search

geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
Creative Commons Attribution 4.0 International
223 stars 40 forks source link

translation factors, various #29089

Open ValWood opened 1 month ago

ValWood commented 1 month ago

I'm trying to build a GO-CAM of mitochondrial translation , and I see many issues with translation factors.

Screenshot 2024-10-23 at 14 18 34

  1. translation initiation factor is under "translation initiation" but is also under regulation fo translation". This seems incorrect, the initiation factors are part_of translation?

  2. We don't have a way to describe the individual activities of "translation initiation factors" These include:

Inhibit the recruitment of the ribosome large subunit to the small subunit (via mtIF3) (until the initiation complex is properly assembled) Recruit the small ribosomal subunit to the initiator tRNA (Formation of the Pre-Initiation Complex (PIC)) involving mtIF2 and fMet-tRNAi). Recruit small ribosomal subunit to the mRNA (no need for cap recognition or extensive mRNA recruitment). Recruit initiator tRNA to the small ribosomal subunit (via mtIF2). Start codon recognition (via mtIF2 and GTP hydrolysis). Recruit the large subunit to form the complete initiation complex.

(for all initiation and a few extra activities for eukaryotic)

  1. The description of "translation iniitation" factor is vague Defined Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide.

but there are factors that act upstream of these iniitation steps in 'pre-initiation' (PPR proteins that act generally to recruit mRNAs, and to recruit TIFs to the ribosome are not themselves considered to be TIFs but fit this definition).

ValWood commented 1 month ago
  1. mRNA regulatory element binding translation repressor activity should be is_a  translation factor activity, RNA binding
ValWood commented 1 month ago
  1. translation initiation factor activity is_a translation factor activity RNA binding but this is not always true
ValWood commented 1 month ago
  1. translation activator activity is a subclass of “translation regulator activity, nucleic acid binding but some translation factors don’t bind mRNA directly
ValWood commented 1 month ago
  1. the positioning of inititation, elongation and termination factors under GO:0008135 translation factor activity, RNA binding is problematic because not all of these factors bind to RNA it seems, for example "mtEFG1: This factor is involved in the translocation of the ribosome along the mRNA after peptide bond formation, similar to EF-G in prokaryotic translation. It interacts with the ribosome but does not bind mRNA directly" mtRRF (Mitochondrial Ribosome Recycling Factor): This factor helps disassemble the ribosomal complex after translation. While it is crucial for terminating translation, it does not bind mRNA directly. there appear to be a number of translation factors that don't bind to RNA (also this doesn't seem to be an ideal way to classify these activities)
ValWood commented 3 weeks ago

Step 1, obsolete the terms with "nucleic acid binding" Step 2 separate "translation factors from translation regulators GO:0008135
translation factor activity, RNA binding Step 3 make the RNA binding terms children of the more general terms