Functional analyses of PAU genes in Saccharomyces cerevisiae
Abstract
PAU genes constitute the largest gene family in Saccharomyces cerevisiae, with 24 members mostly located in the subtelomeric regions of chromosomes. Little information is available about PAU genes, other than expression data for some members. In this study, we systematically compared the sequences of all 24 members, examined the expression of PAU3, PAU5, DAN2, PAU17 and PAU20 in response to stresses, and investigated the stability of all Pau proteins. The chromosomal localization, synteny and sequence analyses revealed that PAU genes could have been amplified by segmental and retroposition duplication through mechanisms of chromosomal end translocation and Ty-associated recombination. The coding sequences diverged through nucleotide substitution and insertion/deletion of one to four codons, thus causing changes in amino acids, truncation or extension of Pau proteins. Pairwise comparison of non-coding regions revealed little homology in flanking sequences of some members. All 24 PAU promoters contain a TATA box, and 22 PAU promoters contain at least one copy of the anaerobic response element and the aerobic repression motif. Differential expression was observed among PAU3, PAU5, PAU17, PAU20 and DAN2 in response to stress, with PAU5 having the highest capacity to be induced by anaerobic conditions, low temperature and wine fermentations. Furthermore, Pau proteins with 124 aa were less stable than those with 120 or 122 aa. Our results indicate that duplicated PAU genes have been evolving, and the individual Pau proteins might possess specific roles for the adaptation of S. cerevisiae to certain environmental stresses.
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Mot3 represses the expression of hypoxic, DAN/TIR/PAU and ERG genes including ERG2, ERG6 and ERG9.
“In addition, to limit Ecm22 function [75], the transcriptional factor Mot3 also represses the expression of hypoxic, DAN/TIR/PAU and ERG genes including ERG2, ERG6 and ERG9 (Figure 3A) [86,89,90,91,92,93].”
From Regulation of Ergosterol Biosynthesis in Saccharomyces cerevisiae (2020) · cites this paper as [93]
Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302 · see citing works
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment
Kumar, S. (2004) · Briefings in Bioinformatics · doi:10.1093/bib/5.2.150 · Cited by 11,642 · see citing works
Ohno, S. (1970) · doi:10.1007/978-3-642-86659-3 · Cited by 7,833 · see citing works
T-Coffee: A novel method for fast and accurate multiple sequence alignment.
Notredame, C., Higgins, D., & Heringa, J. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.4042 · Cited by 7,321 · see citing works
The Evolutionary Fate and Consequences of Duplicate Genes
Lynch, M., & Conery, J. S. (2000) · Science · doi:10.1126/science.290.5494.1151 · Cited by 4,988 · see citing works
Goffeau, A., Barrell, B., Bussey, H., Davis, R. W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J., Jacq, C., Johnston, M., et al. (1996) · Science · doi:10.1126/science.274.5287.546 · Cited by 4,420 · see citing works
Boeke, J. D., Lacroute, F., & Fink, G. R. (1984) · Molecular and General Genetics MGG · doi:10.1007/bf00330984 · Cited by 2,354 · see citing works
Evolution by gene duplication: An update
Zhang, J. (2003) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(03)00033-8 · Cited by 2,201 · see citing works
Sequencing and comparison of yeast species to identify genes and regulatory elements
Kellis, M., Patterson, N. J., Endrizzi, M. G., Birren, B. W., & Lander, E. S. (2003) · Nature · doi:10.1038/nature01644 · Cited by 1,731 · see citing works
Short protocols in molecular biology
(1996) · The Journal of Steroid Biochemistry and Molecular Biology · doi:10.1016/s0960-0760(97)80799-6 · Cited by 1,650 · see citing works
