Comprehensive Analysis of G1 Cyclin Docking Motif Sequences that Control CDK Regulatory Potency In Vivo

Curr Biol. 2020 Nov 16;30(22):4454-4466.e5. doi: 10.1016/j.cub.2020.08.099. Epub 2020 Sep 24.

Abstract

Many protein-modifying enzymes recognize their substrates via docking motifs, but the range of functionally permissible motif sequences is often poorly defined. During eukaryotic cell division, cyclin-specific docking motifs help cyclin-dependent kinases (CDKs) phosphorylate different substrates at different stages, thus enforcing a temporally ordered series of events. In budding yeast, CDK substrates with Leu/Pro-rich (LP) docking motifs are recognized by Cln1/2 cyclins in late G1 phase, yet the key sequence features of these motifs were unknown. Here, we comprehensively analyze LP motif requirements in vivo by combining a competitive growth assay with deep mutational scanning. We quantified the effect of all single-residue replacements in five different LP motifs by using six distinct G1 cyclins from diverse fungi including medical and agricultural pathogens. The results uncover substantial tolerance for deviations from the consensus sequence, plus requirements at some positions that are contingent on the favorability of other motif residues. They also reveal the basis for variations in functional potency among wild-type motifs, and allow derivation of a quantitative matrix that predicts the strength of other candidate motif sequences. Finally, we find that variation in docking motif potency can advance or delay the time at which CDK substrate phosphorylation occurs, and thereby control the temporal ordering of cell cycle regulation. The overall results provide a general method for surveying viable docking motif sequences and quantifying their potency in vivo, and they reveal how variations in docking strength can tune the degree and timing of regulatory modifications.

Keywords: CDK; Cln2; SLiM; Sic1; Ste5; Whi5; cell cycle; cyclin; docking; phosphorylation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs / genetics
  • Consensus Sequence / genetics
  • Cyclin-Dependent Kinases / metabolism*
  • Cyclins / genetics*
  • Cyclins / metabolism
  • DNA Mutational Analysis
  • DNA, Fungal / genetics
  • DNA, Fungal / isolation & purification
  • G1 Phase*
  • Phosphorylation / genetics
  • Protein Binding / genetics
  • Protein Domains / genetics*
  • Saccharomyces cerevisiae
  • Saccharomyces cerevisiae Proteins / genetics*
  • Saccharomyces cerevisiae Proteins / metabolism

Substances

  • CLN1 protein, S cerevisiae
  • CLN2 protein, S cerevisiae
  • Cyclins
  • DNA, Fungal
  • Saccharomyces cerevisiae Proteins
  • Cyclin-Dependent Kinases