# HISTORY 07 May 2016: Updated by: TOUCHUP-v1.18 25 Mar 2016: Updated by: TOUCHUP-v1.15 14 Mar 2016: Updated by: TOUCHUP-v1.14 07 May 2016: Updated by: TOUCHUP-v1.18 # molecular_function 20140729: root_PTN000216478 has function structural constituent of ribosome (GO:0003735) 20140729: root_PTN000216478 has function rRNA binding (GO:0019843) 20140930: Eukaryota_PTN000216482 has function snoRNA binding (GO:0030515) 20140729: Eukaryota_PTN000216482 has LOST/MODIFIED function structural constituent of ribosome (GO:0003735) 20140729: Eukaryota_PTN000216482 has LOST/MODIFIED function rRNA binding (GO:0019843) # cellular_component 20140729: root_PTN000216478 is found in small ribosomal subunit (GO:0015935) 20140930: Eukaryota_PTN000216482 is found in Mpp10 complex (GO:0034457) 20140930: Eukaryota_PTN000216482 is found in small-subunit processome (GO:0032040) 20140729: Eukaryota_PTN000216553 is found in cytosolic small ribosomal subunit (GO:0022627) 20140729: Fungi_PTN000931304 is found in mitochondrial small ribosomal subunit (GO:0005763) 20140729: Eukaryota_PTN000216482 is NOT found in small ribosomal subunit (GO:0015935) # biological_process 20140729: root_PTN000216478 participates in positive regulation of translational fidelity (GO:0045903) 20140729: Eukaryota_PTN000216482 participates in rRNA processing (GO:0006364) 20140729: Eukaryota_PTN000216482 does NOT participate in positive regulation of translational fidelity (GO:0045903) # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES This family is composed largely of ribosomal subunits, bacterial rpsD, mitochondrial ribosome NAM9, Archaeal rps4, eukaryotic Rps9. In addition, it contains the IMP3 subunit of the SSU processome, which appears to be derived from a duplication of the eukaryotic ribosomal subunit Rps9. Additional notes for the IMP3 clade: ======================= The IMP3 clade comprises the IMP3 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. 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 IMP3 subunit is a confirmed subunit of the SSU processome, and specifically part of the Mpp 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 Archae\ al 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). IMP3 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). Annotation comments: --------------------- It has been experimentally shown that Imp3 and Imp4 bind to the 5' domain and adjacent hinge region of the U3 snoRNA; however binding of these proteins to fragments of the pre-rRNA or to the 3' domain of the U3 snoRNA was not observed (PMID:15489263). Therefore, I have blocked propagation from the root of the "rRNA binding" annotation to the IMP3 clade. # 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).