# HISTORY 27 Mar 2016: Updated by: TOUCHUP-v1.15 17 Mar 2016: Updated by: TOUCHUP-v1.14 # molecular_function 20150323: cellular organisms_PTN001149535 has function RNA binding (GO:0003723) # cellular_component 20150323: cellular organisms_PTN001149535 is found in small-subunit processome (GO:0032040) 20150323: cellular organisms_PTN001149535 is found in nucleolus (GO:0005730) 20150323: Euryarchaeota_PTN001149606 is NOT found in small-subunit processome (GO:0032040) 20150323: Euryarchaeota_PTN001149606 is NOT found in nucleolus (GO:0005730) # biological_process # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES This family comprises the RRP5 subunits of the ribosomal Small Subunit Processome, also called the SSU Processome, a large complex which is involved in the initial cleavages of the primary rRNA transcript to separate the small ribosomal subunit (SSU) rRNA from the remainder of the transcript and the biogenesis of the small ribosomal subunit. RRP5 also appears to be involved in maturation of the 5.8S rRNA, which is part of the large ribosomal subunit (LSU; PMID:8896463) The SSU processome was originally identified and characterized from S. cerevisiae (Dragon et al. 2002, PMID:12068309; Gallagher et al. 2004, PMID:15489292; Bernstein et al. 2004, PMID:15590835; and reviewed in Phipps et al. 2011, PMID:21318072). As of September 2014, it has begun to be characterized experimentally from other species such as human (Turner et al. 2012, PMID:22418842; Sato et al. 2013, PMID:24219289; and Hu et al. 2011, PMID:21078665), zebrafish (Wilkins et al. 2013, PMID:24147052), and mouse (Gallenberger et al. 2011, PMID:21051332). The RRP5 subunit is a confirmed subunit of the SSU processome, but is not classified as being part of a specific subcomplex (Phipps et al. 2011, PMID:21318072). Feng et al. 2013 (PMID:24214024) performed an extensive computational analysis from 77 completely sequenced eukaryotic genomes, including representatives of the five eukaryotic supergroups: Opisthokonts, Amoebozoa, Plantae, Excavates, and Chromalveolates, and compared these to sequences from both prokaryotic and Archaeal species for all 51 confirmed and 26 likely SSU processome subunits in S. cerevisiae as indicated in Phipps et al. 2011 (PMID:21318072). In addition, Srivastava et al. have identified SSU processome subunits in the parasitic protist Entamoeba histolytica (PMID:24631428). RRP5 is one of the 51 confirmed proteins of the S. cerevisiae SSU processome (Phipps et al. 2011, PMID:21318072)) and is highly conserved across the 77 eukaryotic species, as listed in Table 1 of Feng et al. 2013 (PMID:24214024). It is also found in the parasitic protist Entamoeba histolytica (Srivastava et al. 2014, PMID:24631428). RRP5 also appears to be involved in maturation of the 5.8S rRNA, which is part of the large ribosomal subunit (LSU; PMID:8896463) Annotation comments: ------------------- There were experimental MF annotations for human PDCD11 to "poly(A) RNA binding" (GO:0044822) from two high throughput studies: PMID:22681889 and PMID:22658674. Between the fact that these were high throughput experiments, the fact that this protein is normally part of a large complex, and the fact that it is not clear that poly(A) RNA binding is biologically relevant, I have chosen not to propagate this MF annotation. All of the papers for two of the Arabidopsis sequences (AT3g23700 and At1g12800) look like large scale proteomics studies (from brief glances at the abstracts). For AT3g23700/MYM9_3, there both chloroplast and nuclear annotations, while for At1g12800, there is only a single chloroplast annotation. However, I am reluctant to propagate these annotations within these plant specific duplication nodes or to block propagation of the SSU processome and rRNA processing related annotations based solely on large scale annotations. large scale papers for Arabipobsis: Q9LK47 - Q9LK47_ARATH = AT3g23700/MYM9_3 - chloroplast (PMID:18431481, PMID:15028209); - chloroplast stroma (PMID:20061580, PMID:18633119) - nucleus (PMID:14617066) Q94AJ9 - Q94AJ9_ARATH = Nucleic acid-binding, OB-fold-like protein = At1g12800 - chloroplast (PMID:18431481) There are also large scale papers for the A. thaliana RRP5 gene, one of which is consistent with SSU processome, while the other is not. I have also not propagated the "plasma membrane" annotation. ARATH_RRP5 - nucleolus (PMID:15496452) - plasma membrane (PMID:14506206) # 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).