Van de Peer, Y. | bioRxiv Science

bioRxiv2017

Network modelling unravels mechanisms of crosstalk between ethylene and salicylate signalling in potato

To provide means for novel crop breeding strategies, it is crucial to understand the mechanisms underlying the interaction between plants and their pathogens. Network modelling represents a powerful tool that can unravel properties of complex biological systems. Here, we build on a reliable Arabidopsis (Arabidopsis thaliana L.) immune signalling model, extending it with the information from diverse publically available resources. The resulting prior knowledge network (20,012 nodes, 70,091 connections) was then translated to potato (Solanum tuberosum L.) and superimposed with an ensemble network inferred from potato time-resolved transcriptomics data. We used different network modelling approaches to generate specific hypotheses of potato immune signalling mechanisms. An interesting finding was the identification of a string of molecular events, illuminating the ethylene pathway modulation of the salicylic acid pathway through NPR1 gene expression. Functional validations confirmed this modulation, thus confirming the potential of our integrative network modelling approach for unravelling molecular mechanisms in complex systems.\n\nOne-sentence summaryAnalysis of integrated prior knowledge and ensemble networks highlights a novel connection between ethylene and salicylic acid signalling modules in potato.

systems biology↗

bioRxiv2017

Ancient duplication and horizontal transfer of a toxin gene cluster reveals novel mechanisms in the cercosporin biosynthesis pathway

Species in the genus Cercospora cause economically devastating diseases in sugar beet, maize, rice, soy bean and other major food crops. Here we sequenced the genome of the sugar beet pathogen C. beticola and found it encodes 63 putative secondary metabolite gene clusters, including the cercosporin toxin biosynthesis (CTB) cluster. We show that the CTB gene cluster has experienced multiple duplications and horizontal transfers across a spectrum of plant pathogenic fungi, including the wide host range Colletotrichum genus as well as the rice pathogen Magnaporthe oryzae. Although cercosporin biosynthesis has been thought to-date to rely on an eight gene CTB cluster, our phylogenomic analysis revealed gene collinearity adjacent to the established cluster in all CTB cluster-harboring species. We demonstrate that the CTB cluster is larger than previously recognized and includes cercosporin facilitator protein (CFP) previously shown to be involved with cercosporin auto-resistance, and four additional genes required for cercosporin biosynthesis including the final pathway enzymes that install the unusual cercosporin methylenedioxy bridge. Finally, we demonstrate production of cercosporin by Colletotrichum fioriniae, the first known cercosporin producer within this agriculturally important genus. Thus, our results provide new insight into the intricate evolution and biology of a toxin critical to agriculture and broaden the production of cercosporin to another fungal genus containing many plant pathogens of important crops worldwide.\n\nSignificance StatementSpecies in the fungal genus Cercospora cause diseases in many important crops worldwide. Their success as pathogens is largely due to the secretion of cercosporin during infection. We report that the cercosporin toxin biosynthesis (CTB) cluster is ancient and was horizontally transferred to diverse fungal pathogens on an unprecedented scale. Since these analyses revealed genes adjacent to the established CTB cluster, we evaluated their role in C. beticola to show that four are necessary for cercosporin biosynthesis. Finally, we confirmed that the apple pathogen Colletotrichum fioriniae produces cercosporin, the first case outside the family Mycosphaerellaceae. Other Colletotrichum plant pathogens also harbor the CTB cluster, which points to a wider concern that this toxin may play in virulence and human health.

evolutionary biology↗