Design principles of acidic transcriptional activation domains

Abstract

Transcription factors activate gene expression with separable DNA binding domains and activation domains (Latchman, 2008). High-throughput studies have uncovered rules for how DNA binding domains recognize their cognate DNA motifs, but the design principles of activation domains remain opaque. For over thirty years it has been a mystery why activation domains are acidic and unstructured (Sigler, 1988). Activation domains require hydrophobic motifs to bind coactivators and join transcriptional condensates, but low evolutionary conservation and intrinsic disorder have made it difficult to identify the design principles that govern the sequence to function relationship (Boija et al., 2018; Chong et al., 2018; Cress and Triezenberg, 1991; Dyson and Wright, 2016). Consequently, activation domains cannot be predicted from amino acid sequence (Finn et al., 2016). Here, we resolve the functional roles of acidity and disorder in activation domains and use these insights to build a new predictor. We designed sequence variants in seven acidic activation domains and measured their activities in parallel with a high-throughput assay in human cell culture. Our results support a flexible model in which acidic residues solubilize hydrophobic motifs so that they can interact with coactivators. This model accurately predicts activation domains in the human proteome. We identify three general rules for activation domain function: hydrophobic motifs must be balanced by acidic residues; acidic residues make large contributions to activity when they are adjacent to motifs; and within motifs, the presence of aromatic or leucine residues reflects the structural constraints of coactivator interactions. We anticipate these design principles will aid efforts to predict activations from amino acid sequence and to engineer new domains.

On the potential of machine learning to examine the relationship between sequence, structure, dynamics and function of intrinsically disordered proteins

“…One such example is the activation domains of transcription factors (Erkine, 2018), whose properties were originally characterized as 'acid blobs and negative noodles' (Sigler, 1988). Recently, a number of multiplexed assays have been used to expand this view and study the functional requirements of the sequence properties of transcriptional activation domains (Staller et al, 2018;Ravarani et al, 2018;Erijman et al, 2020;Tycko et al, 2020;Sanborn et al, 2021;Staller et al, 2021). These results confirm the original observations of a requirement for hydrophobic and negatively charged residues and provide additional information about the role of patterning.…”

Intrinsic Disorder in Plant Transcription Factor Systems: Functional Implications

“…Generally, strong acidic ADs contain multiple clusters of hydrophobic residues near acidic residues, imposing avidity through several weak and dynamic interactions, characteristic of IDR-based fuzzy interactions [ 136 , 137 ]. According to a recently proposed model, acidic residues solubilize hydrophobic motifs enabling their interactions with co-activators [ 138 ]. Thus, hydrophobic motifs are balanced by acidic residues, which constitute important parts of the otherwise hydrophobic motifs.…”

The formation of a fuzzy complex in the negative arm regulates the robustness of the circadian clock

“…We therefore propose that the FRQ/FRH complex meets the definition of a fuzzy complex, although further investigation of the conformational dynamics of this interaction is warranted (Tompa and Fuxreiter, 2008). This combination of positively charged residues that can work in concert with hydrophobic residues is reminiscent of acidic activation domains, where negativelycharged residues conspire with hydrophobic sidechains to determine specificity and affinity (Erijman et al, 2020;Ravarani et al, 2018;Sanborn et al, 2021;Staller et al, 2021Staller et al, , 2018Tuttle et al, 2018). Whether or not these modes of interactions differ only in terms of the charge sign, or if additional chemical and structural nuances emerge, remains an area of open investigation.…”