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Open Access Highly Accessed Research article

An S/T-Q cluster domain census unveils new putative targets under Tel1/Mec1 control

Hannah C Cheung1, F Anthony San Lucas2, Stephanie Hicks3*, Kyle Chang4, Alison A Bertuch5 and Albert Ribes-Zamora6

  • * Corresponding author: Stephanie Hicks sch1@rice.edu

  • † Equal contributors

Author Affiliations

1 Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA

2 University of Texas Graduate School of Biomedical Sciences, Houston, TX, USA

3 Department of Statistics, Rice University, Houston, TX, USA

4 Human Genome Sequencing Center, Departments of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA

5 Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA

6 Department of Pediatrics, Baylor College of Medicine; Department of Biology, University of Saint Thomas, Houston, TX, USA

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BMC Genomics 2012, 13:664  doi:10.1186/1471-2164-13-664

Published: 23 November 2012

Abstract

Background

The cellular response to DNA damage is immediate and highly coordinated in order to maintain genome integrity and proper cell division. During the DNA damage response (DDR), the sensor kinases Tel1 and Mec1 in Saccharomyces cerevisiae and ATM and ATR in human, phosphorylate multiple mediators which activate effector proteins to initiate cell cycle checkpoints and DNA repair. A subset of kinase substrates are recognized by the S/T-Q cluster domain (SCD), which contains motifs of serine (S) or threonine (T) followed by a glutamine (Q). However, the full repertoire of proteins and pathways controlled by Tel1 and Mec1 is unknown.

Results

To identify all putative SCD-containing proteins, we analyzed the distribution of S/T-Q motifs within verified Tel1/Mec1 targets and arrived at a unifying SCD definition of at least 3 S/T-Q within a stretch of 50 residues. This new SCD definition was used in a custom bioinformatics pipeline to generate a census of SCD-containing proteins in both yeast and human. In yeast, 436 proteins were identified, a significantly larger number of hits than were expected by chance. These SCD-containing proteins did not distribute equally across GO-ontology terms, but were significantly enriched for those involved in processes related to the DDR. We also found a significant enrichment of proteins involved in telophase and cytokinesis, protein transport and endocytosis suggesting possible novel Tel1/Mec1 targets in these pathways. In the human proteome, a wide range of similar proteins were identified, including homologs of some SCD-containing proteins found in yeast. This list also included high concentrations of proteins in the Mediator, spindle pole body/centrosome and actin cytoskeleton complexes.

Conclusions

Using a bioinformatic approach, we have generated a census of SCD-containing proteins that are involved not only in known DDR pathways but several other pathways under Tel1/Mec1 control suggesting new putative targets for these kinases.

Keywords:
DNA damage response; Phosphorylation; Proteome; Tel1/Mec1; ATM; ATR