A strategy to disentangle direct and indirect effects on (de)phosphorylation by chemical modulators of the phosphatase PP1 in complex cellular contexts

The Fascinating Intricacy of pSer/Thr-Specific Phosphatases and Their Higher-Order Complexes: Emerging Concepts

The phosphoprotein phosphatase family is responsible for a vast amount of dephosphorylation events on phosphoserine and -threonine in cells. As such, they are involved in key cellular processes, and consequently, disruption of their function contributes to the etiology and progression of diseases. Many of these phosphatases work as holoenzymes, where the catalytic subunit is complexed with regulatory proteins. How these phosphatases are regulated, how they recognize their substrates, and how substrates can be identified are long-standing questions in the field. Here, we lay out recently emerged concepts addressing these questions using examples of the phosphatases PP1, PP2A, and PP5. These new concepts include substrate recruitment through distal complexed proteins, the use of tailored peptide probes and mass spectrometry for substrate identification, substrate recognition through short helical motifs, and insights into holoenzyme assembly, as well as mechanisms of substrate release and phosphatase activation. Furthermore, we discuss future directions enabled by these new insights.

Cell-Penetrating Peptide Based on Myosin Phosphatase Target Subunit Sequence Mediates Myosin Phosphatase Activity

Myosin phosphatase (MP) holoenzyme consists of protein phosphatase-1 (PP1) catalytic subunit (PP1c) associated with myosin phosphatase target subunit-1 (MYPT1) and it plays an important role in mediating the phosphorylation of the 20 kDa light chain (MLC20) of myosin, thereby regulating cell contractility. The association of MYPT1 with PP1c increases the phosphatase activity toward myosin; therefore, disrupting/dissociating this interaction may result in inhibition of the dephosphorylation of myosin. In this study, we probed how MYPT132-58 peptide including major PP1c interactive regions coupled with biotin and cell-penetrating TAT sequence (biotin-TAT-MYPT1) may influence MP activity. Biotin-TAT-MYPT1 inhibited the activity of MP holoenzyme and affinity chromatography as well as surface plasmon resonance (SPR) binding studies established its stable association with PP1c. Biotin-TAT-MYPT1 competed for binding to PP1c with immobilized GST-MYPT1 in SPR assays and it partially relieved PP1c inhibition by thiophosphorylated (on Thr696 and Thr853) MYPT1. Moreover, biotin-TAT-MYPT1 dissociated PP1c from immunoprecipitated PP1c-MYPT1 complex implying its holoenzyme disrupting ability. Biotin-TAT-MYPT1 penetrated into A7r5 smooth muscle cells localized in the cytoplasm and nucleus and exerted inhibition on MP with a parallel increase in MLC20 phosphorylation. Our results imply that the biotin-TAT-MYPT1 peptide may serve as a specific MP regulatory cell-penetrating peptide as well as possibly being applicable to further development for pharmacological interventions.

PP1/PNUTS phosphatase binds the restrictor complex and stimulates RNA Pol II transcription termination

The restrictor ZC3H4/WDR82 terminates antisense transcription from bidirectional promoters, but its mechanism is poorly understood. We report that ZC3H4/WDR82 immunoprecipitates with PP1 phosphatase and its nuclear targeting subunit, PP1 phosphatase nuclear targeting subunit (PNUTS), which binds to WDR82. AlphaFold predicts a complex of PP1/PNUTS with the restrictor where both PNUTS and ZC3H4 contact WDR82. A substrate trap, PP1H66K-PNUTS, comprising inactive PP1 fused to the PNUTS C terminus, antagonizes restrictor-mediated termination, whereas PP1WT-PNUTS has less of an effect, suggesting that phosphatase activity is required for termination. One PP1/PNUTS substrate implicated in termination by the restrictor is RNA polymerase II (RNA Pol II) CTD Ser5-P. PP1H66K-PNUTS induces Ser5-P hyperphosphorylation at 5' ends, presumably by inhibiting dephosphorylation. NET-seq analysis suggests that CTD Ser5 dephosphorylation would promote termination by increasing RNA Pol II pausing. Both inhibition of termination and CTD hyperphosphorylation require the WDR82 binding domain of PP1H66K-PNUTS, which mediates restrictor binding. In summary, the PP1/PNUTS phosphatase associated with the restrictor via WDR82 promotes efficient transcription termination.

Photo-Claisen Rearrangement in a Coumarin-Caged Peptide Leads to a Surprising Enzyme Hyperactivation

Protein phosphatase-1 (PP1) is a ubiquitous enzyme that counteracts hundreds of kinases in cells. PP1 interacts with regulatory proteins via an RVxF peptide motif that binds to a hydrophobic groove on the enzyme. PP1-disrupting peptides (PDPs) compete with these regulatory proteins, leading to the release of the active PP1 subunit and promoting substrate dephosphorylation. Building on previous strategies employing the ortho-nitrobenzyl (o-Nb) group as a photocage to control PDP activity, we introduced coumarin derivatives into a PDP via an ether bond to explore their effects on PP1 activity. Surprisingly, our study revealed that the coumarin-caged peptides (PDP-DEACM and PDP-CM) underwent a photo-Claisen rearrangement, resulting in an unexpected hyperactivation of PP1. Our findings underscore the importance of linker design in controlling uncaging efficiency of photocages and highlight the need for comprehensive in vitro analysis before cellular experiments.