Prochlorococcus requires the capability to accommodate to environmental changes in order to proliferate in oligotrophic oceans, in particular regarding
nitrogen availability. A precise knowledge of the composition and changes in the
proteome can yield fundamental insights into such a response. Here we report a detailed
proteome analysis of the important model cyanobacterium Prochlorococcus marinus SS120
after treatment with
azaserine, an inhibitor of
ferredoxin-dependent glutamate synthase (GOGAT), to simulate extreme
nitrogen starvation. In total, 1,072
proteins, corresponding to 57% of the theoretical
proteome, were identified-the maximum
proteome coverage obtained for any Prochlorococcus strain thus far. Spectral intensity, calibrated quantification by the Hi3 method, was obtained for 1,007
proteins. Statistically significant changes (P value of <0.05) were observed for 408
proteins, with the majority of
proteins (92.4%) downregulated after 8 h of treatment. There was a strong decrease in
ribosomal proteins upon
azaserine addition, while many transporters were increased. The regulatory
proteins PII and PipX were decreased, and the global
nitrogen regulator
NtcA was upregulated. Furthermore, our data for Prochlorococcus indicate that
NtcA also participates in the regulation of photosynthesis. Prochlorococcus responds to the lack of
nitrogen by slowing down translation, while inducing photosynthetic cyclic electron flow and biosynthesis of
proteins involved in
nitrogen uptake and assimilation. IMPORTANCEProchlorococcus is the most abundant photosynthetic organism on Earth, contributing significantly to global primary production and playing a prominent role in biogeochemical cycles. Here we study the effects of extreme
nitrogen limitation, a feature of the oligotrophic oceans inhabited by this organism. Quantitative proteomics allowed an accurate quantification of the Prochlorococcus
proteome, finding three main responses to
nitrogen limitation: upregulation of
nitrogen assimilation-related
proteins, including transporters; downregulation of ribosome
proteins; and induction of the
photosystem II cyclic electron flow. This suggests that
nitrogen limitation affects a range of metabolic processes far wider than initially believed, with the ultimate goal of saving
nitrogen and maximizing the
nitrogen uptake and assimilation capabilities of the cell.