Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
BMC Genomics. 2012 Nov 23;13:664. doi: 10.1186/1471-2164-13-664.
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.
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.
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.
为了维持基因组完整性和正常细胞分裂，细胞对 DNA 损伤的反应是即时且高度协调的。在 DNA 损伤反应 (DDR) 过程中，酿酒酵母中的传感器激酶 Tel1 和 Mec1 以及人类中的 ATM 和 ATR，磷酸化多种介质，激活效应蛋白以启动细胞周期检查点和 DNA 修复。激酶底物的一部分被 S/T-Q 簇结构域 (SCD) 识别，该结构域包含丝氨酸 (S) 或苏氨酸 (T) 之后紧跟一个谷氨酰胺 (Q) 的基序。然而，Tel1 和 Mec1 控制的蛋白质和途径的全部内容尚不清楚。
为了鉴定所有推定的 SCD 包含蛋白质，我们分析了在已验证的 Tel1/Mec1 靶标内 S/T-Q 基序的分布，并得出了一个统一的 SCD 定义，即在 50 个残基的范围内至少有 3 个 S/T-Q。这个新的 SCD 定义被用于一个定制的生物信息学管道，以生成酵母和人类中 SCD 包含蛋白质的普查。在酵母中，鉴定出 436 种蛋白质，比预期的随机命中数量显著增加。这些 SCD 包含蛋白质在 GO 本体论术语中分布不均匀，但在与 DDR 相关的过程中显著富集。我们还发现参与末期和胞质分裂、蛋白质运输和内吞作用的蛋白质显著富集，表明这些途径中可能存在新的 Tel1/Mec1 靶标。在人类蛋白质组中，也鉴定出了广泛的类似蛋白质，包括在酵母中发现的一些 SCD 包含蛋白质的同源物。这个列表还包括 Mediator、纺锤体极体/中心体和肌动蛋白细胞骨架复合物中的高浓度蛋白质。
我们使用生物信息学方法生成了 SCD 包含蛋白质的普查，这些蛋白质不仅参与已知的 DDR 途径，还参与 Tel1/Mec1 控制的其他几种途径，这表明这些激酶的新潜在靶标。
