Bacteria possess a wide range of metabolic pathways, allowing them to adapt to an array of environmental changes. Focusing on these different metabolic pathways allows us to observe how bacteria catabolize substrate or use anabolic pathways to generate biomass. A more in-depth look shows that many of these pathways are redundant, meaning a single organism can conduct the same overall reactions differing only by the types of enzymes or intermediates used. Overlapping pathways are common in bacteria and have become a focal point of metabolism research to determine the advantages of conserving redundant pathways throughout evolution. The metal reducing bacterium Shewanella oneidensis MR-1 is a practical model organism for metabolic studies, as it has substantial branching within its respiratory pathways. In this work, we focused on the extensive electron transport chain (ETC) of S. oneidensis MR-1 to understand the importance of seemingly redundant respiratory complexes and their functions during aerobic growth. The S. oneidensis MR-1 genome encodes four different NADH dehydrogenases (NDHs): a proton-pumping Type I NDH (Nuo), two sodium-pumping NDHs (Nqr1 and Nqr2), and one type II 'uncoupling NDH (Ndh). NDHs oxidize NADH to move electrons into the ETC and generate ion-motive force that drives ATP synthesis, active transport, and motility. We determined that either Nuo or Nqr1 was required for aerobic growth in minimal medium. The presence of theoretically redundant complexes (Nqr2 and Ndh) did not rescue cell growth. Further, we determined that knocking out NDHs led to the inability to properly oxidize NADH. NADH build up inhibited the tricarboxylic acid cycle causing an amino acid synthesis defect and inhibiting growth of the S. oneidensis strain lacking Nuo and Nqr1. Recently, bacterial metabolic models have been developed to explain the use of energetically inefficient pathways during fast growth. Two standout models postulate that energetically inefficient pathways are used to reduce a cell's proteome cost by eliminating thermodynamic barriers or to reduce dependence on the ETC as cells grow larger. We sought to uncover if these models applied to the respiratory chain of S. oneidensis MR-1 during aerobic growth, as the ETC can vary in energetic efficiency based on the combination of NDH and terminal oxidase used. Our findings indicate that the models apply to S. oneidensis MR-1 in the context of overflow metabolism during growth at higher growth rates, while the structuring of the ETC was not in agreement. Most importantly, determined that both carbon metabolism and the ETC were restructured for adaptive growth under differing conditions. As carbon metabolism became less efficient at faster growth rates, the NDH step of the ETC became more efficient, using complexes with higher coupling efficiencies.
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