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Genome-wide Analysis of WD40 Protein Family in Human - PubMed

  • ️Fri Jan 01 2016

Genome-wide Analysis of WD40 Protein Family in Human

Xu-Dong Zou et al. Sci Rep. 2016.

Abstract

The WD40 proteins, often acting as scaffolds to form functional complexes in fundamental cellular processes, are one of the largest families encoded by the eukaryotic genomes. Systematic studies of this family on genome scale are highly required for understanding their detailed functions, but are currently lacking in the animal lineage. Here we present a comprehensive in silico study of the human WD40 family. We have identified 262 non-redundant WD40 proteins, and grouped them into 21 classes according to their domain architectures. Among them, 11 animal-specific domain architectures have been recognized. Sequence alignment indicates the complicated duplication and recombination events in the evolution of this family. Through further phylogenetic analysis, we have revealed that the WD40 family underwent more expansion than the overall average in the evolutionary early stage, and the early emerged WD40 proteins are prone to domain architectures with fundamental cellular roles and more interactions. While most widely and highly expressed human WD40 genes originated early, the tissue-specific ones often have late origin. These results provide a landscape of the human WD40 family concerning their classification, evolution, and expression, serving as a valuable complement to the previous studies in the plant lineage.

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Figures

Figure 1
Figure 1. Domain architectures of hsWD40 proteins.

The schematic domain architectures of representative hsWD40 proteins were roughly depicted. The WD40 domains are coloured in green, and other domain types are filled in other different colours separately. Red texts describe the classes of domain architectures. The number of members in each class is given in the parentheses with the name of the representative protein shown below. Red stars indicate the potential animal-specific domain architectures.

Figure 2
Figure 2. Clusters of highly similar hsWD40 domains.

The nodes represent hsWD40 domains, and the edges indicate that the sequence similarities between them are high. The texts in the nodes are the gene symbols, and the numbers on the edges show the domain sequence identities in percentage. If multiple WD40 domains come from the same protein, a numeric suffix is added to avoid confusion. Domains from tandemly arrayed genes (TAGs) are yellow-shaded, and the red boxes indicate the same domain architecture classes for multi-domain WD40 proteins.

Figure 3
Figure 3. The proportions of hsWD40 genes with different phylogenetic patterns.

The phylogenetic patterns of human WD40 genes and all human protein-coding genes (background genes) were compared. (a) Phylogenetic relationships of the 4 representative species, i.e., human, Drosophila, Arabidopsis, and yeast. The symbols of “+++”, “++−”, “+−−”, and “−−−” denote the different phylogenetic patterns (Methods). The numbers in parentheses give the counts of hsWD40 genes accordingly. (b) Comparison between the proportions of hsWD40 genes and all human protein-coding genes in different phylogenetic patterns. Bars filled with dots and slashes represent the percentages of hsWD40 genes and those of all human protein-coding genes, respectively.

Figure 4
Figure 4. Domain architectures in hsWD40 proteins with four different phylogenetic patterns.

The numbers at the horizontal axis denote the classes of domain architectures, and the vertical axis gives out the four phylogenetic patterns with different time of evolutionary origin. The colour gradient in each cell represents the relative count of proteins matching the two axes, which were adopted to sort the columns through clustering. Red stars at the horizontal axis indicate the potential animal-specific domain architecture classes.

Figure 5
Figure 5. Comparison between the numbers of “Highly expressed in all” and “Tissue-specific” hsWD40 genes in different phylogenetic patterns.

The bars filled with dots and slashes represent the counts of “Highly expressed in all” and those of “Tissue-specific” hsWD40 genes, respectively.

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