Phosphoproteomics reveals essential regulatory roles of phosphorylation in marine oligotrophic bacteria

Oligotrophic bacteria with reduced genomes have relatively few transcriptional regulators and are thought to rely more than other bacteria on post-transcriptional regulation to respond to environmental stimuli. SAR11 bacteria are the most abundant group of heterotrophic bacteria in marine planktonic systems and are a model for understanding genome reduction in other free-living microorganisms. Here, we report a comprehensive, quantitative protein phosphorylation profile for SAR11 strain HTCC1062 grown under various environmentally relevant conditions, including light/dark cycles, temperature differences, and nutrient limitations, to investigate phosphorylation dynamics in this streamlined organism. Nearly half of proteins encoded by the genome were detected in phosphorylated forms under at least one condition. 1014 Ser/Thr/Tyr phosphorylation sites were observed in 1576 phosphopeptides from 555 phosphoproteins. Protein phosphorylation was concentrated in proteins for functions associated with nutrient acquisition and growth, such as ABC transporters, RNA polymerase, and ribosomal proteins. Prominent patterns in protein phosphorylation were detected across a range of culture conditions. In these cells, which previously have been shown to continuously express nearly their entire proteome, protein phosphorylation was more dynamic than protein abundance, supporting the hypothesis that post-transcriptional regulation by protein phosphorylation might play a large role in modulating protein activity. Our findings support a regulatory model characterized by minimal variation in protein expression but extensive protein phosphorylation. This model diverges from bacterial regulatory paradigms reliant on transcriptional control, and may be relevant to understanding other abundant heterotrophs with reduced genomes.