Cildb: a knowledgebase for centrosomes and cilia

Abstract

Ciliopathies, pleiotropic diseases provoked by defects in the structure or function of cilia or flagella, reflect the multiple roles of cilia during development, in stem cells, in somatic organs and germ cells. High throughput studies have revealed several hundred proteins that are involved in the composition, function or biogenesis of cilia. The corresponding genes are potential candidates for orphan ciliopathies. To study ciliary genes, model organisms are used in which particular questions on motility, sensory or developmental functions can be approached by genetics. In the course of high throughput studies of cilia in Paramecium tetraurelia, we were confronted with the problem of comparing our results with those obtained in other model organisms. We therefore developed a novel knowledgebase, Cildb, that integrates ciliary data from heterogeneous sources. Cildb links orthology relationships among 18 species to high throughput ciliary studies, and to OMIM data on human hereditary diseases. The web interface of Cildb comprises three tools, BioMart for complex queries, BLAST for sequence homology searches and GBrowse for browsing the human genome in relation to OMIM information for human diseases. Cildb can be used for interspecies comparisons, building candidate ciliary proteomes in any species, or identifying candidate ciliopathy genes.Database URL: http://cildb.cgm.cnrs-gif.fr

The DPY-30 Domain and Its Flanking Sequence Mediate the Assembly and Modulation of Flagellar Radial Spoke Complexes

“…We discuss only DYDC2 because of the similarity. As expected for an RSP2 orthologue, DYDC2 was found in the human cilium proteome and is listed in the cilium proteome database (2,42). Inferred from expressed sequence tags (EST), it is enriched in the lung and the testis, which contain cells with motile cilia or flagella (Hs.512782 in the UniGene database [http://www.ncbi.nlm.nih.gov/]).…”

The deubiquitinating enzyme CYLD controls apical docking of basal bodies in ciliated epithelial cells

“…At first, ubiquitinated proteins have been reported to be present in cilia and flagella 52 , and the K63-specific E2 ubiquitinconjugating enzyme Ubc13 is present in the ciliome of various species [52][53][54][55] . Next, protein ubiquitination was involved in flagellar disassembly 52 .…”

Switching on cilia: transcriptional networks regulating ciliogenesis

“…A key step in understanding ciliary biology, and thus the etiology of ciliopathies, is to identify the various components that participate in the generation and function of these organelles. Over the years, a variety of strategies have been used to determine the genes and proteins required in different kinds of cilia (Arnaiz et al, 2009;Gherman et al, 2006;Inglis et al, 2006). These screens have revealed that cilia are complex organelles, with hundreds (if not thousands) of components involved in their assembly, structure and function, the expression of which must be precisely coordinated during cilia formation.…”