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Metabolomics. 2014;10(6):1223-1238. doi: 10.1007/s11306-014-0662-x. Epub 2014 Apr 29.

Novel metabolic features in Acinetobacter baylyi ADP1 revealed by a multiomics approach.

Stuani L1,2,3, Lechaplais C1,2,3, Salminen AV1,2,3,4, Ségurens B1,2,3, Durot M1,2,3, Castelli V1,2,3, Pinet A1,2,3, Labadie K1,2,3, Cruveiller S1,2,3, Weissenbach J1,2,3, de Berardinis V1,2,3, Salanoubat M1,2,3, Perret A1,2,3.

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Direction des Sciences du Vivant, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique, Evry, France.
CNRS-UMR8030, Evry, France.
Université d'Evry Val d'Essonne, Evry, France.
Department of Chemistry and Bioengineering, Tampere University of Technology, Korkeakoulunkatu 10, 33720 Tampere, Finland.


Expansive knowledge of bacterial metabolism has been gained from genome sequencing output, but the high proportion of genes lacking a proper functional annotation in a given genome still impedes the accurate prediction of the metabolism of a cell. To access to a more global view of the functioning of the soil bacterium Acinetobacter baylyi ADP1, we adopted a multi 'omics' approach. Application of RNA-seq transcriptomics and LC/MS-based metabolomics, along with the systematic phenotyping of the complete collection of single-gene deletion mutants of A. baylyi ADP1 made possible to interrogate on the metabolic perturbations encountered by the bacterium upon a biotic change. Shifting the sole carbon source from succinate to quinate elicited in the cell not only a specific transcriptional response, necessary to catabolize the new carbon source, but also a major reorganization of the transcription pattern. Here, the expression of more than 12 % of the total number of genes was affected, most of them being of unknown function. These perturbations were ultimately reflected in the metabolome, in which the concentration of about 50 % of the LC/MS-detected metabolites was impacted. And the differential regulation of many genes of unknown function is probably related to the synthesis of the numerous unidentified compounds that were present exclusively in quinate-grown cells. Together, these data suggest that A. baylyi ADP1 metabolism involves unsuspected enzymatic reactions that await discovery.


Bacterial metabolism; Functional genomics; LC/MS-LTQ-Orbitrap; Metabolomics; Transcriptomics

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