Growth-rate dependency of ribosome abundance and translation elongation rate inCorynebacterium glutamicumdiffers fromEscherichia coli

Abstract

The growth rate μ of bacteria depends on the protein synthesis capacity of the cell and thus on the number of active ribosomes and their translation elongation rate. The relationship between these fundamental growth parameters have only been described for a few bacterial species, in particular Escherichia coli, but are missing for most bacterial phyla. In this study, we systematically analysed the growth-rate dependency of ribosome abundance and translation elongation rate for Corynebacterium glutamicum, a gram-positive model species differing from E. coli by a lower growth temperature optimum and a lower μmax. Ribosomes were quantified via single-molecule localization microscopy (SMLM) using fluorescently tagged ribosomal proteins and via RNA/protein ratio. Both methods revealed a non-linear relationship with little change in ribosome abundance below μ = 0.4 h-1 and a steep increase at higher μ. Unlike E. coli, C. glutamicum keeps a large pool of active ribosomes at low μ, but the translation elongation rate declines from ~9 amino acids s-1 at μmax to <2 aa s-1 at μ < 0.1 h-1. A model-based approach shows that depletion of translation precursors at low growth rates can explain the observed decrease in translation elongation rate. Nutrient up-shift experiments support the hypothesis that maintenance of excess ribosomes during poor nutrient conditions enables C. glutamicum to quickly restart growth when conditions improve.

Single-cell heterogeneity in ribosome content and the consequences for the growth laws

“…That is to say, fast growing populations of cells sampled when nutrients are most abundant have the highest heterogeneity in rRNA counts in both yeast and bacteria (Figure 2a). This positive correlation between ribosome heterogeneity and population growth rate appears to be consistent with at least one previous study in another organism 22 . To understand whether heterogeneity in ribosomal content reflects heterogeneity in single-cell growth rates, we sought to find if heterogeneity in single-cell growth rates is positively correlated with the population growth rate.…”

“…That is to say, fast growing populations of cells sampled when nutrients are most abundant have the highest heterogeneity in rRNA counts in both yeast and bacteria ( Figure 2a ). This positive correlation between ribosome heterogeneity and population growth rate appears to be consistent with at least one previous study in another organism 22 . This trend persisted for another measure of data variance or spread ( Figure S4 ).…”

“…In both yeast and bacteria, we find that population growth rate explains 94% and 69% of variance in average rRNA abundance respectively when using a linear model ( Figure 1b , R-squareds). The non-linearity in slow-growing B. subtilis populations, in which ribosomal content appears to be less responsive to changes in nutrient content, has been observed for other bacterial species as well 22 .…”

Stringent Control Over Cytoplasmic and Membrane Densities Defines Cell Geometry inEscherichia coli

“…4,[77][78][79][80][81] Finally, while we focus in this work on E. coli, there is evidence that density maintenance may be a more general property across the microbial world. For example, recent work in Corynebacterium glutamicum, 82 a gram-positive bacterium, reveals a strong correlation between the surface-to-volume ratio and the RNA-to-protein ratio that is consistent with our theoretical predictions. Similarly, the methanogenic archaeon Methanococcus maripaludis demonstrates a fixed composition across growth conditions and, in line with our theory, a fixed cell size.…”

Cellular localization of the hybrid pyruvate/2-oxoglutarate dehydrogenase complex in the actinobacteriumCorynebacterium glutamicum

“…An alternative explanation for the distinct polar spots is nucleoid exclusion ( 43 , 44 ) caused by the unique structural features of the hybrid PDH-ODH complex that might cause the formation of few large assemblies comprising the vast majority of all four subunits. Like many other bacteria, C. glutamicum contains nucleoids ( 45 , 46 ) that probably affect the dynamics and localization of large cellular components, such as ribosomes, whose diffusion is impeded by the DNA meshwork of the nucleoid ( 47 , 48 ). This potential explanation is supported by the observation that the fluorescent spots formed by the PDH-ODH subunits were mainly visible in the DNA-free regions, as observed by SYTOX Orange DNA staining in the integration strains C. glutamicum::odhI-mVenus , C. glutamicum::odhA-mVenus , C. glutamicum::aceE-mVenus , and C. glutamicum::aceF-mVenus ( Fig.…”