Duplication and Divergence: The Evolution of New Genes and Old Ideas
Taylor, J. S., & Raes, J. (2004) · Annual Review of Genetics · doi:10.1146/annurev.genet.38.072902.092831 · Cited by 911 · see citing works
Identification and Distinct Regulation of Yeast TATA Box-Containing Genes
Basehoar, A. D., Zanton, S. J., & Pugh, B. F. (2004) · Cell · doi:10.1016/s0092-8674(04)00205-3 · Cited by 686 · see citing works
Teixeira, M. C. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj013 · Cited by 490 · see citing works
Kong, H., Landherr, L. L., Frohlich, M. W., Leebens‐Mack, J., Mā, H., & dePamphilis, C. W. (2007) · The Plant Journal · doi:10.1111/j.1365-313x.2007.03097.x · Cited by 479 · see citing works
Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast
Wyrick, J. J., Holstege, F. C. P., Jennings, E. G., Causton, H. C., Shore, D., Grunstein, M. R., Lander, E. S., & Young, R. A. (1999) · Nature · doi:10.1038/46567 · Cited by 394 · see citing works
Rapid divergence in expression between duplicate genes inferred from microarray data
Gu, Z., Nicolae, D. L., Lu, H. H.-S., & Li, W. (2002) · Trends in Genetics · doi:10.1016/s0168-9525(02)02837-8 · Cited by 346 · see citing works
Genome‐wide monitoring of wine yeast gene expression during alcoholic fermentation
Rossignol, T., Dulau, L., Julien, A., & Blondin, B. (2003) · Yeast · doi:10.1002/yea.1046 · Cited by 329 · see citing works
Upc2p and Ecm22p, Dual Regulators of Sterol Biosynthesis in <i>Saccharomyces cerevisiae</i>
Vik, Å., & Rine, J. (2001) · Molecular and Cellular Biology · doi:10.1128/mcb.21.19.6395-6405.2001 · Cited by 277 · see citing works
Marks, V. D., Sui, S. J. H., Erasmus, D. J., van der Merwe, G. K., Brumm, J., Wasserman, W. W., Bryan, J., & van Vuuren, H. J. J. (2008) · FEMS Yeast Research · doi:10.1111/j.1567-1364.2007.00338.x · Cited by 191 · see citing works
Chromosome ends: all the same under their caps
Pryde, F. E., Gorham, H. C., & Louis, E. J. (1997) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(97)80046-9 · Cited by 187 · see citing works
Sahara, T., Goda, T., & Ohgiya, S. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m209258200 · Cited by 176 · see citing works
Abramova, N., Sertil, O., Mehta, S., & Lowry, C. V. (2001) · Journal of Bacteriology · doi:10.1128/jb.183.9.2881-2887.2001 · Cited by 157 · see citing works
Comparative Genomics in Hemiascomycete Yeasts: Evolution of Sex, Silencing, and Subtelomeres
Fabre, E., Muller, H., Therizols, P., Lafontaine, I., Dujon, B., & Fairhead, C. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msi070 · Cited by 141 · see citing works
Regulation of Subtelomeric Silencing during Stress Response
Ai, W., Bertram, P. G., Tsang, C. K., Chan, T., & Zheng, X. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00695-0 · Cited by 131 · see citing works
Abramova, N. E., Cohen, B. D., Sertil, O., Kapoor, R., Davies, K. J. A., & Lowry, C. V. (2001) · Genetics · doi:10.1093/genetics/157.3.1169 · Cited by 128 · see citing works
A Role for Sterol Levels in Oxygen Sensing in <i>Saccharomyces cerevisiae</i>
Davies, B. S. J., & Rine, J. (2006) · Genetics · doi:10.1534/genetics.106.059964 · Cited by 123 · see citing works
Blandin, G., Durrens, P., Tekaia, F., Aigle, M., Bolotin‐Fukuhara, M., Bon, E., Casarégola, S., de Montigny, J., Gaillardin, C. M., Lépingle, A., et al. (2000) · FEBS Letters · doi:10.1016/s0014-5793(00)02275-4 · Cited by 92 · see citing works
Saccharomyces cerevisiae PAU genes are induced by anaerobiosis
Rachidi, N., Martinez, M., Barre, P., et al. (2000) · Molecular Microbiology · doi:10.1046/j.1365-2958.2000.01807.x · Cited by 91 · see citing works
Synergistic repression of anaerobic genes by Mot3 and Rox1 in Saccharomyces cerevisiae
Sertil, O. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg792 · Cited by 88 · see citing works
