Fix branch 'modulation of complement activation in another organism'

[pgaudet]

These terms have no annotations:

'modulation of complement activation in another organism' & children:

• 'modulation of complement activation, alternative pathway in another organism'
• 'negative regulation of complement activation, alternative pathway in another organism'
• 'positive regulation of complement activation, alternative pathway in another organism'
• 'modulation of complement activation, classical pathway in another organism'
• 'negative regulation of complement activation, classical pathway in another organism'
• 'positive regulation of complement activation, classical pathway in another organism'
• 'modulation of complement activation, lectin pathway in another organism'
• 'negative regulation of complement activation, lectin pathway in another organism'
• 'positive regulation of complement activation, lectin pathway in another organism'

Need to check

• [ ] if we need to describe the 3 pathways
• [ ] obsolete all positive regulation of complement activation
• [ ] see how GO:0039573 suppression by virus of host complement activation fit in

Action for @genegodbold

• describe the terms needed to define the mechanisms by which complement is suppressed or evaded

[genegodbold]

Unknown mechanism:

• Burkholderia pseudomallei autotransporter C (BpaC): A B. pseudomallei mutant in which the gene encoding BpaC is deleted suffers a 64-fold increase in the median lethal dose (LD50) in a BALB/c mouse model of intraperitoneal infection compared to the isogenic parent strain. The bacterial mutant was attenuated in intracellular replication and was more sensitive to host complement-mediated killing through the classical and/or lectin pathway. Complementation via plasmid-expressed BpaC restored wild-type serum resistance. BpaC also increases survival in macrophages [PMID:25830295].
• Phospholipase D from Acinetobacter baumannii: A mutant A. baumannii in which the gene for PLD is deleted has a decreased ability to survive and proliferate in serum [PMID:20194595].
• Brucella trimeric autotransporter F (BtaF) from Brucella suis: BtaF contributes to serum resistance. Brucella suis mutants in which the gene for BtaF was deleted exhibited a 50% reduction in survival relative to wild-type bacteria in a porcine serum survival assay. Survival was restored by complementation with BtaF [PMID:24236157].
• Outer surface protein B (OspB) from Borrelia burgdorferi: OspB is an abundant lipoprotein on the bacterial surface that significantly reduces the amount of complement component C3bi deposited on the bacterium when exposed to serum [PMID:18068388].

Uses host complement control proteins as a shield to inhibit destruction by host complement

• Bacillus collagen-like protein of anthracis (BclA): BclA, a component of spores of Bacillus anthracis, mediates the attachment of host complement factor H, a complement control protein, to the bacterial spore. This produces a down-regulation of host complement both in vitro and in a mouse model of infection. BclA is the most abundant protein in the exosporium, the outermost layer of B. anthracis spores. BclA improves persistence in mouse lungs and appears to downregulate antibody responses to spores. Both these effects are dependent on its activity against complement through factor H binding [PMID:27304426].
• BhCRASP-1 (CspH) of Borrelia hermsii binds host complement regulators factor H and factor H-related protein 1 (FHR-1) but not factor H-like protein 1 (FHL-1). BhCRASP-1 interacts with the short consensus repeat 20 of the mammalian factor H. Ectopic expression of the protein in a serum-sensitive strain of B burgdorferi rendered it more resistant to human serum. BhCRASP-1 also binds host plasminogen/plasmin [PMID:17513779].
• Complement regulator-acquiring surface protein-1 (CRASP-1; CspA) from Borrelia burgdorferi: CRASP-1 is a lipoprotein that binds human complement factor H and human complement factor H-like protein 1 [PMID:14607842]. CRASP-1 binds to the short consensus repeats 5-7 and 20 of complement factor H [PMID:16925556]. It is essential for bacterial serum-resistance in vitro and for evading deposition of host complement proteins on the bacterial surface. Host factor H subsequently binds C3b of complement, acting as a cofactor for complement factor I which proteolytically destroys it, preventing it from forming a membrane attack complex and thereby destroying the bacterium. CRASP-1 forms a homodimer with the C terminus important for dimerization. It has a coiled coil domain which, when disrupted, prevents binding to complement regulatory factors [PMID:22540535].
• Neisseria surface protein A (NspA): Neisseria meningitidis recruits host human complement inhibitors to its surface to down-regulate complement activation and enhance survival in blood. Deletion of the gene encoding NspA from N. meningitidis renders it more susceptible to destruction by human serum [PMID:25644002]. NspA and fHbp of N. meningitidis both bind human factor H, thereby limiting deposition of human complement component C3 and resisting complement-mediated destruction of the bacteria [PMID:24129254].

