Gene regulatory network plasticity predates a switch in function of a conserved transcription regulator

Abstract

The rewiring of gene regulatory networks can generate phenotypic novelty. It remains an open question, however, how the large number of connections needed to form a novel network arise over evolutionary time. Here, we address this question using the network controlled by the fungal transcription regulator Ndt80. This conserved protein has undergone a dramatic switch in function—from an ancestral role regulating sporulation to a derived role regulating biofilm formation. This switch in function corresponded to a large-scale rewiring of the genes regulated by Ndt80. However, we demonstrate that the Ndt80-target gene connections were undergoing extensive rewiring prior to the switch in Ndt80’s regulatory function. We propose that extensive drift in the Ndt80 regulon allowed for the exploration of alternative network structures without a loss of ancestral function, thereby facilitating the formation of a network with a new function.DOI: http://dx.doi.org/10.7554/eLife.23250.001

The causes of evolvability and their evolution

“…Gene expression patterns themselves are highly robust, not only to mutations in binding sites, but also to wholesale changes in the number, identity, and orientation of binding sites within regulatory regions , and thus to changes in the structure of gene regulatory networks 96 . Modelling work has long anticipated that such robustness can facilitate evolvability 97,98 , but empirical support for this possibility was only recently provided 99 . Specifically, the highly conserved fungal transcription factor Ndt80 underwent a pronounced switch in function from an ancestral role regulating meiosis and sporulation to a derived role regulating biofilm formation.…”

How transcription circuits explore alternative architectures while maintaining overall circuit output

“…For example, the transcription regulator Ndt80 activates hundreds of sporulation and meiosis genes in S. cerevisiae (Hepworth et al 1998) and is required to complete meiosis (Xu et al 1995). Ndt80 is needed for meiosis in multiple ascomycete species (Nocedal et al 2017), including K. lactis (120 million years diverged from S. cerevisiae) and Pichia pastoris (210 million years diverged from S. cerevisiae). ChIP-seq (chromatin immunoprecipitation [ChIP] combined with high-throughput sequencing) analysis of Ndt80 across multiple species shows that, in all species, the Ndt80 regulon is large and consists predominantly of deeply conserved genes; however, the genes controlled by Ndt80 differ greatly across their entire species, with little overlap between them.…”

“…Thus far, we argued here that transcription rewiring is common, and, in this section, we review evidence (predominantly from full-genome experimental and computational studies) that gives a rough idea of the frequency. Based on several independent studies in ascomycetes, it is estimated that, on average, ∼15% of the connections between a transcription regulator and its target genes in S. cerevisiae will be preserved in C. albicans (for example, see Borneman et al 2007;Tuch et al 2008b;Habib et al 2012;Sarda and Hannenhalli 2015;Nocedal et al 2017). Of course, the exact number depends on the particular regulator examined (as well as the methodologies used), but this rough average is a reasonable starting place for appreciating the overall extent of transcriptional rewiring.…”

“…The term "transcriptional rewiring" is sometimes used in the literature to indicate a change in the transcriptional program as development proceeds, but we use the term in a different sense, referring to genetic differences in transcription circuits be-tween one species and another. Despite extensive evolutionary rewiring among even closely related species (Tsong et al 2006;Borneman et al 2007;Martchenko et al 2007;Tuch et al 2008b;Lavoie et al 2009;Weirauch and Hughes 2010;Tirosh et al 2011;Nocedal and Johnson 2015;Villar et al 2015;Nocedal et al 2017), the output from these circuits often remains relatively constant. In the next sections, we discuss specific examples from fungi that illustrate this idea.…”

New transcriptional circuit evolved by coding sequence changes in a master regulator followed by cis-regulatory changes in its target genes

“…Chromatin immunoprecipitation (ChIP) was performed as previously described 11,53 . Briefly, single colonies were grown to saturation overnight in YEPD, diluted to OD 600 = 0.1 in fresh YEPD, then grown at 30°C to OD 600 = 0.4.…”