5 research outputs found
The Gene Ontology of eukaryotic cilia and flagella.
BACKGROUND:
Recent research into ciliary structure and function provides important insights into inherited diseases termed ciliopathies and other cilia-related disorders. This wealth of knowledge needs to be translated into a computational representation to be fully exploitable by the research community. To this end, members of the Gene Ontology (GO) and SYSCILIA Consortia have worked together to improve representation of ciliary substructures and processes in GO.
METHODS:
Members of the SYSCILIA and Gene Ontology Consortia suggested additions and changes to GO, to reflect new knowledge in the field. The project initially aimed to improve coverage of ciliary parts, and was then broadened to cilia-related biological processes. Discussions were documented in a public tracker. We engaged the broader cilia community via direct consultation and by referring to the literature. Ontology updates were implemented via ontology editing tools.
RESULTS:
So far, we have created or modified 127 GO terms representing parts and processes related to eukaryotic cilia/flagella or prokaryotic flagella. A growing number of biological pathways are known to involve cilia, and we continue to incorporate this knowledge in GO. The resulting expansion in GO allows more precise representation of experimentally derived knowledge, and SYSCILIA and GO biocurators have created 199 annotations to 50 human ciliary proteins. The revised ontology was also used to curate mouse proteins in a collaborative project. The revised GO and annotations, used in comparative 'before and after' analyses of representative ciliary datasets, improve enrichment results significantly.
CONCLUSIONS:
Our work has resulted in a broader and deeper coverage of ciliary composition and function. These improvements in ontology and protein annotation will benefit all users of GO enrichment analysis tools, as well as the ciliary research community, in areas ranging from microscopy image annotation to interpretation of high-throughput studies. We welcome feedback to further enhance the representation of cilia biology in GO
Proximity-Induced Covalent Labeling of Proteins with a Reactive Fluorophore-Binding Peptide Tag
Labeling of proteins with fluorescent
dyes in live cells enables
the investigation of their roles in biological systems by fluorescence
microscopy. Because the labeling procedure should not disturb the
native function of the protein of interest, it is of high importance
to find the optimum labeling method for the problem to be studied.
Here, we developed a rapid one-step method to covalently and site-specifically
label proteins with a TexasRed fluorophore in vitro and in live bacteria.
To this end, a genetically encodable TexasRed fluorophore-binding
peptide (TR512) was converted into a reactive tag (ReacTR) by adjoining
a cysteine residue which rapidly reacts with N-α-chloroacetamide-conjugated
TexasRed fluorophore owing to the proximity effect; ReacTR tag first
binds to the TexasRed fluorophore and this interaction brings the
nucleophilic cysteine and the electrophilic N-α-chloroacetamide
groups in close proximity. Our method has several advantages over
existing methods: (i) it utilizes a peptide tag much smaller than
fluorescent proteins, the SNAP, CLIP, or HaLo tags; (ii) it allows
for labeling of proteins with a small, photostable, red-emitting TexasRed
fluorophore; (iii) the probe used is very easy to synthesize; (iv)
no enzyme is required to transfer the fluorophore to the peptide tag;
and (v) labeling yields a stable covalent product in a very fast reaction
L'Auto-vélo : automobilisme, cyclisme, athlétisme, yachting, aérostation, escrime, hippisme / dir. Henri Desgranges
09 octobre 19231923/10/09 (A24,N8333)
MOESM4 of The Gene Ontology of eukaryotic cilia and flagella
Additional file 4. Papers used to make annotations for human ciliary genes. Full list of papers with corresponding PubMed IDs that were used for annotations for human ciliary genes. The first 29 papers comprise the set initially selected for the annotation project. The last four were curated later and specifically targeted to fill in gaps in experimental annotations of certain orthology groups in order to be able to propagate highly specific dynein-related annotations to other sequences within those orthology groups