Global Expression Analysis of the Yeast Lachancea (Saccharomyces) kluyveri Reveals New URC Genes Involved in Pyrimidine Catabolism

Abstract

bPyrimidines are important nucleic acid precursors which are constantly synthesized, degraded, and rebuilt in the cell. Four degradation pathways, two of which are found in eukaryotes, have been described. One of them, the URC pathway, has been initially discovered in our laboratory in the yeast Lachancea kluyveri. Here, we present the global changes in gene expression in L. kluyveri in response to different nitrogen sources, including uracil, uridine, dihydrouracil, and ammonia. The expression pattern of the known URC genes, URC1-6, helped to identify nine putative novel URC genes with a similar expression pattern. The microarray analysis provided evidence that both the URC and PYD genes are under nitrogen catabolite repression in L. kluyveri and are induced by uracil or dihydrouracil, respectively. We determined the function of URC8, which was found to catalyze the reduction of malonate semialdehyde to 3-hydroxypropionate, the final degradation product of the pathway. The other eight genes studied were all putative permeases. Our analysis of double deletion strains showed that the L. kluyveri Fui1p protein transported uridine, just like its homolog in Saccharomyces cerevisiae, but we demonstrated that is was not the only uridine transporter in L. kluyveri. We also showed that the L. kluyveri homologs of DUR3 and FUR4 do not have the same function that they have in S. cerevisiae, where they transport urea and uracil, respectively. In L. kluyveri, both of these deletion strains grew normally on uracil and urea.

Insight on specificity of uracil permeases of the NAT/NCS2 family from analysis of the transporter encoded in the pyrimidine utilization operon of Escherichia coli

“…Pyrimidine degradation is used by cells to control the intracellular pool of nucleotides in concert with biosynthetic ( de novo or salvage) and other catabolic pathways and to obtain nitrogen in the absence or scarcity of other available sources. Four different pyrimidine degradation pathways can be used (Loh et al ., ; Osterman, ; Andersen et al ., ; Andersson Rasmussen et al ., ). The reductive pathway, starting with reduction of uracil to dihydrouracil by a dihydropyrimidine dehydrogenase, is common in most eukaryotes and also in many prokaryotes.…”

Differences in environmental stress response among yeasts is consistent with species-specific lifestyles

“…The description of the transcriptomic response to various conditions has also allowed for the identification of the functions for many genes ( Ashburner et al. , 2000 ; Nieduszynski and Liti, 2011 ; Andersson Rasmussen et al. , 2014 ).…”

Reconstruction and analysis of genome-scale metabolic model of weak Crabtree positive yeast Lachancea kluyveri

“…In the previous published literature, important metabolic phenotypes for L. kluyveri have been reported. Of the four possible modes of pyrimidine degradation known, the uracil (pyrimidine) catabolism (URC) pathway has been uniquely characterized in L. kluyveri 1 , 4 , 48 . Locus URC1-6 and URC8 have been experimentally characterized to be an essential component of the URC pathway for uracil degradation.…”