FEBS Letters 586 (2012) 2732–2739 journal homepage: www.FEBSLetters.org Review The human phosphatase interactome: An intricate family portrait ⇑ Francesca Sacco a,1, Livia Perfetto a,1, Luisa Castagnoli a, Gianni Cesareni a,b, a Department of Biology, University of Rome ‘‘Tor Vergata’’, Rome, Italy b Research Institute ‘‘Fondazione Santa Lucia’’, Rome, Italy article info abstract Article history: The concerted activities of kinases and phosphatases modulate the phosphorylation levels of Received 23 March 2012 proteins, lipids and carbohydrates in eukaryotic cells. Despite considerable effort, we are still miss- Revised 8 May 2012 ing a holistic picture representing, at a proteome level, the functional relationships between Accepted 8 May 2012 kinases, phosphatases and their substrates. Here we focus on phosphatases and we review and inte- Available online 21 May 2012 grate the available information that helps to place the members of the protein phosphatase super- Edited by Marius Sudol, Giulio Superti-Furga families into the human protein interaction network. In addition we show how protein interaction and Wilhelm Just domains and motifs, either covalently linked to the phosphatase domain or in regulatory/adaptor subunits, play a prominent role in substrate selection. Keywords: Ó 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved. Human phosphatome Phosphatase family classification Substrate recognition specificity 1. Introduction protein kinases. 428 are known or predicted to phosphorylate ser- ine and threonine residues, while the remaining 90 are members of Phosphorylation is a widespread post-translational modifica- the tyrosine kinase family [3,12]. By contrast, in the human gen- tion governing signal propagation [1]. Indeed phosphorylation is ome there are only approximately 200 phosphatases, targeting an efficient mean to control cell response to internal and external phosphorylated proteins or lipids. cues: it is rapid, taking as little as a few seconds, it does not require Over the past decades, much of the interest of the scientific com- new proteins to be synthesized or degraded and can be easily munity has focused on protein kinases, protein phosphatases being reverted. Protein phosphorylation plays a key role in controlling considered less interesting house-keeping enzymes playing a non- a variety of cellular processes, such as migration, proliferation, specific role in modulating phosphoprotein homeostasis. Recent apoptosis, differentiation, metabolism, organelle trafficking, findings, however, have led to the emerging recognition that pro- immunity, learning and memory [2–4]. Thus, it is not surprising tein phosphatases play key roles in setting the levels of tyrosine, that aberrant phosphorylation profiles correlate with disease serine and threonine phosphorylation in cells, thus participating conditions such as cancer, diabetes and neurodegenerative or in the regulation of many physiological processes, including cell inflammatory disorders [5–7]. Eukaryotic protein phosphorylation growth, tissue differentiation and inter-cellular communication typically occurs on serine, threonine or tyrosine residues. Olsen [5,13,14]. et al. have found the distribution of pSer, pThr, pTyr sites in the Many excellent comprehensive reviews have discussed the human proteome to be around 79.3%, 16.9% and 3.8% respectively different phosphatase superfamilies, their evolution and the mech- [8]. Furthermore approximately 17000 proteins have at least one anisms underlying substrate recognition specificity [13–17,12]. annotated residue in the Phosphosite database [9]. Indeed protein Despite the progress, identification of functional in vivo substrates kinases are one of the largest gene family in eukaryotes, making up remains a challenge. As a consequence, we are still missing a about 2% of the genome [10,11]. The human genome encodes 518 holistic picture representing, at a proteome level, the functional relationships between phosphatases and substrates. In this short contribution, we propose a phosphatase classification and report Abbreviations: PTP, protein tyrosine phosphatase; LP, lipid phosphatase; PPP, a comprehensive analysis of our current understanding and cover- phosphoprotein phosphatases; PPM, metallo-dependent protein phosphatase; HAD, age of the phosphatase interactome. Finally, we discuss how this haloacid dehalogenase; RS, regulatory subunit intricate network of interactions can help to define the function ⇑ Corresponding author. E-mail address: [email protected] (G. Cesareni). of poorly characterized phosphatases and to identify their sub- 1 These authors contributed equally. strates. 