Kinase consensus sequences: a breeding ground for crosstalk

Abstract

The best characterized examples of crosstalk between two or more different post-translational modifications (PTMs) occur with respect to histones. These examples demonstrate the critical roles that crosstalk plays in regulating cell signaling pathways. Recently, however, non-histone crosstalk has been observed between serine/threonine phosphorylation and the modification of arginine and lysine residues within kinase consensus sequences. Interestingly, many kinase consensus sequences contain critical arginine/lysine residues surrounding the substrate serine/threonine residue. Therefore, we hypothesize that non-histone crosstalk between serine/threonine phosphorylation and arginine/lysine modifications is a global mechanism for the modulation of cellular signaling. In this review, we discuss several recent examples of non-histone kinase consensus sequence crosstalk, as well as provide the biophysical basis for these observations. In addition, we predict likely examples of crosstalk between protein arginine methyltransferase 1 (PRMT1) and Akt and discuss the future implications of these findings.

Figure 1

Serine/Threonine Protein Kinase consensus sequences. A number of serine/threonine protein kinases recognize protein sequences that contain positively charged arginine and lysine residues adjacent to the site of phosphorylation. For example, Akt, prefers substrates that have two arginines (or lysines) at positions −3 and −5 with respect to the modification site that are separated by a variant residue. Each box represents one residue’s position and multiple single letter amino acid codes demonstrate variability within that position. Adapted from (82).

Figure 2

Selected posttranslational modifications of arginine, lysine, serine, threonine, and tyrosine. (a) Arginine residues can be mono- and dimethylated by the PRMTs to form ω-MMA, ADMA, or SDMA. They can also be converted to citrulline by the PADs. (b) Lysine residues can be mono-, di-, and trimethylated by KMTs, acetylated by KATs, or ubiquitinated by ubiquitin ligases. (c) Serine, threonine, and tyrosine residues can be phosphorylated by kinases.

Figure 3

Crosstalk scenarios. (a) The cis-effect refers to crosstalk between two or more modifications located on the same protein. Within the same protein there can be adjacent (i.e., between residues that are close in both primary and tertiary structures) or distal (i.e. between residues that are separated in primary and tertiary structures) crosstalk. (b) The trans-effect refers to crosstalk between two modifications located on two different proteins. (c) Functionally, crosstalk can be direct (i.e., one modification inhibits or enhances the subsequent modification of the same or a different residue) or (d) indirect (i.e., a specific modification inhibits or enhances protein-protein interactions leading to altered downstream effects). Note that while this figure depicts crosstalk involving histones, the same explanations can be applied to non-histone proteins. Adapted from (3).

Figure 4

Structural basis for crosstalk. (a) A structure of Akt (white) bound to a GSK3β (cyan) derived peptide demonstrates that arginine residues in the −5 and −3 positions are critical for Akt substrate recognition. R-5 forms direct and indirect hydrogen bonds with several key residues (i.e. E279, Y316, E342), as well as, with T-2 on the peptide. This residue is also capable of forming a salt bridge with E279. R-3 forms both a hydrogen bond and salt bride with E236. The methylation of both R-5 and R-3 would disrupt these key interactions and thus result in the observed inhibition of serine phosphorylation, which is demonstrated in several examples presented in this review (i.e., FOXO1 (12) and BAD (19)). This figure was prepared with UCSF Chimera using the coordinates for the Akt·GSK3β peptide complex (PDBID 1O6L). (b) A structure of SET7/9 (white) bound to DNMT1 (cyan) provides the structural basis for the inhibition of lysine methylation by phosphorylation of an adjacent serine residue (55). In this case, the potentially phosphorylated residue, i.e. S143 forms a hydrogen bond with K317 and also has van der Waals interactions with L267. The addition of a phosphate group would cause van der Waals respulsions between between the S143 and L267 and thus would prevent methylation. This figure was prepared with UCSF Chimera using the coordinates for the SET7/9·DNMT1 peptide complex (PDBID 3OS5). (c) A structure of SETD6 (white) bound to a RelA peptide (cyan) shows that the potentially phosphorylated S311 forms a hydrogen bond with the backbone carbonyl of Q226 and also has van der Waals interactions with P228. As the authors note, the addition of a phosphate group would likely prevent RelA binding due to sterics and thus abrogate methylation of K310 (69). Note that in all structures a dashed line simply represents the distance between two residues and not necessarily a hydrogen bond. Also note that single letter abbreviations are used to denote residues on the enzyme and three letter abbreviations are used to denote residues on the peptide.