Fungi use ancient proteins to attack plants and microbiomes

Phytopathogenic fungi use ancient antimicrobial proteins to manipulate host plants and alter their microbiomes during infection. This conclusion comes from a study led by Professor Bart Thomma of the Institute of Plant Sciences at the University of Cologne, in collaboration with the MiBiNet Collaborative Research Center and the Ceplas Cluster of Excellence.

The team identified an unexpected evolutionary origin for effector proteins secreted by fungi. These molecules participate in infection by weakening the host's defenses. According to the study, some of them derive from ancient antimicrobial proteins, used by fungi to compete with other microorganisms before the emergence of pathogenic interactions with terrestrial plants.

The result broadens the understanding of fungal disease in plants. The authors indicate a dual strategy. The fungus attacks the plant's immune system and, at the same time, interferes with the microbiota associated with the host. This microbiota includes bacteria, fungi, and other microorganisms. Part of it contributes to protection against diseases.

Vd424Y Effector

The study analyzed the Vd424Y effector, produced by Verticillium dahliae. This pathogen causes vascular wilt in various host plants, including agricultural crops. Researchers have shown that Vd424Y alters the composition of the microbiota during infection and contributes to the development of the disease.

The team also found that mutations gave this effector the ability to penetrate plant cells, reach the cell nucleus, and influence plant immune reactions and other cellular processes. Thus, Vd424Y performs two functions: it manipulates plant immunity and favors the fungus in competition against other microorganisms.

To track proteins with antimicrobial activity, the authors developed a machine learning-based tool called Amapec. The system predicts antimicrobial activity in fungal effector candidates. The tool classified proteins secreted by fungi and indicated a wide presence of antimicrobial candidates in the analyzed secretomes.

Three fungi

The analysis included three fungi with distinct lifestyles: Rhizophagus irregularis, associated with arbuscular mycorrhiza; Coprinopsis cinerea, soil saprophyte; and Verticillium dahliae, phytopathogen. The study indicated that between one-third and half of the secretomes evaluated, after excluding CAZymes and transmembrane proteins, contained proteins with possible antimicrobial activity.

The researchers also analyzed 150 genomes of fungi associated with soil and plants. The set covered three phyla, nine classes, and 24 orders. Many families of secreted proteins with greater conservation throughout evolution showed predictive antimicrobial activity. For the authors, this pattern indicates an ancient origin for these proteins, predating the divergence between fungal phyla.

The study also evaluated effectors already known to modulate plant immunity. Five proteins were selected for experimental validation: Ecp6, of Cladosporium fulvum AGLIP1, from Rhizoctonia solani; AVR-Pita, of magnaporthe oryzae; and Vd424Y and VdCP1, of Verticillium dahliae. All of them showed in vitro antimicrobial activity against plant-associated microorganisms, with distinct spectra of action.

Trials with tomato plants

In tomato trials, the contribution of Vd424Y to the virulence of Verticillium dahliae depended on the presence of host-associated microbiota. Deletion of the Vd424Y gene reduced disease development in the presence of microorganisms, but did not show the same effect in their absence. This result supports the effector's role in manipulating the microbiota during infection.

The bacterial composition of plants infected by Verticillium dahliae wild-type composition differed from that observed in plants infected with the mutant lacking Vd424Y. The authors identified bacterial genera with reduced relative abundance in the presence of the gene, among them Pseudoxanthomonas, Comomonas, Brachybacterium and Sphingobium.

The research also suggests an impact beyond phytopathology. According to the authors, similar mechanisms may occur in fungi capable of infecting animals and humans, as these interactions also involve host-associated microbiota and the immune system.

More information at doi.org/10.1126/sciadv.aec1406