Patterns of Diversifying Selection in the Phytotoxin-like scr74 Gene Family of Phytophthora infestans

Abstract

Phytophthora infestans, the organism responsible for the Irish famine, causes late blight, a re-emerging disease of potato and tomato. Little is known about the molecular evolution of P. infestans genes. To identify candidate effector genes (virulence or avirulence genes) that may have co-evolved with the host, we mined expressed sequence tag (EST) data from infection stages of P. infestans for secreted and potentially polymorphic genes. This led to the identification of scr74, a gene that encodes a predicted 74-amino acid secreted cysteine-rich protein with similarity to the Phytophthora cactorum phytotoxin PcF. The expression of scr74 was upregulated approximately 60-fold 2 to 4 days after inoculation of tomato and was also significantly induced during early stages of colonization of potato. The scr74 gene was found to belong to a highly polymorphic gene family within P. infestans with 21 different sequences identified. Using the approximate and maximum likelihood (ML) methods, we found that diversifying selection likely caused the extensive polymorphism observed within the scr74 gene family. Pairwise comparisons of 17 scr74 sequences revealed elevated ratios of nonsynonymous to synonymous nucleotide-substitution rates, particularly in the mature region of the proteins. Using ML, all 21 polymorphic amino acid sites were identified to be under diversifying selection. Of these 21 amino acids, 19 are located in the mature protein region, suggesting that selection may have acted on the functional portions of the proteins. Further investigation of gene copy number and organization revealed that the scr74 gene family comprises at least three copies located in a region of no more than 300 kb of the P. infestans genome. We found evidence that recombination contributed to sequence divergence within at least one gene locus. These results led us to propose an evolutionary model that involves gene duplication and recombination, followed by functional divergence of scr74 genes. This study provides support for using diversifying selection as a criterion for identifying candidate effector genes from sequence databases.

A Domain-Centric Analysis of Oomycete Plant Pathogen Genomes Reveals Unique Protein Organization

“…The abundance of some domains in plant pathogens is too low to be identified as being overrepresented. For example, the PcF domain (IPR018570), which is present in a small, approximately 50-amino acid necrosis-inducing protein found in various Phytophthora species (Orsomando et al, 2001;Liu et al, 2005), was not identified in the initial overrepresentation analysis. Also in this cluster is the sugar fermentation stimulation domain (IPR005224), which is mainly found in bacteria and involved in the regulation of maltose metabolism (Kawamukai et al, 1991).…”

Molecular Evolution of Pathogenicity-Island Genes in Pseudomonas viridiflava

“…Like Arabidopsis R genes, however, the Phyophthora infestans scr74 gene family of effectors may be subject to diversifying selection (Liu et al 2005). Limited evidence of balancing selection acting upon virulence-related genes is found in Fusarium graminearum (Ward et al 2002) and in Borrelia burgdorferi (Qiu et al 2004).…”

Comparative structural and functional characterization of putative protein effectors belonging to the PcF toxin family from Phytophthora spp

“…1, top), interestingly including all six SSbridged cysteines of PcF recognized as essential for structuring its helix-loop-helix core domain. 22 Notably, only the SCR74 species possess two extra cysteines and thus one presumed additional SS bridge, not shared by other family members 20 ( Fig. 1, bottom).…”

“…20 Overall, these hints suggest conserved protein folds and functions. To date, however, PcF remains the only characterized member within its family.…”

“…14,18 They are encoded by polymorphic genes and identified by the acronym small cysteinerich (SCR) followed by their residues number. 6 At NCBI, three SCR91 gene products 18,19 are currently annotated into the PcF's family, as well as 17 SCR74 isoforms 20 and one SCR70, all from the pathogen P. infestans. More recently, several orthologues from P. sojae and P. ramorum have also been reported and preliminarily annotated at NCBI trace archive.…”