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 rho-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.

FIG. 1.

Growth curves for duplicate samples of “Ca. Pelagibacter ubique” harvested at either mid-exponential or early stationary phase. Approximately 100 μg of protein was produced from each of two 10-liter samples drawn from sterilized seawater medium at stationary phase and each of two 40-liter samples drawn from the medium at exponential phase.

FIG. 2.

Growth in coverage of the AMT tag library with additional culture conditions/samples.

FIG. 3.

Total predicted proteome (blue), detected exponential-phase proteome (red), and detected stationary-phase proteome (yellow) of “Ca. Pelagibacter ubique,” grouped by functional category. Bar heights represent the numbers of proteins or percentages of total proteins (the number of proteins in each functional category divided by the total number of proteins detected for that proteome) for this experiment.