Bacterial translational regulations: high diversity between all mRNAs and major role in gene expression

Abstract

Background: In bacteria, the weak correlations at the genome scale between mRNA and protein levels suggest that not all mRNAs are translated with the same efficiency. To experimentally explore mRNA translational level regulation at the systemic level, the detailed translational status (translatome) of all mRNAs was measured in the model bacterium Lactococcus lactis in exponential phase growth.

Results: Results demonstrated that only part of the entire population of each mRNA species was engaged in translation. For transcripts involved in translation, the polysome size reached a maximum of 18 ribosomes. The fraction of mRNA engaged in translation (ribosome occupancy) and ribosome density were not constant for all genes. This high degree of variability was analyzed by bioinformatics and statistical modeling in order to identify general rules of translational regulation. For most of the genes, the ribosome density was lower than the maximum value revealing major control of translation by initiation. Gene function was a major translational regulatory determinant. Both ribosome occupancy and ribosome density were particularly high for transcriptional regulators, demonstrating the positive role of translational regulation in the coordination of transcriptional networks. mRNA stability was a negative regulatory factor of ribosome occupancy and ribosome density, suggesting antagonistic regulation of translation and mRNA stability. Furthermore, ribosome occupancy was identified as a key component of intracellular protein levels underlining the importance of translational regulation.

Conclusions: We have determined, for the first time in a bacterium, the detailed translational status for all mRNAs present in the cell. We have demonstrated experimentally the high diversity of translational states allowing individual gene differentiation and the importance of translation-level regulation in the complex process linking gene expression to protein synthesis.

Figure 1

Schematic overview of the translatome analysis in exponential phase L. lactis cells. For each step, the size of the gene set is provided.

Figure 2

Polysomal profile of L. lactis cells in exponential phase. (A) 254 nm absorbance profile. The top and bottom of the gradient were indicated on the left and right of the profile, respectively. (B) 16S and 23S rRNA quantifications for peak assignment.

Figure 3

mRNA proportions between fractions B to H for six chosen genes. For a given gene, its proportions of mRNA molecules in each fraction from B to H were calculated as described in Equation 6 of Methods. Square symbols represent data from the three polysomal profile experiments. The black line is the plot of the mean mRNA proportion value.

Figure 4

Ribosome occupancy distribution. The percentage of each mRNA found in ribosome-containing fractions (fractions D to H) was determined for 1619 genes.

Figure 5

Ribosome density distribution. The ribosome density (expressed as ribosomes per 100 nucleotides) was determined for the set of 1049 genes.

Figure 6

Modeling of the cellular process. Genes are first transcribed into mRNA before being translated into proteins. Proteins are then submitted to dilution by growth and degradation. μ: growth rate; k: mRNA degradation constant; k': translation efficiency; k'': protein degradation constant.