Comparative genomic analysis of the DUF71/COG2102 family predicts roles in diphthamide biosynthesis and B12 salvage

Valérie De Crécy-Lagard,John F Hunt,Liang Tong,Farhad Forouhar,Céline Brochier-Armanet

doi:10.1186/1745-6150-7-32

Abstract

BackgroundThe availability of over 3000 published genome sequences has enabled the use of comparative genomic approaches to drive the biological function discovery process. Classically, one used to link gene with function by genetic or biochemical approaches, a lengthy process that often took years. Phylogenetic distribution profiles, physical clustering, gene fusion, co-expression profiles, structural information and other genomic or post-genomic derived associations can be now used to make very strong functional hypotheses. Here, we illustrate this shift with the analysis of the DUF71/COG2102 family, a subgroup of the PP-loop ATPase family.ResultsThe DUF71 family contains at least two subfamilies, one of which was predicted to be the missing diphthine-ammonia ligase (EC 6.3.1.14), Dph6. This enzyme catalyzes the last ATP-dependent step in the synthesis of diphthamide, a complex modification of Elongation Factor 2 that can be ADP-ribosylated by bacterial toxins. Dph6 orthologs are found in nearly all sequenced Archaea and Eucarya, as expected from the distribution of the diphthamide modification. The DUF71 family appears to have originated in the Archaea/Eucarya ancestor and to have been subsequently horizontally transferred to Bacteria. Bacterial DUF71 members likely acquired a different function because the diphthamide modification is absent in this Domain of Life. In-depth investigations suggest that some archaeal and bacterial DUF71 proteins participate in B12 salvage.ConclusionsThis detailed analysis of the DUF71 family members provides an example of the power of integrated data-miming for solving important “missing genes” or “missing function” cases and illustrates the danger of functional annotation of protein families by homology alone.Reviewers’ namesThis article was reviewed by Arcady Mushegian, Michael Galperin and L. Aravind.

Highlights

The availability of over 3000 published genome sequences has enabled the use of comparative genomic approaches to drive the biological function discovery process
The only archaeon lacking both Dph2 and Dph5 was Korarchaeum cryptofilum OPF8 (Figure 2A). We hypothesized that this organism has lost the diphthamide modification pathway even if the K. cryptofilum Elongation Factor 2 (EF-2) still harbors the conserved His residue at the site of the modification (His603 in the K. cryptofilum sequence, Accession B1L7Q0 in UniprotKB)
Because diphthamide is a modification specific to the archaeal and eukaryotic EF-2 proteins and bacteria lack all known diphthamide biosynthesis genes, we propose that cluster 1 in our phylogeny corresponds to bona fide Dph6 enzymes involved in diphthamide synthesis (Figure 4)

Summary

Introduction

The availability of over 3000 published genome sequences has enabled the use of comparative genomic approaches to drive the biological function discovery process. Phylogenetic distribution profiles, physical clustering, gene fusion, co-expression profiles, structural information and other genomic or post-genomic derived associations can be used to make very strong functional hypotheses. We illustrate this shift with the analysis of the DUF71/COG2102 family, a subgroup of the PP-loop ATPase family. In both Archaea and Eucarya, the translation Elongation Factor 2 (EF-2) harbors a complex post-translational modification of a strictly conserved histidine (His699 in yeast) called diphthamide [1]. The diphthamide biosynthesis pathway was described in the early 1980′s [2,3], the corresponding enzymes have only recently A

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Conclusion