# HISTORY 24 Mar 2016: Updated by: TOUCHUP-v1.15 14 Mar 2016: Updated by: TOUCHUP-v1.12 # molecular_function 20131003: cellular organisms_PTN000056680 contributes to function DNA-directed RNA polymerase activity (GO:0003899) 20131003: Eukaryota_PTN000056681 contributes to function RNA polymerase I activity (GO:0001054) 20131003: Eukaryota_PTN000056681 contributes to function RNA polymerase III activity (GO:0001056) 20131003: Eukaryota_PTN000056681 contributes to function RNA polymerase II activity (GO:0001055) 20131003: Magnoliophyta_PTN000056745 has LOST/MODIFIED function RNA polymerase I activity (GO:0001054) 20131003: Magnoliophyta_PTN000056745 has LOST/MODIFIED function RNA polymerase III activity (GO:0001056) 20131003: Magnoliophyta_PTN000056745 has LOST/MODIFIED function RNA polymerase II activity (GO:0001055) # cellular_component 20131003: cellular organisms_PTN000056680 is found in DNA-directed RNA polymerase complex (GO:0000428) 20131003: Eukaryota_PTN000056681 is found in DNA-directed RNA polymerase III complex (GO:0005666) 20131003: Eukaryota_PTN000056681 is found in DNA-directed RNA polymerase I complex (GO:0005736) 20131003: Eukaryota_PTN000056681 is found in DNA-directed RNA polymerase II, core complex (GO:0005665) 20131003: Magnoliophyta_PTN000056745 is NOT found in DNA-directed RNA polymerase III complex (GO:0005666) 20131003: Magnoliophyta_PTN000056745 is NOT found in DNA-directed RNA polymerase I complex (GO:0005736) 20131003: Magnoliophyta_PTN000056745 is NOT found in DNA-directed RNA polymerase II, core complex (GO:0005665) # biological_process # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES this family comprises a conserved subunit of the multisubunit dna-dependent rna polymerases in eukaryotes and archaea, though not in the bacteria. Archaeal RNA polymerases ----------------------------- In the Archaea, which have a single multisubunit RNA polymerase which is more similar to that of eukarya than to that of prokarya, this family contains sequences for subunit H (PMID:23768203). Eukaryotic nuclear RNA polymerases ----------------------------- In the true eukaryotes, which have three conserved nuclear multisubunit RNA polymerases as well as two additional ones in plants, this is the family of the RPABC1 (aka RPB5) subunit of the multisubunit DNA-directed RNA polymerases. In those eukaryotes which have only the three standard nuclear RNA polymerases (I, II, and III), this subunit is found in all three of these RNAPs (PMID:18573085). Within the plants, there are two additional nuclear RNA polymerases, RNAP IV and RNAP V, both derived from RNAP II (PMID:19110459). Comments and issues with the tree --------------------------------- Plant RNAPs IV and V - Within the plants, there are two subnodes: - The first plant node contains three A. thaliana sequences, one of which is characterized as being present in at least RNAPs II, IV, and V: -- ARATH_RPB5C: Q9FJL8 (RP5L1_ARATH) - DNA-directed RNA polymerase subunit 5-like protein 1 -- ARATH_AT3G16680: F4J2R9 (F4J2R9_ARATH) Unreviewed -- ARATH_NRPB5: O81098 (RPB5A_ARATH) - DNA-directed RNA polymerases II and IV subunit 5A The NRPB5 matches peptides found in RNAPs I, II, and III (PMID:19110459), and also two related sequences: At5g57980 (aka RPB5C) and At3g16680. In analysis of the subunit composition of A. thaliana RNAPs II, IV, and V, Ream et al. (PMID:19110459) did not detect At5g57980 (aka RPB5C) in any of these three RNA polymerases; At3g16680 was not included in the Ream et al. analysis. - The second plant node contains three A. thaliana sequences, RPB5D, RPB5E, and NRPE5, which are labeled in the UniProt records as being subunits for RNA polymerases IV and V or just for V, : -- ARATH_RPB5D: Q9ZVB9 (RPD5B_ARATH) - DNA-directed RNA polymerases IV and V subunit 5B -- ARATH_RPB5E: Q9M1H8 (RPE5C_ARATH) - DNA-directed RNA polymerase V subunit 5C -- ARATH_NRPE5: Q9M1J2 (RPE5A_ARATH) - DNA-directed RNA polymerase V subunit 5A While in many RNA polymerase subunit trees, the A. thaliana RNAP IV and/or V subunits group closer to the A. thaliana RNAP II subunit than either does to the O. sativa subunits, in this tree, there appears to be a node for a subunit found in RNAP II as well as in RNAPs IV and IV and another node for subunits found only in RNAP IV and/or V. Therefore, I will block propagation of the RNAP II specific terms to the node (Magnoliophyta_PTN000056745) containing subunits currently only thought to be present in RNAPs IV and/or V. Odd grouping of three sequences outside both the Eukarya and the Archaea - In addition to a node for the eukaryotes (Eukaryota_PTN000056681) and the Archaea (Archaea_PTN000056761), this tree contains a node outside of the common ancestor of the Eukarya and the Archaea (Archaea-Eukaryota_PTN00082955. However, this node contains 1 eukaryotic sequence (from Giardia) and two Archaeal sequences and was pruned due to being misplaced. Annotation Comment ----------------- No direct propagations were made for BP terms since 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).