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

• Main Authors: Brinza Lilia, Calevro Federica, Charles Hubert
• Format: Article
• Language: English
• Published: BMC 2013-02-01
• Series: BMC Genomics
• Subjects: <it>Buchnera aphidicola</it>; Genome reduction; Transcription regulation; DNA-topology; Nucleoid associated proteins (NAPs)
• Online Access: http://www.biomedcentral.com/1471-2164/14/73

<p>Abstract</p> <p>Background</p> <p><it>Buchnera aphidicola</it> is an obligate symbiotic bacterium, associated with most of the aphididae, whose genome has drastically shrunk during intracellular evolution. Gene regulation in <it>Buchnera</it> 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 <it>Buchnera</it>.</p> <p>The goal of this study was to describe the gene transcription regulation capabilities of <it>Buchnera</it> based on the inventory of cis- and trans-regulators encoded in the genomes of five strains from different aphids (<it>Acyrthosiphon pisum</it>, <it>Schizaphis graminum</it>, <it>Baizongia pistacea</it>, <it>Cinara cedri</it> and <it>Cinara tujafilina</it>), as well as on the characterisation of some intrinsic structural properties of the DNA molecule in these bacteria.</p> <p>Results</p> <p>Interaction graph analysis shows that gene neighbourhoods are conserved between <it>E</it>. <it>coli</it> and <it>Buchnera</it> 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 <it>Buchnera</it>. The transcriptional regulatory network in <it>Buchnera</it> 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 <it>Escherichia coli</it>, such as AlaS, PepA and BolA, and the uncharacterized hypothetical regulators YchA and YrbA). The relative positioning of regulatory genes along the chromosome of <it>Buchnera</it> 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 <it>Buchnera</it> in the different aphids. Based on Stress-Induced Duplex Destabilization (SIDD) measurements, unstable σ⁷⁰ promoters were found specifically associated with the regulator and transporter genes.</p> <p>Conclusions</p> <p>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 <it>Buchnera</it>.</p>