Notes for DANRE crppa

• Core function is CDP-ribitol production for dystroglycan-linked O-mannosyl glycosylation [file:DANRE/crppa/crppa-uniprot.txt "Catalyzes the formation of CDP-ribitol"].
• The old isoprenoid-biosynthetic-process annotation is removed because the MEP pathway context is absent in vertebrates PMID:22522421.
• Brain and muscle development annotations are retained as non-core phenotypic consequences of defective alpha-dystroglycan glycosylation.

Re-review 2026-09-28

Full re-review of all 20 GOA rows against the cached primary literature; the earlier
templated summaries ("consistent with the synthesized gene function") were replaced with
row-specific arguments.

• Added two primary references that define the enzyme: Gerin et al. 2016 (PMID:27194101,
  full text) showing recombinant mammalian ISPD is a CDP-ribitol pyrophosphorylase with no
  activity on the MEP substrate PMID:27194101 and that FKTN/FKRP use the
  product PMID:27194101; and
  Riemersma et al. 2015 (PMID:26687144, abstract only) for cytosolic localization and the
  cytidyltransferase domain of human ISPD PMID:26687144. A first attempt to cache the Riemersma paper hit a wrong PMID (26055709 is a
  PDE12 paper); the correct id was found by PubMed search and only 26687144 is cited.
• Three PENDING rows resolved: GO:0009101 glycoprotein biosynthetic process (IEA, ARBA)
  -> MODIFY to GO:0035269, the specific descendant already carried by IBA/IMP; the second
  GO:0010559 IGI row (ispd MO1 x fkrp MO) -> MODIFY to GO:0035269, matching the fktn IGI
  and IMP rows; the second GO:0055001 IMP row (ispd MO2) -> KEEP_AS_NON_CORE, matching
  the MO1 row PMID:22522421.
• The three GO:0010559 "regulation of glycoprotein biosynthetic process" rows stay MODIFY
  -> GO:0035269: the definition of GO:0010559 is a process that modulates the rate of
  glycoprotein biosynthesis, whereas crppa is a pathway enzyme that performs a step
  (donor synthesis), so the evidence supports participation, not regulation
  PMID:22522421.
• GO:0008299 isoprenoid biosynthetic process (IEA, InterPro) stays REMOVE, now with the
  direct enzymatic exclusion from Gerin 2016 in addition to the absence of the MEP pathway
  in vertebrates PMID:22522421.
• Brain morphogenesis and muscle cell development IMP rows stay KEEP_AS_NON_CORE: the
  phenotypes are penetrant and specific but downstream of alpha-dystroglycan
  hypoglycosylation PMID:22522421.
• Cytosol rows (IBA/IEA/ISS) are now supported by the human localization experiment rather
  than the FUNCTION line. Protein homodimerization (ISS) remains KEEP_AS_NON_CORE with only
  the by-similarity SUBUNIT line as support.
• Description rewritten as standalone biology; reference_review added to every PMID;
  core_functions re-supported with primary quotes; two suggested questions and
  experiments added (direct assay of zebrafish Crppa; ribitol rescue in a mutant line).
• Validation: zero errors.