, in excitable cells, are responsible for propagating action potentials. One of the nine human NaV isoforms, NaV1.8, is a promising target for analgesics, and selective inhibitors are of interest as therapeutics. One such inhibitor, the gating-modifier peptide Protoxin-I derived from tarantula venom, blocks channel opening by shifting the activation voltage threshold to more depolarised potentials, but the structural basis for this inhibition has not previously been determined. Using monolayer graphene grids, we report the cryogenic electron microscopy structures of full-length human apo-NaV1.8 and the Protoxin-I-bound complex at 3.1 [A] and 2.8 [A] resolution, respectively. The apo structure shows an unexpected movement of the Domain I S4-S5 helix, and VSDI was unresolvable. We find that Protoxin-I binds to and displaces the VSDII S3-S4 linker, hindering translocation of the S4II helix during activation.

biophysics↗

bioRxiv2024

Enhanced Suppression of Stenotrophomonas maltophilia by a Three-Phage Cocktail: Genomic Insights and Kinetic Profiling

In our era of rising antibiotic resistance, Stenotrophomonas maltophilia (STM) is an understudied, gram-negative, aerobic bacterium widespread in the environment and increasingly causing opportunistic infections. Treating STM infections remains difficult, leading to an increase in disease severity and higher hospitalization rates in people with Cystic Fibrosis (pwCF), cancer, and other immunocompromised health conditions. The lack of effective antibiotics has led to renewed interest in phage therapy; however, there is a need for well-characterized phages. In response to an oncology patient with a respiratory infection, we collected 18 phages from Southern California wastewater influent that exhibit different plaque morphology against STM host strain B28B, cultivated from a blood sample. Here, we characterize the genomes and life cycle kinetics of our STM phage collection. We hypothesize that genetically distinct phages give rise to unique lytic life cycles that can enhance bacterial killing when combined into a phage cocktail compared to the individual phages alone. We identified three genetically distinct clusters of phages, and a representative from each group was screened for potential therapeutic use and investigated for infection kinetics. The results demonstrated that the three-phage cocktail significantly suppressed bacterial growth compared to individual phages when observed for 48 hours. We also assessed the lytic impacts of our three-phage cocktail against a collection of 46 STM strains to determine if a multi-phage cocktail can expand the host range of individual phages. Our phages remained strain-specific and infect >50% of tested strains. The multi-phage cocktail maintains bacterial growth suppression and prevents the emergence of phage-resistant strains throughout our 40-hour assay. These findings suggest specialized phage cocktails may be an effective avenue of treatment for recalcitrant STM infections resistant to current antibiotics. IMPORTANCEPhage therapy could provide a vital strategy in the fight against antimicrobial resistance (AMR) bacterial infections; however, significant knowledge gaps remain. This study investigates phage cocktail development for the opportunistic pathogen Stenotrophomonas maltophilia (STM). Our findings contribute novel phages, their lytic characteristics, and limitations when exposed to an array of clinically relevant STM strains. Eighteen bacteriophages were isolated from wastewater influent from Escondido, California, and subjected to genomic analysis. We investigated genetically distinct phages to establish their infection kinetics and developed them into a phage cocktail. Our findings suggest that a genetically distinct STM phage cocktail provides an effective strategy for bacterial suppression of host strain B28B and five other clinically relevant STM strains. Phage therapy against STM remains poorly understood, as only 39 phages have been previously isolated. Future research into the underlying mechanism of how phage cocktails overwhelm the host bacteria will provide essential information that could aid in optimizing phage applications and impact alternative treatment options.

microbiology↗

bioRxiv2024

Phollow: Visualizing Gut Bacteriophage Transmission within Microbial Communities and Living Animals

