A Bacillales-specific tubular scaffold essential for NADH dehydrogenase activity

Respiratory type II NADH:quinone oxidoreductases (NDH-II) are typically monotopic flavoproteins that make direct contact with the membrane to access the quinone pool. Here, we show that in Bacillus subtilis, one NDH-II, termed Ndh, assembles with the helical membrane plugin (HMP) protein YjlC and forms supramolecular fibers. Genetic and biochemical analyses demonstrate that Ndh and YjlC proteins are essential for NADH oxidation. Cryo-EM analysis reveals that YjlC forms a tubular scaffold onto which multiple Ndh subunits are regularly docked via their C-terminal domain, repurposed from its classical role in direct membrane binding. These fibers can extend up to ~1000 Å, creating a continuous hydrophobic tunnel filled with lipids and quinones, thereby mimicking the membrane environment. Comparative genomics unveils that this partnership arose exclusively within Bacillales through the recruitment of an ancestral HMP originally associated with sulfide:quinone reductases. Together, our findings uncover a lineage-specific structural adaptation in which NDH-II enzymes depend on an HMP scaffold, expanding their functional diversity beyond the classical monotopic paradigm.