Development of a Substrate Identification Method for Human Scp1 Phosphatase Using Phosphorylation Mimic Phage Display

Background: Protein phosphorylation is strictly regulated by protein kinases and protein phosphatases, and disordered regulation of protein phosphorylation often causes serious diseases, such as cancer. Protein phosphatases are divided into two major groups: tyrosine (Tyr) phosphatases and serine/threonine (Ser/Thr) phosphatases. Substrate trapping mutants are frequently used to characterize Tyr phosphatases and identify their substrates; however, a rapid and simple method to identify substrates for Ser/Thr phosphatases has yet to be developed. Recently it has reported that AlF4 -/AlF3 and BeF3 - form a complex with Mg2+ in the catalytic center of FCP/SCP phosphatases, and that the Mg2+-AlF4 -/AlF3 complex mimics the transition state of the hydrolysis step, while the Mg2+-BeF3 - complex mimics the aspartylphosphate intermediate.

Objectives: The main objective of this study was to develop a novel methodology, termed Phosphorylation Mimic Phage Display (PMPD), to identify substrates for Ser/Thr phosphatase Scp1 using peptide phage display libraries with Mg2+ and AlF4 -.

Methods: Recombinant protein of human full-length Scp1 (rScp1) expressed in E. coli system was purified by Co2+ chelated affinity column, and then confirmed by SDS-PAGE and Western-blot analysis. The Ph.D.-C7C or M12 Phage Display Libraries (New England BioLabs, Beverly, MA) were screened using purified rScp1 immobilized on ELISA plate. Then, the plate was blocked with 0.5% (w/v) BSA in maleate buffer at 4°C for 3 h, before adding approximately 1×1010 plaque-forming units (pfu) of the phages in maleate blocking AlF4 - buffer to each well. After incubating, the wells were washed with maleate AlF4 - buffer to remove unbound phages. Then, phages were eluted with Mg2+ and AlF4 - free maleate buffer or with excess rScp1. After the third round of screening, the isolated phages were sequenced and subjected to binding analyses.

Results: After panning by PMPD method, 46 and 60 clones were isolated from the Ph.D. C7C and Ph.D. 12 phage libraries, respectively, as Mg2+ or/and AlF4 - -dependent binding clones. The binding analyses showed that M12-1 and Dep-3 specifically bind to Scp1 in an AlF4 --dependent manner. Notably, the Dep-3 peptide contained a Thr-Pro-Met-Ser sequence, which is similar to the Ser2-Pro3-Thr4-Ser5 (Ser/Thr-Pro-partially hydrophobic residue-Ser) sequence found in CTD, which is an endogenous substrate for Scp1. Binding analyses also showed that both BP-14 and M12-6a bound to Scp1 in a Mg2+-dependent manner. BP-14 peptide contained Ser- Thr-Tyr and Pro-Phe-Glu sequences, which are similar to the Ser-Thr-Trp and Ile-Phe-Glu sequences found in M12-6a, suggesting that one or both of these tripeptides may be the binding motif(s) recognized by Scp1.

Conclusion: We developed a substrate identification method for the Ser/Thr phosphatase Scp1 using a novel phage display method with AlF4 -. Dep-3 showed a core sequence similar to that of the CTD of RNA polymerase II, an endogenous Scp1 substrate, suggesting that this method is applicable for identifying novel Scp1 substrate candidates. This method will also be applicable for other FCP/SCP-type phosphatases, allowing us to better understand the substrate recognition mechanisms of Ser/Thr phosphatases.