Bacterial viruses (known as "phages") shape the ecology and evolution of microbial communities, making them promising targets for microbiome engineering. However, knowledge of phage biology is constrained because it remains difficult to study phage transmission dynamics within multi-member communities and living animal hosts. We therefore created "Phollow": a live imaging-based approach for tracking phage replication and spread in situ with single-virion resolution. Combining Phollow with optically transparent zebrafish enabled us to directly visualize phage outbreaks within the vertebrate gut. We observed that virions can be rapidly taken up by intestinal tissues, including by enteroendocrine cells, and quickly disseminate to extraintestinal sites, including the liver and brain. Moreover, antibiotics trigger waves of interbacterial transmission leading to sudden shifts in spatial organization and composition of defined gut communities. Phollow ultimately empowers multiscale investigations connecting phage transmission to transkingdom interactions that have the potential to open new avenues for viral-based microbiome therapies.

microbiology↗

bioRxiv2024

Delta-Conotoxin Structure Prediction and Analysis through Large-scale Comparative and Deep Learning Modeling Approaches

The {delta}-conotoxins, a class of peptide produced in the venom of cone snails, are of interest due to their ability to inhibit the inactivation of voltage-gated sodium channels causing paralysis and other neurological responses, but difficulties in their isolation and synthesis have made structural characterization challenging. Taking advantage of recent breakthroughs in computational algorithms for structure prediction that have made modeling especially useful when experimental data is sparse, this work uses both the deep-learning based algorithm AlphaFold and comparative modeling method RosettaCM to model and analyze 18 previously uncharacterized {delta}-conotoxins derived from piscivorous, vermivorous, and molluscivorous cone snails. The models provide useful insights into structural aspects of these peptides and suggest features likely to be significant in influencing their binding and different pharmacological activities against their targets, with implications for drug development. Additionally, the described protocol provides a roadmap for the modeling of similar disulfide-rich peptides by these complementary methods.

biochemistry↗

bioRxiv2020

Structure of human ferroportin reveals molecular basis of iron homeostasis

The serum iron level in humans is tightly controlled by the action of the hormone hepcidin on the iron efflux transporter ferroportin. Hepcidin negatively regulates iron absorption and recycling by inducing ferroportin internalization and degradation. Aberrant ferroportin activity can lead to diseases of iron overload, like hemochromatosis, or iron limitation anemias. Here, we determined cryogenic electron microscopy (cryo-EM) structures of ferroportin in lipid nanodiscs, both in the apo state and in complex with cobalt, an iron mimetic, and hepcidin. These structures and accompanying molecular dynamics simulations identify two divalent metal binding sites within the N- and C-domains of ferroportin. Hepcidin binds ferroportin in an outward-open conformation and completely occludes the iron efflux pathway. The carboxy-terminus of hepcidin directly contacts the divalent metal in the FPN C-domain. We further show that hepcidin binding to ferroportin is coupled to iron binding, with an 80-fold increase in hepcidin affinity in the presence of iron. These results suggest a new model for hepcidin regulation of ferroportin, where only iron loaded ferroportin molecules are targeted for degradation. More broadly, our structural and functional insights are likely to enable more targeted manipulation of the hepcidin-ferroportin axis in disorders of iron homeostasis.

biochemistry↗

bioRxiv2020

Phasing and imputation of single nucleotide polymorphism data of missing parents of bi-parental plant populations

