Decay of Genes Encoding the Oomycete Flagellar Proteome in the Downy Mildew Hyaloperonospora arabidopsidis

Abstract

Zoospores are central to the life cycles of most of the eukaryotic microbes known as oomycetes, but some genera have lost the ability to form these flagellated cells. In the plant pathogen Phytophthora infestans, genes encoding 257 proteins associated with flagella were identified by comparative genomics. These included the main structural components of the axoneme and basal body, proteins involved in intraflagellar transport, regulatory proteins, enzymes for maintaining ATP levels, and others. Transcripts for over three-quarters of the genes were up-regulated during sporulation, and persisted to varying degrees in the pre-zoospore stage (sporangia) and motile zoospores. Nearly all of these genes had orthologs in other eukaryotes that form flagella or cilia, but not species that lack the organelle. Orthologs of 211 of the genes were also absent from a sister taxon to P. infestans that lost the ability to form flagella, the downy mildew Hyaloperonospora arabidopsidis. Many of the genes retained in H. arabidopsidis were also present in other non-flagellates, suggesting that they play roles both in flagella and other cellular processes. Remnants of the missing genes were often detected in the H. arabidopsidis genome. Degradation of the genes was associated with local compaction of the chromosome and a heightened propensity towards genome rearrangements, as such regions were less likely to share synteny with P. infestans.

Novel core promoter elements in the oomycete pathogen Phytophthora infestansand their influence on expression detected by genome-wide analysis

“…By selecting the best hit with >97% identity, 7,862 T30-4 genes were matched to the array data. Expression calls from Affymetrix MAS 5.0 software were normalized before analysis, resulting in values that showed good concordance with data from SybrGreen reverse transcription-qPCR studies ([62]; Additional file 2). Analyses of changes during development and variance calculations used per-gene normalized data, set to a mean of 1.0.…”

Gene Expression and Silencing Studies in Phytophthora infestans Reveal Infection-Specific Nutrient Transporters and a Role for the Nitrate Reductase Pathway in Plant Pathogenesis

“…infestans ranged from 4.1 to 39.8% (Fig 2B; Table 1). To help assess these preliminary tests, we examined the expression of the genes encoding effector Avr3A and haustorial protein Hmp1 which are markers of biotrophic growth, Npp1 which is a marker of necrotrophic growth, and a flagella-associated centrin which is a marker of sporulation [3, 30]. In both leaves and tubers, Avr3A and Hmp1 mRNAs were >10-fold higher in the leaf and tuber samples at 3 dpi than 6 dpi (Fig 2B).…”

“…Pathogens accomplish this through mechanisms that include manipulating hosts to shift nutrients to sites of infection, generating feeding structures, expressing transporters for the nutrients, and making metabolic enzymes for assimilating the nutrients [1–3]. Studies in fungi and bacteria have identified transporters and metabolic pathways that contribute to pathogenesis [4–10].…”

Phosphagen kinase function in flagellated spores of the oomycete Phytophthora infestans integrates transcriptional regulation, metabolic dynamics and protein retargeting

“…Analyses across the breadth of eukaryotic diversity indicate that the role of PKs in flagella is not universal, however. While all PK-bearing eukaryotes (animals, alveolates, choanoflagellates, excavates and stramenopiles) contain flagella or cilia, our current and prior (Judelson et al, 2012) searches of genome databases indicate that the reverse is not true: groups with flagellated life-stages that lack PK genes include chytrids, amoeba and lower plants, e.g. Batrachochytrium, Acanthamoeba and Chlamydomonas respectively.…”

“…In prior studies of the potato late blight pathogen Phytophthora infestans, we identified genes encoding PKs (Kim and Judelson, 2003;Randall et al, 2005). The premise that these may help maintain energy homeostasis in zoospores was supported by our discovery that genes encoding PKs were absent from the azoosporic oomycete Hyaloperonospora arabidopsidis (Judelson et al, 2012). Biochemical analyses subsequently indicated that the phosphagen in Phytophthora is taurocyamine (Uda et al, 2013).…”