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

Abstract

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 σ70 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.

Figure 1

Spatial organisation of the BAp chromosome compared with that of E. coli. First line bars: genes involved in aerobic/anaerobic metabolism (dark blue), DNA replication (orange), rrn genes (upper red), and transition phase (brown). Second line bars: selected genes involved in the control of DNA topology (green). Third line bars: selected genes encoding NAPs (light blue). Fourth line bars: selected genes involved in modulating RNAP activity, including σ factor-utilization regulators (light green), secondary channel-binding proteins (pink), termination/elongation factors (red), and RNAP subunits (black). Grey dotted lines link pairs of orthologous genes between BAp and E. coli. Selected genes are those described by Sobetzko et al. [39].

Figure 2

SIDD profile of the 400 bp located around the start codon of all CDS.BAp: black, continuous curve; E. coli: red, continuous curve. The upper curves (dotted lines) depict the densities of the length of the 5’ UTR regions in BAp (black) and in E. coli (red), as determined by BPROM. No Y-coordinate scale is given for these curves: the density peaks correspond to the most frequent transcription start site positions (relative to the start codon) in the two bacteria.

Figure 3

General comparison, between BAp and E. coli, of four physical properties of the DNA molecule. A: intrinsic curvature; B: base-stacking energy; C: base-pair propeller twist and D: SIDD. Global and local null models are described in the Methods section. Parameter values were estimated using 300 bp non-overlapping sliding windows.

Figure 4

SIDD distribution in the different intergenic regions of the BAp DNA molecule. (A): CDS (black), divergent (blue), convergent (yellow), tandem (green). (B): same as A, separating the tandem region intra- transcription unit (yellow) from the inter-transcription unit regions (black).