Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validationsReport as inadecuate




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BMC Genomics

, 8:245

First Online: 23 July 2007Received: 05 December 2006Accepted: 23 July 2007

Abstract

BackgroundFolate synthesis and salvage pathways are relatively well known from classical biochemistry and genetics but they have not been subjected to comparative genomic analysis. The availability of genome sequences from hundreds of diverse bacteria, and from Arabidopsis thaliana, enabled such an analysis using the SEED database and its tools. This study reports the results of the analysis and integrates them with new and existing experimental data.

ResultsBased on sequence similarity and the clustering, fusion, and phylogenetic distribution of genes, several functional predictions emerged from this analysis. For bacteria, these included the existence of novel GTP cyclohydrolase I and folylpolyglutamate synthase gene families, and of a trifunctional p-aminobenzoate synthesis gene. For plants and bacteria, the predictions comprised the identities of a -missing- folate synthesis gene folQ and of a folate transporter, and the absence from plants of a folate salvage enzyme. Genetic and biochemical tests bore out these predictions.

ConclusionFor bacteria, these results demonstrate that much can be learnt from comparative genomics, even for well-explored primary metabolic pathways. For plants, the findings particularly illustrate the potential for rapid functional assignment of unknown genes that have prokaryotic homologs, by analyzing which genes are associated with the latter. More generally, our data indicate how combined genomic analysis of both plants and prokaryotes can be more powerful than isolated examination of either group alone.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-8-245 contains supplementary material, which is available to authorized users.

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Author: Valérie de Crécy-Lagard - Basma El Yacoubi - Rocío Díaz de la Garza - Alexandre Noiriel - Andrew D Hanson

Source: https://link.springer.com/article/10.1186/1471-2164-8-245







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