# Genome-Wide Identification of CFEM Proteins in Sclerotinia sclerotiorum Reveals Effector Candidates with Cell Death Suppression Activity

## TL;DR

This study identifies and characterizes CFEM proteins in the fungus Sclerotinia sclerotiorum, revealing some as potential virulence factors that suppress cell death in plants.

## Contribution

The first comprehensive identification and functional analysis of CFEM proteins in Sclerotinia sclerotiorum, including their roles in suppressing cell death.

## Key findings

- Thirteen CFEM proteins were identified in Sclerotinia sclerotiorum with diverse properties and predicted functions.
- SsCFEM4 and SsCFEM9 were shown to suppress cell death in Nicotiana benthamiana, indicating their role as effectors.
- Transcriptomic data revealed upregulation of most SsCFEM genes during early plant infection.

## Abstract

The CFEM (Common in Fungal Extracellular Membrane) domain defines a family of cysteine-rich proteins unique to fungi, playing pivotal roles in host–pathogen interactions. However, the repertoire and functions of CFEM proteins in the broad-host-range necrotrophic pathogen Sclerotinia sclerotiorum remain largely unexplored. Through genome-wide bioinformatic analysis, we identified 13 CFEM-containing proteins (SsCFEM1–13) in S. sclerotiorum. Characterization revealed substantial diversity in their physicochemical properties, domain architecture, and predicted subcellular localization. Ten proteins possess a secretion signal, with six predicted to be GPI-anchored and three classified as high-confidence effectors. Members lacking transmembrane domains were predicted to adopt the conserved CFEM “helical-basket” fold. Phylogenetic analysis grouped SsCFEMs into two distinct clades and indicated a complex evolutionary history involving both conserved ancestry and lineage-specific expansion. Transcriptomic profiling showed that most genes were upregulated during early infection of various host plants, with SsCFEM8 exhibiting particularly strong and consistent induction. Crucially, transient expression assays in Nicotiana benthamiana revealed that several SsCFEM proteins, notably SsCFEM4 and SsCFEM9, function as cell death suppressors, validating their predicted effector roles and identifying key virulence candidates. This study provides the first comprehensive catalog and functional prediction of the CFEM protein family in S. sclerotiorum, establishing a foundation for future mechanistic studies on their roles in the pathogenesis of this devastating fungal pathogen.