Fig. 2: E. coli recycles its cytoplasmic proteins when nitrogen is limited.

A Histogram of protein total half-lives for E. coli grown in chemostats under C-lim, P-lim, and N-lim. The vertical line marks the dilution limit set by the 6-h doubling time. Total half-lives greater than doubling time indicate measurement noise. Under C-lim and P-lim, most proteins have total half-lives equal to the doubling time, suggesting they are stable. However, under N-lim many proteins are actively degraded. B Separation of the proteome into stable proteins (grey) and actively degrading proteins (yellow). All proteins with p-value < 0.05 are called confidently degrading (t-test, one-sided, n = 2). In C-lim and P-lim, 15% of the proteome turns over with high confidence. In contrast, under N-lim, 43% of the proteome turns over. C Distribution of total half-lives for proteins from different subcellular localizations overlayed against the entire proteome. Most proteins are stable under C-lim and P-lim, irrespective of localization. However, nearly all cytoplasmic proteins slowly degrade under N-lim while the membrane and periplasmic proteomes are largely stable. D Scatter plots of protein total half-lives in different nutrient limitations. The dotted black lines mark the dilution limit, the solid black line denotes perfect agreement. Contour plots contain 50% of the probability mass for each subcellular compartment. The contour plots of membrane and periplasmic proteins are centered around the dilution limit in all the binary comparisons, indicating that most of these proteins are stable under all limitations. However, the shift in the contour plots of the cytoplasmic proteins on comparing N-lim with P-lim and C-lim suggests that the cytoplasmic proteins are degraded in N-lim. E Measurement of protein turnover rates under complete nutrient starvation in batch. In batch, like the N-lim chemostat, the cytoplasmic proteins are degrading with high confidence as compared to the membrane and periplasmic proteins (ANOVA, p-value = 9E–16, n = 2114 proteins). The box extends from the first quartile to the third quartile of the data, with a line at the median. The whiskers extend from the box to the farthest data point lying within 1.5× the inter-quartile range from the box.