# HISTORY 26 Mar 2016: Updated by: TOUCHUP-v1.15 16 Mar 2016: Updated by: TOUCHUP-v1.14 # molecular_function # cellular_component 20150121: Eukaryota_PTN000412421 is found in BBSome (GO:0034464) 20150121: Eukaryota_PTN000412421 is found in membrane (GO:0016020) 20150121: Eukaryota_PTN000412421 is found in axoneme (GO:0005930) 20150121: Eukaryota_PTN000412421 is found in ciliary basal body (GO:0036064) # biological_process 20150121: Eukaryota_PTN000412421 participates in protein localization (GO:0008104) 20150121: Eukaryota_PTN000412421 participates in intracellular transport (GO:0046907) 20150121: Eukaryota_PTN000412421 participates in cilium assembly (GO:0042384) # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES This family contains the BBS7 subunit of the highly conserved seven-member BBSome complex, a membrane coat complex that traffics membrane proteins to the primary cilium (PMID:19575670, PMID:20697559, PMID:20603001). Whether this trafficking of transmembrane receptors occurs by a vesicular mechanism or as a planar patch that moves laterally within the membrane is not yet clear as of August 2014. The BBSome also appears to be an adaptor for some retrograde intraflagellar traffic (IFT) within the cilium (PMID:20697559). Comments on the tree & sequences ---------------------------- This tree looks very straightforward. All four duplication nodes look like sequence issues rather than true duplications: - From Strongylocentrotus purpuratus, all three sequences (H3IIR3_STRPU, H3HUD8_STRPU, and H3JB57_STRPU) are partial; they are also obsolete in UniProt. - From Pristionchus pacificus (Parasitic nematode), both sequences (H3FME0_PRIPA and H3FMD9_PRIPA) look like partial sequences. - From Schistosoma mansoni (Blood fluke), both sequences (G4LWA1_SCHMA and G4LWA2_SCHMA) look like partial sequences. - From Nematostella vectensis (Starlet sea anemone), both sequences (A7T6T2_NEMVE and A7S3C1_NEMVE) look like partial sequences. Comments on annotations and propagations ----------------------------------- - I decided not to propagate the MF annotation of the human BBS7 to the term "RNA polymerse II repressing transcription factor binding (GO:0001103 from PMID:22302990) because this was done by yeast two-hybrid with isolated subunits of the BBSome complex against the RNF2 transcription factor and multiple subunits showed the same effect, suggesting that the interaction might be at the level of the BBSome complex, rather than an individual subunit. In addition, they say that they "have shown recently that depletion of BBS4 results in defective proteasome-mediated protein clearance, leading to the accumulation of β-catenin in BBS4 knockdown cells (Gerdes et al., 2007).", and show similar accumulation of RNF2 protein in BBS knockdown cells. Basically, this seems somewhat preliminary and potentially indirect, so I have not chosen to propagate this annotation. - I did not propagate a large number of BP annotations based on developmental phenotypes because they are all downstream of the primary defect in trafficking to the cilium and the resulting defect in cilary function. # REFERENCE Annotation inferences using phylogenetic trees The goal of the GO Reference Genome Project, described in PMID 19578431, is to provide accurate, complete and consistent GO annotations for all genes in twelve model organism genomes. To this end, GO curators are annotating evolutionary trees from the PANTHER database with GO terms describing molecular function, biological process and cellular component. GO terms based on experimental data from the scientific literature are used to annotate ancestral genes in the phylogenetic tree by sequence similarity (ISS), and unannotated descendants of these ancestral genes are inferred to have inherited these same GO annotations by descent. The annotations are done using a tool called PAINT (Phylogenetic Annotation and INference Tool).