Biology subjects

Kraege, A.

Publications and source records attributed to Kraege, A..

6 recordsLinked to original sources

bioRxiv2026

Structural homology reveals cerato-platanins as conserved antimicrobials repeatedly co-opted for fungal host colonization

Fungal cerato-platanins (CPs) are small ([~]12 kDa) secreted proteins broadly conserved across filamentous fungi and implicated in a striking diversity of biological processes, ranging from fungal development to interactions with plant hosts. However, a core molecular activity unifying these diverse functions has remained elusive. Fungal pathogens secrete effector proteins, including CPs, to manipulate host physiology and promote colonization. Increasing evidence demonstrates that particular fungal effectors possess antimicrobial activity that enables pathogens to reshape host-associated microbiota during infection, and that antimicrobial activity is strongly enriched among evolutionarily conserved secreted proteins. These findings suggests that intermicrobial competition represents an ancient and fundamental fungal trait, and that several effectors that manipulate plant hosts evolved from ancient antimicrobials. Here, we identify antimicrobial activity as the conserved core function of the CP family, from which diverse roles in environmental adaptation and host interaction evolved. Structural analysis of the Verticillium dahliae secretome identified a structural cluster containing the CP protein CP1 and the previously characterized antimicrobial effector Ave1, providing the first structural link between CPs and antimicrobial activity. Accordingly, functional assays demonstrate that V. dahliae CPs exhibit selective antimicrobial activity in vitro. Expanding this analysis to a wide diversity of phylogenetic lineages and ecological lifestyles revealed that antimicrobial features are broadly conserved across the CP family. Together, our findings identify antimicrobial activity as an ancient and conserved molecular function that unifies the CP family and support a model in which host-manipulating effector functions evolved from ancestral proteins that mediate inter-microbial competition.

microbiology↗

bioRxiv2025

Differential contributions of an antimicrobial effector from Verticillium dahliae to virulence and tomato microbiota assembly across natural soils

Throughout their life cycle plants associate with diverse and complex microbial communities, known as their microbiota. These microbiota contribute to plant performance and health, in part by providing a microbial barrier against invading plant pathogens. To colonize plant hosts, pathogens not only have to overcome host immune responses, but also breach the microbial barrier, for which they secrete so-called effector proteins. Accordingly, the soil-borne fungal plant pathogen Verticillium dahliae secretes the antimicrobial effector Ave1 to suppress antagonistic microbes and facilitate host colonization. Notably, many pathogens, including V. dahliae, have life stages outside their host plants, for instance in soil, where they encounter diverse microbial communities. Yet, how antimicrobial effectors support establishment across these environments remains poorly understood. To address this, we established a collection of natural soil samples with diverse physicochemical properties and microbiota compositions. Using this collection, we show for three plant species, barley, tomato and cotton, that root-associated bacterial and fungal communities are primarily shaped by the type of soil, whereas the phyllosphere microbiota is mainly determined by plant species. On tomato, we furthermore show that Ave1 differentially contributes to virulence on diverse soils, as Ave1 altered the tomato microbiota on all soils tested, but the taxa affected by these shifts varied depending on the specific soils. Our findings suggest that while Ave1-mediated microbiota manipulation occurs across soils, its impact on fungal virulence is influenced by the specific composition of the soil-derived microbiota assembled by the host.

plant biology↗

bioRxiv2025

Undermining the cry for help: The phytopathogenic fungus Verticillium dahliae secretes an antimicrobial effector protein to undermine host recruitment of antagonistic Pseudomonas bacteria

During pathogen attack, plants recruit beneficial microbes in a "cry for help" to mitigate disease development. Simultaneously, pathogens secrete effectors to promote host colonization through various mechanisms, including targeted host microbiota manipulation. Here, we characterize the Av2 effector of the vascular wilt fungus Verticillium dahliae as a suppressor of the cry for help. Inspired by in silico antimicrobial activity prediction, we investigated the antimicrobial activity of Av2 in vitro. Furthermore, its role in V. dahliae virulence was assessed through microbiota sequencing of inoculated plants, microbial co-cultivation assays, and inoculations in a gnotobiotic plant cultivation system. We show that Av2 inhibits bacterial growth, and acts as a virulence factor during host colonization. Microbiota sequencing revealed involvement of Av2 in suppression of Pseudomonas spp. recruitment upon plant inoculation with V. dahliae, suggesting that Av2 suppresses the cry for help. We show that several Pseudomonas spp. are antagonistic to V. dahliae and sensitive to Av2 treatment. We conclude that V. dahliae secretes Av2 to supress the cry for help by inhibiting the recruitment of antagonistic Pseudomonas spp. to pave the way for successful plant invasion.

