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Open Access Research article

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

Lilia Brinza123, Federica Calevro1 and Hubert Charles12*

Author Affiliations

1 UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, INSA-Lyon, INRA, Université de Lyon, Villeurbanne, France

2 BAMBOO, INRIA Rhône-Alpes, Montbonnot Saint-Martin, France

3 Present address: Université de Lyon, Université Lyon1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Lyon, France

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BMC Genomics 2013, 14:73  doi:10.1186/1471-2164-14-73

Published: 1 February 2013

Additional files

Additional file 1:

(Figure): Functional analysis (GO terms) of BAp genes.

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Additional file 2:

(Figure): Conservation of the protein sequences of the six NAP encoding genes found in Buchnera.

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Additional file 3:

(Table): Number (#) of specific NAP target genes in E. coli (as found in the RegulonDB) and of the orthologous genes (putative conserved targets) in the four Buchnera strains BAp, BSg, BBp and BCc.

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Additional file 4:

(Table): Number (#) of predicted σ70 promoters in the four strains of Buchnera.

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Additional file 5:

(Figure): Distribution of σ70 prediction scores and 5’UTR lengths in BAp and E. coli.

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Additional file 6:

(Figure): Venn-diagram of the putative σ32 regulons in Buchnera.

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Additional file 7:

(Table): Transporter (T) and regulatory (R) genes of BAp significantly correlated with low SIDD values (i.e., associated with unstable promoter regions).

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