# HISTORY
25 Mar 2016: Updated by: TOUCHUP-v1.15
15 Mar 2016: Updated by: TOUCHUP-v1.14

# molecular_function
20130911: cellular organisms_PTN000358822 contributes to function DNA-directed RNA polymerase activity (GO:0003899) 
20130911: Eukaryota_PTN000358824 contributes to function RNA polymerase I activity (GO:0001054) 
20130911: Eukaryota_PTN000358824 contributes to function RNA polymerase III activity (GO:0001056) 
20130911: Eukaryota_PTN000358883 contributes to function RNA polymerase II activity (GO:0001055) 

# cellular_component
20130911: cellular organisms_PTN000358822 is found in DNA-directed RNA polymerase complex (GO:0000428) 
20130911: Eukaryota_PTN000358824 is found in DNA-directed RNA polymerase I complex (GO:0005736) 
20130911: Eukaryota_PTN000358824 is found in DNA-directed RNA polymerase III complex (GO:0005666) 
20130911: Eukaryota_PTN000358883 is found in DNA-directed RNA polymerase II, core complex (GO:0005665) 

# biological_process

# WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED

# NOTES
Background & Phylogeny
This family comprises a highly conserved small 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_PTN000358944), this tree contains the L subunits (PMID:23768203).
Eukaryotic nuclear RNA polymerases
---------------------------------
Within the eukaryota, this family contains the smaller of two subunits of eukaryotic nuclear RNA polymerases with similarity to the bacterial alpha subunit (the other is RPB3 in RNAP II or RPAC1/RPC40 in RNAPs I and III; PMID:19896367). There are two large subgroupings within the Eukaryota in this family:
- the RPB11 subunits (Eukaryota_PTN000358883), which are found in RNA polymerase II
- the RPAC2 (aka RPC19) subunits (Eukaryota_PTN000358824), which are found in both RNAPs I and III
Comments and issues with the tree
---------------------------------
Note that 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). However, there is only a single sequence within this clade for both Arabidopsis thaliana and  Oryza sativa so it may be that RPB11 is present within all five nuclear RNA polymerases in plants.
Annotations
-----------
MF
- to top level node (Archaea-Eukaryota_PTN000358822) to propagate down to Archaea
contributes_to "DNA-directed RNA polymerase activity" (GO:0003899)
- to top of RNAP II clade (Eukaryota_PTN000358883)
contributes_to "RNA polymerase II activity" (GO:0001055)
- to the top of the RNAP I & RNAP III clade (Eukaryota_PTN000358824)
contributes_to "RNA polymerase I activity" (GO:0001054) - to top of RNAP I clade (Eukaryota _PTN000453524)
contributes_to "RNA polymerase III activity" (GO:0001056) - to top of RNAP III clade (Eukaryota_PTN000453624)
CC
- to top level node (Archaea-Eukaryota_PTN000358822) to propagate down to Archaea
"DNA-directed RNA polymerase complex" (GO:0000428)
- to top of RNAP II clade (Eukaryota_PTN000358883)
"DNA-directed RNA polymerase I complex" (GO:0005736)
- to the top of the RNAP I & RNAP III clade (Eukaryota_PTN000358824)
"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 inferred 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).