Genome-wide alternative splicing profiling in the fungal plant pathogen Sclerotinia sclerotiorum during the colonization of diverse host families.

Heba M.M Ibrahim,Marie Didelon,Stefan Kusch,Sylvain Raffaele

doi:10.1111/mpp.13006

Heba M.M Ibrahim, Marie Didelon + Show 2 more

Open Access

https://doi.org/10.1111/mpp.13006

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Abstract

Sclerotinia sclerotiorum is a notorious generalist plant pathogen that threatens more than 600 host plants, including wild and cultivated species. The molecular bases underlying the broad compatibility of S. sclerotiorum with its hosts is not fully elucidated. In contrast to higher plants and animals, alternative splicing (AS) is not well studied in plant‐pathogenic fungi. AS is a common regulated cellular process that increases cell protein and RNA diversity. In this study, we annotated spliceosome genes in the genome of S. sclerotiorum and characterized their expression in vitro and during the colonization of six host species. Several spliceosome genes were differentially expressed in planta, suggesting that AS was altered during infection. Using stringent parameters, we identified 1,487 S. sclerotiorum genes differentially expressed in planta and exhibiting alternative transcripts. The most common AS events during the colonization of all plants were retained introns and the alternative 3′ receiver site. We identified S. sclerotiorum genes expressed in planta for which (a) the relative accumulation of alternative transcripts varies according to the host being colonized and (b) alternative transcripts harbour distinct protein domains. This notably included 42 genes encoding predicted secreted proteins showing high‐confidence AS events. This study indicates that AS events are taking place in the plant pathogenic fungus S. sclerotiorum during the colonization of host plants and could generate functional diversity in the repertoire of proteins secreted by S. sclerotiorum during infection.

Highlights

Sclerotinia sclerotiorum is a plant-parasitic fungus that causes white mould disease
The superimposition of TCONS_00002254 and TCONS_00002255 protein models revealed that the C-terminal extension in TCONS_00002255 corresponds to a surface-exposed unstructured loop reaching the neighbourhood of the catalytic site cleft (Figure 6e). This additional exposed loop could modify protein–protein interactions in TCONS_00002255 or modify access to its catalytic site. These results suggest that alternative splicing (AS) is a mechanism to generate functional diversity in the repertoire of proteins secreted by S. sclerotiorum during the colonization of host plants
The pipeline we used in this study combines two fundamentally different strategies to detect true novel splicing events and reduce algorithm bias

Summary

| INTRODUCTION

Sclerotinia sclerotiorum is a plant-parasitic fungus that causes white mould disease. The two pipelines identified a common set of 250 genes of S. sclerotiorum encoding more than one transcript and expressed differentially in planta (“common set” of candidates, Figures 2b and S2). This analysis suggested that the relative accumulation of alternative transcripts produced by a given gene could vary according to the host being colonized We tested whether this was the case for the gene Sscle03g026100, encoding a predicted phosphoenolpyruvate kinase-like protein. The alternatively spliced gene Sscle11g080920 was predicted to encode two secreted protein isoforms derived from the reference transcript TCONS_00002255. This additional exposed loop could modify protein–protein interactions in TCONS_00002255 or modify access to its catalytic site These results suggest that AS is a mechanism to generate functional diversity in the repertoire of proteins secreted by S. sclerotiorum during the colonization of host plants

| DISCUSSION

Findings

| EXPERIMENTAL PROCEDURES