[genegodbold]

Inhibits complement activation by direct association with complement proteins:

• Bordetella serum-resistance killing protein (BrkA): BrkA from Bordetella pertussis provides serum resistance by inhibiting the host classical pathway of complement activation. It prevents deposition of host C3 and accumulation of deposited C4 while not affecting C1 deposition [PMID:11292725]. A B. pertussis mutant strain in which the gene encoding BrkA is deleted exhibits a severe defect in colonization of the respiratory tract that manifests after three days following inoculation in a mouse model of infection. BrkA resists both antibody-dependent and -independent killing by complement. However, C3-deficient mice are still more effectively colonized by wild type bacteria when compared to mutants in which BrkA is deleted. Thus the colonization defect does not appear to be related to the ability of BrkA to provide serum resistance [PMID:15385494].
• Complement inhibitor via C4 binding protein (CihC) from Borrelia recurrentis: CihC is expressed on the outer surface of the bacterium in a patch-like manner. Expression of CihC significantly increases the serum resistance of the bacteria. CihC binds to both the C4 binding protein and the C1 inhibitor protein--the activity of both is retained upon binding. The central domain extends from residues 145 to 185 and mediates these interactions [PMID:20532227].
• BBK32 of Borrelia burgdorferi inhibits host complement activation by blocking activation of the C1 complement complex. The C terminal globular domain of BBK32 binds with high affinity to C1 and C1r. This may be the first report of a biomolecule that specifically and noncovalently inhibits C1/C1r [PMID:26808924].
• Vag8 from Bordetella bronchiseptica: Bordetella pertussis autotransporter Vag8 is a serine protease that binds human host C1 esterase inhibitor and confers serum resistance. Vag8 was disrupted in two different B. pertussis strains, BP338 and 18-323, and the mutants were tested for their ability to bind C1inh in a surface-binding assay. Neither mutant strain was capable of binding C1inh, whereas a complemented strain successfully bound C1inh [PMID:21695123]. Vag8 binding to human C1inh inhibits C1inh binding to C1s, C1r and MASP-2 resulting in the release of active proteinases that subsequently cut C2 and C4 away from the surface of the bacterium. This depletion of complement components result in decreased complement deposition on the bacteria and also less complement-mediated bacterial killing [PMID:28742139].
• Collagen binding protein (Cna) from Staphylococcus aureus: Cna binds to host complement protein C1q (UniProtP02745) and inhibits activation of the classical pathway of complement fixation on the bacterial surface [PMID:23720782].
• Extracellular complement-binding protein (Ecb, Efb-homologous protein, Ehb) from Staphylococcus aureus: Ecb blocks host complement convertase activity but not by accelerating their decay like host factor H. Rather, Ecb prevents the cutting of C3 and C5 by host convertases of the alternate pathway of complement activation. Ecb binds to the C3d domain of host C3 and blocks C3 convertases of the alternative pathway and C5 convertases of all complement pathways. Inhibition of C5 convertases blocks generation of the chemoattractant C5a and subsequent migration of neutrophils. Ecb is the most effective inhibitor of C5a generation [PMID:20304920]. In a mouse model of infection, a mutant S. aureus bacterium lacking both Ecb and Efb was attenuated relative to the WT bacteria. Wild type S. aureus killed 79% of the mice upon intravenous injection while the isogenic double deletion mutant only killed 29% of the mice. Ecb and Efb together block recruitment of neutrophils during S. aureus pneumonia. Ecb and Efb together are required for S. aureus virulence after intravenous injection. Ecb and Efb together are required for bacterial persistence and abscess formation [PMID:22327617].
• Extracellular fibrinogen binding protein (Efb, Fib) from Staphylococcus aureus: Efb is a secreted protein that binds to the complement component C3b and fibrinogen. Efb inhibits complement activation and blocks opsonization (and subsequent phagocytosis) in a dose-dependent manner. Efb binds to the alpha-chain of C3 and inhibits both the classical and lectin pathways of complement activation. Efb blocks deposition of C3 on the bacterial surface [PMID:15243934]. Efb blocks the formation of the functional C3b opsonin by binding tightly to the thioester-containing domain of the native C3 and by altering its conformation such that it becomes incapable of being processed into C3b [PMID:17351618]. Together Sbi and Efb bind complement components C3 and C3b simultaneously with human plasminogen. The bound plasminogen is converted by secreted staphylokinase or by a host-specific urokinase to plasmin which in turn leads to degradation of both C3 and C3b. The bound plasmin also degrades C3a. Sbi and Efb comprise a platform for recruitment of plasminogen, C3 and C3b for efficient degradation of the complement components. Efb enhances the degradation of C3/C3b more than Sbi, probably because it has a higher binding affinity for C3d (Efb dissociation constant for C:Cd3 = 0.3 nanomolar while Sbi = 1.4 micromolar). Plasmin cleaves C3b at several sites and generates C3c and C3d [PMID:23071827].
• Extracellular serine protease (EspP, protease secreted by STEC, PssA) from Escherichia coli: EspP can also cleave complement factors C3/C3b and C5 with the effect of diminishing the host's ability to activate complement [PMID:20643852].
• Complement evasion factor (CEF; Spy0136) from Streptococcus pyogenes: Recombinant CEF, of 221 residues, used in a pull-down assay with human plasma associated with four host complement components: C1r, C1s, C3, and C5. Glycan chains appear to be important for binding as treatment with PNGase F abolished association with all but C1r. Recombinant CEF inhibited complement-mediated hemolysis of bacteria and inhibited deposition of the C3b opsonin and the membrane attack complex on the surface of Streptococcus pyogenes [PMID:35094646].

