Proteomic Analysis of Stationary Phase in the Marine Bacterium “Candidatus Pelagibacter ubique”

ABSTRACT “Candidatus Pelagibacter ubique,” an abundant marine alphaproteobacterium, subsists in nature at low ambient nutrient concentrations and may often be exposed to nutrient limitation, but its genome reveals no evidence of global regulatory mechanisms for adaptation to stationary phase. High-resolution capillary liquid chromatography coupled online to an LTQ mass spectrometer was used to build an accurate mass and time (AMT) tag library that enabled quantitative examination of proteomic differences between exponential- and stationary-phase “Ca. Pelagibacter ubique” cells cultivated in a seawater medium. The AMT tag library represented 65% of the predicted protein-encoding genes. “Ca. Pelagibacter ubique” appears to respond adaptively to stationary phase by increasing the abundance of a suite of proteins that contribute to homeostasis rather than undergoing a major remodeling of its proteome. Stationary-phase abundances increased significantly for OsmC and thioredoxin reductase, which may mitigate oxidative damage in “Ca. Pelagibacter,” as well as for molecular chaperones, enzymes involved in methionine and cysteine biosynthesis, proteins involved in ρ-dependent transcription termination, and the signal transduction enzyme CheY-FisH. We speculate that this limited response may enable “Ca. Pelagibacter ubique” to cope with ambient conditions that deprive it of nutrients for short periods and, furthermore, that the ability to resume growth overrides the need for a more comprehensive global stationary-phase response to create a capacity for long-term survival.