Abstract
Protein synthesis is a template polymerization process composed by three main steps: initiation, elongation, and termination. During translation, ribosomes are engaged into polysomes whose size is used for the quantitative characterization of translatome. However, simultaneous transcription and translation in the bacterial cytosol complicates the analysis of translatome data. We established a procedure for robust estimation of the ribosomal density in hundreds of genes from Lactococcus lactis polysome size measurements. We used a mechanistic model of translation to integrate the information about the ribosomal density and for the first time we estimated the protein synthesis rate for each gene and identified the rate limiting steps. Contrary to conventional considerations, we find significant number of genes to be elongation limited. This number increases during stress conditions compared to optimal growth and proteins synthesized at maximum rate are predominantly elongation limited. Consistent with bacterial physiology, we found proteins with similar rate and control characteristics belonging to the same functional categories. Under stress conditions, we found that synthesis rate of regulatory proteins is becoming comparable to proteins favored under optimal growth. These findings suggest that the coupling of metabolic states and protein synthesis is more important than previously thought.
Highlights
Translation is involved in the multi-layer process of the gene expression and allows the transfer of gene coding information from RNA to protein through ribosome action
We used a mechanistic model of protein synthesis to analyze the translatome in L. lactis cells in exponential phase and under stress condition using experimentally determined ribosomal densities
Other groups have previously studied translatome in eukaryotic systems, with help of various techniques [7,8,16,36,37]
Summary
Translation is involved in the multi-layer process of the gene expression and allows the transfer of gene coding information from RNA to protein through ribosome action. Translation is composed of three successive steps: initiation, elongation and termination. A ribosome binds to an mRNA at the ribosomebinding site to initiate translation at the beginning of the coding sequence (Figure 1). The ribosome moves forward on the mRNA reading the sequence of codons and synthesizes the corresponding sequence of amino acids. Several ribosomes are translating simultaneously the same mRNA molecule, and this mRNA-ribosome complex is called polyribosomes or polysomes. When a ribosome reaches the stop codon translation ends with the termination step during which the native protein and the ribosome are released from the mRNA
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