Parasites

Bottom line: parasites have gene biology that free-living models lack:
host invasion, immune evasion and nutrient theft at the host interface.
This umbrella project collects GO reviews of such genes. Because parasite
species have very few reviewed UniProt entries, we anchored it on the one
Swiss-Prot entry in the genus Steinernema (the S. carpocapsae astacin
nas-8) and on five secreted or surface proteins of the filarial nematode
Brugia malayi (cpi-2, far-1, dpy-31, gp29, mf1). All six have completed
reviews covering 35 GOA rows (21 ACCEPT, 6 KEEP_AS_NON_CORE, 4
MARK_AS_OVER_ANNOTATED, 3 MODIFY, 1 REMOVE), although the gene list and
status below still call them PENDING. The most substantive correction is on
the CPI-2 cystatin, where an IDA aspartic-type endopeptidase inhibitor
activity row was changed to cysteine-type, because the inhibited enzyme
(asparaginyl endopeptidase, legumain) is a cysteine protease. No gene has
deep research or notes yet, and S. hermaphroditum has not been started.

Overview

This project is a broad umbrella for gene reviews of parasitic and
host-associated organisms — species whose biology is defined by a parasitic
(or otherwise intimate host-exploiting) lifestyle. It collects the gene biology
that is specific to parasitism: host invasion, host-immune evasion/modulation,
nutrient acquisition from the host, and the molecular machinery of the
parasite–host (and parasite–symbiont) interface.

It serves as a hub that ties together more focused parasite-related efforts
rather than duplicating them — see Related projects.

Scope

• Animal-parasitic and insect-parasitic nematodes, including
  entomopathogenic nematodes (EPNs) such as Steinernema, which kill insect
  hosts in mutualistic partnership with Xenorhabdus/Photorhabdus bacteria.
• Other metazoan and protozoan parasites as gene reviews accrue
  (helminths, apicomplexans, etc.).
• Host-modulating secreted proteins of parasites and blood-feeders —
  these are the subject of the existing
  PARASITE_IMMUNE_MODULATORS project, treated
  here as a sub-topic.

A note on boundaries: not every host-associated nematode is a parasite.
Necromenic associates (e.g. Pristionchus pacificus, which rides live beetles
but only feeds after they die) and free-living comparators (e.g.
Caenorhabditis briggsae) are not parasites and are tracked under
SATELLITE_MODEL_ORGANISMS. True insect-parasitic
nematodes that are also used as comparative models are cross-listed.

Species in scope

The EPNs most biologically aligned with Steinernema (Heterorhabditis
bacteriophora, HETBA) and Strongyloides ratti (STRRB) have 0 reviewed
entries, so B. malayi was chosen as the reviewed-rich nematode anchor.
Additional parasites (other filariae — Onchocerca volvulus ONCVO 43,
Ascaris suum ASCSU 67 — parasitic helminths, protozoan parasites) to be added
as reviews are scoped.

Genes for review

• [x] Steinernema carpocapsae STECR nas-8 (D2KBH9, zinc metalloproteinase
  / astacin, EC 3.4.24.21) — seeded into genes/STECR/nas-8/; annotations are
  PENDING review. Secreted protease relevant to host invasion; carries an EXP
  metalloendopeptidase-activity annotation from PMID:20670659 (Sc-AST
  characterization) plus IEA terms.
• [ ] Steinernema hermaphroditum (9BILA, NCBITaxon:289476) — seed gene(s)
  TBD; not yet fetched into the repo. No reviewed entries, so any seed is a
  TrEMBL accession. Candidate areas: infective-juvenile development, host-immune
  evasion, and the Xenorhabdus symbiosis interface.
• BRUMA (B. malayi) host-interaction / immune-evasion set — reviewed,
  protein-level (PE=1) filarial genes; seeded, annotations PENDING:
• [ ] cpi-2 (A0A0K0IP23) — cystatin; secreted immunomodulator (inhibits
  host cysteine proteases / modulates antigen presentation). Has experimental
  annotations.
• [ ] far-1 (Q93142) — fatty-acid & retinol-binding protein (Bm20), a
  classic secreted excretory–secretory immunomodulator. Has experimental
  annotations.
• [ ] dpy-31 (A8Q2D1) — zinc metalloproteinase / astacin (procollagen
  C-proteinase), cuticle biogenesis — parallels the Steinernema nas-8 astacin.
• [ ] gp29 (P67877) — cuticular glutathione peroxidase, major surface
  antigen (oxidative defense at the host interface).
• [ ] mf1 (P29030) — endochitinase (MF1 antigen), microfilarial
  sheath / vaccine candidate.

Status / next steps

• SCOPING. Parasite seeds present: S. carpocapsae nas-8 (EPN anchor) and
  a 5-gene B. malayi host-interaction set (reviewed-rich filarial anchor) — all
  PENDING review.
• Annotation availability (UniProt, 2026-06): across the whole genus
  Steinernema there is exactly 1 reviewed (Swiss-Prot) entry — D2KBH9
  (NAS8_STECR, S. carpocapsae astacin metalloprotease). S. hermaphroditum
  (9BILA) has 0 reviewed entries (~36,000 TrEMBL); S. carpocapsae
  (STECR) has 1 reviewed + ~35,200 TrEMBL.
• Next: complete the PENDING annotation review of S. carpocapsae nas-8
  (start from the EXP PMID:20670659 evidence), then expand to S. hermaphroditum
  TrEMBL genes paired with literature + bioinformatics rather than relying on
  existing GO annotation.
• Pull the PARASITE_IMMUNE_MODULATORS candidate
  list under this umbrella's "host-modulation" sub-topic.

Related projects

• PARASITE_IMMUNE_MODULATORS — parasite/
  blood-feeder secreted proteins that modulate host immunity (sub-topic).
• SATELLITE_MODEL_ORGANISMS — non-parasitic
  comparative nematodes (C. briggsae) and necromenic associates
  (P. pacificus); some insect-parasitic nematodes are cross-listed there.

Slides

• Slides (Marp source: PARASITES-slides.md) — AI generated