Biology subjects

Villa, E.

Publications and source records attributed to Villa, E..

At least 19 recordsLinked to original sources

bioRxiv2026

A bacteriophage split DNA polymerase incorporates a sliding clamp-derived processivity subunit

Viruses that infect bacteria, termed bacteriophages or phages, typically encode their own DNA replication machinery that rapidly generates many copies of the phage genomic DNA in an infected cell. Nucleus-forming phages of the chimallivirus family possess a distinctive repertoire of predicted DNA replication proteins, with two proteins annotated as DNA polymerases plus a DnaB-like replicative helicase, but lacking an identified primase or sliding clamp protein. Here, we demonstrate that in the Pseudomonas aeruginosa-infecting chimallivirus PhiKZ, the core DNA polymerase comprises a stable 1:1 complex of two DNA polymerase subunits, termed DNAPN and DNAPC. A 2.1 A resolution cryoelectron microscopy structure of this core complex reveals homology to other phage and bacterial B-family DNA polymerases. Next, we identify a direct but transient interaction between the core DNA polymerase complex and a third protein termed Rhc, which possesses an N-terminal RNase H domain and a C-terminal domain related to DNA sliding clamp proteins. Cryoelectron microscopy structures of a stabilized DNA polymerase-Rhc complex, and of this complex bound to a primer-template DNA, reveal a single Rhc subunit that cooperates with the DNA polymerase thumb domain to bind double-stranded DNA emerging from the DNA polymerase active site. While the Rhc RNase H domain is not resolved in our structures, this domain is situated such that it could degrade RNA associated with an incoming template DNA strand. In vitro primer-extension assays show that Rhc strongly boosts DNA polymerase activity, and that this boost relies on the Rhc-DNA polymerase interface we observe in our structures. Overall, our findings reveal a distinctive chimallivirus-specific DNA replication machine with an integrated DNA-binding subunit related to sliding clamp proteins, and a flexibly-linked RNase H domain.

biochemistry↗

bioRxiv2026

A bifunctional RNase H protein supports DNA replication and transcription in nucleus-forming Chimalliviridae phages

Jumbo bacteriophages of the Chimalliviridae family replicate their genomes within a proteinaceous phage nucleus that spatially segregates viral DNA replication and transcription from translation. While the phage nucleus protects viral DNA from host defenses, it also imposes unique constraints on genome replication and gene expression. Here we identify the phage-encoded protein Rhc (RNase H-clamp) as a central mediator of genome transactions within the phage nucleus. Using the Escherichia coli infecting bacteriophage Goslar, we show that Rhc functions as an essential component of a non-canonical three-subunit DNA polymerase complex composed of DNAPN, DNAPC and Rhc. Rhc physically interacts with the DNAPC subunit, and both the catalytic activity of Rhc's N-terminal RNase H domain and its C-terminal sliding clamp-derived DNA binding domain are required for genome replication, nuclear maturation, and productive infection. Further, Goslar Rhc also supports transcription within the phage nucleus through a function that is separable from its DNA replication function. Rhc depletion results in reduced transcription of a subset of late genes, in a pattern that suggests a role for Rhc in resolving R-loops. Imaging and cryo-electron tomography reveal that loss of Rhc arrests phage development at a nascent nuclear stage, uncoupling nuclear assembly from maturation. Together, these findings identify Rhc as a multifunctional nuclear factor that mediates both DNA replication and transcription in nucleus-forming jumbo phages, revealing how viruses repurpose a conserved enzymatic activity to coordinate gene expression within a compartmentalized replication environment.

cell biology↗

bioRxiv2026

Cell cycle control of chromatin creates a therapeutic window for epigenetic therapy in tumors

