In Silico Study of Rett Syndrome Treatment-Related Genes, MECP2, CDKL5, and FOXG1, by Evolutionary Classification and Disordered Region Assessment

Abstract

Rett syndrome (RTT), a neurodevelopmental disorder, is mainly caused by mutations in methyl CpG-binding protein 2 (MECP2), which has multiple functions such as binding to methylated DNA or interacting with a transcriptional co-repressor complex. It has been established that alterations in cyclin-dependent kinase-like 5 (CDKL5) or forkhead box protein G1 (FOXG1) correspond to distinct neurodevelopmental disorders, given that a series of studies have indicated that RTT is also caused by alterations in either one of these genes. We investigated the evolution and molecular features of MeCP2, CDKL5, and FOXG1 and their binding partners using phylogenetic profiling to gain a better understanding of their similarities. We also predicted the structural order-disorder propensity and assessed the evolutionary rates per site of MeCP2, CDKL5, and FOXG1 to investigate the relationships between disordered structure and other related properties with RTT. Here, we provide insight to the structural characteristics, evolution and interaction landscapes of those three proteins. We also uncovered the disordered structure properties and evolution of those proteins which may provide valuable information for the development of therapeutic strategies of RTT.

Keywords: Rett syndrome; cyclin-dependent kinase-like 5; forkhead box protein G1; intrinsically disordered region; methyl-CpG-binding protein 2; phylogenetic profile analysis; post-transcriptional modification.

Figure 1

The order–disorder propensity of RTT and RTT-like causing proteins in chordates. Heat maps of the order–disorder propensity were generated according to the taxonomic positions in the phylogenetic tree (rows) and multiple sequence alignment (columns). The heat maps show a color gradient of blue (ordered) to red (disordered), with white as the boundary between the two and black as gaps. Colored boxes between the trees and heat maps indicate the taxonomic group, and bars above the heat maps indicate domain position in the multiple sequence alignment, with light blue and black areas indicating the domain and absence of a domain, respectively. (A–C) Heat maps for MeCP2 (A), CDKL5 (B), and FOXG1 (C) are shown. MBD, TRD, NID, FBD, GBD, JBD, NLS, and NES indicate methyl-CpG-binding domain, transcriptional repression domain, NCoR/SMRT interaction domain, forkhead binding domain, Groucho-binding domain, JARID1B binding domain, nuclear localization signal, and nuclear export signal, respectively.

Figure 2

Rate of evolution per site in human RTT-related proteins. (A–C) Rates of amino acid substitution in MeCP2 (A), CDKL5 (B), and FOXG1 (C) are shown as blue areas. The bars above charts indicate the position of the domain in the human sequence, with light blue areas indicating the domain and black lines indicating no domain. Conserved phosphorylation sites, disordered region, single nucleotide polymorphisms in the general population, and pathogenic missense point mutation are plotted in green, purple, blue, and red lines, respectively. The x and y axes represent the sequence length and Z score of the evolutionary rates, respectively.

Figure 3

Phylogenetic profiling of MeCP2, CDKL5, and FOXG1 proteins and their interaction partners. The horizontal axis shows 326 eukaryotes for which whole genome sequences are available, and the vertical axis shows 240 human proteins related to RTT. Bar in a1 and a2 shows MeCP2-interactor (red), CDKL5-interactor (green), FOXG1-interactor (blue), respectively. The human orthologous proteins in each species are shown in black. The phylogenetic tree was divided into four clusters (Class 1–4); those conserved across chordates, metazoan, multicellular, and eukaryotes are shown.

Figure 4

Subcellular localization and specific GO categories of human RTT-related proteins: Phylogenetic trees show interactors, subcellular localization, and specific GO categories for each protein. The vertical axis shows 240 RTT-related proteins, and each bar shows MeCP2-interactor (red), CDKL5-interactor (green), and FOXG1-interactor (blue) (a1 and a2); cellular localization (b); epigenetic regulation of gene expression (c1); transcriptional regulation (c2); and organogenesis (c3).