Cohen, B. D. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.3.799 · Cited by 88 · see citing works
ALIMARDANI, P., RÉGNACQ, M., MOREAU-VAUZELLE, C., FERREIRA, T., ROSSIGNOL, T., BLONDIN, B., & BERGÈS, T. (2004) · Biochemical Journal · doi:10.1042/bj20040297 · Cited by 84 · see citing works
Yeast gene expression during growth at low temperature
Homma, T., Iwahashi, H., & Komatsu, Y. (2003) · Cryobiology · doi:10.1016/s0011-2240(03)00028-2 · Cited by 83 · see citing works
Hongay, C., Jia, N., Bard, M., & Winston, F. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf415 · Cited by 72 · see citing works
Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser
Byrne, K. P. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj041 · Cited by 64 · see citing works
Viswanathan, M., Muthukumar, G., Cong, Y.-S., & Lenard, J. (1994) · Gene · doi:10.1016/0378-1119(94)90249-6 · Cited by 56 · see citing works
Tandemly Arrayed Genes in Vertebrate Genomes
Pan, D., & Zhang, L. (2008) · Comparative and Functional Genomics · doi:10.1155/2008/545269 · Cited by 49 · see citing works
An evolutionary scenario for one of the largest yeast gene families
Despons, L., Wirth, B., Leh, V., Potier, S., & Souciet, J. (2005) · Trends in Genetics · doi:10.1016/j.tig.2005.10.001 · Cited by 31 · see citing works
Luo, Z., & van Vuuren, H. J. J. (2008) · FEMS Yeast Research · doi:10.1111/j.1567-1364.2008.00355.x · Cited by 19 · see citing works
Self-citationWirth, B., Louis, V. L., Potier, S., et al. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi170 · Cited by 8 · see citing works
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Regulation of Ergosterol Biosynthesis in Saccharomyces cerevisiae
Jordá, T., & Puig, S. (2020) · Genes · doi:10.3390/genes11070795 · Cited by 489 · see citing works
Hickman, M. J., Spatt, D., & Winston, F. (2011) · Genetics · doi:10.1534/genetics.111.128322 · Cited by 68 · see citing works
Joshua, I., & Höfken, T. (2017) · International Journal of Molecular Sciences · doi:10.3390/ijms18040772 · Cited by 40 · see citing works
Serratore, N. D., Baker, K. M., Macadlo, L. A., Gress, A. R., Powers, B. L., Atallah, N., Westerhouse, K. M., Hall, M. C., Weake, V. M., & Briggs, S. D. (2018) · Genetics · doi:10.1534/genetics.117.300554 · Cited by 33 · see citing works
- Authors
- Luo, Z., & van Vuuren, H. J. J.
- Affiliations
- University of British Columbia (CA)
- Wine Research Centre, Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Venue
- Microbiology
- Publisher
- Microbiology Society
- Published
- 2009-12-01
- Volume
- 155
- Issue
- 12
- Pages
- 4036-4049
- ISSN
- 1350-0872 (ISSN-L)
- 1465-2080
- OpenAlex
- W2125683634
- Cited by
- 54
- References
- 39
- Citations by year
- 2025: 2 · 2024: 6 · 2023: 4 · 2022: 2 · 2021: 3 · 2020: 2 · 2019: 7 · 2018: 4 · 2017: 5 · 2016: 2 · 2015: 3 · 2014: 3 · 2013: 4 · 2012: 1
- FWCI
- 0.94
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Microbiology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Natural Sciences and Engineering Research Council of Canada
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Yeasts and Rust Fungi Studies
- Keywords
- Saccharomyces cerevisiae, subtelomeric regions, gene family evolution, segmental duplication, retroposition, stress response, anaerobic conditions, cold stress, wine fermentation, protein stability, promoter analysis
- MeSH terms
- Amino Acid Sequence, Base Sequence, Chromosome Mapping, DNA, Fungal, Genes, Fungal, Multigene Family, Molecular Sequence Data, Phylogeny, Saccharomyces cerevisiae, Sequence Homology, Nucleic Acid, Stress, Physiological, Gene Expression, Sequence Homology, Amino Acid, Evolution, Molecular, Gene Duplication, 5' Flanking Region, Saccharomyces cerevisiae Proteins, Protein Stability
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