# HISTORY 26 Mar 2016: Updated by: TOUCHUP-v1.15 16 Mar 2016: Updated by: TOUCHUP-v1.14 # molecular_function # cellular_component 20150121: Eukaryota_PTN000424645 is found in small-subunit processome (GO:0032040) 20150121: Eukaryota_PTN000424645 is found in Mpp10 complex (GO:0034457) # biological_process 20150121: Eukaryota_PTN000424645 participates in maturation of SSU-rRNA (GO:0030490) # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES This family is comprised of the MPP10 (aka MPHOSPH10) family of proteins involved in rRNA processing, specifically as part of the Mpp10 subcomplex 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 MPP10 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 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). MPP10 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). Comments on the tree & sequences ---------------------------- This tree looks very straightforward. Most of seven duplication nodes look like sequence issues rather than true duplications: - From Macaca mulatta (Rhesus macaque), the sequence F6VJQ2_MACMU (named as MPHOSPH10) looks complete, while the other two (F7HL07_MACMU and F6WIT3_MACMU) look like partials. - From Ornithorhynchus anatinus (Duckbill platypus), both sequences (F7AAZ1_ORNAN and F7G278_ORNAN) look like partials. - From Strongylocentrotus purpuratus (purple sea urchin), the H3HF48_STRPU sequence looks nearly complete (possibly missing a small bit of N-terminus), while the other three sequences (H3HQ59_STRPU, H3I922_STRPU, and H3JQE5_STRPU) are partial. However, all are obsolete since March 2014. - From Entamoeba histolytica, both sequences (B1N5H2_ENTHI and C4LW64_ENTHI) look partial. - From Phytophthora infestans (strain T30-4) (Potato late blight fungus), both sequences (D0MWR0_PHYIT and D0MWQ9_PHYIT) look partial. - From Oryza sativa subsp. japonica (Rice), the Q2QY33_ORYSJ sequence looks complete, or nearly so, while Q0IUS6_ORYSJ looks partial. One sequence issue is less clear cut whether this is a sequence error, allelic variation, or an actual duplication: - From Candida albicans (strain SC5314 / ATCC MYA-2876) (Yeast), both sequences (Q59L48_CANAL and Q59L68_CANAL) look essentially complete with some small sequence differences between the two. Comments on annotations and propagations ----------------------------------- - I did not propagate MF annotations to the term "poly(A) RNA binding (GO:0044822)" for human MPHOSPH10 (UniProtKB:MPP10_HUMAN) from PMID:22658674 or PMID:22681889 because both are large scale papers and I doubt the biological relevance of this annotation. # 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).