The relationship between cell cycle length and differentiation competence is well established in developmental biology, particularly in embryonic stem cells, where a short G1 phase maintains pluripotency and G1 lengthening permits lineage commitment. Whether this principle operates in cancer cells, where the cell cycle is deregulated and G1 is frequently shortened, and whether it can be pharmacologically exploited for therapy, has not been tested. Here we show that the duration of G1 is a causal determinant of chromatin state in cancer cells and that extending G1 creates a therapeutic window for epigenetic drugs. Using acute myeloid leukemia (AML) as a model, we demonstrate that low-dose palbociclib, at concentrations well below those required for cytostatic arrest, extends G1 without halting proliferation. This modest prolongation reshapes the histone modification landscape: repressive marks (H3K9me2/3, H4K20me2/3) increase while acetylation decreases, and chromatin accessibility rises broadly in the euchromatic compartment. Naturally slow-cycling AML lines share this epigenetic signature regardless of their oncogenic driver mutations, and pharmacologically extending G1 in fast-cycling cells recapitulates it, establishing G1 length as a causal regulator of the cancer epigenome rather than a passive correlate. To identify epigenetic vulnerabilities created by G1 extension, we performed complementary drug and CRISPR-Cas9 screens in G1-extended AML cells. Both approaches converged on LSD1 (KDM1A): slow-cycling AML cells are intrinsically sensitive to LSD1 inhibition, while fast-cycling cells become sensitive when G1 is prolonged. The combination of low-dose palbociclib and LSD1 inhibition triggers differentiation and significantly prolongs survival in AML xenograft models. p21 (CDKN1A) emerges as the central molecular determinant of this response. In slow-cycling AML cells, p21 is highly expressed and its knockdown abolishes LSD1 inhibitor sensitivity. Structure-function analysis using p21 mutants separates the two known activities of p21: the CDK-inhibitory function (which extends G1) is required for sensitization, whereas the PCNA-binding function is dispensable. Three pharmacological routes converge on the same endpoint, CDK inhibition, G1 extension, and a differentiation-competent chromatin state: direct CDK4/6 inhibition by palbociclib, p21 overexpression, and p21 induction through HDAC or EZH1/2 inhibitors. Palbociclib bypasses the requirement for p21 entirely, confirming that G1 length itself, not p21 as a protein, is the critical variable. Mechanistically, the combination of G1 extension and LSD1 inhibition produces a qualitatively distinct chromatin state rather than an additive one. ATAC-seq reveals thousands of combination-exclusive accessible regions, enriched for footprints of myeloid differentiation transcription factors including SPI1/PU.1, IRF1, and STAT1/2. A double-lock principle governs this remodeling: palbociclib drives the removal of repressive marks (H3K9me3 and H3K27me3), while LSD1 inhibition installs active marks at the newly accessible regions. The ncBAF chromatin remodeling complex, identified in our CRISPR screen and validated by knockout of its essential subunits BRD9 and SMARCD1, is specifically required for this response. Loss of ncBAF abolishes the combination-induced chromatin remodeling and differentiation program but does not affect the initial G1 extension or retinoic acid-induced differentiation, indicating that ncBAF specifically couples cell-cycle modulation to chromatin remodeling rather than acting as a general differentiation factor. The principle generalizes beyond AML. In melanoma, breast cancer, and small-cell lung cancer (SCLC), sensitivity to LSD1 inhibition tracks with p21 expression and cycling speed. Primary melanoma samples stratified by p21 recapitulate the same pattern: p21-high, slow-cycling cells are sensitive; p21-low, fast-cycling cells are resistant but can be sensitized by palbociclib cotreatment. Cisplatin-induced drug-tolerant persister (DTP) cells, which emerge as a slow-cycling, chemo-resistant population and upregulate both p21 and LSD1, become vulnerable to LSD1 inhibition and are eradicated by the combination. In melanoma patient-derived xenograft (PDX) models, p21-high tumors respond to LSD1 inhibitor monotherapy, while p21-low tumors are sensitized by palbociclib cotreatment, with p21 knockdown abolishing the response. Together, these findings establish cell-cycle duration as a tunable regulator of the cancer epigenome and demonstrate that pharmacological G1 extension converts cytostatic CDK4/6 inhibition into an epigenetic sensitization strategy. Both fast-proliferating and slow-cycling tumor compartments (including drug-resistant persisters) can be targeted by matching the epigenomic state to the appropriate combination of cell-cycle modulators and epigenetic drugs. p21 emerges as a candidate biomarker for patient stratification. More broadly, our work repositions the cell cycle from a passive conduit for proliferation signals to an active, druggable regulator of chromatin fate, with implications that extend from cancer therapy to stem cell biology and regenerative medicine.

cancer biology↗

bioRxiv2026

A DNA damage-activated kinase controls bacterial immune pathway expression

Bacteria encode myriad stress-response pathways that protect their hosts against both internal and external threats. A key question is how these pathways are regulated, especially anti-phage immune pathways that mediate host cell killing. Here, we identify two proteins termed CapK and CapS that are encoded upstream of diverse immune operons, and regulate their expression in response to DNA damage. CapK resembles bacterial anti-sigma factor kinases, and CapS resembles these proteins STAS domain antagonists. CapS is a DNA-binding transcriptional repressor, and phosphorylation of CapS by CapK results in dissociation of a CapS homodimer and de-repression of transcription. CapKs kinase activity is directly activated by single-stranded DNA generated as a by-product of DNA repair. Finally, we show that CapK and CapS-like proteins have been co-opted into an anti-phage toxin-antitoxin system with a VapC-like protein, where they similarly respond to DNA damage to activate VapCs nuclease activity. Overall, our results reveal how a kinase-substrate pair can regulate expression of an adjacent operon in response to DNA damage, and highlight the modularity of immune and other stress-response pathways.