plant biology↗

bioRxiv2025

A gnotobiotic system reveals multifunctional effector roles in plant-fungal pathogen dynamics

Plants host diverse microbiota that influence physiological processes and can enhance resilience against invading pathogens that, in turn, evolved effector proteins to manipulate host microbiota in their favor. However, the complexity of microbial communities and their interactions complicates mechanistic research on processes governing microbiota assembly and function. Gnotobiotic systems are valuable tools to study plant microbiota by reducing complexity and enabling controlled microbiota reconstitution experiments. Despite their utility, no gnotobiotic systems have been established to investigate the role of antimicrobial effector proteins in the interactions between plants, their microbiota, and fungal pathogens. Here, we present a refined gnotobiotic system designed to study these interactions, establishing protocols for infections with the fungal pathogen Verticillium dahliae across multiple host plants under sterile conditions. We demonstrate that a synthetic microbial community (SynCom) derived from a culture collection generated for this study can be applied in this system where it interferes with fungal infections. Additionally, using our gnotobiotic system we reveal that specific antimicrobial effectors of V. dahliae, like Ave1L2, contribute to fungal virulence in a microbiota-dependent manner, whereas other antimicrobial effectors, such as Ave1, seem to possess functions beyond microbiota manipulation.

plant biology↗

bioRxiv2023

High quality genome assembly and annotation (v1) of the eukaryotic terrestrial microalga Coccomyxa viridis SAG 216-4

Unicellular green algae of the genus Coccomyxa are recognized for their worldwide distribution and ecological versatility. Most species described to date live in close association with various host species, such as in lichen associations. However, little is known about the molecular mechanisms that drive such symbiotic lifestyles. We generated a high-quality genome assembly for the lichen photobiont Coccomyxa viridis SAG 216-4 (formerly C. mucigena). Using long-read PacBio HiFi and Oxford Nanopore Technologies in combination with chromatin conformation capture (Hi-C) sequencing, we assembled the genome into 21 scaffolds with a total length of 50.9 Mb, an N50 of 2.7 Mb and a BUSCO score of 98.6%. While 19 scaffolds represent full-length nuclear chromosomes, two additional scaffolds represent the mitochondrial and plastid genomes. Transcriptome-guided gene annotation resulted in the identification of 13,557 protein-coding genes, of which 68% have annotated PFAM domains and 962 are predicted to be secreted.

genomics↗

bioRxiv2023

The soil-borne white root rot pathogen Rosellinia necatrix expresses antimicrobial proteins during host colonization

Rosellinia necatrix is a prevalent soil-borne plant-pathogenic fungus that is the causal agent of white root rot disease in a broad range of host plants. The limited availability of genomic resources for R. necatrix has complicated a thorough understanding of its infection biology. Here, we sequenced nine R. necatrix strains with Oxford Nanopore sequencing technology, and with DNA proximity ligation we generated a gapless assembly of one of the genomes into ten chromosomes. Whereas many filamentous pathogens display a so-called two-speed genome with more dynamic and more conserved compartments, the R. necatrix genome does not display such genome compartmentalization. It has recently been proposed that fungal plant pathogens may employ effectors with antimicrobial activity to manipulate the host microbiota to promote infection. In the predicted secretome of R. necatrix, 26 putative antimicrobial effector proteins were identified, nine of which are expressed during plant colonization. Two of the candidates were tested, both of which were found to possess selective antimicrobial activity. Intriguingly, some of the inhibited bacteria are antagonists of R. necatrix growth in vitro and can alleviate R. necatrix infection on cotton plants. Collectively, our data show that R. necatrix encodes antimicrobials that are expressed during host colonization and that may contribute to modulation of host-associated microbiota to stimulate disease development.

plant biology↗