Escherichia coli translation strategies differ across carbon, nitrogen and phosphorus limitation conditions

Abstract

For cells to grow faster they must increase their protein production rate. Microorganisms have traditionally been thought to accomplish this increase by producing more ribosomes to enhance protein synthesis capacity, leading to the linear relationship between ribosome level and growth rate observed under most growth conditions previously examined. Past studies have suggested that this linear relationship represents an optimal resource allocation strategy for each growth rate, independent of any specific nutrient state. Here we investigate protein production strategies in continuous cultures limited for carbon, nitrogen and phosphorus, which differentially impact substrate supply for protein versus nucleic acid metabolism. Unexpectedly, we find that at slow growth rates, Escherichia coli achieves the same protein production rate using three different strategies under the three different nutrient limitations. Under phosphorus (P) limitation, translation is slow due to a particularly low abundance of ribosomes, which are RNA-rich and thus particularly costly for phosphorous-limited cells. Under nitrogen (N) limitation, translation elongation is slowed by processes including ribosome stalling at glutamine codons. Under carbon (C) limitation, translation is slowed by accumulation of inactive ribosomes not bound to messenger RNA. These extra ribosomes enable rapid growth acceleration during nutrient upshift. Thus, bacteria tune ribosome usage across different limiting nutrients to enable balanced nutrient-limited growth while also preparing for future nutrient upshifts.

Modeling microbial metabolic trade-offs in a chemostat

“…The method for total RNA and protein measurements is described in (Li et al, 2018 Chemostat variables _ = +,_ , 3,_ , … 5,_ Nutrient environment inside the -th chemostat.…”

Flexible open-source automation for robotic bioengineering

“…3C). 24 , we observe that the total amount of protein is generally not affected by limiting carbon or nitrogen, nor by supplementing the cells with excess of either nutrient. However, perhaps most interestingly, we additionally find that when phosphorus is limited (0.25X), excess carbon supplementation not only rescues the growth rate of the culture (Fig.…”

“…It has traditionally been thought that cells regulate protein production by allocating their resources to optimize for both expression and growth 22,23 . However, it has recently been shown that in either carbon-, nitrogen-or phosphorus-limiting conditions, cells are able to fine-tune their ribosomal usage to maintain equal levels of protein 24 . Thus, we hypothesized that exploration of the entire metabolite landscape (Fig.…”

(p)ppGpp directly regulates translation initiation during entry into quiescence

“…For example, some species exhibit a loss of ribosomes during extended periods of stationary phase (Deutscher, 2003; Piir et al, 2011) which would be expected to decrease overall protein synthesis. However, recent work suggests that ribosomes are actually in excess, and that only a fraction are active, especially under non-exponential growth (Dai et al, 2016; Li et al, 2018). This excess would be particularly useful for the exit from quiescence, since the ability to transition to maximal protein synthesis as quickly as possible would provide a clear selective advantage (Korem Kohanim et al, 2018; Remigi et al, 2019).…”