Insights into the versatile metabolism of the Alphaproteobacterium Paracoccus denitrificans
Two distinct metabolic modes provide bacteria with energy (i.e., catabolism) and cellular building blocks (i.e., anabolism). At the interface between both lie the central metabolite acetyl-CoA, as well as the amphibolic tricarboxylic acid (TCA) cycle. The fate of acetyl-CoA in catabolism is its comp...
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|Summary:||Two distinct metabolic modes provide bacteria with energy (i.e., catabolism) and cellular building blocks (i.e., anabolism). At the interface between both lie the central metabolite acetyl-CoA, as well as the amphibolic tricarboxylic acid (TCA) cycle. The fate of acetyl-CoA in catabolism is its complete oxidation in the TCA cycle for the generation of reducing equivalents and energy, whereby the carbon backbone of the metabolite is fully lost to CO2. To assimilate acetyl-CoA into biomass in anabolism, instead, additional help of so-called replenishment (i.e., anaplerotic) pathways is therefore needed. These pathways circumvent the oxidative, CO2-producing steps of the TCA cycle, thereby allow the incorporation of acetyl-CoA into biomass, and ultimately enable bacterial growth on small carbon compounds such as acetate.
While the old picture of metabolism has assumed a biochemical unity, according to which each organism possesses the same dedicated metabolic route for the conversion of a certain substrate, multiple distinct replenishment routes have been discovered in bacteria by today. Amongst them are the glyoxylate cycle (GC) and the ethylmalonyl-CoA pathway (EMCP). Most bacterial species possess only one of the two acetyl-CoA assimilation pathways as standalone route. However, the Alphaproteobacterium Paracoccus denitrificans, like only few others, has the genetic potential for both. This raised the questions what the biological purpose behind this apparent functional degeneracy in the metabolism of this organism is and how it is coordinated in the cell.
This work shows that both routes the GC and the EMCP are employed by P. denitrificans during different stages of growth on acetate. While the EMCP is constitutively expressed on various substrates and additionally upregulated in the lag phase after growth switch to acetate, the GC is specifically induced on this substrate and only few others that are solely assimilated via acetyl-CoA as well. Each acetyl-CoA assimilation strategy alone confers distinct advantages on the cell. The EMCP allows metabolization of a great variety of carbon substrates and its action results in high growth yields of P. denitrificans on acetate. The GC, in contrast, is specialized for the rapid metabolization of acetyl-CoA and enables fast exponential growth of the bacterium on the carbon source.
A fine-tuned genetic regulation controls expression of both pathways in P. denitrificans and thereby mediates dynamic metabolic rewiring between the two acetyl-CoA assimilation routes. This metabolic plasticity provides the organism with the ability to respond to changes in the nature and availability of carbon sources in a highly flexible manner to meet its physiological requirements.
Using a combination of genetic, molecular biological, and biochemical methods, this work shows that RamB, a transcription factor of the ScfR family, senses CoA-ester intermediates of the EMCP to activate expression of the GC. This demonstrates a so-far undescribed phenomenon in bacterial metabolism, in which one seemingly degenerate metabolic pathway directly drives expression of the other.
In all, this work expands our understanding of microbial metabolism and presents the molecular basis of plasticity in the central carbon metabolism of bacterial cells. Complete elucidation of the underlying mechanisms hereafter may open possibilities to develop new regulatory modules for application in synthetic pathways and metabolic engineering in the future.|