microbiology↗

bioRxiv2025

In-cell cryo-electron tomography reveals differential effects of type I and type II kinase inhibitors on LRRK2 filament formation and microtubule association

Mutations in Leucine-Rich Repeat Kinase 2 (LRRK2) are a leading contributor to developing familial and idiopathic Parkinsons disease (PD). Most PD-causing LRRK2 mutations increase the kinase activity, leading to increased phosphorylation of Rab GTPases, disrupting vesicular trafficking, cytoskeletal dynamics, and autophagy. Under homeostatic conditions, the bulk of WT and PD-mutant LRRK2 is found in the cytosol. However, exogenously expressed LRRK2 can form microtubule-associated filaments that have been shown to affect molecular transport along microtubules in vitro. While the physiological relevance of microtubule binding has not been established yet, inhibitors being designed and tested as therapeutics have been shown to either promote or prevent filament formation of LRRK2. In this study, we examine the localization and resulting molecular organization of hyperactive LRRK2-I2020T, a common PD mutant, in cells treated with type I (MLi-2) or type II (GZD-824) kinase inhibitors. Treatment with a type I kinase inhibitor results in extensive LRRK2-I2020T decoration around microtubules and microtubule bundling. Stabilization of LRRK2-I2020T filaments by type I inhibitor treatment allowed us to build a full-length closed-kinase model of LRRK2-I2020T in its cellular environment. Conversely, treatment with a type II inhibitor resulted in minimal microtubule decoration by LRRK2-I2020T compared to Type I inhibitor treated cells. This study provides a structural framework for understanding how type I and type II kinase inhibitors differentially modulate LRRK2 filament formation, demonstrating that type I inhibitor treatment promotes a distinct filament architecture, whereas such assemblies are not observed with type II inhibitors.

biophysics↗

bioRxiv2025

RobPicker: A Meta Learning Framework for Robust Identification of Macromolecules in Cryo-Electron Tomograms

Accurate particle picking of macromolecules of all kinds, shapes, and sizes in cryogenic electron tomograms (cryo-ET) is critical for understanding the molecular architecture of biological systems in their native state. Current deep learning methods have shown potential in identifying macromolecules from tomograms, but they are vulnerable to issues of noise in the training dataset obtained through human or automatic labeling and imbalanced distribution of macromolecule species. To address these limitations, we developed RobPicker, a meta-learning framework that effectively mitigates these issues by automatically learning deep neural networks to correct label errors and give greater emphasis to underrepresented macromolecule species. In evaluations across diverse cryo-ET datasets with noisy labels and imbalanced species distributions, RobPicker substantially outperforms state-of-the-art methods, particularly in identifying small and rare macromolecules. The efficiency and robustness of RobPicker can also be used for rapid fine-tuning of the tilt-series alignment, leading to improved tomogram reconstruction and enabling high-resolution cellular structural biology analysis.

bioinformatics↗

bioRxiv2025

N-Glycans Modulate HIV-1 Env Conformational Plasticity

Human immunodeficiency virus-1 (HIV-1) remains a global health crisis, with over 39 million people living with the virus and no effective vaccine available. Central to HIV infection and immune evasion is the envelope glycoprotein (Env), a heavily glycosylated class I fusion protein that mediates viral entry and is the sole immunogenic target. Despite the recent advancements provided by imaging techniques, the characterization of Envs structure and dynamics within its native membrane environment remains incomplete. Here, we present microsecond-long, all-atom molecular dynamics simulations of the full-length Env glycoprotein embedded in a biologically relevant lipid bilayer with a complete glycosylation profile. Our simulations reveal a pronounced tilting motion of Env relative to the membrane, with supporting evidence from cryo-electron tomography, which also captures Env tilting within the native membrane. Importantly, we identify a critical role for N-linked glycans at N88 and N611 in modulating the tilting transition. These findings highlight the dual role of Envs glycan shield as both a protective barrier against neutralizing antibodies and a structural modulator of conformational plasticity. While providing an atomically detailed view of Env in a native membrane environment and advancing the general understanding of its glycan shield and its vulnerabilities, this work also suggests a possible strategy to modulate Envs conformational plasticity.

