Cellular proteins are subject to numerous post-translational modifications (PTMs), which control many aspects of cellular function. Such modifications can regulate protein activity through allosteric effects, but can also create binding sites for a number of modular protein-interaction domains, which recognize, for example, phosphorylated, methylated, acetylated, ubiquitylated or hydroxylated sites. We propose that such PTM-dependent protein?protein interactions represent a fundamental mechanism through which the state of the proteome is interpreted.
Although the selective recognition of modified sites by interaction domains is, in principle, rather simple, such interactions can be used to yield more complex responses. For example, they can mediate cooperative or switch-like effects, intramolecular autoregulation, or function in mutually exclusive or antagonistic modes. Furthermore, they often function sequentially to create extended signalling pathways or networks.
Protein phosphorylation on Tyr or Ser/Thr residues creates binding sites for a range of interaction domains that provide many examples of the strategies noted above. Strikingly, there are numerous distinct domains that have converged on the common recognition of phosphorylated sites. Phosphorylation-dependent binding to interaction domains functions as a mechanism to couple the multi-site phosphorylation of a single protein to various downstream effectors and regulators, and it can also mediate the effects of multiple different types of PTM. For example, activated receptor tyrosine kinases recruit proteins with multiple phosphotyrosine-recognition domains (such as Src-homology-2 (SH2) and phosphotyrosine-binding (PTB) domains), as well as ubiquitin-binding domains (such as ubiquitin-interacting motifs (UIMs)), to activate signalling pathways and control receptor internalization.
PTM-dependent interactions have similar consequences in histone biology. In this case, the predominant modifications involve the acetylation or methylation of Lys residues, which primarily recruit proteins that contain bromodomains or chromodomains. These interactions can be modified by distinct PTMs, such as phosphorylation or sumoylation, and provide a versatile mechanism for the control of chromatin organization and gene expression.
The ubiquitylation of proteins creates binding sites for a large number of ubiquitin-binding domains. These can control a wide range of cellular activities, including regulated protein degradation, receptor internalization, the activation of specific signalling pathways and translesion DNA synthesis. We propose that the interactions that are regulated by ubiquitylation follow similar rules to those that apply to phosphorylation-, acetylation- and methylation-dependent interactions.
Proteins are controlled by a vast and dynamic array of post-translational modifications, many of which create binding sites for specific protein-interaction domains. We propose that these domains, working together, read the state of the proteome and therefore couple post-translational modifications to cellular organization. We also identify common strategies through which modification-dependent interactions synergize to regulate cell behaviour.
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We are indebted to C. Lim and M. Rabiller for assistance with the figures, and to R. Linding and M. Tyers for insightful comments. B.T.S. is funded by a fellowship from the Cancer Research Institute (New York, USA). Work in the authors' laboratories is funded by the Canadian Institutes for Health Research (CIHR) and the National Cancer Institute of Canada and Genome Canada (T.P.), the Deutsche Forschungsgemeinschaft and the German?Israeli Foundation (I.D.), and the United States National Institutes of Health (M.-M.Z). T.P. is a distinguished investigator of the CIHR.
The authors declare no competing financial interests.
A phosphorylated derivative of the glycerolipid phosphatidylinositol.
- Allosteric regulation
The regulation of a protein's activity through a conformational change that is induced by the binding of a ligand or the addition of a post-translational modification at a region other than the substrate-binding site.
- Src-homology-2 (SH2) domain
A 100-residue domain that binds to particular phosphorylated Tyr sequences in proteins.
- Pleckstrin-homology domain
(PH domain). The PH domain is ∼120 amino acids. It typically interacts with various phosphoinositides, and is thereby involved in targeting proteins to membranes.
- WD40-repeat domain
A repeat sequence of 40?60 amino acids that usually ends with Trp and Asp (WD). Consecutive repeats fold into a circular β-propeller structure.
- E3 ubiquitin ligase
An enzyme that functions with a ubiquitin-conjugating enzyme (E2) to link one or more ubiquitin molecules to a target protein, which marks the protein for subsequent recognition by ubiquitin-binding domains. SCF-type ubiquitin ligases are one of the principal classes of E3 ligase. They are complexes that consist of SKP1, cullin and F-box proteins.
A large multiprotein complex that is responsible for degrading intracellular proteins that have been tagged for destruction by the addition of ubiquitin.
- Breast-cancer-susceptibility protein-1 C-terminal domain
(BRCT domain). The BRCT domain is 90?100 amino acids and occurs either as a single element or as multiple repeats. It binds to phosphopeptides in several proteins that are involved in DNA-damage response and DNA repair.
- Ubiquitin-binding domains
The collective term that is given to modular interaction domains that bind to ubiquitin.
A protein that supports the assembly of a multiprotein complex through interactions with other proteins.
A protein domain that often binds to methylated Lys residues in target proteins.
- 14-3-3 proteins
A family of proteins that bind to phosphorylated Ser/Thr residues in a context-specific manner.
- Src-family kinases
Kinases that belong to the Src family of tyrosine kinases, which is the largest of the non-receptor-tyrosine-kinase families. Members include Src, Yes, Fyn, Lck, Lyn, Blk, Hck, Fgr and Yrk.
- Src-homology-3 (SH3) domain
A protein sequence of ∼50 amino acids that binds to Pro-rich regions of proteins. Some SH3 domains have been identified that bind to atypical non-Pro-based motifs.
- Phosphotyrosine-binding domain
(PTB domain). A domain of 100?150 amino acids. Some PTB domains bind to specific phosphotyrosine sites, which usually have the consensus sequence Asn-Pro-X-pTyr (NPXpY).
- Conserved region-2 of protein kinase C domain
(C2 domain). A domain that was originally found to bind to lipids in a Ca2+-dependent manner. However, an exception has been identified in the C2 domain of protein kinase Cδ, which binds to specific phosphotyrosine-containing peptides.
- WW domain
A protein domain of ∼35 amino acids that binds to Pro-rich peptide motifs or, in some cases, to pSer/pThr-Pro motifs.
- FF domain
A protein domain of 50?60 amino acids. FF domains are always arranged in tandem repeats and bind to acidic or phosphorylated peptide motifs.
- SRI domain
(Set2 Rpb1 interacting domain). An ∼100-amino-acid domain that is conserved among a number of putative Set2 homologues. The SRI domain of Set2 binds to the phosphorylated C-terminal domain of RNA polymerase II.
- C-terminal-interaction domains
(CIDs). CIDs are domains that bind to phosphorylated heptad repeats in the C-terminal domain of RNA polymerase II.
- Histone deacetylase
An enzyme that removes acetyl groups from Lys residues of a histone protein. Histone acetyltransferases function in the opposite manner to add acetyl groups to Lys residues of a histone protein.
An evolutionarily conserved protein domain that often binds to acetylated Lys residues in target proteins.
Heritable information that is encoded by modifications of the genome and chromatin components, which affect gene expression without changing the nucleotide sequence.
- TUDOR domain
A conserved chromodomain-like protein domain. Some TUDOR domains bind to methylated Lys or Arg residues.
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Seet, B., Dikic, I., Zhou, MM. et al. Reading protein modifications with interaction domains. Nat Rev Mol Cell Biol 7, 473–483 (2006). https://doi.org/10.1038/nrm1960
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