Nine Phosphatomes

We define the phosphotomes of human, three other bilaterians (sea urchin, fruit fly, and Caenorhabditis elegans), two basal metazoans (the anemone Nematostella vectensis and the sponge Amphimedon queenslandica), the unicellular choanoflagellate (Monosiga brevicollis) which is the closest living lineage to metazoans, a yeast (Saccharomyces cerevisiae), and Dictyostelium discoideum.

Through searching genomic and protein sequences followed by extensive gene model curation, we identified 1229 protein phosphatases in the nine organisms, including 43 phosphatases that are not present in the predicted proteomes. These phosphatases are further classified by their sequence similarity, domain combination, and known molecular function (see here).

Conservation of protein phosphatases

Phylogenetic comparison of the human phosphatome with those of eight other species shows that all phosphatase superfamilies found in human are shared from Dictyostelium to human. Of 85 human subfamilies, 59 are conserved as deep as to sponge, and these presumably serve functions essential for the existence of metazoans. We found 44 subfamilies present in both human and the single-cellular organism Monosiga, and even 24 between human and yeast, and 27 between human and Dictyostelium.

Gains and losses of subfamilies

We inferred the gains and losses of subfamilies by predicting whether ancestral genome has a subfamily by its presence and absence in the extant genomes in this study. The phosphatome expanded dramatically during the emergence of holozoa and metazoa, with the number of subfamilies increasing by one half and one third, respectively. These increases are mainly due to the expansion of Class I Cys-based superfamily. Around two-thirds of the subfamilies gained in holozoa and metazoa (19 and 21, respectively) belong to this superfamily (11 and 13). Dramatic gains and/or losses of subfamilies also happened in individual lineages. In C. elegans, more than a dozen subfamilies were gained, meanwhile more than a dozen were lost. In contrast to the similar extent of gains and losses in C. elegans, fruit fly lost 8 subfamilies but only gained 1 subfamily.

Subfamilies gained or lost of selected clade: PPM1L Auxilin R_Ecdysozoa FCP1 R_Urchin_1 PHLPP UBLCP1 N_Nematode_eak PRL PPP4C RD RG RA RB RC N23 MTMR6 MTMR5 N20 MTMR3 MTMR1 RK EYA R_Nematode_3 R_Nematode_2 PPP3C PTEN DSP15 TPIP DSP12 DSP11 DSP10 PHP TIM50 DSP19 OCA PTPMT1 SSU72 RNGTT R_Arthropoda PPM1G PPM1E PPM1D Ank-MTMR1 PPM1A DULLARD STYXL1 Slingshot N5_RR PPM1K PPM1H DSP14 PPP6C PPP7C SCP N_Nematode_1 N_Nematode_6 N_Nematode_5 MTM_Dicty1 PTPDC1 R_Choan_EGF LRR-PP2C N12 N13 N14 PPP5C CDC25 N_Nematode_egg PPP_Nematode_7 PPP_Nematode_6 PPP_Nematode_5 LRR-DSP N_Choan_2 N_Choan_1 PPM1G2 RTR1 HSPC129 N_Fungi_PTP1 R_Choan_DeathReceptor Laforin CUT MTMR9 STYX MTMR10 R_Anemone_1 R_Anemone_2 PDP N9 N1 N3 RN N6 C2-MTMR1 LMWPTP TM-FCP R_Choan_CA(n) DSP3 DSP1 MTMR14 DSP6 DSP8 Tensin PPP2C PP2D1 LHPP PPP1C Ptc6_Fungi PGP CYR1_Fungi N_Nematode_4 Acr2 DSP23 PPP_Nematode_3 PPP_Nematode_2 PPP_Nematode_1 ILKAP R_Sponge_1 R_Sponge_2 PPP_Nematode_4 MDP1 CDC14 pats1 TAB1 CDKN3 PTC7