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Obsolete GO:0044076 'positive regulation by symbiont of host vacuole organization' #26251

Closed pgaudet closed 11 months ago

pgaudet commented 1 year ago

No annotations, no mappings, not describing any known process that occurs between host and symbiont.

Also, change label of parent 'modulation by symbiont of host vacuole organization' to symbiont-mediated perturbation of host vacuole organization

@genegodbold

pgaudet commented 1 year ago

@genegodbold We dont have any references on that term, if you have suggestions that'd be appreciated.

genegodbold commented 1 year ago

Hey @pgaudet, see if you think these work for this; some may be a little off-target:

  1. Anaplasma phagocytophilum post-translationally modified protein A (AmpA; APH_1387) is a secreted effector that is poly-SUMOylated in the host cell and localizes to the membrane of the A. phagocytophilum-occupied vacuolar membrane (AVM) and in the cytosol of host cells. Inhibition of SUMOylation, decreases the number of bacteria in the host cell [PMID:25308709].
  2. Anaplasma translocated substrate 1 (Ats-1; APH_0859): Ats-1 nucleates autophagosomes and is involved in the creation and/or maintenance of Anaplasma inclusions. Ats-1 enhances bacterial replication and may contribute to the acquisition of nutrients from the host cell through its subversion of autophagy [PMID:23197835]. Ats-1 induces the formation of autophagosome-like vesicles containing multiple host autophagy proteins by binding host BECN1, a core component in the PtdIns3K complex that initiates host cell autophagy. The intracellular bacteria appear to use these autophagic inclusions to proliferate [PMID:23388398].
  3. IncB from Chlamydia psittaci interacts with host cytoplasmic protein snapin which is involved in intracellular trafficking. IncB, snapin, and host dynein co-localize near the inclusion body of C. psittaci-infected Hep-2 cells. Snapin may connect chlamydial inclusions with the microtubule network via IncB and dynein [PMID:24751478].
  4. ChlaDUB1 and the related ChlaDUB2 from Chlamydia trachomatis are chlamydial effectors that can perform both lysine deubiquitination and lysine acetyltransferase reactions using the same conserved Cys residue and a unique inserted helix (VR3). The His203Tyr mutation inactivates both enzymatic activities. The deubiquitinase activity of these effectors is responsible for the redistribution of the Golgi around the inclusion body in host cells infected with bacteria. The effector localizes to the Golgi during infection [PMID:30397340].
  5. Chlamydia promoter of survival (CpoS; CT_229) from C. trachomatis: CpoS is a chlamydial T3SS effector that recruits host Rab small GTPases and Rab effectors to the periphery of the inclusion body in infected cells. In doing so it redirects and intercepts host clathrin-coated vesicles from the recycling pathway to the periphery of the inclusion [PMID:30893609].
  6. CT_813 from C. trachomatis associates with the endoplasmic reticulum and interacts prominently with host SNARE protein VAMP7 that governs fusion between late endosomes and other compartments. CT_813 contains a SNARE motif (residues 191-264) [PMID:18369472]. InaC recruits Arf1 and Arf4 to the inclusion membrane where they induce posttranslationally modified microtubules. Both isoforms of Arf are necessary for the repositioning of host Golgi complex fragments around the inclusion. Chlamydia are obligate intracellular pathogens that stimulates actin polymerization at the plasma membrane to induce its own uptake into a membrane-bound inclusion. The developing inclusion moves along host microtubules to the microtubule-organizing center (MTOC), where it resides for the duration of the Chlamydia life cycle. At the MTOC, Chlamydia establishes extensive interactions with the host Golgi complex. C. trachomatis fragments the Golgi complex into ministacks, which are then repositioned around the inclusion [PMID:28465429].
  7. TepP (CT_875) from C. trachomatis is one of the most abundant T3SS effectors secreted by Chlamydia [PMID:22014092]. TepP requires Slc1 as a chaperone and is phosphorylated by host cell kinases at multiple Ser and Tyr residues. Two tyrosine phosphorylation sites generate consensus pYxxP motifs that provide a docking site for host proteins with SH2 domains, including two spliced forms of the host signaling adaptor protein Crk (CrkI and CrkII) which are recruited to pathogen-containing inclusions within the infected host cell [PMID:24586162]. TepP recruits both host class I phosphoinositide 3-kinases (PI3K) and the host adaptor protein CrkL to pathogen-containing inclusions within host cells. TepP also activates PI3K on internal membranes and nascent inclusion membranes to generate phosphoinositide-(3,4,5)-triphosphate (PIP3) on those membranes [PMID:28744480].
  8. Cbu0513 from Coxiella burnetii is a T4SS Dot/Icm effector that appears to be involved in biogenesis of the Coxiella containing vacuole that localizes to the host cell cytosol. Loss of function results in a bacterial mutant with a small-vacuole phenotype. The defect in CCV biogenesis arrests vacuole maturation prior to fusion with autophagosomes [PMID:29339460].
  9. Cig57 (Cbu1751) from Coxiella burnetii is important for development of the Coxiella containing vacuole [PMID:25080348]. Cig57 binds, via its endocytic sorting motif, to host FCHO2 protein via , to interfere with clathrin-dependent vesciular transport. Clathrin is found around CCV and clathrin recruitment to the CCV is attenuated in the absence of FCHO2 [PMID:28002452].
  10. Coxiella vacuolar protein E (CvpE) from Coxiella burnetii is a T4SS effector protein that localizes to the Coxiella-containing vacuole and appears to be involved in its formation [PMID:25422265].
  11. Ehrlichia translocated factor-2 (Etf-2; Ech0261) from Ehrlichia chaffeensis is a T4SS effector that localizes to ehrlichial inclusions and sequesters the host Rab5 small GTPase in its GTP-bound form. Etf-2 delays Rab5 dissociation from (and Rab7 localization to) phagosomes from endosomes. Binding of Etf-2 to Rab5-GTP delays Rab5 inactivation and avoids routing of ehrlichial inclusions to host phagosomes. Etf-2 delays the maturation of phagosomes to phagolysosomes [PMID:30181274].
pgaudet commented 11 months ago

Hi @genegodbold I think the 3 papers about Coxiella burnetii (# 8, 9 and 10) rather talk about entry into host cell by a symbiont-containing vacuole than GO:0044075 symbiont-mediated perturbation of host vacuole organization ?

Anyways, I am closing this ticket, no more GO work or GO-PathGO mapping to do for this term.