# HISTORY 07 May 2016: Updated by: TOUCHUP-v1.18 14 Mar 2016: Updated by: TOUCHUP-v1.12 24 Mar 2016: Updated by: TOUCHUP-v1.15 # molecular_function 20150122: cellular organisms_PTN000036740 has function rRNA methyltransferase activity (GO:0008649) 20150122: cellular organisms_PTN000036740 has function histone-glutamine methyltransferase activity (GO:1990259) 20150122: cellular organisms_PTN000036740 has function RNA binding (GO:0003723) # cellular_component 20150122: cellular organisms_PTN000036740 is found in small-subunit processome (GO:0032040) 20150122: cellular organisms_PTN000036740 is found in box C/D snoRNP complex (GO:0031428) 20150122: Eukaryota_PTN000036741 is found in Cajal body (GO:0015030) 20150122: Archaea_PTN000036825 is NOT found in small-subunit processome (GO:0032040) 20150122: Archaea_PTN000036825 is NOT found in box C/D snoRNP complex (GO:0031428) # biological_process 20150122: cellular organisms_PTN000036740 participates in histone glutamine methylation (GO:1990258) 20150122: cellular organisms_PTN000036740 participates in rRNA methylation (GO:0031167) 20150122: cellular organisms_PTN000036740 participates in box C/D snoRNA 3'-end processing (GO:0000494) # PRUNED 07 May 2016: Ascomycota_PTN001308271 has been pruned from tree # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES 24 Mar 2016: Ascomycota_PTN001308271 has been pruned from tree 14 Mar 2016: Ascomycota_PTN001308271 has been pruned from tree This family contains fibrillarin, aka NOP1, FBL, FIB, in the eukaryotes, or flpA in the Archaea. Nop1 is the catalytic methyltransferase in the box C/D type snoRNAs that methylate various RNA substrates, including rRNA, snoRNA, and others, including tRNAs in the Archaea. It has also been shown to methylate histone glutamine residues. Tree and Sequence Comments =================== - Node Ascomycota_PTN001308271 - The sequences under this node look out of place. The Archael sequences are more homologous to the rest of this family than these six sequences are to the rest of the fungi. There is also a really long branch length to this node from the branch node separating this from the rest of the fungi. Annotation comments: =============== Extent of conservation to the Archaea ----------------- I did some research to decide how much could be propagated to the Archaea: - Pereira SL et al. 1997 (PMID:9356501) indicates that Archaea have eukaryotic type histones. - This book available via NCBI books that indicates that Archaea do have snoRNAs, but I did not see any indication that they have Cajal bodies, so most annotations have been propagated to the root of the tree, but the CC annotation to "Cajal body" was propagated only up to the root node of the eukaryotes. - Edouard Bertrand and Maurille J. Fournier. The snoRNPs and Related Machines: Ancient Devices That Mediate Maturation of rRNA and Other RNAs - http://www.ncbi.nlm.nih.gov/books/NBK6107/ MF term "RNA binding" ------------------ While there are are a number of different annotations to "RNA binding" or to more specific terms, I have chosen to propagate only "RNA binding". PMID:21785141 demonstrates binding of A. thaliana FIB2 to a variety of types of RNA. - While the rat gene Fbl is also annotated to "RNA binding" by IDA from PMID:10679015, when I look at the paper, it seems to me that the coIP really only shows that these proteins come down together as part of the Box H/ACA and Box C/D snoRNP complexes, not direct evidence of which protein(s) is/are binding RNA. - There were also experimental MF annotations for human FBL to "poly(A) RNA binding" (GO:0044822) from two high throughput studies: PMID:22681889 and PMID:22658674. Between the fact that these were high throughput experiments, the fact that this protein is normally part of a large complex, and the fact that it is not clear that poly(A) RNA binding is biologically relevant, I have chosen not to propagate this MF annotation. # 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).