Functional Degeneracy in Paracoccus denitrificans Pd1222 Is Coordinated via RamB, Which Links Expression of the Glyoxylate Cycle to Activity of the Ethylmalonyl-CoA Pathway

• Published in: Applied and environmental microbiology Vol. 89; no. 7; p. e0023823
• Main Authors: Kremer, Katharina, Meier, Doreen, Theis, Lisa, Miller, Stephanie, Rost-Nasshan, Aerin, Naing, Yadanar T, Zarzycki, Jan, Paczia, Nicole, Serrania, Javier, Blumenkamp, Patrick, Goesmann, Alexander, Becker, Anke, Thanbichler, Martin, Hochberg, Georg K A, Carter, Michael S, Erb, Tobias J
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 26-07-2023
• Subjects: Catabolism; Environmental Microbiology; Glyoxylate cycle; Intermediates; Metabolic pathways; Metabolism; Oxidation; Paracoccus denitrificans; Plastic properties; Plasticity; Substrates; Tricarboxylic acid cycle; ethylmalonyl-CoA pathway; anaplerosis; proteobacteria; transcriptional regulation; glyoxylate cycle; Paracoccus denitrificans; carbon metabolism; metabolic regulation
• ISSN: 0099-2240; 1098-5336
• DOI: 10.1128/aem.00238-23

Metabolic degeneracy describes the phenomenon that cells can use one substrate through different metabolic routes, while metabolic plasticity, refers to the ability of an organism to dynamically rewire its metabolism in response to changing physiological needs. A prime example for both phenomena is the dynamic switch between two alternative and seemingly degenerate acetyl-CoA assimilation routes in the alphaproteobacterium Paracoccus denitrificans Pd1222: the ethylmalonyl-CoA pathway (EMCP) and the glyoxylate cycle (GC). The EMCP and the GC each tightly control the balance between catabolism and anabolism by shifting flux away from the oxidation of acetyl-CoA in the tricarboxylic acid (TCA) cycle toward biomass formation. However, the simultaneous presence of both the EMCP and GC in P. denitrificans Pd1222 raises the question of how this apparent functional degeneracy is globally coordinated during growth. Here, we show that RamB, a transcription factor of the ScfR family, controls expression of the GC in P. denitrificans Pd1222. Combining genetic, molecular biological and biochemical approaches, we identify the binding motif of RamB and demonstrate that CoA-thioester intermediates of the EMCP directly bind to the protein. Overall, our study shows that the EMCP and the GC are metabolically and genetically linked with each other, demonstrating a thus far undescribed bacterial strategy to achieve metabolic plasticity, in which one seemingly degenerate metabolic pathway directly drives expression of the other.
Carbon metabolism provides organisms with energy and building blocks for cellular functions and growth. The tight regulation between degradation and assimilation of carbon substrates is central for optimal growth. Understanding the underlying mechanisms of metabolic control in bacteria is of importance for applications in health (e.g., targeting of metabolic pathways with new antibiotics, development of resistances) and biotechnology (e.g., metabolic engineering, introduction of new-to-nature pathways). In this study, we use the alphaproteobacterium P. denitrificans as model organism to study functional degeneracy, a well-known phenomenon of bacteria to use the same carbon source through two different (competing) metabolic routes. We demonstrate that two seemingly degenerate central carbon metabolic pathways are metabolically and genetically linked with each other, which allows the organism to control the switch between them in a coordinated manner during growth. Our study elucidates the molecular basis of metabolic plasticity in central carbon metabolism, which improves our understanding of how bacterial metabolism is able to partition fluxes between anabolism and catabolism.