Remote homology clustering identifies lowly conserved families of effector proteins in plant-pathogenic fungi

Abstract

Plant diseases caused by fungal pathogens are typically initiated by molecular interactions between ‘effector’ molecules released by a pathogen and receptor molecules on or within the plant host cell. In many cases these effector-receptor interactions directly determine host resistance or susceptibility. The search for fungal effector proteins is a developing area in fungal-plant pathology, with more than 165 distinct confirmed fungal effector proteins in the public domain. For a small number of these, novel effectors can be rapidly discovered across multiple fungal species through the identification of known effector homologues. However, many have no detectable homology by standard sequence-based search methods. This study employs a novel comparison method (RemEff) that is capable of identifying protein families with greater sensitivity than traditional homology-inference methods, leveraging a growing pool of confirmed fungal effector data to enable the prediction of novel fungal effector candidates by protein family association. Resources relating to the RemEff method and data used in this study are available from https://figshare.com/projects/Effector_protein_remote_homology/87965.

Comparative computational structural genomics highlights divergent evolution of fungal effectors

“…We proposed computational structural genomics as a framework to reveal such evolutionary connections obscured by sequence dissimilarity with predicted structures (Seong and Krasileva, 2021). The success of the methodology was exemplified by the identification of the MAX effector cluster, which could not be revealed by remote homology searches alone (Jones et al, 2021). With the availability of AlphaFold (Senior et al, 2020; Jumper et al, 2021), secretome-wide structure prediction and analysis has provided further insights.…”

WideEffHunter: An Algorithm to Predict Canonical and Non-Canonical Effectors in Fungi and Oomycetes

“…Effectoromics is a central research area in plant pathology, but identification of effectors has been slow, difficult, and even confusing. There are several criteria used for effector identification, but not all effectors perfectly match the established criteria, making effector identification a challenge [ 9 , 30 , 34 , 43 , 44 ]. Effector identification pipelines are quite variable; the identification of effectors in fungi and oomycetes can permit the presence of one or two TMDs [ 33 ] or entirely exclude TMDs altogether [ 12 , 32 ].…”

“…Recent reports have shown in some fungal effectors the existence of previously believed oomycete effector exclusive motifs. Conversely, domains from fungal proteins have been identified in oomycete effectors [ 22 , 29 , 30 ]. Similarly, WideEffHunter found classical motifs of oomycete effectors in fungal effector candidates, meanwhile in Phytophthora infestans , the algorithm was able to identify LysM and other domains commonly found in fungal effectors.…”

Fungal Effectoromics: A World in Constant Evolution

“…The motifs RXLR, LFLAK, Y/F/WxC, and CRN motifs are commonly used for identifying effectors in oomycetes, but recently, Zhao et al, (2020) used this strategy on the fungus Puccinia graminis and found 719 RXLR, 19 CRN, and 138 Y/F/WxC new effector candidates [ 89 ]. Recently, the Predector [ 90 ] pipeline, which was created for ranking effector candidates, was able to identify MoCDIP8, a non-canonical Magnaporthe oryzae effector with two predicted transmembrane domains and no signal peptide; the predictors EffHunter, EffectorP 1.0 or EffectorP 2.0 fail to recognize this protein as an effector. Predector also recognizes MoCDIP13 which is retrieved by EffectorP 1.0 but not by Effhunter and EffectorP 2.0.…”

“…ToxA, first identified in Pyrenophora tritici-repentis, has homologs in Parastagonospora nodorum , and Bipolaris sorokiniania , among other species, that most likely originated through horizontal transfer of these genes [ 123 ]. Similarly, AvrLm6 first reported in Leptosphaeria maculans , has been reported in Leptosphaeria biglobosa , Fusarium oxysporum , Colletotrichum sp., Venturia inaequalis and V. pirina [ 90 ]. Lastly, a Crinkler effector candidate CRN13, from the legume root pathogen Aphanomyces euteiches , is also found in the genome of the amphibian fungal pathogen, Batrachochytrium dendrobatidis .…”