biophysics↗

bioRxiv2025

Multi-scale structure of chromatin condensates rationalizes phase separation and material properties

Biomolecular condensates, compartments that concentrate molecules without surrounding membranes, are integral to numerous cellular processes. The structure and interaction networks of molecules within condensates remain poorly understood. Using cryo-electron tomography and molecular dynamics simulations we elucidated the structure of phase separated chromatin condensates across scales, from individual amino acids to network architecture. We found that internucleosomal DNA linker length controls nucleosome arrangement and histone tail interactions, shaping the structure of individual chromatin molecules both within and outside condensates. This structural modulation determines the balance between intra- and intermolecular interactions, which in turn governs the molecular network, thermodynamic stability, and material properties of chromatin condensates. Mammalian nuclei contain dense clusters of nucleosomes whose non-random organization is mirrored by the reconstituted condensates. Our work explains how the structure of individual chromatin molecules ultimately determines physical properties of chromatin condensates, with implications for cellular chromatin organization.

biophysics↗

bioRxiv2024

Quantitative Spatial Analysis of Chromatin Biomolecular Condensates using Cryo-Electron Tomography

Phase separation is an important mechanism to generate certain biomolecular condensates and organize the cell interior. Condensate formation and function remain incompletely understood due to difficulties in visualizing the condensate interior at high resolution. Here we analyzed the structure of biochemically reconstituted chromatin condensates through cryo-electron tomography. We found that traditional blotting methods of sample preparation were inadequate, and high-pressure freezing plus focused ion beam milling was essential to maintain condensate integrity. To identify densely packed molecules within the condensate, we integrated deep learning-based segmentation with novel context-aware template matching. Our approaches were developed on chromatin condensates, and were also effective on condensed regions of in situ native chromatin. Using these methods, we determined the average structure of nucleosomes to 6.1 and 12 [A] resolution in reconstituted and native systems, respectively, and found that nucleosomes form heterogeneous interaction networks in both cases. Our methods should be applicable to diverse biochemically reconstituted biomolecular condensates and to some condensates in cells.

biophysics↗

bioRxiv2024

ExoSloNano: Multi-Modal Nanogold Tags for identi-fication of Macromolecules in Live Cells & Cryo-Electron Tomograms

In situ cryo-Electron Microscopy (cryo-EM) enables the direct interrogation of structure-function relationships by resolving macromolecular structures in their native cellular environment. Tremendous progress in sample preparation, imaging and data processing over the past decade has contributed to the identification and determination of large biomolecular complexes. However, the majority of proteins are of a size that still eludes identification in cellular cryo-EM data, and most proteins exist in low copy numbers. Therefore, novel tools are needed for cryo-EM to identify the vast majority of macromolecules across multiple size scales (from microns to nanometers). Here, we introduce and validate novel nanogold probes that enable the detection of specific proteins using cryo-ET (cryo-Electron Tomography) and resin-embedded correlated light and electron microscopy (CLEM). We demonstrate that these nanogold probes can be introduced into live cells, in a manner that preserves intact molecular networks and cell viability. We use this system to identify both cytoplasmic and nuclear proteins by room temperature EM, and resolve associated structures by cryo-ET. We further employ gold particles of different sizes to enable future multiplexed labeling and structural analysis. By providing high efficiency protein labeling in live cells and molecular specificity within cryo-ET tomograms, we establish a broadly enabling tool that significantly expands the proteome available to electron microscopy.

biophysics↗

bioRxiv2024

ProteinAligner: A Multi-modal Pretraining Framework for Protein Foundation Models

Protein foundation models, particularly protein language models, have demonstrated strong success in learning meaningful representations of proteins using transformer architectures pretrained on large-scale protein datasets with self-supervised learning. These representations have been highly effective for downstream tasks such as predicting protein functions and properties. However, most current protein foundation models focus on pretraining with amino acid sequences, often neglecting additional modalities like protein structures and related literature, both of which provide valuable insights. To address this gap, we propose a multi-modal pretraining approach that integrates three key modalities - protein sequences, structures, and literature text. In our framework, the protein sequence modality serves as the anchor, with the other two modalities aligned to it, enhancing the models capacity to capture more comprehensive protein information. ProteinAligner out-performed state-of-the-art protein foundation models in predicting protein functions and properties across diverse down-stream tasks.

