ArticlePLoS computational biology2013
A genome-scale integration and analysis of Lactococcus lactis translation data.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 27 citations in OpenAlex.
- A combination of mRNA features influence the efficiency of leaderless mRNA translation initiation.NAR genomics and bioinformatics · 2021Article
- Networks of ribosome flow models for modeling and analyzing intracellular traffic.Scientific reports · 2019Article
- Translational control plays an important role in the adaptive heat-shock response of Streptomyces coelicolor.Nucleic acids research · 2018Article
- Ribosome flow model with extended objects.Journal of the Royal Society, Interface · 2017Article
- Optimal Translation Along a Circular mRNA.Scientific reports · 2017Article
- Predictive biophysical modeling and understanding of the dynamics of mRNA translation and its evolution.Nucleic acids research · 2016Article
- Codon optimality controls differential mRNA translation during amino acid starvation.RNA (New York, N.Y.) · 2016Article
- Analysis of Translation Elongation Dynamics in the Context of an Escherichia coli Cell.Biophysical journal · 2016Article
- Article
- Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data.PLoS computational biology · 2015Article
- Amino Acid Flux from Metabolic Network Benefits Protein Translation: the Role of Resource Availability.Scientific reports · 2015Article
- Maximizing protein translation rate in the non-homogeneous ribosome flow model: a convex optimization approach.Journal of the Royal Society, Interface · 2014Article
- Entrainment to periodic initiation and transition rates in a computational model for gene translation.PloS one · 2014Article
- The significance of translation regulation in the stress response.BMC genomics · 2013Article
- Controllability Analysis and Control Synthesis for the Ribosome Flow Model.IEEE/ACM transactions on computational biology and bioinformaticsArticle
- Translational reprogramming in cellular stress response.Wiley interdisciplinary reviews. RNAReview
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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