Translation elicits a growth rate‐dependent, genome‐wide, differential protein production in Bacillus subtilis

Abstract

Complex regulatory programs control cell adaptation to environmental changes by setting condition‐specific proteomes. In balanced growth, bacterial protein abundances depend on the dilution rate, transcript abundances and transcript‐specific translation efficiencies. We revisited the current theory claiming the invariance of bacterial translation efficiency. By integrating genome‐wide transcriptome datasets and datasets from a library of synthetic gfp‐reporter fusions, we demonstrated that translation efficiencies in Bacillus subtilis decreased up to fourfold from slow to fast growth. The translation initiation regions elicited a growth rate‐dependent, differential production of proteins without regulators, hence revealing a unique, hard‐coded, growth rate‐dependent mode of regulation. We combined model‐based data analyses of transcript and protein abundances genome‐wide and revealed that this global regulation is extensively used in B. subtilis. We eventually developed a knowledge‐based, three‐step translation initiation model, experimentally challenged the model predictions and proposed that a growth rate‐dependent drop in free ribosome abundance accounted for the differential protein production.

Combinatorial impact of Sec signal peptides from Bacillus subtilis and bioprocess conditions on heterologous cutinase secretion by Corynebacterium glutamicum

“…Such an inverse correlation was also reported in various other studies, for example on the production of a nuclease with E. coli (Cheng et al, ), a β‐aminopeptidase with E. coli (Heyland, Blank, & Schmid, ), GFP with B. subtilis (Borkowski et al, ), GFP with E. coli (Bienick et al, ), or LacZ with E. coli (Klumpp, Zhang, & Hwa, ). In these studies, the observed relations were explained by the redirection of metabolic flux to meet the increased energy demand from heterologous protein production (Heyland et al, ) and modeling of growth‐rate‐dependent ribosomal capacity (Bienick et al, ; Borkowski et al, ; Klumpp et al, ). However, these reports concerned intracellular protein production in batch cultivations, meaning that the observed reduced growth rates were a result of heterologous protein biosynthesis.…”

“…Such an inverse correlation was also reported in various other studies, for example on the production of a nuclease with E. coli (Cheng et al, 2003), a β-aminopeptidase with E. coli (Heyland, Blank, & Schmid, 2011), GFP with B. subtilis (Borkowski et al, 2016), GFP with E. coli (Bienick et al, 2014), or LacZ with E. coli (Klumpp, Zhang, & Hwa, 2009). In these studies, the observed…”

“…explained by the redirection of metabolic flux to meet the increased energy demand from heterologous protein production (Heyland et al, 2011) and modeling of growth-rate-dependent ribosomal capacity (Bienick et al, 2014;Borkowski et al, 2016;Klumpp et al, 2009).…”

Depletion of Shine-Dalgarno Sequences Within Bacterial Coding Regions Is Expression Dependent

“…Normalizing to the genome-wide average should help to mitigate this effect. Second, research has shown that at higher growth rates, ribosomal protein genes make up an increasingly larger fraction of bacterial proteomes (Borkowski et al 2016). Thus, relative differences in S between ribosomal protein coding genes and the genome as a whole should reflect the selective pressure for increased ribosomal protein production during periods of rapid growth.…”

Large-scale reduction of the Bacillus subtilis genome: consequences for the transcriptional network, resource allocation, and metabolism

“…3A). The use of resources for the synthesis of ribosomal proteins typically reflects the growth rate of the bacteria (Bremer and Dennis 1996;Borkowski et al 2016). Indeed, we observe a precise linear correlation between the growth rate of the strains and the fraction of ribosomal proteins (Fig.…”