Carbon monoxide-driven proton respiration enables facultative anaerobes to survive electron acceptor limitation

Abstract

Diverse microorganisms couple the oxidation of carbon monoxide gas (CO) to the reduction of protons, producing hydrogen gas (H2). This energy-conserving process is mediated by the nickel-containing CO dehydrogenase/energy-converting hydrogenase (Ni-CODH/ECH). Yielding only a small supply of energy, the physiological role of this process at environmentally relevant CO levels remains unresolved. Here, we show that Ni-CODH/ECH enables metabolically flexible facultative anaerobes within the Anoxybacillaceae to survive electron acceptor limitation. Analysis of 387 Anoxybacillaceae genomes revealed that Ni-CODH/ECH had a patchy distribution and, with one exception, was mutually exclusive with the aerobic molybdenum-containing CODH. Culture experiments using the three isolates (Parageobacillus sp. G301, P. thermoglucosidasius NBRC 107763, and Thermolongibacillus altinsuensis B1-1) demonstrated that CO-dependent proton respiration is activated during stationary phase when exogenous electron acceptors are limiting, enhancing cell density 1.2-to 1.5-fold under 25% CO, whereas no effect was observed in a Ni-CODH knockout ({Delta}cooCSF) strain. RNA-seq analysis of strain G301 under twelve conditions revealed that Ni-CODH genes reached 2,000-12,500 TPM (top 0.2-1.9% of all genes) during stationary phase, independent of CO presence, under the predicted control of the redox-dependent transcriptional repressor Rex. {Delta}cooCSF cultures accumulated more trace CO than the wild-type, suggesting trace CO uptake by the wild-type. Thus, Ni-CODH/ECH is a redox-regulated auxiliary energy-conservation system that supports adaptation to electron acceptor limitation. Given the continual environmental supply of the two substrates for this enzyme, we propose CO-dependent proton respiration is a dependable way for metabolically flexible microorganisms to stay energized in spatiotemporally variable environments. Significance statementMicroorganisms are frequently challenged to survive in environments where both energy sources and electron acceptors are limited. We reveal that facultative anaerobes activate a respiratory process that utilizes carbon monoxide (CO) and protons to survive under electron acceptor limitation. This hydrogenogenic CO-oxidizing reaction, termed CO-dependent proton respiration, is catalyzed by an ancient and minimal complex, the nickel-containing CO dehydrogenase/energy-converting hydrogenase. Although the reaction yields barely enough energy to translocate protons, this complex provides a reliable lifeline by extracting energy from trace CO and protons that are ubiquitous in nature, even when other electron acceptors are depleted. The widespread distribution of this complex across bacteria and archaea suggests that it provides a universal adaptive advantage for life under energy-limited conditions.