GPS-ARM: computational analysis of the APC/C recognition motif by predicting D-boxes and KEN-boxes

Abstract

Anaphase-promoting complex/cyclosome (APC/C), an E3 ubiquitin ligase incorporated with Cdh1 and/or Cdc20 recognizes and interacts with specific substrates, and faithfully orchestrates the proper cell cycle events by targeting proteins for proteasomal degradation. Experimental identification of APC/C substrates is largely dependent on the discovery of APC/C recognition motifs, e.g., the D-box and KEN-box. Although a number of either stringent or loosely defined motifs proposed, these motif patterns are only of limited use due to their insufficient powers of prediction. We report the development of a novel GPS-ARM software package which is useful for the prediction of D-boxes and KEN-boxes in proteins. Using experimentally identified D-boxes and KEN-boxes as the training data sets, a previously developed GPS (Group-based Prediction System) algorithm was adopted. By extensive evaluation and comparison, the GPS-ARM performance was found to be much better than the one using simple motifs. With this powerful tool, we predicted 4,841 potential D-boxes in 3,832 proteins and 1,632 potential KEN-boxes in 1,403 proteins from H. sapiens, while further statistical analysis suggested that both the D-box and KEN-box proteins are involved in a broad spectrum of biological processes beyond the cell cycle. In addition, with the co-localization information, we predicted hundreds of mitosis-specific APC/C substrates with high confidence. As the first computational tool for the prediction of APC/C-mediated degradation, GPS-ARM is a useful tool for information to be used in further experimental investigations. The GPS-ARM is freely accessible for academic researchers at: http://arm.biocuckoo.org.

Figure 1. The Sequence logos of ARM(2, 6) and ARM(8, 15) were generated by the HMM-Logo (LogoMat-M) for the (A) D-box and (B) KEN-box, respectively.

Figure 2. Screen snapshot of the GPS-ARM 1.0 software.

The default thresholds were chosen for the D-box (high) and KEN-box (low). As an example, the prediction results for the human centromere protein F/CENP-F (UniProt ID: P49454) are shown.

Figure 3. The prediction performance of GPS-ARM 1.0.

The LOO validation and 4-, 6-, 8- and 10-fold cross-validations were performed for (A) the D-box and (B) the KEN-box.