Chromosome organisation in Buchnera: a dynamic active structure involved in gene expression regulation

International audienceMost bacterial chromosomes consist of a single closed-circular DNA molecule folded into a compact and dynamic structure called the nucleoid. Variations of chromosome 3D-structure act as a global regulatory factor of gene expression. More particularly, the modulation of genome architecture is admitted to belong to the class of mechanisms allowing genome-wide transcriptional profile variation in response to environmental changes [1, 2].We searched for evidences of spatial organization of the chromosome in an extremely intriguing bacterial model: Buchnera aphidicola. Associated with most agricultural pest aphids and being partly responsible for their harmfulness, Buchnera are one of the most studied intracellular symbiotic bacteria of insects. Their genomes present all the characteristics of intracellular bacteria: (1) small size of 400 - 600 kb depending on aphid species, (2) highly biased base composition towards A and T and (3) high evolutionary rate due to the isolation of Buchnera populations within the host cells combined with the drastic bottlenecks that occur in the population dynamics of the bacteria during their transmission to the aphid progeny.A crucial stage for the symbiosis comprehension passes through the understanding of symbiont gene expression regulation, and yet little is known about the transcriptional regulation capabilities of the bacteria. Given the “poor” catalogue of transcriptional factors it was suggested that the bacteria are no longer able to regulate their gene expression. Also, Buchnera conserved target genes for regulatory proteins absent in their genome. Nevertheless, recent works using a dedicated microarray showed that Buchnera respond specifically to somenutritional stresses imposed to their host [3].The aim of this work was to study potential structural units of the Buchnera chromosome and the impact they could have on the gene expression regulation. For this purpose, we analysed the potential structural domains of the chromosome at different scales and the main contributor proteins for the organization and maintenance of these domains. Our study brings evidences for (1) the existence of structural chromosomal units at several scales, (2) a functionally complete set of proteins essential for nucleoid organization and (3) the tight interdependence between these proteins, the chromosome architecture and the gene expression profile.Basic genomic structural elements in bacteria participating to the chromosome organization are transcription units (operons). A transcription unit contains one or several adjacent genes transcribed as a single mRNA. Thus, genes belonging to the same transcriptional unit display strong correlated transcription levels. A first annotation of Buchnera transcription units was available in BioCyc (http://biocyc.org/). We found that some of these transcriptional units were not consistent with the analysis of the gene expression profile. Thus, we decided to re-annotate the transcription units of Buchnera taking into account gene expression levels, gene order conservation, sequence features of Buchnera, like Rho-independent terminators inferred by the bioinformatics tool (TransTermHP, [4]) and specific intergenic distances. We tested this new annotation with microarray gene expression data.A higher level of structural units in bacterial genomes is represented by the organization in topological domains (~10kbp in E. coli [5]). These structures are mainly organized and maintained by Nucleoid Associated Proteins (NAPs). Analysis of the NAP set of Buchnera pointed out that, despite genome reduction, the bacteria retains the most important members of the group (IHF, H-NS, Fis, DnaA and HU). Our bioinformatics analysis of these proteins confirms a strong conservation of structural domains and 3D structure. Moreover, key amino acids (their mutation compromises NAPs function in E. coli) are also well conserved. As NAPs must frequently bind DNA (every 10 kbp) to form dynamic inter-domains barriers, they rather recognize specific topologic structures (i.e., bend DNA) than specific motive binding sites. By using Curvature program [6]), we showed that Buchnera have a more curved DNA than E. coli (this result may be partially explained by the strong A-T bias) , that might influence the size and shape of their topological domains.Combination of topological domains and DNA fold are at the origin of a third class of larger structural units in bacterial chromosomes. Previous results of our team pointed out a periodic transcriptional pattern that supports the existence of these kinds of structures in Buchnera [7]. We completed this work by using a more realistic distance on the chromosome (i.e., physical distance (bp), instead of the “gene number” distance).Our work brings several evidences that Buchnera chromosome is a functional structure probably playing an active role in gene expression regulation. This kind of regulation was often neglected in free-living bacteria but might be central in shrunken genomes of endosymbionts. A short-term perspective of our work will be to inactivate in vivo specific NAP proteins of Buchnera and analyse the induced modifications within the gene expression profile of the symbiotic bacteria

Chromosome organisation in Buchnera: a dynamic active structure involved in gene expression regulation