0014-5793/$36.00 Ó 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.febslet.2012.05.008 F. Sacco et al. / FEBS Letters 586 (2012) 2732–2739 2733 3 NRPTPs (21) Classical PTPs (41) PTPs (108) 3 RPTPs (20) 2 VH1-like (63) MKPs (12) Atypical DSPs (18) CDC14s (4) PRLs (3) MTMRs (14) PTENs (9) LM-PTP (1) SSHs (3) CDC25C (3) PPPs (13) Phosphatase classification 1 PPMs (15) HADs (11) HADs (21) 2,3 FCPs (6) EYAs (4) LPTs (15) 2 LPs (37) Li-sensitive (7) INPP5 (15) NUDT (5) Fig. 1. Classification of protein phosphatase superfamilies. Protein phosphatases were first classified into six different families according to the catalytic domain InterPro annotation (1). Next each phosphatase family was further subdivided into different classes according to their preferred substrates (2) or literature annotation (3). The number of phosphatases in each family or class is in parenthesis. 2. Phosphatase classification - PPP by the serine/threonine-specific protein phosphatase domain (IPR006186); 2.1. A complete compendium of phosphatase domains - PPM by the Protein phosphatase 2C-like domain (IPR001932); - HAD by the Haloacid dehalogenase-like hydrolase domain A number of reports have discussed in detail the different phos- (IPR005834) or HD domain (IPR023279); phatase superfamilies. Here we aim at a catalogue of all the en- - LP by one of the following three domains: phosphatidic acid zymes removing a phosphate group from proteins or lipids, phosphatase (IPR000326), inositol monophosphatase including their accessory subunits. To obtain such a comprehen- (IPR000760) and inositol polyphosphate-related phosphatase sive list, we first screened the literature and protein databases to (IPR000300); retrieve a list of 250 proteins 194 of which contain a phosphatase - NUDT by the NUDIX hydrolase domain (IPR000086). catalytic domain, while the remaining 56 where classified as regu- latory subunits (RSs). These six main families were further subdivided into classes, Next, to achieve proteome wide coverage of the proteins con- according to different criteria: sequence homology in the catalytic taining phosphatase domains we used a three step procedure: domain, substrate specificity and literature annotation (Fig. 1). The (i) we first recovered from InterPro [18] the sequences of the cat- 211 catalytic domains captured by this procedure were aligned alytic domains and aligned them with the ClustalW2 program with ClustalW2 and the resulting sequence similarity tree is shown [19]; (ii) clustering analysis allowed the classification of the phos- in Fig. 2. This graphic representation should not be interpreted as phatase domains into 13 different subgroups; (iii) each subgroup representing an evolutionary relationship between the different alignment was used for a PSI-BLAST search, against the human phosphatase superfamilies. proteome [20]. Hits with a p-value <0.001 were either retained in the group they were already assigned to, or added as new en- 4. Catalytic specificity and substrate selection tries to our phosphatase compendium. This strategy resulted in a collection of 211 Phosphatase catalytic domains distributed in 199 Phosphatases have been considered promiscuous enzymes, dis- proteins. playing little intrinsic substrate specificity when assayed in vitro. Some published evidence, on the contrary, indicates that they may 3. Phosphatase classification show remarkable preference for specific substrates in vivo. The reac- tion rate for a specific substrate is defined by the Michaelis Menten The 211 phosphatase domains in the compendium were next equation linking the rate of enzymatic reaction to substrate concen- assigned to 6 families defined by catalytic domain sequence simi- tration and to the rate constant kcat. Thus, enzymatic specificity may larity, after taking into account InterPro annotations: be achieved by increasing the ratio of the catalytic activity of the enzyme toward physiological substrates over the ‘‘background’’ - PTP membership is defined by the protein-tyrosine phospha- catalytic activity for similar non-physiological substrates. Such tase domain (IPR016130); intrinsic catalytic specificity can be obtained by shaping the 2734 F. Sacco et al. / FEBS Letters 586 (2012) 2732–2739 P PPP1CA-P62136 9 PPP2CB-P6271 PPP6C-O00743 PPP2CA-P67775 P PPP4C-P6051 P EPM2A-O95278 P CDKN3-Q16667 9 TP 298 0 1 1 STYXL1 2 6 8454 2 C DUSP 0 DUSP3-P51452 J8 M1 C 81 9 Q DUSP26-Q9BV47 P4 64 - 1 - M P 0 6 - A20 P53041 51 DUSP13- C- Q8WUK - 14 2 5 D 3 DUPD1-Q68J44 D 27-Q5VZP5 3 USP22-Q9NRW 6 1-O148 S - DUSP15-Q9H1R2 -Q P3 8 6 Q9Y6 F DUSP19-Q8WTR2 P D1-B0Y P3C 7 E 928 - EF2-O1483 5A B- Q01968 3 Q PP5C - 0 5 5 4 PPP1CB-P62140 PPP3C 8 P PPP3CB-P1 DUSP8-Q1320 PP 0 P -O15056 DUSP16-Q9BY8 6 PP P 0 PP Q B J HAC 5 PPA1-Q1 9UI 8 PPA2-Q9H2U2 5D-Q D 8 INP I INP P 94 DUSP2-Q0592USP5-Q16