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

Abstract

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/MSdetected 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.

MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes

“…This soil bacterium is able to metabolize a wide range of plant secondary metabolites as the sole source of carbon and energy. Shifting the carbon source from succinate to quinate induced not only a specific transcriptional response necessary to catabolize the new carbon source, but also a tremendous upheaval of the transcription pattern affecting the expression of more than 12 % of the total number of genes, most of them being of unknown function (41). These perturbations were ultimately reflected in the metabolome, in which the concentration of about 50% of the LC/MS-detected metabolites was impacted.…”

Rapid and assured genetic engineering methods applied to Acinetobacter baylyi ADP1 genome streamlining

“…While it does not delete any genes that are essential for viability in minimal media, it does remove two genes that are essential for fitness in LB, cysK and dcaS. In this case, it is possible that there could be a fitness balancing effect of simultaneously deleting multiple pathways involved in the degradation of aromatic compounds including the pca-qui-pob-hca gene cluster (28,32).…”

“…Multiple studies have also highlighted its useful innate metabolic abilities, particularly related to degradation of aromatic compounds (28)(29)(30)(31)(32) and production of triacylglycerols and wax esters (33,34). ADP1's natural transformability has been leveraged to perform targeted mutagenesis and disruption of genes in its chromosome for metabolic engineering of these pathways (35,36), as well as to add novel genes to its genome and evolve them to improve these functions (33,34,37).…”

Development of a genetic toolset for the highly engineerable and metabolically versatile Acinetobacter baylyi ADP1

“…Similarly, the bacterial portion of a group of broad-spectrum promoters from a recent work 12 show expression, however not in the order and strength expected. Finally, using the 300-500 upstream bases 5' to genes with known high mRNA abundance in ADP1, 13 the gene with the highest transcriptomic expression from previous work (gltI) gives the strongest expression on par with T5 and below Trc. Other native promoters did not show strong expression.…”