# HISTORY 07 May 2016: Updated by: TOUCHUP-v1.18 14 Mar 2016: Updated by: TOUCHUP-v1.14 25 Mar 2016: Updated by: TOUCHUP-v1.15 # molecular_function 20130909: cellular organisms_PTN000210279 contributes to function DNA-directed RNA polymerase activity (GO:0003899) 20130909: Eukaryota_PTN000210281 contributes to function RNA polymerase II activity (GO:0001055) 20130909: Eukaryota_PTN000210383 contributes to function RNA polymerase I activity (GO:0001054) 20130909: Eukaryota_PTN000210383 contributes to function RNA polymerase III activity (GO:0001056) # cellular_component 20130909: cellular organisms_PTN000210279 is found in DNA-directed RNA polymerase complex (GO:0000428) 20130909: Eukaryota_PTN000210281 is found in DNA-directed RNA polymerase II, core complex (GO:0005665) 20130909: Eukaryota_PTN000210383 is found in DNA-directed RNA polymerase I complex (GO:0005736) 20130909: Eukaryota_PTN000210383 is found in DNA-directed RNA polymerase III complex (GO:0005666) # biological_process # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES Background & Phylogeny This family comprises a highly conserved subunit of multisubunit DNA-dependent RNA polymerases in the Archaea and Eukaryota, one of two with similarity to the bacterial alpha subunit. Archaeal RNA polymerases ----------------------------- Within the Archaea (Archaea_PTN000927851), this tree contains the D subunits (PMID:23768203). Eukaryotic nuclear RNA polymerases ---------------------------------- Within the eukaryota, this family contains the third largest subunit of eukaryotic nuclear RNA polymerases and the larger of two with similarity to the bacterial alpha subunit (the other is RPB11 in RNAP II or RPAC2/RPC19 in RNAPs I and III; PMID:19896367). There are two large subgroupings within this family: - RPB3, the third largest subunit of RNA polymerase II enzymes (Eukaryota_PTN000210281) - RPAC1 (aka RPC40), the third largest subunit in both RNA polymerases I and III (Eukaryota_PTN000210383) Comments and issues with the tree --------------------------------- Although the bacterial alpha subunits, which are prsent in a stoichiometry of 2 subunits per core bacterial RNA polymerase complex, are considered to be the equivalent of the RPB3 and RPB11 subunit pair in RNAP II and the RPAC1 and RPAC2 (aka RPC40 and RPC19) subunit pair in both RNAP I and RNAP III, the bacterial-type alpha subunits, including those for chloroplast enzymes, are not present within this tree. In plants, there are two additional nuclear RNA polymerases called RNAP IV and RNAP V, both of which are thought to be derived from RNAP II (PMID:19110459). Arabidopsis has two genes within the RNAP II clade (RPB3-A and RPB3-B); RPB3-A is annotated as being present within both the RNAP IV and RNAP V complexes as well as the RNAP II complex. However, there is only a single Oryza sativa sequence within this clade as currently built. Within the RNAP I/III clade, the plants, both A. thaliana (named RPAC42 and RPAC43; PMID:8566778) and O. sativa each contain two genes. It is not clear whether these genes can each be present in either RNAP I or RNAP III, or whether each is specific to a single RNAP. There is an additional clade (parent node PTN000210347) within this tree containing Cript genes encoding "Cysteine-rich PDZ-binding protein". It has a significantly longer branch length than either the RPB3 or RPAC1 (aka RPC40) clades. I think this branch should be completely removed from this tree so I have pruned it. Annotations ----------- MF - to top level node (Archaea-Eukaryota_PTN000210279) to propagate down to Archaea contributes_to "DNA-directed RNA polymerase activity" (GO:0003899) - to top of RNAP II clade (Eukaryota_PTN000210281) contributes_to "RNA polymerase II activity" (GO:0001055) - to the top of the RNAP I & RNAP III clade (Eukaryota_PTN000210383) contributes_to "RNA polymerase I activity" (GO:0001054) contributes_to "RNA polymerase III activity" (GO:0001056) CC - to top level node (Archaea-Eukaryota_PTN000210279) to propagate down to Archaea "DNA-directed RNA polymerase complex" (GO:0000428) - to top of RNAP II clade (Eukaryota_PTN000210281) "DNA-directed RNA polymerase I complex" (GO:0005736) - to the top of the RNAP I & RNAP III clade (Eukaryota_PTN000210383) "DNA-directed RNA polymerase II, core complex" (GO:0005665) "DNA-directed RNA polymerase III complex" (GO:0005666) BP - no direct propagations, the appropriate terms can all be inferred by the Function-Process links from the propagated MF terms # 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).