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

Bailly M, de Crécy-Lagard V - Biol. Direct (2010)

Bottom Line: Our hypotheses, if confirmed, will lead to the discovery of a new post-translational modification pathway.Zhulin and Mikhail Gelfand.For the full reviews, please go to the Reviewers' reports section.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA.

ABSTRACT

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.

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Wenn diagram. Red representing bacteria with efp; orange, a subset of those with the conserved. lysine; blue, bacteria with yjeA; and green, bacteria with yjeK (the colors, of course, are arbitrary, whereas the topology is not).
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Figure 5: Wenn diagram. Red representing bacteria with efp; orange, a subset of those with the conserved. lysine; blue, bacteria with yjeA; and green, bacteria with yjeK (the colors, of course, are arbitrary, whereas the topology is not).

Mentions: Since only 125 of 722 studied bacterial species have both candidate genes, an obvious question is, whether these genes always co-occur (if they are often found solo, this would be suspicious), whether they occur in species without the conserved lysine (if they do, what are they doing there?), and how many of 597 = 722-125 genomes have this lysine. Such analysis would allow the authors to verify the conclusions obtained by positional clustering using the phylogenetic profiles. The answer is best represented by a Wenn diagram (Fig. 5).


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

Bailly M, de Crécy-Lagard V - Biol. Direct (2010)

Wenn diagram. Red representing bacteria with efp; orange, a subset of those with the conserved. lysine; blue, bacteria with yjeA; and green, bacteria with yjeK (the colors, of course, are arbitrary, whereas the topology is not).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2821294&req=5

Figure 5: Wenn diagram. Red representing bacteria with efp; orange, a subset of those with the conserved. lysine; blue, bacteria with yjeA; and green, bacteria with yjeK (the colors, of course, are arbitrary, whereas the topology is not).
Mentions: Since only 125 of 722 studied bacterial species have both candidate genes, an obvious question is, whether these genes always co-occur (if they are often found solo, this would be suspicious), whether they occur in species without the conserved lysine (if they do, what are they doing there?), and how many of 597 = 722-125 genomes have this lysine. Such analysis would allow the authors to verify the conclusions obtained by positional clustering using the phylogenetic profiles. The answer is best represented by a Wenn diagram (Fig. 5).

Bottom Line: Our hypotheses, if confirmed, will lead to the discovery of a new post-translational modification pathway.Zhulin and Mikhail Gelfand.For the full reviews, please go to the Reviewers' reports section.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA.

ABSTRACT

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.

Show MeSH
Related in: MedlinePlus