BONCAT (nascent) proteomes of starved Pseudomonas aeruginosa

We have characterized the responses of the opportunistic pathogen Pseudomonas aeruginosa to prolonged starvation for carbon or nitrogen sources, and to transitions between these states. We find that most cells survive both types of starvation for more than a week and maintain low but robustly detectable levels of protein synthesis in the absence of growth. Nitrogen-starved cells are larger, make more proteins and retain fewer ribosomes than carbon-starved cells, indicating that distinct physiological strategies are adopted during the two starvation types. We used bio-orthogonal non-canonical amino acid tagging (BONCAT) to enrich for proteins that were newly synthesised during prolonged starvation for nitrogen, during the transition from nitrogen to carbon starvation conditions, and during prolonged starvation for carbon. We found that the newly synthesized proteomes of each starvation type are distinct, although many of the most highly synthesized proteins are shared across conditions. Interestingly, we observed a temporary burst of protein synthesis as cells were transitioned between the two starvation conditions, which may reflect active remodelling of the proteome during growth arrest. Combining this dataset with quantification of total proteomes and identification of genes required for fitness using Tn-Seq, we highlight proteases and chaperones; flagellar motility; and the nitrogen-related phosphotransferase system as key fitness-impacting functions that are actively maintained by growth arrested Pseudomonas aeruginosa.