Inhibits complement activation indirectly

• Complement-inhibitor and Plg-binding protein of Acinetobacter baumannii (CipA) is a host plasminogen-binding protein. Plasminogen bound to the surface of A. baumannii by CipA, upon conversion to plasmin, degrades both host fibrinogen and host complement C3b and contributes to serum resistance. Besides its ability to bind plasminogen, CipA inhibits the alternative pathway of complement activation in vitro. Inactivation of CipA renders the bacterium sensitive to serum. CipA interacts with host plasminogen through its C terminal 18 residues [PMID:26681776].
• Cronobacter plasminogen activator (Cpa) from Cronobacter sakazakii: Cpa can activate plasminogen and is required for resistance to complement-mediated killing. A mutant C. sakazakii in which the gene encoding Cpa was deleted demonstrated decreased serum resistance as the concentration of serum increased [PMID:21245266].
• Plasminogen surface receptor (hPg/hPm-binding M-protein; plasminogen binding groupA streptococcal M-like protein; PAM; antiphagocytic M protein; fibronectin binding protein; MRP4 protein; Ig-binding protein) from Streptococcus: Fibrils of M protein form a dense, covalently attached coat on the streptococcal surface blocking the deposition of antibodies and complement [PMID:18323455].
• Endopeptidase O (PepO; Neprilysin) from Streptococcus suis: Host plasminogen bound to PepO can be converted to plasmin via proteolysis by host uPA and can then degrade host complement C3b and enabling the control of complement activation. A bacterial mutant lacking PepO has impaired adherence to plasminogen, invasion of rat brain microvessel endothelial cells, and is efficiently killed by human serum and blood [PMID:34305859].
• Elongation factor-Tu (EF-Tu; LIC12875) from Leptospira sp: Leptospiral elongation factor-Tu can be found on the bacterial surface where it binds plasminogen in a dose-dependent manner. The plasminogen is converted to plasmin which can cut host complement component C3b as well as fibrinogen. EF-Tu can also bind the host complement regulator factor H which can mediated C3b degradation by host Factor I. Thus EF-Tu can protect the bacterium from complement-mediated destruction [PMID:24312361].

Other

• Ubiquitous surface protein A1 (and A2) of Moraxella catarrhalis: Both UspA2 and UspA1 inhibit the generation of the anaphylatoxin C3a [PMID:21270401].

