# HISTORY 07 May 2016: Updated by: TOUCHUP-v1.18 14 Mar 2016: Updated by: TOUCHUP-v1.14 24 Mar 2016: Updated by: TOUCHUP-v1.15 # molecular_function 20140124: cellular organisms_PTN000109455 has function protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242) 20140123: cellular organisms_PTN000109455 has function histone-arginine N-methyltransferase activity (GO:0008469) 20140207: Eukaryota_PTN000109694 has function protein-arginine omega-N monomethyltransferase activity (GO:0035241) # cellular_component 20140207: cellular organisms_PTN000109455 is found in cytosol (GO:0005829) 20140207: Euteleostomi_PTN000109526 is found in plasma membrane (GO:0005886) # biological_process 20140207: cellular organisms_PTN000109455 participates in regulation of transcription, DNA-templated (GO:0006355) 20140207: Eukaryota_PTN000109694 participates in peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918) 20140124: Euteleostomi_PTN000109551 participates in histone H4-R3 methylation (GO:0043985) # PRUNED 07 May 2016: Eumetazoa_PTN000865239 has been pruned from tree # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES 24 Mar 2016: Eumetazoa_PTN000865239 has been pruned from tree 14 Mar 2016: Eumetazoa_PTN000865239 has been pruned from tree reviews: PMID:19150423 PMID:18057026 PMID:23697934 (histone methylation) Type I PRMTs form omega-NG-monomethylarginine and asymmetric omega-NG,NG-dimethylarginine (ADMA) residues; Type I = PRMT1, 2, 3, 4, 6, 8 Type II PRMTs form omega-NG-monomethylarginine and symmetric omega-NG,NGomega-dimethylarginine (SDMA) residues; Type II = PRMT5 (PTHR10738) Type III and type IV PRMTs synthesize only delta-NG-monomethylarginine (MMA) and delta-NG-monomethylarginine, respectively = PRMT7. All PRMT's seem to have activity against histone, but it may not be the physiological substrate for all. For example, Km of PRMT8 is 200-fold lower than PRMT1 (PMID:23946480). Pruned PRMT10 (AKA FBXO11) since there is conflicting data about its methyltransferase activity (see PMID:16487488 and PMID:17336909); also, that clade is more diverged that its 'sister' PRMT7 that arose after the duplication PTHN000109695, and PRMT7 has already a changed subtrate specificity. MF - Transferred histone-arginine N-methyltransferase activity (GO:0008469) to the root; since the activity is found across several branches, in particular PMRT1 and PRMT7; also, histones are present in Euryarchaea. - NOT'ed the PRMT10/PRMT9 branch as its activity is controversial (PMID:18057026) "FBXO11, also referred to as PRMT9 (2p16.3), was identified as a potential PRMT because it has regions that display weak sequence similarity to the I, post-I, II and III amino acid sequence motifs (Cook et al., 2006). Unlike other PRMTs, it does not harbor a THW loop; however, FLAG-tagged hFBXO11 has been reported to have type II activity (Cook et al., 2006), but HA-tagged hFBXO11 and its C. elegans ortholog (DRE-1) have been reported not to have PRMT activity (Fielenbach et al., 2007). " - PRMT7: NOT protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242); but has protein-arginine omega-N monomethyltransferase activity (GO:0035241) (see PMID: 2225144) ** CANNOT PROPAGATE - PRMT1: histone methyltransferase activity (H4-R3 specific) (not annotated) BP - Transferred histone methylation (GO:0016571) to the root; since the activity is found across several branches, in particular PMRT1 and PRMT7; also, histones are present in Euryarchaea. - Transferred regulation of transcription, DNA-templated (GO:0006355), since that's the process regulated by histone methylation. ** Annotations to correct: Only PRMT7 is a Type II Arg methlytransferase. Other annotations to "protein-arginine omega-N monomethyltransferase activity (GO:0035241)" probably just represent a step in the di-methylation. SO the momomethyltransferase annotations should be reviewed by all groups. ** Substrate specificity Data is complicated. Histone methylation seems to be used generally to test activity, but it's not clear whether it's the physiological susbtrate. Also, many sustrates are missing. So didn't annotate for now. Some suggestions for annotations: - PRMT1 family: H4-R3 methylation (GO:0043985) (PMID:23697934). - PRMT6 family: histone methyltransferase activity (H3-R2 specific) (GO:0070611) (PMID:23697934; PMID:18079182). - PRMT6: Histone H3R2 methylation (PMID:23697934). # 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).