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Background   Buchnera aphidicola  is an obligate symbiotic bacterium, associated with most of the aphididae, whose genome has drastically shrunk during intracellular evolution. Gene regulation in  Buchnera  has been a matter of controversy in recent years as the combination of genomic information with the experimental results has been contradictory, refuting or arguing in favour of a functional and responsive transcription regulation in  Buchnera .  The goal of this study was to describe the gene transcription regulation capabilities of  Buchnera  based on the inventory of cis- and trans-regulators encoded in the genomes of five strains from different aphids ( Acyrthosiphon pisum ,  Schizaphis graminum ,  Baizongia pistacea ,  Cinara cedri  and  Cinara tujafilina ), as well as on the characterisation of some intrinsic structural properties of the DNA molecule in these bacteria.    Results  Interaction graph analysis shows that gene neighbourhoods are conserved between  E .  coli  and  Buchnera  in structures called transcriptons, interactons and metabolons, indicating that selective pressures have acted on the evolution of transcriptional, protein-protein interaction and metabolic networks in  Buchnera . The transcriptional regulatory network in  Buchnera  is composed of a few general DNA-topological regulators (Nucleoid Associated Proteins and topoisomerases), with the quasi-absence of any specific ones (except for multifunctional enzymes with a known gene expression regulatory role in  Escherichia coli , such as AlaS, PepA and BolA, and the uncharacterized hypothetical regulators YchA and YrbA). The relative positioning of regulatory genes along the chromosome of  Buchnera  seems to have conserved its ancestral state, despite the genome erosion. Sigma-70 promoters with canonical thermodynamic sequence profiles were detected upstream of about 94% of the CDS of  Buchnera  in the different aphids. Based on Stress-Induced Duplex Destabilization (SIDD) measurements, unstable σ 70  promoters were found specifically associated with the regulator and transporter genes.    Conclusions  This genomic analysis provides supporting evidence of a selection of functional regulatory structures and it has enabled us to propose hypotheses concerning possible links between these regulatory elements and the DNA-topology (i.e., supercoiling, curvature, flexibility and base-pair stability) in the regulation of gene expression in the shrunken genome of  Buchnera .

Genomic analysis of the regulatory elements and links with intrinsic DNA structural properties in the shrunken genome of Buchnera