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

# molecular_function
20130822: root_PTN000453461 contributes to function DNA-directed RNA polymerase activity (GO:0003899) 
20130822: Eukaryota_PTN000453524 contributes to function RNA polymerase I activity (GO:0001054) 
20130822: Eukaryota_PTN000453624 contributes to function RNA polymerase III activity (GO:0001056) 
20130822: Eukaryota_PTN000453465 contributes to function RNA polymerase II activity (GO:0001055) 

# cellular_component
20130821: root_PTN000453461 is found in DNA-directed RNA polymerase complex (GO:0000428) 
20130821: Eukaryota_PTN000453524 is found in DNA-directed RNA polymerase I complex (GO:0005736) 
20130821: Eukaryota_PTN000453624 is found in DNA-directed RNA polymerase III complex (GO:0005666) 
20130821: Eukaryota_PTN000453465 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 the largest subunits of the multisubunit DNA-dependent RNA polymerases, including eubacteria, archaea, and eukaryota.
Bacterial type RNA polymerases
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In the eubacteria (Eubacteria_PTN000453445), this family primarily consists of the largest beta' (beta prime) subunits. However, in the cyanobacteria (here represented by Gloeobacter violaceus and Synechocystis), the rpoC gene has been split into two genes, rpoC1 and rpoC2, where the rpoC1 gene (encoding the gamma subunit) corresponds to the amino-terminal half of the E. coli beta' subunit (PMID:1904436).
The chloroplasts (aka plastids) of plants also contain a multisubunit RNAP, which is thought to to be derived from the cyanobacterial RNA polymerase (PMID:1904436).
Archaeal RNA polymerases
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Within the Archaea (PTN001065866), this tree contains both the A and A' subunits which together represent the equivalent of the bacterial beta' and eukaryotic largest subunits (PMID:23768203).
Eukaryotic nuclear RNA polymerases
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Within the eukaryota, there are three large subgroupings for the largest subunits of:
- RNAP I ( Eukaryota _PTN000453524)
- RNAP II (Eukaryota_PTN000453465),  including plant RNAP IV (or RNAP D) and RNAP V (or RNAP E), both of which are thought to be derived from RNAP II (PMID:19110459).
- RNAP III (Eukaryota_PTN000453624)
Comments and issues with the tree
---------------------------------
Euacterial subunits:
- Note that the E. coli subunit rpoC is represented twice in the tree, once with a MetaCyc ID and once with an EcoCyc ID.
Plastid beta subunits:
- The chloroplast subunit sequences originally present within the tree are not placed properly. Placed within the RNAP I clade, the node Viridiplantae_PTN000453619 contains beta' subunits, including ORYSJ_rpoC2 and ARATH_RPOC2 (both in node Magnoliophyta_PTN001065671).
- The Arabidopsis subunit ARATH_RPOC1 is found in the RNAP II clade.
- These three sequences have been pruned due to their inappropriate positions within the tree structure.
RNAP IV and RNAP V:
- 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). In this tree, the largest subunits of the Arabidopsis RNAP IV and V subunits (ARATH_NRPD1 and ARATH_NRPE1) group with the largest subunit of RNAP II (ARATH_RPB1) as expected. However, this tree contains only a single sequence for rice (Oryza sativa) within the RNAP II clade.
Annotation Comment
---------------------------------
No direct BP propagations made since the appropriate BP terms are all inferred via the MF-BP 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).