Structure and dynamics of the operon map of Buchnera aphidicola sp. strain APS.
BACKGROUND
Gene expression regulation is still poorly documented in bacteria with highly reduced genomes. Understanding the evolution and mechanisms underlying the regulation of gene transcription in Buchnera aphidicola, the primary endosymbiont of aphids, is expected both to enhance our understanding of this nutritionally based association and to provide an intriguing case-study of the evolution of gene expression regulation in a reduced bacterial genome.


RESULTS
A Bayesian predictor was defined to infer the B. aphidicola transcription units, which were further validated using transcriptomic data and RT-PCR experiments. The characteristics of B. aphidicola predicted transcription units (TUs) were analyzed in order to evaluate the impact of operon map organization on the regulation of gene transcription.On average, B. aphidicola TUs contain more genes than those of E. coli. The global layout of B. aphidicola operon map was mainly shaped by the big reduction and the rearrangements events, which occurred at the early stage of the symbiosis. Our analysis suggests that this operon map may evolve further only by small reorganizations around the frontiers of B. aphidicola TUs, through promoter and/or terminator sequence modifications and/or by pseudogenization events. We also found that the need for specific transcription regulation exerts some pressure on gene conservation, but not on gene assembling in the operon map in Buchnera. Our analysis of the TUs spacing pointed out that a selection pressure is maintained on the length of the intergenic regions between divergent adjacent gene pairs.


CONCLUSIONS
B. aphidicola can seemingly only evolve towards a more polycistronic operon map. This implies that gene transcription regulation is probably subject to weak selection pressure in Buchnera conserving operons composed of genes with unrelated functions.
INSA-Lyon, UMR203 BF2I, INRA, Biologie Fonctionnelle Insectes et Interactions, Bât, Louis Pasteur 20 ave, Albert Einstein, F-69621 Villeurbanne, France. lilia.brinza@insa-lyon.fr
Lilia
L
Brinza
Federica
F
Calevro
Gabrielle
G
Duport
Karen
K
Gaget
Christian
C
Gautier
Hubert
H
Charles
D001483:Base Sequence; D020635:Buchnera / Q000235:genetics*; D003062:Codon / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D021901:DNA, Intergenic / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D019143:Evolution, Molecular; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames / Q000235:genetics; D009876:Operon / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics; D012372:ROC Curve; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013728:Terminator Regions, Genetic / Q000235:genetics; D014158:Transcription, Genetic
D003062:Codon; D021901:DNA, Intergenic