Evolution and functional cross-talk of protein post-translational modifications

Abstract

Protein post-translational modifications (PTMs) allow the cell to regulate protein activity and play a crucial role in the response to changes in external conditions or internal states. Advances in mass spectrometry now enable proteome wide characterization of PTMs and have revealed a broad functional role for a range of different types of modifications. Here we review advances in the study of the evolution and function of PTMs that were spurred by these technological improvements. We provide an overview of studies focusing on the origin and evolution of regulatory enzymes as well as the evolutionary dynamics of modification sites. Finally, we discuss different mechanisms of altering protein activity via post-translational regulation and progress made in the large-scale functional characterization of PTM function.

Figure 1. Phylogenetic distribution for the Top 15 most frequent PTMs annotated in UniProt

We selected the 15 PTM types annotated in UniProt with at least 1000 occurrences and with one annotated instance in at least 10 species. For these we obtained a list of all species with at least one occurrence. The species distribution of these 15 PTM types was mapped to a phylogenetic tree using the Interactive Tree of Life tool (http://itol.embl.de/). Presence or absence of at least one occurrence is displayed using a PTM color code next to each species leaf in the tree. Absence of a PTM occurrence in any given species has to be cautiously interpreted since this could be simply due to a lack of coverage.

Figure 2. Evolution of PTM regulation at different time scales

PTM evolution can be studied at different levels: from the origin of the PTMs and their enzymes (bottom) to the evolution of PTM enzymes and binding domains (middle) and their interactions (top). Many PTM types appear to be ancient and the origin of novel PTM type and their regulatory enzymes is likely to be a rare evolutionary event. The study of the ancient origin of protein phosphorylation has been aided by structural analysis where the conserved structural motifs of different phosphorylation enzymes can shed light on the origin of these enzymes. This is illustrated by the structural similarity between an aminoglycoside phosphotransferase (Kinase A, PDB: 1J7U) and a cAMP‐dependent protein kinase (Kinase B, PDB: 1CDK). Once a PTM type is established, the evolution of its regulators is likely to progress via gene‐duplication and divergence. Given the functional inter‐dependencies of the different effector domains (e.g. reader, writer and eraser) a high degree of co‐evolution is expected. This was observed for the phospho‐tyrosine effector domains (middle) where the three domain types typically display an all‐or‐none pattern of occurrence in the proteomes. The divergence of domain‐site interactions can occur at a faster rate than the divergence of effector domains since only a few mutations are required to create or destroy a PTM site. A hypothetical case illustrates how a few point mutations would be sufficient to significantly re‐wire a kinase‐substrate interaction network composed of three proteins and two kinases (top).

Figure 3. Functional role of post‐translational modifications

PTMs act to change the activity of proteins through different mechanism and in response to different conditions. (A) Different mechanism used by PTMs to regulate protein activity. (B) Example of conditional regulation of phosphorylation sites. A hypothetical dataset of conditional regulation of phosphosites under different conditions was subjected to hierarchical clustering. The cluster shows a set of co‐regulated sites that is up‐regulated during mitosis and down‐regulated during stem‐cell differentiation and G1/S/G2. This cluster illustrates how patterns of co‐regulation provide additional functional annotation to PTMs. (C) Mechanism of cross‐regulation between different PTM types. Two different PTM types have been observed to cross‐regulate each other in the same protein where for example a phosphosite may recruit an E3‐ligase promoting protein ubiquitylation. The regulatory enzyme of one type can be regulated by modification of another type such as the regulation of protein kinases via acetylation (regulation of regulators). Additionally, a binder for one PTM type may be regulated by a modification site of a different type. This has been observed for 14‐3‐3 domains which can bind phosphosites and have been shown to be regulated by acetylation (regulation of regulators).

Figure 4. A depiction of cell‐decision making at the convergence of different approaches to cell biology

Cell signaling systems are often depicted as highly logical and engineered circuits in a representation that tries to capture the main design principles of a cellular function. However, this representation may hinder our progress in studying systems that are not engineered but are highly cooperative and evolved. A second paradigm has recently been put forward, based on large scale studies of cellular networks. A view where each component is a node and each association between components is an edge. This simple network view has been useful in describing the high degree of complexity and cooperativity inside the cell but is not informative of the logic observed in these systems. We suggest that a useful and realistic description of cell biology must be informed by these two view‐points.