[pgaudet]

NTR

• 1. suppression of complement activation in another organism
• • (def) by inhibition of complement protein activity either by binding (sequestering) and inhibiting complement protein, or by cleaving it and inactivating it, or or by binding and inhibiting complement control protein
• • 2. inactivation of complement proteins (PMID:24312361; PMID:34305859)
• • (def) complement not yet assembled, such that the complement doesn't reach the microbe surface
• • 3. sequestration of complement away from the microbial surface ? (hPg/hPm-binding M-protein; PMID:18323455)
• • • microbial proteins hold the host complement away from the surface
• • 4. suppression of complement activation by complement control protein binding (PMID:27304426, PMID:17513779, PMID:22540535, PMID:24129254)
• • • (def) microbial protein binds a host complement control protein complement control protein (CCP) prevents complement activation, such that if a microbial surface protein bind to a CCP, the complement will fail to activate on the microbial surface (https://en.wikipedia.org/wiki/Complement_control_protein)

[pgaudet]

• GO:0141114 suppression of complement activation by another organism

+[Term] GO:0141115 suppression of complement activation by another organism by inactivation of complement proteins +namespace: biological_process +def: "A process in which another organism another organism disrupts or prematurely activates complement so that its microbial-destroying activities fail." [PMID:24312361, PMID:34305859] +is_a: GO:0141114 ! suppression of complement activation by another organism +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26389" xsd:anyURI +created_by: pg +creation_date: 2023-11-22T15:32:58Z + +[Term] GO:0141116 suppression of complement activation by another organism by complement sequestering +namespace: biological_process +def: "A process in which another organism prevents the activation of complement by sequestering it away from its surface." [PMID:18323455] +is_a: GO:0141114 ! suppression of complement activation by another organism +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26389" xsd:anysd:anyURI +created_by: pg +creation_date: 2023-11-22T15:34:16Z + +[Term] GO:0141117 suppression of complement activation by another organism by recuitement of complement control protein +namespace: biological_process ctivate." [PMID:17513779, PMID:22540535, PMID:24129254, PMID:27304426] +is_a: GO:0141114 ! suppression of complement activation by another organism sd:anyURI +created_by: pg +creation_date: 2023-11-22T15:35:52Z

[pgaudet]

Dear all,

The proposal has been made to obsolete

GO:0044645 modulation of complement activation in another organism GO:0044630 modulation of complement activation, lectin pathway in another organism GO:0044627 modulation of complement activation, classical pathway in another organism GO:0044633 modulation of complement activation, alternative pathway in another organism GO:0044632 negative regulation of complement activation, lectin pathway in another organism GO:0044631 positive regulation of complement activation, lectin pathway in another organism GO:0044629 negative regulation of complement activation, classical pathway in another organism GO:0044628 positive regulation of complement activation, classical pathway in another organism GO:0044634 negative regulation of complement activation, alternative pathway in another organism GO:0044635 positive regulation of complement activation, alternative pathway in another organism GO:0044646 envenomation resulting in modulation of complement activation in another organism GO:0044639 envenomation resulting in modulation of complement activation, lectin pathway in another organism GO:0044636 envenomation resulting in modulation of complement activation, classical pathway in another organism GO:0044642 envenomation resulting in modulation of complement activation, alternative pathway in another organism GO:0044640 envenomation resulting in negative regulation of complement activation, lectin pathway in another organism GO:0044641 envenomation resulting in positive regulation of complement activation, lectin pathway in another organism GO:0044637 envenomation resulting in negative regulation of complement activation, classical pathway in another organism GO:0044638 envenomation resulting in positive regulation of complement activation, classical pathway in another organism GO:0044644 envenomation resulting in negative regulation of complement activation, alternative pathway in another organism GO:0044643 envenomation resulting in positive regulation of complement activation, alternative pathway in another organism

The reason for obsoletion is that we are replacing these terms by GO:0141114 suppression of complement activation by another organism GO:0141116 suppression of complement activation by another organism by complement sequestering GO:0141115 suppression of complement activation by another organism by inactivation of complement proteins GO:0141117 suppression of complement activation by another organism by recruitment of complement control protein

There are no annotations to these terms; these terms are not present in any subsets.

You can comment on the ticket: https://github.com/geneontology/go-ontology/issues/26389

Thanks, Pascale

[pgaudet]

Changing back to 'symbiont-mediated' xx

[genegodbold]

Let's do this @pgaudet!!! 🥇🥇🥇