Probing the Phylogenomics and Putative Pathogenicity Genes of Pythium insidiosum by Oomycete Genome Analyses

Abstract

Pythium insidiosum is a human-pathogenic oomycete. Many patients infected with it lose organs or die. Toward the goal of developing improved treatment options, we want to understand how Py. insidiosum has evolved to become a successful human pathogen. Our approach here involved the use of comparative genomic and other analyses to identify genes with possible functions in the pathogenicity of Py. insidiosum. We generated an Oomycete Gene Table and used it to explore the genome contents and phylogenomic relationships of Py. insidiosum and 19 other oomycetes. Initial sequence analyses showed that Py. insidiosum is closely related to Pythium species that are not pathogenic to humans. Our analyses also indicated that the organism harbours secreted and adhesin-like proteins, which are absent from related species. Putative virulence proteins were identified by comparison to a set of known virulence genes. Among them is the urease Ure1, which is absent from humans and thus a potential diagnostic and therapeutic target. We used mass spectrometric data to successfully validate the expression of 30% of 14,962 predicted proteins and identify 15 body temperature (37 °C)-dependent proteins of Py. insidiosum. This work begins to unravel the determinants of pathogenicity of Py. insidiosum.

Prediction and Characterization of RXLR Effectors inPythiumSpecies

“…No Pythium RXLR effector has been previously identified despite the numerous reports of RXLRs in their phylogenetically close species [21,22,23,24]. Here we developed a de novo identification method with stringent threshold to screen RXLR candidates in 9 Pythium species (Fig 1A).…”

“…The genome sequences of H. arabidopsidis [28], Ph. vexans [22], P. aphanidermatum [22], P. arrhenomanes [22], P. irregulare [22], P. iwayamai [22], P. oligandrum [39], P. periplocum [39], P. ultimum [21], P insidiosum [23], P. guiyangense [24], S. parasitica [40], P. tricornutum [41], T. pseudonana [42], S. cerevisiae [43], S. sclerotiorum [44], U. maydis [45], P. graminis [46], B. cinerea [47], C. elegans [48], M. hapla [49], E. coli [50], E. amylovora [51] and Ca L. asiaticus [52] were obtained from the National Center for Biotechnology Information (NCBI, https://www.ncbi.nlm.nih.gov/). Detailed genomic information of all species is listed in S7 Table.…”

“…All these RXL-containing oomycetes are phylogenetically close to Pythium species. Nevertheless, previously reported Pythium genome analyses did not reveal any RXLR-encoding genes [21,22,23,24].…”

“…Unlike Phytophthora species which are mostly plant-infecting pathogens, Pythium species occupy multiple ecological niches. Many Pythium species, including P. ultmum, P. iwayamai , and P. aphanidermatum , cause a wide variety of diseases in plants [21,22], whereas P. insidiosum is a notorious pathogen infecting human and animals [23]. Interestingly, Some Pythium species, such as P. oligandrum and P. periplocum , are used as mycoparasitic biocontrol agents since they can infect fungal hosts and induce plant defense response as well [25,26,27].…”

The Repurposed Drug Disulfiram Inhibits Urease and Aldehyde Dehydrogenase and Prevents In Vitro Growth of the Oomycete Pythium insidiosum

“…In the present study, we performed an in vitro susceptibility assay and showed that all 27 P. insidiosum strains tested were susceptible to disulfiram. In addition, we identified some putative target enzymes in the genome of P. insidiosum (27,28) and initially assessed a potential inhibitory mechanism of disulfiram against the pathogen by homology modeling, molecular docking, and biochemical analyses.…”