Niche-specific metabolic adaptation in biotrophic and necrotrophic oomycetes is manifested in differential use of nutrients, variation in gene content, and enzyme evolution.

The use of host nutrients to support pathogen growth is central to disease. We addressed the relationship between metabolism and trophic behavior by comparing metabolic gene expression during potato tuber colonization by two oomycetes, the hemibiotroph Phytophthora infestans and the necrotroph Pythium ultimum. Genes for several pathways including amino acid, nucleotide, and cofactor biosynthesis were expressed more by Ph. infestans during its biotrophic stage compared to Py. ultimum. In contrast, Py. ultimum had higher expression of genes for metabolizing compounds that are normally sequestered within plant cells but released to the pathogen upon plant cell lysis, such as starch and triacylglycerides. The transcription pattern of metabolic genes in Ph. infestans during late infection became more like that of Py. ultimum, consistent with the former's transition to necrotrophy. Interspecific variation in metabolic gene content was limited but included the presence of -amylase only in Py. ultimum. The pathogens were also found to employ strikingly distinct strategies for using nitrate. Measurements of mRNA, N-15 labeling studies, enzyme assays, and immunoblotting indicated that the assimilation pathway in Ph. infestans was nitrate-insensitive but induced during amino acid and ammonium starvation. In contrast, the pathway was nitrate-induced but not amino acid-repressed in Py. ultimum. The lack of amino acid repression in Py. ultimum appears due to the absence of a transcription factor common to fungi and Phytophthora that acts as a nitrogen metabolite repressor. Evidence for functional diversification in nitrate reductase protein was also observed. Its temperature optimum was adapted to each organism's growth range, and its K-m was much lower in Py. ultimum. In summary, we observed divergence in patterns of gene expression, gene content, and enzyme function which contribute to the fitness of each species in its niche. Author summary A key feature of disease is the pathogen's consumption of host metabolites to support its growth and multiplication. Understanding how host nutrients are used by pathogens may lead to strategies for limiting disease, for example by developing inhibitors of metabolic pathways needed for pathogen growth. Feeding strategies of plant pathogens range between two extremes: necrotrophs kill host cells and consume the released nutrients, while biotrophs do not injure host cells but instead acquire nutrients from extracellular spaces in the plant. In this study, a comparison was made between the metabolism of Phytophthora infestans (the infamous Irish Famine pathogen) and Pythium ultimum during potato tuber colonization. These microbes have close evolutionary histories, but while Py. ultimum is a necrotroph, Ph. infestans is a biotroph for most of the disease cycle. It was discovered that distinct patterns of metabolic gene expression, gene content, and enzyme behavior underlie these lifestyles. For example, genes for utilizing compounds that are normally stored within plant cells were expressed more by Py. ultimum, while Ph. infestans appeared to synthesize more biosubstances from precursors. Several differences in carbon and nitrogen metabolism were linked to variation in enzyme content and gene expression regulators in the two species.