Abstract
As an ancient protein family, the WD40 repeat proteins often play essential roles in fundamental cellular processes in eukaryotes. Although investigations of eukaryotic WD40 proteins have been frequently reported, prokaryotic ones remain largely uncharacterized. In this paper, we report a systematic analysis of prokaryotic WD40 proteins and detailed comparisons with eukaryotic ones. About 4,000 prokaryotic WD40 proteins have been identified, accounting for 6.5% of all WD40s. While their abundances are less than 0.1% in most prokaryotes, they are enriched in certain species from Cyanobacteria and Planctomycetes, and participate in various functions such as prokaryotic signal transduction and nutrient synthesis. Comparisons show that a higher proportion of prokaryotic WD40s tend to contain multiple WD40 domains and a large number of hydrogen bond networks. The observation that prokaryotic WD40 proteins tend to show high internal sequence identity suggests that a substantial proportion of them (~20%) should be formed by recent or young repeat duplication events. Further studies demonstrate that the very young WD40 proteins, i.e., Highly-Repetitive WD40s, should be of higher stability. Our results have presented a catalogue of prokaryotic WD40 proteins, and have shed light on their evolutionary origins.
Highlights
WD40 domain-containing proteins, constituting one of the most abundant protein families in eukaryotes, often serve as scaffolds in assembling functional complexes by interacting with other macromolecules[1]
WD40 proteins had been considered rare in prokaryotes[7], but we identified a considerable number of prokaryotic WD40 proteins
In Planctomycetes, DUF1501 and RNA polymerase sigma-70 factor family are often annotated to the protein products of the neighbours of WD40-coding genes (Fig. 4b). These analyses suggest that many prokaryotic WD40 proteins may function in pervasive catalytic machineries that are involved in signal transduction, protein folding, transcription, etc
Summary
WD40 domain-containing proteins, constituting one of the most abundant protein families in eukaryotes, often serve as scaffolds in assembling functional complexes by interacting with other macromolecules[1]. WD40 blades are featured with two prevalent structure motifs, one of which is the stability-contributing side chain hydrogen bond network, formed by residues of aspartic acid, histidine, serine (or threonine), and tryptophan (DH[S/T]W, or tetrad)[11, 12]. Another is the β-bulge, which in combination with the tetrad creates a strategy for prediction of hotspot residues and potential interactions[13]. The current repertoire of WD40 domains is expected to contain both ancient and young ones, and the sequence identity between repeats within the same domain can be adopted to roughly measure the time that has passed since the intra-gene duplication event happened. Further depiction of the abundance of young WD40 domains and their taxonomic preference remains largely undetermined
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