Evaluation of Secretion Prediction Highlights Differing Approaches Needed for Oomycete and Fungal Effectors

Frontiers in Plant Science
Jana SperschneiderJennifer M Taylor

Abstract

The steadily increasing number of sequenced fungal and oomycete genomes has enabled detailed studies of how these eukaryotic microbes infect plants and cause devastating losses in food crops. During infection, fungal and oomycete pathogens secrete effector molecules which manipulate host plant cell processes to the pathogen's advantage. Proteinaceous effectors are synthesized intracellularly and must be externalized to interact with host cells. Computational prediction of secreted proteins from genomic sequences is an important technique to narrow down the candidate effector repertoire for subsequent experimental validation. In this study, we benchmark secretion prediction tools on experimentally validated fungal and oomycete effectors. We observe that for a set of fungal SwissProt protein sequences, SignalP 4 and the neural network predictors of SignalP 3 (D-score) and SignalP 2 perform best. For effector prediction in particular, the use of a sensitive method can be desirable to obtain the most complete candidate effector set. We show that the neural network predictors of SignalP 2 and 3, as well as TargetP were the most sensitive tools for fungal effector secretion prediction, whereas the hidden Markov model predictors of Si...Continue Reading

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Citations

Mar 17, 2017·Scientific Reports·Jana SperschneiderJennifer M Taylor
Dec 5, 2017·MSphere·Jamie McGowan, David A Fitzpatrick
Mar 24, 2018·Molecular Plant Pathology·Jana SperschneiderJennifer M Taylor
Apr 6, 2019·Molecular Plant-microbe Interactions : MPMI·Javier F Tabima, Niklaus J Grünwald
Dec 12, 2018·Genome Biology and Evolution·Jamie McGowanDavid A Fitzpatrick
May 8, 2020·Biomolecules·Karla Gisel Carreón-AnguianoBlondy Canto-Canché
Nov 25, 2018·International Journal of Molecular Sciences·Michał BurdukiewiczPaweł Mackiewicz
Aug 28, 2020·Frontiers in Genetics·Savithri PurayannurLina M Quesada-Ocampo
Dec 16, 2017·The New Phytologist·Jana SperschneiderJennifer M Taylor
Apr 14, 2019·Planta·Pramod PrasadSubodh Kumar
Aug 21, 2021·Molecular Plant-microbe Interactions : MPMI·Kyungyong Seong, Ksenia V Krasileva

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Methods Mentioned

BETA
in silico methods

Software Mentioned

WoLF PSORT
PexFinder ( Phytophthora Extracellular Proteins Finder )
SecretomeP
PSORT
Phobius
TMHMM
PexFinder
ProtComp
PrediSi
TargetP

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