bioinformatics↗

bioRxiv2024

Multi-Modal Large Language Model Enables Protein Function Prediction

Predicting the functions of proteins can greatly accelerate biological discovery and applications, where deep learning methods have recently shown great potential. However, these methods predominantly predict protein functions as discrete categories, which fails to capture the nuanced and complex nature of protein functions. Furthermore, existing methods require the development of separate models for each prediction task, a process that can be both resource-heavy and time-consuming. Here, we present ProteinChat, a versatile, multi-modal large language model that takes a proteins amino acid sequence as input and generates comprehensive narratives describing its function. ProteinChat is trained using over 1,500,000 (protein, prompt, answer) triplets curated from the Swiss-Prot dataset, covering diverse functions. This novel model can universally predict a wide range of protein functions, all within a single, unified framework. Furthermore, ProteinChat supports interactive dialogues with human users, allowing for iterative refinement of predictions and deeper exploration of protein functions. Our experimental results, evaluated through both human expert assessment and automated metrics, demonstrate that ProteinChat outperforms general-purpose LLMs like GPT-4, one of the flagship LLMs, by over ten-fold. In addition, ProteinChat exceeds or matches the performance of task-specific prediction models.

bioinformatics↗

bioRxiv2024

Cryo-electron tomography reveals the microtubule-bound form of inactive LRRK2

Parkinsons Disease (PD) is the second most common neurodegenerative disorder. Mutations in leucine-rich repeat kinase 2 (LRRK2), a multi-domain protein containing both a kinase and a GTPase, are a leading cause of the familial form of PD. Pathogenic LRRK2 mutations increase LRRK2 kinase activity. While the bulk of LRRK2 is found in the cytosol, the protein associates with membranes where its Rab GTPase substrates are found, and under certain conditions, with microtubules. Integrative structural studies using single-particle cryo-electron microscopy (cryo-EM) and in situ cryo-electron tomography (cryo-ET) have revealed the architecture of microtubule-associated LRRK2 filaments, and that formation of these filaments requires LRRK2s kinase to be in the active-like conformation. However, whether LRRK2 can interact with and form filaments on microtubules in its autoinhibited state, where the kinase domain is in the inactive conformation and the N-terminal LRR domain covers the kinase active site, was not known. Using cryo-ET, we show that full-length LRRK2 can oligomerize on microtubules in its autoinhibited state. Both WT-LRRK2 and PD-linked LRRK2 mutants formed filaments on microtubules. While these filaments are stabilized by the same interfaces seen in the active-LRRK2 filaments, we observed a new interface involving the N-terminal repeats that were disordered in the active-LRRK2 filaments. The helical parameters of the autoinhibited-LRRK2 filaments are different from those reported for the active-LRRK2 filaments. Finally, the autoinhibited-LRRK2 filaments are shorter and less regular, suggesting they are less stable.

biophysics↗

bioRxiv2024

Asesino: a nucleus-forming phage that lacks PhuZ

As nucleus-forming phages become better characterized, understanding their unifying similarities and unique differences will help us understand how they occupy varied niches and infect diverse hosts. All identified nucleus-forming phages fall within the proposed Chimalliviridae family and share a core genome of 68 unique genes including chimallin, the major nuclear shell protein. A well-studied but non-essential protein encoded by many nucleus-forming phages is PhuZ, a tubulin homolog which aids in capsid migration, nucleus rotation, and nucleus positioning. One clade that represents 24% of all currently known chimalliviruses lacks a PhuZ homolog. Here we show that Erwinia phage Asesino, one member of this PhuZ-less clade, shares a common overall replication mechanism with other characterized nucleus-forming phages despite lacking PhuZ. We show that Asesino replicates via a phage nucleus that encloses phage DNA and partitions proteins in the nuclear compartment and cytoplasm in a manner similar to previously characterized nucleus-forming phages. Consistent with a lack of PhuZ, however, we did not observe active positioning or rotation of the phage nucleus within infected cells. These data show that some nucleus-forming phages have evolved to replicate efficiently without PhuZ, providing an example of a unique variation in the nucleus-based replication pathway.

