Modular evolution of phosphorylation-based signalling systems

Abstract

Phosphorylation sites are formed by protein kinases ('writers'), frequently exert their effects following recognition by phospho-binding proteins ('readers') and are removed by protein phosphatases ('erasers'). This writer-reader-eraser toolkit allows phosphorylation events to control a broad range of regulatory processes, and has been pivotal in the evolution of new functions required for the development of multi-cellular animals. The proteins that comprise this system of protein kinases, phospho-binding targets and phosphatases are typically modular in organization, in the sense that they are composed of multiple globular domains and smaller peptide motifs with binding or catalytic properties. The linkage of these binding and catalytic modules in new ways through genetic recombination, and the selection of particular domain combinations, has promoted the evolution of novel, biologically useful processes. Conversely, the joining of domains in aberrant combinations can subvert cell signalling and be causative in diseases such as cancer. Major inventions such as phosphotyrosine (pTyr)-mediated signalling that flourished in the first multi-cellular animals and their immediate predecessors resulted from stepwise evolutionary progression. This involved changes in the binding properties of interaction domains such as SH2 and their linkage to new domain types, and alterations in the catalytic specificities of kinases and phosphatases. This review will focus on the modular aspects of signalling networks and the mechanism by which they may have evolved.

Figure 1.

The eukaryotic phosphorylation-based network is operated by a modular kinase–phosphatase-interaction domain toolkit. (a) The writer–reader–eraser toolkit system in protein phosphorylation. Phosph-bind. dom., phospho-binding domain. (b) Different evolutionary passages for the kinases (divergent from a common ancestor), the phosphatases (both convergent and divergent) and the phospho-binding domains (mostly from sporadic and unpredictable inventions). (c) Representative pTyr and pSer/pThr binding domains.

Figure 2.

Many protein-tyrosine kinases (TKs) share non-catalytic modular domain types with classical type I protein-tyrosine phosphatases—domain architectures of human proteins are shown. (a) Non-receptor type TKs and PTPs. (b) Receptor type TKs and PTPs. (c) The interaction domains of cytoplasmic TKs (i.e. SH2, SH3, F-BAR) regulate the activity of the adjacent kinase domain either through intramolecular interactions or through targeted binding to primed substrates or membranes. The Src, Abl and Fps/Fes TKs are shown as examples. Myri, myristoyl group. In the slime mould Shk kinases, a dual-specificity kinase domain (Ser/Thr/Tyr kin) is joined to a C-terminal SH2 domain.

Figure 3.

Examples of signalling pathways illustrating modular networks controlled by protein phosphorylation. Kinases are shown in red; phosphatases in blue; and phospho-binding domains in green. (a) The signalling system in response to EGF at the plasma membrane: pTyr-binding domains, such as SH2 and PTB, play a key role. (b) DNA damage and repair responses via a network of pSer/pThr-dependent interactions: specific pSer/pThr-recognition by FHA and BRCT domains mediates the formation of protein complexes. FHA domain-containing RNF8 relays phosphorylation events to the ubiquitylation of histone H2A.

Figure 4.

Roles for linked domains in the evolution of kinases and phosphatases. (a) Gene duplication without domain rearrangement. Following duplication, one copy of the gene has been freed from the constraint to maintain its original function. This provides the chance for the new copy to explore mutational space, which may opportunistically give rise to novel functions (represented by the white stripes in the box). (b) A new domain (shown in yellow) joins a system within which a resident domain (in grey) operates. The resident domain may then acquire modified functions more compatible with its new partner, provided that these changes promote the overall fitness of the species to the selective pressure. Such directional changes in function are indicated by yellow stripes. (c) A stepwise evolution of the pTyr signalling system. (d) PTK and classical type 1 PTP sharing non-catalytic domain types.

Figure 5.

Evolution of the PI3K-Akt pathway from a modular perspective: focusing on the role of the SH2 domains of p85. (a–c) These panels show a gradation of organismal complexity as represented by modern organisms. (a) Total absence of the PI3K system in the fungi (Saccharomyces cerevisiae). (b) The limited PI3K-Akt system in the slime mould (Dictyostelium discoideum) responds primarily to GPCR activation, with no direct pTyr involvement. The N- to C-terminal order of domains in p110 (Dd_PIKA/B, type class I_B) is Ras-binding domain (Ras_bind.), C2 domain, Helical domain (unmarked) and the kinase domain (catalytic). PH domain-containing Akt Ser/Thr kinase is recruited by the products of PI3K, PtdIns(3,4)P and PtdIns(3,4,5)P, and is activated. Akt directs limited downstream signalling responses. Arrows indicate directions of the pathways. (c) The fully evolved PI3K class I enzymes (shown with human proteins) are able to mediate RTK signalling via the functions of the SH2 adaptor p85 (for the class I_A type PI3K). In N- to C-terminal order, p85 contains an SH3 domain, a BH domain, an SH2 domain, a p110-binding domain (p110_bind.) and a second SH2 domain. The SH2 domains of p85 bind pTyr on membrane receptors and adaptors. The new class I_A type p110 enzyme contains an N-terminal p85-binding domain (p85_bind.). The activation of class I_B type p110γ remains GPCR- (and Ras-) responsive with p101 acting as its adaptor; however, its role in Akt activation has become less prominent (as indicated by shading). The new catalytic class I_A type of p110α/β/δ is activated primarily in response to RTK signalling, and mediates potent Akt activation, which in turn leads to a broad range of downstream pSer/pThr events.

Figure 6.

A model for reciprocal interactions between a subcellular system and its protein domains. (a) Modular interactions control compartmentalization (schematized with the yellow sphere), and delineate coordination of subsystems via the process of modular domain entrance and exit following shuffling or formation of new interactions. Yellow stripe marking is intended to indicate a modified function of the domain that is compatible with the new molecular environment. (b) A model for the reciprocal evolutionary forces between modular domains and the signalling system they operate within.