# HISTORY 26 Mar 2016: Updated by: TOUCHUP-v1.15 16 Mar 2016: Updated by: TOUCHUP-v1.14 # molecular_function 20140415: Eukaryota_PTN000480538 contributes to function single-stranded RNA binding (GO:0003727) 20140415: Eukaryota_PTN000480538 contributes to function DNA-directed RNA polymerase activity (GO:0003899) 20140415: Eukaryota_PTN000480538 has function translation initiation factor binding (GO:0031369) 20140415: Eukaryota_PTN000480538 contributes to function single-stranded DNA binding (GO:0003697) 20140415: Magnoliophyta_PTN001467212 has LOST/MODIFIED function translation initiation factor binding (GO:0031369) # cellular_component 20140415: Eukaryota_PTN000480538 is found in DNA-directed RNA polymerase II, core complex (GO:0005665) 20140415: Eukaryota_PTN000480538 is found in cytoplasmic mRNA processing body (GO:0000932) 20140415: Magnoliophyta_PTN001467212 is NOT found in DNA-directed RNA polymerase II, core complex (GO:0005665) 20140415: Magnoliophyta_PTN001467212 is NOT found in cytoplasmic mRNA processing body (GO:0000932) # biological_process 20140415: Eukaryota_PTN000480538 participates in transcription initiation from RNA polymerase II promoter (GO:0006367) 20140415: Eukaryota_PTN000480538 participates in positive regulation of translational initiation (GO:0045948) 20140415: Eukaryota_PTN000480538 participates in nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288) 20140415: Eukaryota_PTN000480538 participates in mRNA export from nucleus in response to heat stress (GO:0031990) 20140415: Eukaryota_PTN000480538 participates in recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex (GO:0034402) 20140415: Magnoliophyta_PTN001467212 does NOT participate in transcription initiation from RNA polymerase II promoter (GO:0006367) 20140415: Magnoliophyta_PTN001467212 does NOT participate in positive regulation of translational initiation (GO:0045948) 20140415: Magnoliophyta_PTN001467212 does NOT participate in nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288) 20140415: Magnoliophyta_PTN001467212 does NOT participate in mRNA export from nucleus in response to heat stress (GO:0031990) 20140415: Magnoliophyta_PTN001467212 does NOT participate in recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex (GO:0034402) # PRUNED 26 Mar 2016: Embryophyta_PTN001083844 has been pruned from tree # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES 16 Mar 2016: Embryophyta_PTN001083844 has been pruned from tree Background & Phylogeny This family comprises the conserved Rpb4 subunit of eukaryotic multisubunit DNA-dependent RNA polymerase II, which is part of the conserved 4/7 subcomplex. It is considered homologous to the RNAP I subunit Rpa14 (A14), the RNAP III subunit Rpc17 (C17), and the Archaeal F subunit, though these homologous/equivalent sequences are not present within this family. It is similar to the Spt4/5 transcription factors that are conserved across both Archaea and Eukarya (PMID:20473037). The Rpb4 and Rpb7 subunits form the Rpb4/7 subcomplex that can diss\ ociate from the rest of the 10 subunit RNA polymerase II enzyme. In addition to its role in transcription itself, the 4/7 subcomplex is also involved in mRNA export and decay, regulation of translation, as well as transcription-coupled DNA repair (PMID:22917057). Comments and issues with the tree --------------------------------- 1. Sequences not present within this tree, though they might have been expected to be here Despite the fact that the RNAP I subunit Rpa14 (A14), the RNAP III subunit Rpc17 (C17), and the Archaeal F subunit are generally considered homologous to Rpb4 (PMID:18573085), sequences for these homolous sequences are not found within this tree. However, as part of the Rpb4/7, F/E subcomplex, which as acquired numerous additional functions, it might not be completely surprising to see more divergence in this family. As of April 2014, here are some comments about the Rpc17, Rpa14, and Archaeal subunit F sequences. - Rpc17 sequences are found in a separate tree (PTHR15561). - For Rpa14 (using Rpa14 as a search keyword), I can find the S.cerevisiae and S.pombe sequences in Panther, but not any other sequences or a family. I also haven't been able to identify an appropriate human Rpa14 sequence in UniProt via keyword searches or via BLAST using the S.cerevisiae sequence. - For the Archaea (using RpoF as a search keyword), in Panther, I can find a single Archaeal RpoF sequence: Q7LXK4 (Q7LXK4_SULSO). Using this as a BLAST query in UniProt finds a number of other Archaeal sequences, some of which are labelled as RpoF, and which share good similarity with each other and also some similarity with the S.cerevisiae Rpb4 sequence. Here is a selection of Archaeal sequences that come up in the results using Q7LXK4_SULSO as a BLAST query at UniProt: -- C3NHD8_SULIN -- Q4JB12_SULAC -- F9VMZ3_SULTO -- F4B8A3_ACIHW -- A4YCT7_METS5 -- F4G1T9_METCR -- H2C6N1_9CREN -- Q9YEM9_AERPE -- A2BNB2_HYPBU -- U3TCX7_9CREN 2. Pruned node Embryophyta_PTN001083844 I have pruned this node (which contains two Oryza sativa, two A. thaliana, and one Physcomitrella patens sequence) because they look significantly divergent from the rest of the sequences in the MSA. These five sequences are all significantly longer than any of the other sequences in this tree, and visually they look like they lack a large number of key conserved residues compared to all other sequences. In addition, both of the sequences I would expect to see in A. thaliana (NRPB4 found in RNAP II and NRPD4 found in RNAPs IV and V) are found in the other node Embryophyta_PTN001083846, which is the sibling node of the pruned node under the duplication node root_PTN000480594. Annotation Comments --------------------------------- I blocked propagation of the MF term "translation initiation factor binding" and all of the BP annotations since they were all characterized for Rpb4 in the context of RNAP II and this node contains the A. thaliana gene NRPD4, which is characterized as being a subunit of both RNAP IV and RNAP V, which are involved in transcription of small RNAs, but not in mRNA transcription. # 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).