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PMID: 15534694 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

Conservation and evolution of cis-regulatory systems in ascomycete fungi.

PLoS biology ·Vol. 2 ·No. 12 ·2004-12-00 ·Pages e398

Gasch AP, Moses AM, Chiang DY, Fraser HB, Berardini M, Eisen MB

Abstract

Relatively little is known about the mechanisms through which gene expression regulation evolves. To investigate this, we systematically explored the conservation of regulatory networks in fungi by examining the cis-regulatory elements that govern the expression of coregulated genes. We first identified groups of coregulated Saccharomyces cerevisiae genes enriched for genes with known upstream or downstream cis-regulatory sequences. Reasoning that many of these gene groups are coregulated in related species as well, we performed similar analyses on orthologs of coregulated S. cerevisiae genes in 13 other ascomycete species. We find that many species-specific gene groups are enriched for the same flanking regulatory sequences as those found in the orthologous gene groups fromS. cerevisiae, indicating that those regulatory systems have been conserved in multiple ascomycete species. In addition to these clear cases of regulatory conservation, we find examples of cis-element evolution that suggest multiple modes of regulatory diversification, including alterations in transcription factor-binding specificity, incorporation of new gene targets into an existing regulatory system, and cooption of regulatory systems to control a different set of genes. We investigated one example in greater detail by measuring the in vitro activity of the S. cerevisiae transcription factor Rpn4p and its orthologs from Candida albicans and Neurospora crassa. Our results suggest that the DNA binding specificity of these proteins has coevolved with the sequences found upstream of the Rpn4p target genes and suggest that Rpn4p has a different function in N. crassa.

MeSH Terms
Amino Acid Motifs Amino Acid Sequence Ascomycota/genetics Binding, Competitive Candida albicans/genetics Cloning, Molecular Conserved Sequence DNA/chemistry,metabolism DNA-Binding Proteins/metabolism Evolution, Molecular Gene Expression Regulation, Fungal Genes, Regulator Genome, Fungal Models, Statistical Molecular Sequence Data Multigene Family Neurospora crassa/genetics Open Reading Frames Phylogeny Plasmids/metabolism Proteasome Endopeptidase Complex/metabolism Protein Binding Saccharomyces cerevisiae/genetics Saccharomyces cerevisiae Proteins/metabolism Sequence Homology, Amino Acid Species Specificity Transcription Factors/metabolism
Chemicals
DNA-Binding Proteins RPN4 protein, S cerevisiae Saccharomyces cerevisiae Proteins Transcription Factors DNA Proteasome Endopeptidase Complex
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Gasch Audrey P
Genome Sciences Department, Genomics Division, Lawrence Berkeley National Laboratory , Berkeley, California, USA. agasch@wisc.edu <agasch@wisc.edu>
Moses Alan M
Chiang Derek Y
Fraser Hunter B
Berardini Mark
Eisen Michael B
Conflict of Interest

The authors have declared that no conflicts of interest exist.

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Article Info
Journal
PLoS biology
Abbr.
PLoS Biol
ISSN
1545-7885
Published
2004-12-00
Epub
2004-00-09
Pages
e398
Language
English
Region
United States
NLM ID
101183755
PMCID
PMC526180
Subset
IM
Grants
NCI NIH HHS · P01 CA092584 · United States
NCI NIH HHS · 5P01CA092584-03 · United States
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