Transcriptome and Metabolite Profiling of the Infection Cycle of Zymoseptoria tritici on Wheat Reveals a Biphasic Interaction with Plant Immunity Involving Differential Pathogen Chromosomal Contributions and a Variation on the Hemibiotrophic Lifestyle Definition  

Abstract

The hemibiotrophic fungus Zymoseptoria tritici causes Septoria tritici blotch disease of wheat (Triticum aestivum). Pathogen reproduction on wheat occurs without cell penetration, suggesting that dynamic and intimate intercellular communication occurs between fungus and plant throughout the disease cycle. We used deep RNA sequencing and metabolomics to investigate the physiology of plant and pathogen throughout an asexual reproductive cycle of Z. tritici on wheat leaves. Over 3,000 pathogen genes, more than 7,000 wheat genes, and more than 300 metabolites were differentially regulated. Intriguingly, individual fungal chromosomes contributed unequally to the overall gene expression changes. Early transcriptional down-regulation of putative host defense genes was detected in inoculated leaves. There was little evidence for fungal nutrient acquisition from the plant throughout symptomless colonization by Z. tritici, which may instead be utilizing lipid and fatty acid stores for growth. However, the fungus then subsequently manipulated specific plant carbohydrates, including fructan metabolites, during the switch to necrotrophic growth and reproduction. This switch coincided with increased expression of jasmonic acid biosynthesis genes and large-scale activation of other plant defense responses. Fungal genes encoding putative secondary metabolite clusters and secreted effector proteins were identified with distinct infection phase-specific expression patterns, although functional analysis suggested that many have overlapping/redundant functions in virulence. The pathogenic lifestyle of Z. tritici on wheat revealed through this study, involving initial defense suppression by a slow-growing extracellular and nutritionally limited pathogen followed by defense (hyper) activation during reproduction, reveals a subtle modification of the conceptual definition of hemibiotrophic plant infection.

The Biotrophic Development of Ustilago maydis Studied by RNA-Seq Analysis

“…In Zymoseptoria tritici, Colletotrichum higginsianum and Puccinia striiformis f. sp. tritici 28%, 44% and 50% of the genes were differentially expressed, respectively (O'Connell et al, 2012;Rudd et al, 2015;Dobon et al, 2016). We consider it likely that the coupling between pathogenic and sexual development in U. maydis and the associated morphological changes contribute to this high percentage of differentially expressed U. maydis genes.…”

“…To promote the respective colonization strategy pathogens secrete a large arsenal of effector proteins. In recent years the study of lifestyle transitions in plant pathogenic fungi by time resolved transcriptome analyses through RNAseq provided deep insights into the processes associated with stages of fungal development on and inside the host (Kawahara et al, 2012;O'Connell et al, 2012;Hacquard et al, 2013;Jupe et al, 2013;Dong et al, 2015;Fondevilla et al, 2015;Kong et al, 2015;Rudd et al, 2015;Dobon et al, 2016;Thatcher et al, 2016;Copley et al, 2017;Wang et al, 2017;Zeng et al, 2017;Massonnet et al, 2018). These and other studies (Toruno et al, 2016) have shown that different sets of effectors are synthesized and presumably needed during discrete developmental stages in fungal pathogens.…”

A fungal avirulence factor encoded in a highly plastic genomic region triggers partial resistance to septoria tritici blotch

“…Avr3D1 and the three other genes in the effector gene cluster are located on the right arm of chromosome 7, which is distinctive because of its low overall expression levels (Rudd et al ., 2015) and its enrichment in heterochromatin (Schotanus et al ., 2015). In fact, it was postulated that this region originated from a fusion between an accessory chromosome and a core chromosome (Schotanus et al ., 2015).…”

“…It is possible that the role of Avr3D1 is more pronounced under field conditions or at different developmental stages, for example in adult plants. An additional hypothesis to explain the apparent dispensability of Avr3D1 is that functional redundancy masks phenotypic effects in the knockout mutants (Marshall et al ., 2011; Win et al ., 2012; Mirzadi Gohari et al ., 2015; Rudd et al ., 2015). …”

“…We used RNA sequencing (RNA‐seq) raw data of IPO323 infecting wheat seedlings (Rudd et al ., 2015) to manually annotate the gene Zt09_7_00581 . To annotate the other genes in the cluster, we used RNA‐seq raw data of 3D7 from two different experiments and at six different time points (Palma‐Guerrero et al ., 2016).…”