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Background  The bacterial elongation factor P (EF-P) is strictly conserved in bacteria and essential for protein synthesis. It is homologous to the eukaryotic translation initiation factor 5A (eIF5A). A highly conserved eIF5A lysine is modified into an unusual amino acid derived from spermidine, hypusine. Hypusine is absolutely required for eIF5A's role in translation in  Saccharomyces cerevisiae . The homologous lysine of EF-P is also modified to a spermidine derivative in  Escherichia coli . However, the biosynthesis pathway of this modification in the bacterial EF-P is yet to be elucidated.    Presentation of the Hypothesis  Here we propose a potential mechanism for the post-translational modification of EF-P. By using comparative genomic methods based on physical clustering and phylogenetic pattern analysis, we identified two protein families of unknown function, encoded by  yjeA  and  yjeK  genes in  E. coli , as candidates for this missing pathway. Based on the analysis of the structural and biochemical properties of both protein families, we propose two potential mechanisms for the modification of EF-P.    Testing the hypothesis  This hypothesis could be tested genetically by constructing a bacterial strain with a tagged  efp  gene. The tag would allow the purification of EF-P by affinity chromatography and the analysis of the purified protein by mass spectrometry.  yjeA  or  yjeK  could then be deleted in the  efp  tagged strain and the EF-P protein purified from each mutant analyzed by mass spectrometry for the presence or the absence of the modification. This hypothesis can also be tested by purifying the different components (YjeK, YjeA and EF-P) and reconstituting the pathway  in vitro .    Implication of the hypothesis  The requirement for a fully modified EF-P for protein synthesis in certain bacteria implies the presence of specific post-translational modification mechanism in these organisms. All of the 725 bacterial genomes analyzed, possess an  efp  gene but only 200 (28%) possess both  yjeA  and  yjeK  genes. In the other organisms, EF-P may be modified by another pathway or the translation machinery must have adapted to the lack of EF-P modification. Our hypotheses, if confirmed, will lead to the discovery of a new post-translational modification pathway.    Reviewers  This article was reviewed by Céline Brochier-Armanet, Igor B. Zhulin and Mikhail Gelfand. For the full reviews, please go to the Reviewers' reports section.

Predicting the pathway involved in post-translational modification of Elongation factor P in a subset of bacterial species