This paper presents an extension to a heuristic method for phasing and imputation of genotypes of descendants in bi-parental populations so that it can phase and impute genotypes of parents of bi-parental populations that are fully ungenotyped or partially genotyped. The imputed genotypes of the parent are then used to impute low-density genotyped descendants of the bi-parental population to high-density. The extension works in three steps. First, it identifies whether a parent has no or low-density genotypes available and it identifies all of its relatives that have high-density genotypes. Second, using the high-density information of relatives, it determines whether the parent is homozygous or heterozygous for a given locus. Third, it phases heterozygous positions of the parent by matching haplotypes to its relatives. We implemented the new algorithm in an extension of the AlphaPlantImptue software and tested its accuracy of imputing missing parent genotypes in simulated bi-parental populations from different scenarios. We also tested the accuracy of imputation of the missing parents descendants using the true genotype of the parent and compared this to using the imputed genotypes of the parent. Our results show that across all scenarios, the accuracy of imputation of a parent, measured as the correlation between true and imputed genotypes, was > 0.98 and did not drop below [~] 0.96. The imputation accuracy of a parent was always higher when it was inbred than when it was outbred and when it had low-density genotypes. Including ancestors of the parent at HD, increasing the number of crosses and the number of high-density descendants all increased the accuracy of imputation. The high imputation accuracy achieved for the parent across all scenarios translated to little or no impact on the accuracy of imputation of its descendants at low-density. Key MessageNew fast and accurate method for phasing and imputation of SNP chip genotypes within diploid bi-parental plant populations.

genetics↗

bioRxiv2018

A family-based phasing algorithm for sequence data

This paper describes a family-based phasing algorithm, for variable-coverage sequence data, that first minimises phasing errors and then maximises the proportion of alleles phased. This algorithm is one of the essential tools that underpin an overall strategy for generating highly accurate sequence data on whole populations at low cost.\n\nThe algorithm is called AlphaFamSeq. It uses sequence data on the focal individual and at least two generations of ancestors to phase alleles. In the first step, AlphaFamSeq calculates allele probabilities using iterative peeling. In subsequent steps, the alleles are phased using heuristics deriving information from the sequence data of parents, grandparents and progenies and, if available, from other families in the pedigree. AlphaFamSeq was tested on a range of simulated data sets.\n\nAlphaFamSeq gives low phasing error rates and, if there is sufficient sequence information and haplotype sharing amongst individuals, it can give a high yield of correctly phased alleles.\n\nThe allele threshold had a large effect and window size had a small effect on performance. When all individuals in a single family were sequenced at different coverages the highest correctly phased alleles reached 90% of the possible maximum (98.9%) at ~1/6 of the maximum aggregate coverage. Adding sequence information from other related individuals increased the percentage of correctly phased alleles. Imputation performance was high across all allele frequencies (average correlation by marker of 0.94), except for a slight decrease at very low frequencies ([≤]0.01 MAF).\n\nWithin an overall strategy for generating highly accurate sequence data on whole populations at low cost the role of AlphaFamSeq is to provide very accurately phased haplotypes on focal individuals, who are individuals whose haplotypes are very common in the population.

genomics↗

bioRxiv2018

A heuristic method for fast and accurate phasing and imputation of single nucleotide polymorphism data in bi-parental plant populations

This paper presents a new heuristic method for phasing and imputation of genomic data in diploid plant species. Our method, called AlphaPlantImpute, explicitly leverages features of plant breeding programs to maximise the accuracy of imputation. The features are a small number of parents, which can be inbred and usually have high-density genomic data, and few recombinations separating parents and focal individuals genotyped at low-density (i.e. descendants that are the imputation targets). AlphaPlantImpute works roughly in three steps. First, it identifies informative low-density genotype markers in parents. Second, it tracks the inheritance of parental alleles and haplotypes to focal individuals at informative markers. Finally, it uses this low-density information as anchor points to impute focal individuals to high-density.\n\nWe tested the imputation accuracy of AlphaPlantImpute in simulated bi-parental populations across different scenarios. We also compared its accuracy to existing software called PlantImpute. In general, AlphaPlantImpute had better or equal imputation accuracy as PlantImpute. The computational time and memory requirements of AlphaPlantImpute were tiny compared to PlantImpute. For example, accuracy of imputation was 0.96 for a scenario where both parents were inbred and genotyped at 25,000 markers per chromosome and a focal F2 individual was genotyped with 50 markers per chromosome. The maximum memory requirement for this scenario was 0.08 GB and took 37 seconds to complete.

