A genomic survey of nitrogen assimilation pathways in budding yeasts (sub‐phylum Saccharomycotina)

Abstract

Sequenced genomes of 149 species of budding yeast (including 62 species with draft genomes that currently lack gene annotations) were surveyed for the presence of 24 genes associated with the assimilation of amines, uracil, dihydropyrimidines, purines, uric acid, allantoin, and nitrate as nitrogen sources. Genes for the assimilation of primary amines were distributed broadly across the Saccharomycotina while choline assimilation appeared to be mostly restricted to the families Debaryomycetaceae, Metschnikowiaceae, and Pichiaceae. Conversely, the uracil catabolic pathway was completely absent in Debaryomycetaceae and Metschnikowiaceae but present in the majority of the remaining Saccharomycotina. The super-pathway for assimilation of purines, uric acid, and allantoin was present in the majority of surveyed species.Genes for the assimilation of nitrate were restricted to a minority of species in families Phaffomycetaceae, Pichiaceae, and Trichomonascaceae as well as some currently unassigned genera. This study also successfully identified yeast homologs of all six previously known eukaryotic genes involved in the biosynthesis of the molybdenum cofactor, which is required for the activity of the nitrogen assimilation-associated enzymes nitrate reductase and xanthine oxidoreductase. Analysis of 1,187 upstream intergenic regions identified three novel putative regulatory motifs for the assimilation of uracil, purines, and uric acid as well as a possible role for the MADS-box transcription factor Mcm1 in the regulation of amine assimilation genes.

Ornithine decarboxylase of the fungal pathogen Colletotrichum higginsianum plays an important role in regulating global metabolic pathways and virulence

“…5A; Table S4). In fungi, another nitrogen metabolism pathway, purine catabolism, has been extensively studied (Reinert and Marzluf, 1975; Gournas et al ., 2011; Linder, 2019). In particular, adenine and the nucleotides AMP, GMP, UMP, dCMP, dAMP, dIMP and dGMP were found at lower abundances in the Δ ChODC mutant than in the wild‐type strain (Table S3).…”

Natural trait variation across Saccharomycotina species

“…The latter has led to new insights into the evolutionary history of metabolic gains and losses across Saccharomycotina , and the discovery of associations with ecology and genome content (Novo et al 2009 , Gonçalves et al 2016 , Opulente et al 2018 ). Among the many advantages of this approach, it has put the evolutionary study of nitrogen utilization well within reach (Wang et al 2015 , Filteau et al 2017 , Linder 2019b ) as a complement to the classic focus on variation in carbon source preferences.…”

What makes Komagataella phaffii non-conventional?

“…Recently, a genomic survey of nitrogen assimilation pathways in budding yeast has been published (Linder 2019 ). By contrast to S. cerevisiae , the genome of K. phaffii contains the gene AMO1 encoding amine oxidase that catalyzes the deamination of aliphatic primary amine (R-NH 2 ) with the release of ammonia.…”

“…At least six genes, MOC1 – MOC6 are involved in molybdenum cofactor biosynthesis in eukaryotic cells. The homologs of these six genes were identified in K. phaffii but not in S. cerevisiae (Linder 2019 ).…”