International audienceMost bacterial chromosomes consist of a single closed-circular DNA molecule folded into a compact and dynamic structure called the nucleoid. Variations of chromosome 3D-structure act as a global regulatory factor of gene expression. More particularly, the modulation of genome architecture is admitted to belong to the class of mechanisms allowing genome-wide transcriptional profile variation in response to environmental changes [1, 2].We searched for evidences of spatial organization of the chromosome in an extremely intriguing bacterial model: Buchnera aphidicola. Associated with most agricultural pest aphids and being partly responsible for their harmfulness, Buchnera are one of the most studied intracellular symbiotic bacteria of insects. Their genomes present all the characteristics of intracellular bacteria: (1) small size of 400 - 600 kb depending on aphid species, (2) highly biased base composition towards A and T and (3) high evolutionary rate due to the isolation of Buchnera populations within the host cells combined with the drastic bottlenecks that occur in the population dynamics of the bacteria during their transmission to the aphid progeny.A crucial stage for the symbiosis comprehension passes through the understanding of symbiont gene expression regulation, and yet little is known about the transcriptional regulation capabilities of the bacteria. Given the “poor” catalogue of transcriptional factors it was suggested that the bacteria are no longer able to regulate their gene expression. Also, Buchnera conserved target genes for regulatory proteins absent in their genome. Nevertheless, recent works using a dedicated microarray showed that Buchnera respond specifically to somenutritional stresses imposed to their host [3].The aim of this work was to study potential structural units of the Buchnera chromosome and the impact they could have on the gene expression regulation. For this purpose, we analysed the potential structural domains of the chromosome at different scales and the main contributor proteins for the organization and maintenance of these domains. Our study brings evidences for (1) the existence of structural chromosomal units at several scales, (2) a functionally complete set of proteins essential for nucleoid organization and (3) the tight interdependence between these proteins, the chromosome architecture and the gene expression profile.Basic genomic structural elements in bacteria participating to the chromosome organization are transcription units (operons). A transcription unit contains one or several adjacent genes transcribed as a single mRNA. Thus, genes belonging to the same transcriptional unit display strong correlated transcription levels. A first annotation of Buchnera transcription units was available in BioCyc (http://biocyc.org/). We found that some of these transcriptional units were not consistent with the analysis of the gene expression profile. Thus, we decided to re-annotate the transcription units of Buchnera taking into account gene expression levels, gene order conservation, sequence features of Buchnera, like Rho-independent terminators inferred by the bioinformatics tool (TransTermHP, [4]) and specific intergenic distances. We tested this new annotation with microarray gene expression data.A higher level of structural units in bacterial genomes is represented by the organization in topological domains (~10kbp in E. coli [5]). These structures are mainly organized and maintained by Nucleoid Associated Proteins (NAPs). Analysis of the NAP set of Buchnera pointed out that, despite genome reduction, the bacteria retains the most important members of the group (IHF, H-NS, Fis, DnaA and HU). Our bioinformatics analysis of these proteins confirms a strong conservation of structural domains and 3D structure. Moreover, key amino acids (their mutation compromises NAPs function in E. coli) are also well conserved. As NAPs must frequently bind DNA (every 10 kbp) to form dynamic inter-domains barriers, they rather recognize specific topologic structures (i.e., bend DNA) than specific motive binding sites. By using Curvature program [6]), we showed that Buchnera have a more curved DNA than E. coli (this result may be partially explained by the strong A-T bias) , that might influence the size and shape of their topological domains.Combination of topological domains and DNA fold are at the origin of a third class of larger structural units in bacterial chromosomes. Previous results of our team pointed out a periodic transcriptional pattern that supports the existence of these kinds of structures in Buchnera [7]. We completed this work by using a more realistic distance on the chromosome (i.e., physical distance (bp), instead of the “gene number” distance).Our work brings several evidences that Buchnera chromosome is a functional structure probably playing an active role in gene expression regulation. This kind of regulation was often neglected in free-living bacteria but might be central in shrunken genomes of endosymbionts. A short-term perspective of our work will be to inactivate in vivo specific NAP proteins of Buchnera and analyse the induced modifications within the gene expression profile of the symbiotic bacteria

Genomic DNA: an attractive candidate for microarray data normalization

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Spatial transcriptomic patterns in the genome of the endosymbiotic bacterium Buchnera aphidicola

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Relationship between gene expression and genome properties in Buchnera aphidicola, the primary endosymbiont of the pea aphid Acyrthosiphon pisum

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Régulation génétique et métabolique chez Buchnera aphidicola (AgroBi 2006)

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Different levels of transcriptional regulation due to trophic constraints in the reduced genome of Buchnera aphidicola APS

1-ACL (articles avec comité de lecture)Symbiotic associations involving intracellular microorganisms and animals are widespread, especially for species feeding on poor or unbalanced diets. Buchnera aphidicola, the obligate intracellular bacterium associated with most aphid species, provides its hosts with essential amino acids (EAAs), nutrients in short supply in the plant phloem sap. The Buchnera genome has undergone severe reductions during intracellular evolution. Genes for EAA biosynthesis are conserved, but most of the transcriptional regulatory elements are lost. This work addresses two main questions: is transcription in Buchnera (i) regulated and (ii) scaled to aphid EAA demand? Two microarray experiments were designed for profiling the gene expression in Buchnera. The first one was characterized by a specific depletion of tyrosine and phenylalanine in the aphid diet, and the second experiment combined a global diminution of EAAs in the aphid diet with a sucrose concentration increase to manipulate the aphid growth rate. Aphid biological performance and budget analysis (the balance between EAAs provided by the diet and those synthesized by Buchnera) were performed to quantify the nutritional demand from the aphids toward their symbiotic bacteria. Despite the absence of known regulatory elements, a significant transcriptional regulation was observed at different levels of organization in the Buchnera genome : between genes, within putative transcription units, and within specific metabolic pathways. However, unambiguousevidence for transcriptional changes underpinning the scaling of EAA biosynthesis to aphid demand was not obtained. The phenotypic relevance of the transcriptional response from the reduced genome of Buchnera is addressed

Regulation of expression following nutritional stresses in the reduced genome of Buchnera aphidicola, "Is there any life left?"

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Regulation of expression following nutritional stresses in the reduced genome of Buchnera aphidicola, "Is there any life left?"

3-INV (conférences invitées