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

# molecular_function
20130915: root_PTN000465875 contributes to function DNA-directed RNA polymerase activity (GO:0003899) 
20130915: Eukaryota_PTN000465942 contributes to function RNA polymerase I activity (GO:0001054) 
20130915: Eukaryota_PTN000465879 contributes to function RNA polymerase III activity (GO:0001056) 
20130915: Eukaryota_PTN000466005 contributes to function RNA polymerase II activity (GO:0001055) 

# cellular_component
20130915: root_PTN000465875 is found in DNA-directed RNA polymerase complex (GO:0000428) 
20130915: Eukaryota_PTN000465942 is found in DNA-directed RNA polymerase I complex (GO:0005736) 
20130915: Eukaryota_PTN000465879 is found in DNA-directed RNA polymerase III complex (GO:0005666) 
20130915: Eukaryota_PTN000466005 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
This family comprises a highly conserved subunit of the multisubunit DNA-dependent RNA polymerases.
Bacterial type RNA polymerases
-----------------------------
In the eubacteria (Eubacteria_PTN000466095), this family consists of the second largest beta subunits.
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
-----------------------------
Within the Archaea (Archaea_PTN000466083), this family contains the B subunits (PMID:23768203), which in some species is split into two subunits designated B' and B'' (PMID:10400604).
Eukaryotic nuclear RNA polymerases
-----------------------------
Within the eukaryota, there are three large subgroupings for the second largest subunits:
- RNAP I (Eukaryota _PTN000465942)
- RNAP II (Eukaryota_PTN000466005), 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_PTN000465879)
Comments and issues with the tree
-----------------------------
Within the bacteria, note that the E. coli subunit rpoB is represented twice in the tree, once with a MetaCyc ID and once with an EcoCyc ID.
Plastid beta subunit node:
- In this tree, the plastid RNAP beta subunits (encoded by rpoB genes) for both Arabidopsis and Oryza sativa are grouped together, under a node (Eukaryota_PTN001074406) that is in between the Eubacteria and the common ancestor of Eukaryota and Archaea, as seems appropriate for the cyanobacterial origin of the plastid RNAP.
- However, this node also contains sequences from Ixodes scapularis (ticks), Nemotastella vectensis (starlet sea anemone), and Trichoplax adhaerens (a basal group of multicellular metazoan animals). These sequences seem misplaced, so I have pruned them.
RNAP IV and RNAP V:
- Arabidopsis has two genes encoding the second largest subunit (NRPD2A and NRPD2B), only one of which (ARATH_RPD2B) appears in this tree in the RNAP II clade, along with sequences from Oryza sativa and Physcomitrella patens. The node Embryophyta_PTN001074367 contains the NRPD2B sequence, encoding a subunit of RNAP IV in A. thaliana, so the sequences in this node should not have RNAP II annotations. Therefore, propagation of the RNAP II terms has been blocked for this node.
- I don't see any sign of RNAP V subunits in the tree.
Annotation comment
-----------------
No direct propagations 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).