Pelotomaculum-Methanocella propionate syntrophy: curate causal graph

docs/communities/Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.html

@@ -409,6 +409,7 @@ <h1>Pelotomaculum-Methanocella Propionate RNA-Seq Coculture</h1>
                     </span>
                 </div>
 
+
             </div>
         </section>
 
@@ -655,6 +656,15 @@ <h3>Propionate Oxidation Coupled to Methanogenesis</h3>
 
 
 
+                <div class="interaction-flow">
+                    <strong>Downstream Effects:</strong>
+
+                    <div class="flow-item">
+                        <span class="flow-arrow">→</span> Catabolism and Methanogenesis Upregulation in Coculture
+                    </div>
+
+                </div>
+
 
 
                 <h4>Evidence</h4>
@@ -726,6 +736,19 @@ <h3>Catabolism and Methanogenesis Upregulation in Coculture</h3>
 
 
 
+                <div class="interaction-flow">
+                    <strong>Downstream Effects:</strong>
+
+                    <div class="flow-item">
+                        <span class="flow-arrow">→</span> Formate and Electron Bifurcation Strategy
+                    </div>
+
+                    <div class="flow-item">
+                        <span class="flow-arrow">→</span> Signal Transduction and Amino Acid Exchange
+                    </div>
+
+                </div>
+
 
 
                 <h4>Evidence</h4>
@@ -799,6 +822,19 @@ <h3>Formate and Electron Bifurcation Strategy</h3>
 
 
 
+                <div class="interaction-flow">
+                    <strong>Downstream Effects:</strong>
+
+                    <div class="flow-item">
+                        <span class="flow-arrow">→</span> Propionate Oxidation Coupled to Methanogenesis
+                    </div>
+
+                    <div class="flow-item">
+                        <span class="flow-arrow">→</span> Propionate Oxidation Coupled to Methanogenesis
+                    </div>
+
+                </div>
+
 
 
                 <h4>Evidence</h4>

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