# HISTORY 26 Apr 2016: Updated by: TOUCHUP-v1.15 19 Mar 2016: Updated by: TOUCHUP-v1.14 # molecular_function # cellular_component 20150120: Eukaryota_PTN000795297 is found in membrane (GO:0016020) 20150120: Eukaryota_PTN000795297 is found in BBSome (GO:0034464) 20150120: Eukaryota_PTN000795297 is found in ciliary basal body (GO:0036064) 20150120: Eukaryota_PTN000795297 is found in motile cilium (GO:0031514) # biological_process 20150120: Eukaryota_PTN000795297 participates in cilium assembly (GO:0042384) 20150120: Eukaryota_PTN000795297 participates in protein localization to ciliary membrane (GO:1903441) # PRUNED 26 Apr 2016: node_PTN001286762 has been pruned from tree # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES 19 Mar 2016: node_PTN001286762 has been pruned from tree This family contains the BBS2 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 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 Ornithorhynchus anatinus (Duckbill platypus), the sequence K7EGX4_ORNAN appears to be a fragment, while F6UN54_ORNAN looks complete. - From Strongylocentrotus purpuratus, both sequences (H3HWJ6_STRPU and H3JLA0_STRPU) are obsolete and were pruned. - From Pristionchus pacificus (Parasitic nematode), both sequences (H3FFN0_PRIPA and H3FAC9_PRIPA) look to be short partial sequences. - From Chlamydomonas reinhardtii (Chlamydomonas smithii), both sequences (A8HY02_CHLRE and A8HY05_CHLRE) appear to be partial sequences. Comments on annotations and propagations ----------------------------------- - I decided not to propagate the MF annotation of the human BBS2 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 decided not to propagate the BP annotation of the human BBS2 to the term "Golgi to plasma membrane protein transport" from PMID:19150989 because while the authors said "most likely between the Golgi and the ciliary and/or plasma membrane" and thus did not seem certain exactly which membrane is the target of BBSome mediated trafficking. - 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).