title: 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.
authors.affiliation: Micalis Institute, INRA AgroParisTech Université Paris-Saclay, Jouy-en-Josas, 78350, France MaIAGE, INRA Université Paris-Saclay, Jouy-en-Josas, 78350, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Borkowski
authors.affiliation: MaIAGE, INRA Université Paris-Saclay, Jouy-en-Josas, 78350, France.
authors.forename: Anne
authors.initials: A
authors.lastname: Goelzer
authors.affiliation: Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.
authors.forename: Marc
authors.initials: M
authors.lastname: Schaffer
authors.affiliation: Micalis Institute, INRA AgroParisTech Université Paris-Saclay, Jouy-en-Josas, 78350, France.
authors.forename: Magali
authors.initials: M
authors.lastname: Calabre
authors.affiliation: Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.
authors.forename: Ulrike
authors.initials: U
authors.lastname: Mäder
authors.affiliation: Micalis Institute, INRA AgroParisTech Université Paris-Saclay, Jouy-en-Josas, 78350, France.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Aymerich
authors.affiliation: Micalis Institute, INRA AgroParisTech Université Paris-Saclay, Jouy-en-Josas, 78350, France Matthieu.Jules@grignon.inra.fr vincent.fromion@jouy.inra.fr.
authors.forename: Matthieu
authors.identifier: 0000-0003-0817-8949
authors.initials: M
authors.lastname: Jules
authors.affiliation: MaIAGE, INRA Université Paris-Saclay, Jouy-en-Josas, 78350, France Matthieu.Jules@grignon.inra.fr vincent.fromion@jouy.inra.fr.
authors.forename: Vincent
authors.initials: V
authors.lastname: Fromion
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics / Q000254:growth & development*; D001426:Bacterial Proteins / Q000378:metabolism*; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D008962:Models, Theoretical; D014176:Protein Biosynthesis; D020543:Proteome / Q000378:metabolism; D012329:RNA, Bacterial / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D020543:Proteome; D012329:RNA, Bacterial; D012333:RNA, Messenger
keywords: Bacillus subtilis; global regulation; growth rate; protein production; translation efficiency