genomics↗

bioRxiv2017

Near-Atomic Cryo-EM Imaging of a Small Protein Displayed on a Designed Scaffolding System

Current single particle electron cryo-microscopy (cryo-EM) techniques can produce images of large protein assemblies and macromolecular complexes at atomic level detail without the need for crystal growth. However, proteins of smaller size, typical of those found throughout the cell, are not presently amenable to detailed structural elucidation by cryo-EM. Here we use protein design to create a modular, symmetrical scaffolding system to make protein molecules of typical size amenable to cryo-EM. Using a rigid continuous alpha-helical linker, we connect a small 17 kDa protein (DARPin) to a protein subunit that was designed to self-assemble into a cage with cubic symmetry. We show that the resulting construct is amenable to structural analysis by single particle cryo-EM, allowing us to identify and solve the structure of the attached small protein at near-atomic detail, ranging from 3.5 to 5 [A] resolution. The result demonstrates that proteins considerably smaller than the theoretical limit of 50 kDa for cryo-EM can be visualized clearly when arrayed in a rigid fashion on a symmetric designed protein scaffold. Furthermore, because the amino acid sequence of a DARPin can be chosen to confer tight binding to various other protein or nucleic acid molecules, the system provides a future route for imaging diverse macromolecules, potentially broadening the application of cryoEM to proteins of typical size in the cell.\n\nSignificance statementNew electron microscopy methods are making it possible to view the structures of large proteins and nucleic acid complexes at atomic detail, but the methods are difficult to apply to molecules smaller than about 50 kDa, which is larger than the size of the average protein in the cell. The present work demonstrates that a protein much smaller than that limit can be successfully visualized when it is attached to a large protein scaffold designed to hold 12 copies of the attached protein in symmetric and rigidly defined orientations. The small protein chosen for attachment and visualization can be modified to bind to other diverse proteins, opening up a new avenue for imaging cellular proteins by cryo-EM.

molecular biology↗

bioRxiv2017

A method for allocating low-coverage sequencing resources by targeting haplotypes rather than individuals

BackgroundThis paper describes a heuristic method for allocating low-coverage sequencing resources by targeting haplotypes rather than individuals. Low-coverage sequencing assembles high-coverage sequence information for every individual by accumulating data from the genome segments that they share with many other individuals into consensus haplotypes. Deriving the consensus haplotypes accurately is critical for achieving a high phasing and imputation accuracy. In order to enable accurate phasing and imputation of sequence information for the whole population we allocate the available sequencing resources among individuals with existing phased genomic data by targeting the sequencing coverage of their haplotypes.\n\nResultsOur method, called AlphaSeqOpt, prioritizes haplotypes using a score function that is based on the frequency of the haplotypes in the sequencing set relative to the target coverage. AlphaSeqOpt has two steps: (1) selection of an initial set of individuals by iteratively choosing the individuals that have the maximum score conditional to the current set, and (2) refinement of the set through several rounds of exchanges of individuals. AlphaSeqOpt is very effective for distributing a fixed amount of sequencing resources evenly across haplotypes, which results in a reduction of the proportion of haplotypes that are sequenced below the target coverage. AlphaSeqOpt can provide a greater proportion of haplotypes sequenced at the target coverage by sequencing less individuals, as compared with other methods that use a score function based on the haplotypes population frequency. A refinement of the initially selected set can provide a larger more diverse set with more unique individuals, which is beneficial in the context of low-coverage sequencing. We extend the method with an approach to filter rare haplotypes based on their flanking haplotypes, so that only those that are likely to derive from a recombination event are targeted.\n\nConclusionsWe present a method for allocating sequencing resources so that a greater proportion of haplotypes are sequenced at a coverage that is sufficiently high for population-based imputation with low-coverage sequencing. The haplotype score function, the refinement step, and the new approach of filtering rare haplotypes make AlphaSeqOpt more effective for that purpose than methods reported previously for reducing sequencing redundancy.

genomics↗