Gene duplication and the evolution of ribosomal protein gene regulation in yeast

Abstract

Coexpression of genes within a functional module can be conserved at great evolutionary distances, whereas the associated regulatory mechanisms can substantially diverge. For example, ribosomal protein (RP) genes are tightly coexpressed in Saccharomyces cerevisiae, but the cis and trans factors associated with them are surprisingly diverged across Ascomycota fungi. Little is known, however, about the functional impact of such changes on actual expression levels or about the selective pressures that affect them. Here, we address this question in the context of the evolution of the regulation of RP gene expression by using a comparative genomics approach together with cross-species functional assays. We show that an activator (Ifh1) and a repressor (Crf1) that control RP gene regulation in normal and stress conditions in S. cerevisiae are derived from the duplication and subsequent specialization of a single ancestral protein. We provide evidence that this regulatory innovation coincides with the duplication of RP genes in a whole-genome duplication (WGD) event and may have been important for tighter control of higher levels of RP transcripts. We find that subsequent loss of the derived repressor led to the loss of a stress-dependent repression of RPs in the fungal pathogen Candida glabrata. Our comparative computational and experimental approach shows how gene duplication can constrain and drive regulatory evolution and provides a general strategy for reconstructing the evolutionary trajectory of gene regulation across species. T he coordinated expression of modules of functionally related genes, such as ribosomal proteins or oxidative phosphorylation enzymes, is often conserved at great evolutionary distances (1). This is consistent with a selective pressure to conserve coordinated transcript levels to maintain functional cellular modules. Recent studies have shown that the regulatory mechanisms controlling conserved modules can diverge, most notably by switching from one regulatory system to another while preserving coregulation (1, 2). However, because previous studies have typically relied on functional expression data from only one or two species, it is unknown whether these changes in regulatory mechanisms affect the expression levels of a module's genes at all or whether both coexpression and expression levels are conserved.A prominent example of a conserved regulatory module is the ribosomal protein (RP) module. Genes encoding RPs are tightly coexpressed in organisms from bacteria to humans (3, 4), consistent with a selective pressure to conserve coordinated transcript levels to maintain a stoichoimetric balance in ribosome assembly. The transcription factors controlling RP gene expression have changed several times since the last common ancestor of the Ascomycota fungi, which span Saccharomyces cerevisiae and Schizosaccharomyces pombe (4-6). These dramatic changes include the loss of the ancestral regulator Tbf1, the emergence of Rap1 as a key activator among the Hemiascomycota (4, 5), as well as the add...

Saccharomyces cerevisiae Forms d-2-Hydroxyglutarate and Couples Its Degradation to d-Lactate Formation via a Cytosolic Transhydrogenase

“…Finally, it is also interesting to note that the only post-duplication species, of those that we analyzed, not encoding the Dld3 protein is the pathogenic species C. glabrata. Similarly, for the ohnologous gene pair IFH1 and CRF1 (both genes are involved in the regulation of expression of ribosomal proteins), only IFH1 is maintained in the C. glabrata genome (54). All of the Dld3-like sequences found in the post-duplication species lack the MTS that is present in the Dld2-like sequences in yeasts but also in other eukaryotic species such as mammals.…”

Zinc Cluster Transcription Factors Alter Virulence in Candida albicans

“…Phylogenetic analysis of (B) ZCF15 and (C) ZCF29 in Candida and related fungi. Orthologs of ZCF15 and ZCF29 in Candida and related fungi were previously identified (Wapinski et al 2010). Phylogenies inferred with RAxML from aligned protein sequences are shown with the fraction of 1000 bootstrap replicates supporting each node.…”

“…Protein sequences were aligned using MUSCLE (Edgar 2004), and converted to codon alignments with PAL2NAL (Suyama et al 2006); d N /d S ratios were calculated with Codeml (Yang 2007). For phylogenetic analysis of ZCF15 or ZCF29 with related orthologs (Wapinski et al 2010), protein sequences were aligned with MUSCLE (Edgar 2004), and gap regions removed with TrimAl (CapellaGutierrez et al 2009). The best model was identified with Protest v3.4 (Darriba et al 2011) (PROTGAMMAJTT for ZCF15 and PROTGAMMALG for ZCF29), and used by RAxML v7.7.8 (Stamatakis 2006) to infer the phylogenetic relationship of each ZCF gene.…”

Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules

“…Such studies measure and compare genomic profiles, including mRNA levels (Bergmann et al 2003b;Tirosh et al 2006;Wapinski et al 2010;Brawand et al 2011;Fowlkes et al 2011;Rhind et al 2011;Tirosh et al 2011), chromatin organization (Segal et al 2006;Tsankov et al 2010;Xiao et al 2012), or protein-DNA interactions (Borneman et al 2007;Schmidt et al 2010Schmidt et al , 2012Kutter et al 2011) across two or more species.…”