Identification of New Substrates of the Protein-tyrosine Phosphatase PTP1B by Bayesian Integration of Proteome Evidence

Abstract

There is growing evidence that tyrosine phosphatases display an intrinsic enzymatic preference for the sequence context flanking the target phosphotyrosines. On the other hand, substrate selection in vivo is decisively guided by the enzyme-substrate connectivity in the protein interaction network. We describe here a system wide strategy to infer physiological substrates of protein-tyrosine phosphatases. Here we integrate, by a Bayesian model, proteome wide evidence about in vitro substrate preference, as determined by a novel high-density peptide chip technology, and “closeness” in the protein interaction network. This allows to rank candidate substrates of the human PTP1B phosphatase. Ultimately a variety of in vitro and in vivo approaches were used to verify the prediction that the tyrosine phosphorylation levels of five high-ranking substrates, PLC-γ1, Gab1, SHP2, EGFR, and SHP1, are indeed specifically modulated by PTP1B. In addition, we demonstrate that the PTP1B-mediated dephosphorylation of Gab1 negatively affects its EGF-induced association with the phosphatase SHP2. The dissociation of this signaling complex is accompanied by a decrease of ERK MAP kinase phosphorylation and activation.

Metastasis-associated PRL-3 induces EGFR activation and addiction in cancer cells

“…PTP1B has been reported to reduce the phosphorylation of multiple EGFR signaling pathway components, including PLC-γ1, GAB1, SHP2, SHP, and EGFR itself (45). Although the involvement of other EGFR phosphatases (26) cannot be discounted, our study suggests that PTP1B is the primary EGFR phosphatase causally involved in PRL-3-driven EGFR hyperphosphorylation.…”

HUPHO: the human phosphatase portal

“…Placing phosphatases in such an interaction web would help to infer the function of poorly characterized phosphatases and to identify potential substrates [12][13][14]. In order to offer a proteome-wide perspective of the phosphatase interactome, we have embarked on an extensive text-mining-assisted literature curation effort to extend phosphatase interaction information that was not yet covered by protein-protein interaction (PPI) databases.…”

A Conserved Rod Domain Phosphotyrosine That Is Targeted by the Phosphatase PTP1B Promotes Keratin 8 Protein Insolubility and Filament Organization*

“…PTP1B (50). The model was highly effective in predicting actual PTP1B substrates, such as EGFR, but in addition, it predicted K8 as a very high ranking substrate with a score near that of EGFR (0.897 for K8 versus 0.926 for EGFR) (50).…”

“…The model was highly effective in predicting actual PTP1B substrates, such as EGFR, but in addition, it predicted K8 as a very high ranking substrate with a score near that of EGFR (0.897 for K8 versus 0.926 for EGFR) (50). Our present findings demonstrate that PTP1B is a bona fide K8 phosphatase and raise the possibility that PTP1B may be an important regulator of K8 function under various types of epithelial cell stress, including in the liver, which is a major site of PTP1B action (51).…”