Biology subjects

Klein-Sousa, V.

Publications and source records attributed to Klein-Sousa, V..

3 recordsLinked to original sources

bioRxiv2026

Genome delivery of a contractile tailed phage and its superinfection exclusion mechanism

Successful viral infection requires efficient adsorption to the target cell, followed by membrane penetration for genome translocation into the host cytoplasm. Bacteriophage T4 initiates infection by binding to Escherichia coli receptors, triggering sequential conformational changes that culminate in genome delivery through viral channels spanning the host cell envelope. Here, we resolved structures of bacteriophage T4 at discrete stages. This revealed how long tail fiber extension affects the baseplate to initiate tail contraction, and the channel formation by the tape measure protein for genome translocation. We further demonstrate that the virus-encoded superinfection exclusion protein Imm binds to the tape measure protein to prevent secondary infections. Our findings offer insights into the coordinated process of genome delivery and phage-encoded superinfection exclusion proteins that prevent genome translocation.

microbiology↗

bioRxiv2024

Towards a complete phage tail fiber structure atlas.

Bacteriophages use receptor-binding proteins (RBPs) to adhere to bacterial hosts. Understanding the structure of these RBPs can provide insights into their target interactions. Tail fibers, a prominent type of RBP, are typically elongated, flexible, and trimeric proteins, making it challenging to obtain high-resolution experimental data of their full-length structures. Recent advancements in deep learning-based protein structure prediction, such as AlphaFold2-multimer (AF2M) and ESMfold, allow for the generation of high-confidence predicted models of complete tail fibers. In this paper, we introduce RBPseg, a method that combines monomeric ESMfold predictions with a novel sigmoid distance pair (sDp) protein segmentation technique. This method segments the tail fiber sequences into smaller fractions, preserving domain boundaries. These segments are then predicted in parallel using AF2M and assembled into a full fiber model. We demonstrate that RBPseg significantly improves AF2M v2.3.2 in terms of model confidence, running time, and memory usage. To validate our approach, we used single-particle cryo-electron microscopy to analyze five tail fibers from three phages of the BASEL collection. Additionally, we conducted a structural classification of 67 fibers and their domains, which identified 16 well-defined tail fiber classes and 89 domains. Our findings suggest the existence of modular fibers as well as fibers with different sequences and shared structure, indicating possible sequence convergence, divergence, and domain swapping. We further demonstrate that these structural classes account for at least 24% of the known tail fiber universe.

microbiology↗

bioRxiv2023

Agtrevirus phage AV101 infect diverse extended spectrum β-lactamase E. coli by recognizing four different O-antigens

Bacteriophages in the Agtrevirus genus are known for expressing multiple tail spike proteins (TSPs), but little is known about their genetic diversity and host recognition apart from their ability to infect diverse Enterobacteriaceae species. Here we aim to determine the genetic differences that may account for the diverse host ranges of Agrevirus phages. We performed comparative genomics of 14 Agtrevirus and identified only a few genetic differences including genes involved in nucleotide metabolism. Most notably was the diversity of the tsp gene cluster, specifically in the receptor binding domains that were unique among most of the phages. We further characterized agtrevirus AV101 infecting nine diverse Extended Spectrum {beta}-lactamase (ESBL) E. coli and demonstrated that this phage encoded four unique TSPs among Agtrevirus. Purified TSPs formed translucent zones and inhibited AV101 infection of specific hosts, demonstrating that TSP1, TSP2, TSP3, and TSP4 recognize O8, O82, O153, and O159 O-antigens of ESBL E. coli, respectively. BLASTp analysis showed that the receptor binding domain of TSP1, TSP2, TSP3 and TSP4 are similar to TSPs encoded by E. coli prophages and distant related virulent phages. Thus, Agtrevirus may have gained their receptor binding domains by recombining with prophages or virulent phages. Overall, combining bioinformatic and biological data expands the understanding of TSP host recognition of Agtrevirus and give new insight into the origin and acquisition of receptor binding domains of Ackermannviridae phages. One sentence summaryAgtrevirus phage AV101 express four unique tail spike proteins that recognize different O-antigens of Extended Spectrum {beta}-Lactamase producing E. coli.

microbiology↗