ArticleBMC genomics2013
Genomic analysis of the regulatory elements and links with intrinsic DNA structural properties in the shrunken genome of Buchnera.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 42 citations in OpenAlex.
- Emergence of supercoiling-mediated regulatory networks through the evolution of bacterial chromosome organization.PLoS computational biology · 2025Article
- A complete DNA repair system assembled by two endosymbionts restores heat tolerance of the insect host.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Host-specific co-evolution likely driven by diet in Buchnera aphidicola.BMC genomics · 2024Article
- Assessing in vivo the impact of gene context on transcription through DNA supercoiling.Nucleic acids research · 2023Article
- Spatiotemporal Coupling of DNA Supercoiling and Genomic Sequence Organization-A Timing Chain for the Bacterial Growth Cycle?Biomolecules · 2022Review
- Role of the Discriminator Sequence in the Supercoiling Sensitivity of Bacterial Promoters.mSystems · 2021Article
- Composition of Transcription Machinery and Its Crosstalk with Nucleoid-Associated Proteins and Global Transcription Factors.Biomolecules · 2021Review
- Spatial and morphological reorganization of endosymbiosis during metamorphosis accommodates adult metabolic requirements in a weevil.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Coherent Domains of Transcription Coordinate Gene Expression During Bacterial Growth and Adaptation.Microorganisms · 2019Review
- Determination of the Gene Regulatory Network of a Genome-Reduced Bacterium Highlights Alternative Regulation Independent of Transcription Factors.Cell systems · 2019Article
- Bacterial genome architecture shapes global transcriptional regulation by DNA supercoiling.Nucleic acids research · 2019Article
- DNA Supercoiling: an Ancestral Regulator of Gene Expression in Pathogenic Bacteria?Computational and structural biotechnology journal · 2019Review
- Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655.Nucleic acids research · 2018Article
- Transcription Factors Exhibit Differential Conservation in Bacteria with Reduced Genomes.PloS one · 2016Article
- Integration of syntactic and semantic properties of the DNA code reveals chromosomes as thermodynamic machines converting energy into information.Cellular and molecular life sciences : CMLS · 2013Review
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3 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundBuchnera 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.
resultsInteraction 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.
conclusionsThis 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.
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