microbiology↗

bioRxiv2024

The Molecular Architecture of the Nuclear Basket

The nuclear pore complex (NPC) is the sole mediator of nucle-ocytoplasmic transport. Despite great advances in understanding its conserved core architecture, the peripheral regions can exhibit considerable variation within and between species. One such structure is the cage-like nuclear basket. Despite its crucial roles in mRNA surveillance and chromatin organization, an architectural understanding has remained elusive. Using in-cell cryo-electron tomography and subtomogram analysis, we explored the NPCs structural variations and the nuclear basket across fungi (yeast; S. cerevisiae), mammals (mouse; M. musculus), and protozoa (T. gondii). Using integrative structural modeling, we computed a model of the basket in yeast and mammals that revealed how a hub of Nups in the nuclear ring binds to basket-forming Mlp/Tpr proteins: the coiled-coil domains of Mlp/Tpr form the struts of the basket, while their unstructured termini constitute the basket distal densities, which potentially serve as a docking site for mRNA preprocessing before nucleocytoplasmic transport

biophysics↗

bioRxiv2024

An essential and highly selective protein import pathway encoded by nucleus-forming phage

Targeting proteins to specific subcellular destinations is essential in prokaryotes, eukaryotes, and the viruses that infect them. Chimalliviridae phages encapsulate their genomes in a nucleus-like replication compartment composed of the protein chimallin (ChmA) that excludes ribosomes and decouples transcription from translation. These phages selectively partition proteins between the phage nucleus and the bacterial cytoplasm. Currently, the genes and signals that govern selective protein import into the phage nucleus are unknown. Here we identify two components of this novel protein import pathway: a species-specific surface-exposed region of a phage intranuclear protein required for nuclear entry and a conserved protein, PicA, that facilitates cargo protein trafficking across the phage nuclear shell. We also identify a defective cargo protein that is targeted to PicA on the nuclear periphery but fails to enter the nucleus, providing insight into the mechanism of nuclear protein trafficking. Using CRISPRi-ART protein expression knockdown of PicA, we show that PicA is essential early in the chimallivirus replication cycle. Together our results allow us to propose a multistep model for the Protein Import Chimallivirus (PIC) pathway, where proteins are targeted to PicA by amino acids on their surface, and then licensed by PicA for nuclear entry. The divergence in the selectivity of this pathway between closely-related chimalliviruses implicates its role as a key player in the evolutionary arms race between competing phages and their hosts. Significance StatementThe phage nucleus is an enclosed replication compartment built by Chimalliviridae phages that, similar to the eukaryotic nucleus, separates transcription from translation and selectively imports certain proteins. This allows the phage to concentrate proteins required for DNA replication and transcription while excluding DNA-targeting host defense proteins. However, the mechanism of selective trafficking into the phage nucleus is currently unknown. Here we determine the region of a phage nuclear protein that targets it for nuclear import and identify a conserved, essential nuclear shell-associated protein that plays a key role in this process. This work provides the first mechanistic model of selective import into the phage nucleus.

microbiology↗

bioRxiv2024

Integrative spatiotemporal map of nucleocytoplasmic transport

Nuclear Pore Complexes (NPCs) enable rapid, selective, and robust nucleocytoplasmic transport. To explain how transport emerges from the system components and their interactions, we used experimental data and theoretical information to construct an integrative Brownian dynamics model of transport through an NPC, coupled to a kinetic model of transport in the cell. The model recapitulates key aspects of transport for a wide range of molecular cargos, including pre-ribosomes and viral capsids. It quantifies how flexible phenylalanine-glycine (FG) repeat proteins raise an entropy barrier to passive diffusion and how this barrier is selectively lowered in facilitated diffusion by the many transient interactions of nuclear transport receptors with the FG repeats. Selective transport is enhanced by "fuzzy" multivalent interactions, redundant FG repeats, coupling to the energy-dependent RanGTP concentration gradient, and exponential dependence of transport kinetics on the transport barrier. Our model will facilitate rational modulation of the NPC and its artificial mimics.

cell biology↗

bioRxiv2023

A mobile intron facilitates interference competition between co-infecting viruses

Mobile introns containing homing endonucleases are widespread in nature and have long been assumed to be selfish elements that provide no benefit to the host organism. These genetic elements are common in viruses, but whether they confer a selective advantage is unclear. Here we studied a mobile intron in bacteriophage {Phi}PA3 and found its homing endonuclease gp210 contributes to viral competition by interfering with the virogenesis of co-infecting phage {Phi}KZ. We show that gp210 targets a specific sequence in its competitor {Phi}KZ, preventing the assembly of progeny viruses. This work reports the first demonstration of how a mobile intron can be deployed to engage in interference competition and provide a reproductive advantage. Given the ubiquity of introns, this selective advantage likely has widespread evolutionary implications in nature.

microbiology↗