The conserved GTPase LepA contributes mainly to translation initiation in Escherichia coli.
LepA is a paralog of EF-G found in all bacteria. Deletion of lepA confers no obvious growth defect in Escherichia coli, and the physiological role of LepA remains unknown. Here, we identify nine strains (ΔdksA, ΔmolR1, ΔrsgA, ΔtatB, ΔtonB, ΔtolR, ΔubiF, ΔubiG or ΔubiH) in which ΔlepA confers a synthetic growth phenotype. These strains are compromised for gene regulation, ribosome assembly, transport and/or respiration, indicating that LepA contributes to these functions in some way. We also use ribosome profiling to deduce the effects of LepA on translation. We find that loss of LepA alters the average ribosome density (ARD) for hundreds of mRNA coding regions in the cell, substantially reducing ARD in many cases. By contrast, only subtle and codon-specific changes in ribosome distribution along mRNA are seen. These data suggest that LepA contributes mainly to the initiation phase of translation. Consistent with this interpretation, the effect of LepA on ARD is related to the sequence of the Shine-Dalgarno region. Global perturbation of gene expression in the ΔlepA mutant likely explains most of its phenotypes.
Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
Rohan
R
Balakrishnan
Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA Department of Physics, The Ohio State University, Columbus, OH 43210, USA.
Kenji
K
Oman
Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
Shinichiro
S
Shoji
Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA Department of Physics, The Ohio State University, Columbus, OH 43210, USA.
Ralf
R
Bundschuh
Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA fredrick.5@osu.edu.
Kurt
K
Fredrick
D020134:Catalytic Domain; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D020558:GTP Phosphohydrolases / Q000378:metabolism; D017353:Gene Deletion; D010441:Peptide Chain Elongation, Translational; D010442:Peptide Chain Initiation, Translational; D010448:Peptide Initiation Factors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D010641:Phenotype; D039662:Prokaryotic Initiation Factors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D017434:Protein Structure, Tertiary; D012333:RNA, Messenger / Q000032:analysis; D012270:Ribosomes / Q000378:metabolism
D029968:Escherichia coli Proteins; C515651:LepA protein, E coli; D010448:Peptide Initiation Factors; D039662:Prokaryotic Initiation Factors; D012333:RNA, Messenger; D020558:GTP Phosphohydrolases