Comparative genomic and transcriptional analyses of the carbohydrate-active enzymes and secretomes of phytopathogenic fungi reveal their significant roles during infection and development

Xueliang Lyu,Jiatao Xie,Cuicui Shen,Jiasen Cheng,Yanping Fu,Daohong Jiang,Guoqing Li

doi:10.1038/srep15565

Abstract

Our comparative genomic analysis showed that the numbers of plant cell wall (PCW)- and fungal cell wall (FCW)-degradation-associated carbohydrate-active enzymes (CAZymes) in necrotrophic and hemibiotrophic fungi are significantly larger than that in most biotrophic fungi. However, our transcriptional analyses of CAZyme-encoding genes in Melampsora larici-populina, Puccinia graminis and Sclerotinia sclerotiorum showed that many genes encoding PCW- and FCW-degradation-associated CAZymes were significantly up-regulated during the infection of both necrotrophic fungi and biotrophic fungi, indicating an existence of a universal mechanism underlying PCW degradation and FCW reorganization or modification, which are both intimately involved in necrotrophic and biotrophic fungal infection. Furthermore, our results showed that the FCW reorganization or modification was also related to the fungal development. Additionally, our transcriptional analysis of the secretome of S. sclerotiorum showed that many secreted protein-encoding genes were dramatically induced during infection. Among them, a small, cysteine-rich protein SsCVNH was experimentally confirmed to be essential for the virulence and sclerotial development, indicating that the small secreted proteins might also play crucial roles as potential effectors in host-non-specific necrotrophic fungi.

Highlights

Our results showed that the numbers of genes encoding plant cell wall (PCW)- and fungal cell wall (FCW)-degradation-associated carbohydrate-active enzymes (CAZymes) and their respective related carbohydrate-binding modules (CBMs) in necrotrophic and hemibiotrophic fungi were both significantly larger than that in most of biotrophic fungi except for C. fulvum (Fig. 1, Table S1), indicating both PCW- and FCW-degradation-associated CAZymes may play crucial roles during the infection and development of necrotrophic and hemibiotrophic fungi
To explore the expression patterns of CAZyme-encoding genes during the infection and development of necrotrophic fungi, we used digital gene expression profiling (DGE) based on deep sequencing technology to illuminate the transcriptional responses of CAZyme-encoding genes during the infection stage and different developmental stages of the necrotrophic fungus S. sclerotiorum, which is used as an example
Our results indicated different kinds of FCW-degrading enzymes participated in this biological process and their proportions varied during different infection stages, indicating the FCW reorganization or modification process is sophisticatedly and stringently regulated

Summary

Introduction

There are a large number of genes encoding FCW-degrading enzymes in phytopathogenic fungal genomes, the expression patterns and the exact roles of these FCW-degrading CAZymes during fungal infection and development are unknown. There are several key steps in the life cycle of S. sclerotiorum, including vegetative growth, infection, sclerotial development, sclerotial myceliogenic germination, sclerotial carpogenic germination and apothecium formation (stipe). Secretome analysis revealed large numbers of predicted effector candidates in the genome of S. sclerotiorum[21], and recent studies demonstrated that the non-CWDE secreted proteins played crucial roles during infection[22,23]. Our results increase the understanding of the roles of CAZymes and the secretomes in the infection and development of phytopathogenic fungi and facilitate the discovery of novel effector candidates in host-non-specific necrotrophic fungi

Methods

Results

Conclusion