| | Pathway ID | Pathway Name | Chemical Compounds | Proteins | Pathway Description |
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| PW431827 | Phosphatidylethanolamine (PE) biosynthesis | Reaction compounds not found | | Phosphatidylethanolamine (PE) biosynthesis is an essential metabolic pathway in bacteria that produces PE, a key phospholipid component of cellular membranes. The pathway involves the condensation of ethanolamine with CDP-diacylglycerol (CDP-DAG), catalyzed by the enzyme phosphatidylethanolamine synthase (PES). In some bacteria, an alternative biosynthetic route also exists, where PE is synthesized from phosphatidylserine (PS) by decarboxylation, a process catalyzed by phosphatidylserine decarboxylase (PSD). In the CDP-DAG pathway, the first step is the synthesis of CDP-DAG from diacylglycerol (DAG) and CDP, which then reacts with ethanolamine to form PE. This phospholipid plays a crucial role in maintaining membrane fluidity and integrity, enabling bacterial cells to adapt to environmental changes. PE is also involved in the formation of lipid rafts, membrane fusion, and the function of membrane-associated proteins. Given its central role in membrane architecture, PE biosynthesis is tightly regulated, and disruptions to this pathway can significantly impact bacterial survival and pathogenicity. Additionally, PE is a precursor for the synthesis of other phospholipids, such as phosphatidylcholine in some organisms. | | PW431858 | Phosphatidylcholine (PC) biosynthesis | Reaction compounds not found | | Phosphatidylcholine (PC) biosynthesis in bacteria is a key metabolic pathway that contributes to the formation of one of the major phospholipids in bacterial cell membranes. In many bacteria, PC is synthesized via two primary routes: the CDP-choline pathway and the methylation pathway. The CDP-choline pathway begins with the phosphorylation of choline to form phosphocholine, which then reacts with CDP-diacylglycerol (CDP-DAG) to form PC. This process is catalyzed by the enzyme phosphatidylcholine synthase. Alternatively, in some bacteria, PC can be synthesized from phosphatidylethanolamine (PE) by a methylation reaction, where three methyl groups are added to PE, ultimately forming PC. This methylation pathway is catalyzed by phosphatidylethanolamine N-methyltransferase (PmtA). Phosphatidylcholine is crucial for membrane integrity, providing stability and flexibility, and it also plays a role in regulating membrane protein function and lipid signaling. PC biosynthesis is especially important in bacteria that inhabit environments requiring robust membrane structure, such as those with fluctuating temperatures or osmotic stress. In some bacteria, PC also contributes to pathogenesis, aiding in host interaction and immune evasion. Thus, PC biosynthesis is an essential process for bacterial growth, survival, and adaptability. | | PW528286 | Quorum Sensing: Biosynthesis of Diffusible Signal Factors (DSFs) (RpfF/R operon Activation) | Reaction compounds not found | | The RpfF/R quorum sensing system is a sophisticated communication mechanism utilized by bacteria, such as Xanthomonas campestris and Lysobacter enzymogenes, to coordinate collective behaviors in response to changes in population density. At its core, the gene rpfF encodes an enzyme that synthesizes diffusible signal factors (DSFs) and their variants, such as BDSF, which are critical signaling molecules capable of diffusing through bacterial cell membranes.DSFs are fatty acid-based signaling molecules and include compounds like DSF (cis-11-methyl-2-dodecenoic acid) and BDSF (Burkholderia DSF, cis-2-dodecenoic acid). At low cell density, the extracellular concentration of DSF is below a certain threshold. In this state, the unphosphorylated histidine kinase, RpfC, actively participates in the negative regulation of DSF synthesis. This is achieved through a direct interaction with the DSF synthase RpfF, inhibiting the synthesis of DSF, which remains at a basal level. This regulatory mechanism does not involve the phosphorelay system and is independent of RpfG, allowing the bacteria to maintain a low signaling state. As the bacterial population grows, the concentration of DSFs increases, leading to their eventual accumulation in the extracellular environment. Upon reaching a critical concentration threshold, DSFs bind to the sensor domain of RpfC, triggering a crucial transition in the signaling pathway. At high cell density, the binding of DSF to RpfC activates autophosphorylation of the kinase, subsequently facilitating the transfer of the phosphate group to the response regulator RpfR. This transfer results in the phosphorylation of RpfR, which functions as a transcriptional regulator that orchestrates the expression of various downstream genes involved in multiple processes, such as virulence factor production, biofilm formation, and the biosynthesis of antimicrobial compounds, exemplified by the heat-stable antifungal factor (HSAF).Moreover, RpfC acts as a hybrid sensor kinase that integrates diverse biological functions through distinct molecular mechanisms. Its involvement in both the negative regulation of DSF production at low cell densities and the positive signaling pathway at high cell densities illustrates its versatility. In the positive feedback loop initiated by DSF binding, RpfC releases RpfF and activates RpfG through a four-step phosphorelay. The activation of RpfG subsequently leads to positive regulation of biofilm dispersal and enhances the production of virulence factors.Crucially, as the RpfR response regulator influences the transcription of genes related to virulence and biofilm characteristics, it can also feedback to modulate the biosynthesis of DSF itself. This feedback mechanism allows the bacterial community to finely tune its response to environmental conditions, ensuring optimal survival and competitiveness in fluctuating environments. Overall, the RpfF/R system exemplifies a complex and dynamic regulatory network whereby bacterial cells exploit quorum sensing to adaptively regulate gene expression and synchronize population-wide behaviors, such as enhanced virulence during host infection, modification of biofilm characteristics, and secretion of exopolysaccharides. The integration of these multifaceted regulatory pathways underscores the importance of the RpfF/R system in bacterial adaptability and ecological success |
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