Biology subjects

van der Lee, T.

Publications and source records attributed to van der Lee, T..

3 recordsLinked to original sources

bioRxiv2025

The evolutionary tale of tailocins in Pectobacterium show genus-wide homologous recombination and inversions of tail fiber genes

Due to their ability to kill closely related strains, phage tail-like bacteriocins, also called tailocins, play an important role in shaping bacterial communities. One such tailocin, called carotovoricin, is also known to be present in the Pectobacterium genus. However, little is known about its evolutionary dynamics and the scope of impact on species interactions in this genus. To investigate the diversity and evolution of carotovoricin, we performed a genus-wide, phylogenetically-structured pangenome study. This analysis inferred that the gene cluster responsible for carotovoricin biosynthesis is conserved across the genus and is located in the same gene neighborhood in all the species. Within the carotovoricin cluster, the tail fiber genes, which determine the host range specificity, exhibit high variability and discordance with the species phylogeny. We show evidence for an evolutionary mechanism involving recombination-mediated exchange of these tail fiber loci across the entire Pectobacterium genus, which complements the previously known mechanism for DNA sequence inversion to maintain tailocin polymorphism at the population level. In addition, the ability to exchange tail-fiber loci in a highly targeted and genus-wide manner could influence the community dynamics in nutrient rich environments such as infected plant tissues. In conclusion, the strong signal for carotovoricin retention and ability to exchange tail fibers indicates that it significantly contributes to the community interactions of the Pectobacterium phytopathogens. Significance StatementA widespread presence of tailocins among various gram-negative bacteria and maintenance of their tail fiber diversity underscore their role in inter-bacterial interactions. A tailocin is also found to be conserved in Pectobacterium, a pathogen causing soft rot. However, the mechanism maintaining the diversity of the tailocin tail fibers, which enable recognition of the target bacteria, is not yet completely understood. Here, we characterized the genomic diversity of this tailocin and discovered that the diversity is maintained through the exchange of the tail fiber locus DNA across the genus.

evolutionary biology↗

bioRxiv2025

Temporal Shifts in Gene Expression Drive Quantitative Resistance to a Necrotrophic Fungus in a Tomato Crop Wild Relative

Resistance breeding against generalist necrotrophic pathogens heavily relies on quantitative disease resistance (QDR). Lesion growth dynamics involve distinct phases (e.g., lag phase duration or lesion doubling time), each independently affecting the overall symptom severity. While the genetic and regulatory basis of lesion growth rate has been studied, the host-derived regulation of the lag-phase duration remains largely uncharacterised. In this study, we tested the regulatory response of Solanum pennellii genotypes exhibiting different lag-phase durations. We conducted a time-series gene expression profiling experiment dissecting genotype-specific regulatory responses to Sclerotinia sclerotiorum inoculation. We observed genotype-specific regulatory trajectories, with resistant plants displaying early activation of defence-related genes during the asymptomatic phase. These genes, regulated by a WRKY6-centered gene regulatory network, exhibited elevated basal expression in resistant genotypes and a fine-tuned longitudinal expression with induction before lesion onset. In contrast, susceptible genotypes lacked this early response, showing gene induction only post-infection. This study is the first to link host regulatory dynamics to lag-phase duration, suggesting that elevated basal expression of receptor genes and a WRKY6-mediated gene regulatory network may enhance QDR. These findings provide insights into the regulatory foundation of QDR and establish a functional basis for more focused breeding of QDR traits.

plant biology↗

bioRxiv2024

Pangenomics to understand prophage dynamics in the Pectobacterium genus and the radiating lineages of P. brasiliense

Bacterial pathogens of the genus Pectobacterium are responsible for soft rot and blackleg disease in a wide range of crops and have a global impact on food production. The emergence of new lineages and their competitive succession is frequently observed in Pectobacterium species, in particular in P. brasiliense. With a focus on one such recently emerged P. brasiliense lineage in the Netherlands that causes blackleg in potatoes, we studied genome evolution in this genus using a reference-free graph-based pangenome approach. We clustered 1,977,865 proteins from 454 Pectobacterium spp. genomes into 30,156 homology groups. The Pectobacterium genus pangenome is open and its growth is mainly contributed by the accessory genome. Bacteriophage genes were enriched in the accessory genome and contributed 16% of the pangenome. Blackleg-causing P. brasiliense isolates had increased genome size with high levels of prophage integration. To study the diversity and dynamics of these prophages across the pangenome, we developed an approach to trace prophages across genomes using pangenome homology group signatures. We identified lineage-specific as well as generalist bacteriophages infecting Pectobacterium species. Our results capture the ongoing dynamics of mobile genetic elements, even in the clonal lineages. The observed lineage-specific prophage dynamics provide mechanistic insights into Pectobacterium pangenome growth and contribution to the radiating lineages of P. brasiliense.

bioinformatics↗