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Updated: Jul 27, 2026

Oligopeptide Competition Assay for Phosphorylation Site Determination
Published on: May 18, 2017
Multi-site phosphorylation of Pho4 by the cyclin-CDK Pho80-Pho85 is semi-processive with site preference
D A Jeffery1, M Springer, D S King
1Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143, USA.
Abstract:
As part of a nutrient-responsive signaling pathway, the budding yeast cyclin-CDK complex Pho80-Pho85 phosphorylates the transcription factor Pho4 on five sites and inactivates it. Here, we describe the kinetic reaction between Pho80-Pho85 and Pho4. Through experimentation and computer modeling we have determined that Pho80-Pho85 phosphorylates Pho4 in a semi-processive fashion that results from a balance between kcat and k(off). In addition, we show that Pho80-Pho85 phosphorylates certain sites preferentially. Phosphorylation of the site with the highest preference inhibits the transcriptional activity of Pho4 when it is in the nucleus, while phosphorylation of the lowest-preference sites is required for export of Pho4 from the nucleus. This method of phosphorylation may allow Pho80-Pho85 to quickly inactivate Pho4 in the nucleus and efficiently phosphorylate Pho4 to completion.
Insights
The Pho80-Pho85 cyclin-CDK complex controls transcription factor Pho4 activity by semi-processive phosphorylation. This regulation balances inactivation and nuclear export, optimizing nutrient response.
Area of Science:
- Molecular Biology
- Biochemistry
- Cell Biology
Background:
- The Pho80-Pho85 complex is a cyclin-dependent kinase (CDK) that regulates nutrient signaling pathways.
- Transcription factor Pho4 is a key target, and its phosphorylation by Pho80-Pho85 leads to inactivation.
Purpose of the Study:
- To elucidate the kinetic mechanism of Pho80-Pho85 phosphorylation of Pho4.
- To understand how site-specific phosphorylation impacts Pho4 activity and localization.
Main Methods:
- Experimental kinetic analysis of the Pho80-Pho85/Pho4 interaction.
- Computer modeling to simulate and interpret phosphorylation dynamics.
Main Results:
- Pho80-Pho85 phosphorylates Pho4 in a semi-processive manner, influenced by catalytic rate (kcat) and dissociation rate (koff).
- Preferential phosphorylation of specific sites on Pho4 was observed.
- High-affinity site phosphorylation inhibits nuclear Pho4 activity, while low-affinity site phosphorylation promotes nuclear export.
Conclusions:
- The semi-processive and site-selective phosphorylation mechanism allows for rapid inactivation and efficient completion of Pho4 phosphorylation.
- This regulatory strategy enables precise control of the nutrient-responsive signaling pathway.
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