Gene duplication and co-evolution of G1/S transcription factor specificity in fungi are essential for optimizing cell fitness

Abstract

Transcriptional regulatory networks play a central role in optimizing cell survival. How DNA binding domains and cis-regulatory DNA binding sequences have co-evolved to allow the expansion of transcriptional networks and how this contributes to cellular fitness remains unclear. Here we experimentally explore how the complex G1/S transcriptional network evolved in the budding yeast Saccharomyces cerevisiae by examining different chimeric transcription factor (TF) complexes. Over 200 G1/S genes are regulated by either one of the two TF complexes, SBF and MBF, which bind to specific DNA binding sequences, SCB and MCB, respectively. The difference in size and complexity of the G1/S transcriptional network across yeast species makes it well suited to investigate how TF paralogs (SBF and MBF) and DNA binding sequences (SCB and MCB) co-evolved after gene duplication to rewire and expand the network of G1/S target genes. Our data suggests that whilst SBF is the likely ancestral regulatory complex, the ancestral DNA binding element is more MCB-like. G1/S network expansion took place by both cis- and trans- co-evolutionary changes in closely related but distinct regulatory sequences. Replacement of the endogenous SBF DNA-binding domain (DBD) with that from more distantly related fungi leads to a contraction of the SBF-regulated G1/S network in budding yeast, which also correlates with increased defects in cell growth, cell size, and proliferation.

G1/S Transcription Factor Copy Number Is a Growth-Dependent Determinant of Cell Cycle Commitment in Yeast

“…Our mathematical model of the Start transition extends previous models based solely on the relief of SBF/MBF inhibition by Cln-Cdc28-mediated phosphorylation and Whi5 nuclear export (Cross et al, 2002;Di Talia et al, 2009;Huang et al, 2009;Wang et al, 2009;Charvin et al, 2010;Adames et al, 2015;Liu et al, 2015;Laomettachit et al, 2016;Palumbo et al, 2016;Aldea et al, 2017) by incorporating SBF/MBF accumulation as cells grow in G1 phase and the enhanced expression of SBF/MBF in poor nutrients. Our model thus accommodates specialized functions of SBF and MBF (Hendler et al, 2017), unlike prior models that treat SBF and MBF activity as a single parameter (Laomettachit et al, 2016). We also find that Cln2 amplification is damped due to an increased contribution from MBF in glycerol medium.…”

The evolution of a G1/S transcriptional network in yeasts

“…Further support for the functional division of the SBF regulon to "modern" genes containing SCB motifs and "ancient" genes containing MCB motifs came from chromatin immunoprecipitation (ChIP) experiments. We found that Sc Swi4 exhibits much higher affinity for the SCB motif relative to the MCB-like motif while the chimeric TFs containing distantly related DBDs can only bind the MCB-like motif (Hendler, et al 2017). These results suggest that the Sc Swi4 evolved for optimized binding to the SCB motif to enable normal cell growth and morphogenesis.…”

“…Despite extensive studies in different organisms, relatively little was known regarding how Swi4 and Mbp1 DNA binding domains (DBDs) co-evolved to recognize the SCB and MCB DNA binding sequences, respectively, to synchronize the expression of a large set of genes during the G1 to S transition. To address these questions, we recently generated and examined the function of different chimeric Mbp1 and Swi4 TFs in Sc (Hendler, et al 2017). Specifically, we generated to slow growth rate and severe morphological defects upon cell growth, budding and division (Hendler, et al 2017).…”

“…To address these questions, we recently generated and examined the function of different chimeric Mbp1 and Swi4 TFs in Sc (Hendler, et al 2017). Specifically, we generated to slow growth rate and severe morphological defects upon cell growth, budding and division (Hendler, et al 2017).…”

“…Despite extensive research little is known regarding the evolution of the G1/S transcription regulation including the co-evolution of the DNA binding domains with their respective DNA binding sequences. We have recently examined the coevolution of the G1/S TF specificity through the systematic generation and examination of chimeric Mbp1/Swi4 TFs containing different orthologue DNA binding domains in S. cerevisiae (Hendler, et al 2017). Here, we review the co-evolution of G1/S transcriptional network and discuss the evolutionary dynamics and specificity of the MBF-MCB and SBF-SCB interactions in different fungal species.…”