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Global expression analysis of the yeast Lachancea (Saccharomyces) kluyveri reveals new URC genes involved in pyrimidine catabolism

Rasmussen, Anna LU ; Kandasamy, Dineshkumar LU ; Beck, Halfdan LU ; Crosby, Seth D ; Björnberg, Olof LU ; Schnackerz, Klaus LU and Piskur, Jure LU (2014) In Eukaryotic Cell 13(1). p.31-42
Abstract

Pyrimidines 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.... (More)

Pyrimidines 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.

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author
; ; ; ; ; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Catabolite Repression, Fungal Proteins/genetics, Gene Expression Profiling, Genome, Fungal, Nitrogen/metabolism, Nucleoside Transport Proteins/genetics, Saccharomyces/genetics, Uracil/metabolism
in
Eukaryotic Cell
volume
13
issue
1
pages
31 - 42
publisher
American Society for Microbiology
external identifiers
  • wos:000329193900004
  • pmid:24186952
  • scopus:84891606430
  • pmid:24186952
ISSN
1535-9778
DOI
10.1128/EC.00202-13
language
English
LU publication?
yes
id
1a3dca38-655b-4d0b-8fce-ba9025dfab3f (old id 4179818)
date added to LUP
2016-04-01 10:05:54
date last changed
2021-11-02 08:14:52
@article{1a3dca38-655b-4d0b-8fce-ba9025dfab3f,
  abstract     = {<p>Pyrimidines 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. </p>},
  author       = {Rasmussen, Anna and Kandasamy, Dineshkumar and Beck, Halfdan and Crosby, Seth D and Björnberg, Olof and Schnackerz, Klaus and Piskur, Jure},
  issn         = {1535-9778},
  language     = {eng},
  number       = {1},
  pages        = {31--42},
  publisher    = {American Society for Microbiology},
  series       = {Eukaryotic Cell},
  title        = {Global expression analysis of the yeast Lachancea (Saccharomyces) kluyveri reveals new URC genes involved in pyrimidine catabolism},
  url          = {http://dx.doi.org/10.1128/EC.00202-13},
  doi          = {10.1128/EC.00202-13},
  volume       = {13},
  year         = {2014},
}