From 7bb5e392625ebca6d690046dbe7291ee2f447ce2 Mon Sep 17 00:00:00 2001 From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com> Date: Tue, 21 Jul 2026 19:10:48 -0700 Subject: [PATCH] Pelotomaculum-Methanocella propionate syntrophy: curate causal graph MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Add directed `downstream` causal edges to the four existing ecological_interactions of CommunityMech:000190, from the Edison causal-graph run (PaperQA3; PMID:30038609 / DOI:10.3389/fmicb.2018.01551). Wiring (all grounded in the cited abstract; InteractionDownstream carries target + causal description, evidence stays on the parent nodes): - Propionate Oxidation Coupled to Methanogenesis → Catabolism and Methanogenesis Upregulation (syntrophic coculture drives the concerted catabolic/methanogenesis transcriptional shift). - Catabolism and Methanogenesis Upregulation → Formate and Electron Bifurcation Strategy, and → Signal Transduction and Amino Acid Exchange (the upregulation activates FDH/electron-bifurcation transfer and the flagellar-signaling / amino-acid-exchange mechanisms). - Formate and Electron Bifurcation Strategy → Propionate Oxidation Coupled to Methanogenesis, twice: a positive edge (formate/H2 transfer sustains methanogenesis, thermodynamically pulling propionate oxidation; 2-BES abolishes both) and a NEGATIVE product-inhibition edge (excess formate halts syntrophic activity). Forms the syntrophic feedback loop 1->2->3->1 with a negative regulatory edge. Regenerate the record's HTML page (single file). Schema validates; no new evidence snippets or terms introduced. Co-Authored-By: Claude Opus 4.8 (1M context) --- ...hanocella_Propionate_RNASeq_Coculture.html | 36 +++++++++++++++++++ ...hanocella_Propionate_RNASeq_Coculture.yaml | 31 ++++++++++++++++ 2 files changed, 67 insertions(+) diff --git a/docs/communities/Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.html b/docs/communities/Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.html index 02080172..f78d54ca 100644 --- a/docs/communities/Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.html +++ b/docs/communities/Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.html @@ -409,6 +409,7 @@

Pelotomaculum-Methanocella Propionate RNA-Seq Coculture

+ @@ -655,6 +656,15 @@

Propionate Oxidation Coupled to Methanogenesis

+
+ Downstream Effects: + +
+ → Catabolism and Methanogenesis Upregulation in Coculture +
+ +
+

Evidence

@@ -726,6 +736,19 @@

Catabolism and Methanogenesis Upregulation in Coculture

+
+ Downstream Effects: + +
+ → Formate and Electron Bifurcation Strategy +
+ +
+ → Signal Transduction and Amino Acid Exchange +
+ +
+

Evidence

@@ -799,6 +822,19 @@

Formate and Electron Bifurcation Strategy

+
+ Downstream Effects: + +
+ → Propionate Oxidation Coupled to Methanogenesis +
+ +
+ → Propionate Oxidation Coupled to Methanogenesis +
+ +
+

Evidence

diff --git a/kb/communities/Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.yaml b/kb/communities/Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.yaml index fec452fa..82c62081 100644 --- a/kb/communities/Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.yaml +++ b/kb/communities/Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.yaml @@ -149,6 +149,13 @@ ecological_interactions: term: id: GO:0015948 label: methanogenesis + downstream: + - target: Catabolism and Methanogenesis Upregulation in Coculture + description: > + Establishing the syntrophic coculture (versus monoculture) drives the + concerted transcriptional upregulation of catabolic genes — the + methylmalonyl-CoA pathway in P. thermopropionicum and methanogenesis + genes in M. conradii. evidence: - reference: PMID:30038609 supports: SUPPORT @@ -185,6 +192,17 @@ ecological_interactions: term: id: GO:0015948 label: methanogenesis + downstream: + - target: Formate and Electron Bifurcation Strategy + description: > + The catabolic upregulation includes formate dehydrogenase and flavin-based + electron bifurcation/confurcation genes in both partners, activating + formate as an alternate interspecies electron carrier alongside H2. + - target: Signal Transduction and Amino Acid Exchange + description: > + The same coculture transcriptional shift upregulates flagellum-induced + signal transduction and amino-acid exchange that accompany syntrophic + growth. evidence: - reference: PMID:30038609 supports: SUPPORT @@ -222,6 +240,19 @@ ecological_interactions: term: id: GO:0044419 label: biological process involved in interspecies interaction between organisms + downstream: + - target: Propionate Oxidation Coupled to Methanogenesis + description: > + Interspecies formate and H2 transfer to M. conradii sustains + hydrogenotrophic methanogenesis, keeping the shared electron-carrier + partial pressure low and thermodynamically pulling P. thermopropionicum + propionate oxidation; inhibiting methanogenesis with 2-BES abolished both + methane production and propionate oxidation. + - target: Propionate Oxidation Coupled to Methanogenesis + description: > + NEGATIVE (product inhibition) — accumulation of excess formate inhibits + syntrophic activity and halts propionate oxidation, so formate transfer + must stay balanced by continuous methanogenic consumption. evidence: - reference: PMID:30038609 supports: SUPPORT