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Background  The  Burkholderia cepacia  complex (Bcc) groups bacterial species with beneficial properties that can improve crop yields or remediate polluted sites but can also lead to dramatic human clinical outcomes among cystic fibrosis (CF) or immuno-compromised individuals. Genome-wide regulatory processes of gene expression could explain parts of this bacterial duality. Transcriptional σ 70  factors are components of these processes. They allow the reversible binding of the DNA-dependent RNA polymerase to form the holoenzyme that will lead to mRNA synthesis from a DNA promoter region. Bcc genome-wide analyses were performed to investigate the major evolutionary trends taking place in the σ 70  family of these bacteria.    Results  Twenty σ 70  paralogous genes were detected in the  Burkholderia cenocepacia  strain J2315 ( Bcen -J2315) genome, of which 14 were of the ECF (extracytoplasmic function) group. Non-ECF paralogs were related to primary ( rpoD ), alternative primary, stationary phase ( rpoS ), flagellin biosynthesis ( fliA ), and heat shock ( rpoH ) factors. The number of σ 70  genetic determinants among this genome was of 2,86 per Mb. This number is lower than the one of  Pseudomonas aeruginosa , a species found in similar habitats including CF lungs. These two bacterial groups showed strikingly different σ 70  family architectures, with only three ECF paralogs in common ( fecI -like,  pvdS  and  algU ).  Bcen -J2315 σ 70  paralogs showed clade-specific distributions. Some paralogs appeared limited to the ET12 epidemic clone ( ecfA2 ), particular Bcc species ( sigI ), the  Burkholderia  genus ( ecfJ ,  ecfF , and  sigJ ), certain proteobacterial groups ( ecfA1 ,  ecfC ,  ecfD ,  ecfE ,  ecfG ,  ecfL ,  ecfM  and  rpoS ), or were broadly distributed in the eubacteria ( ecfI ,  ecfK ,  ecfH ,  ecfB , and  rpoD -,  rpoH -,  fliA -like genes). Genomic instability of this gene family was driven by chromosomal inversion ( ecfA2 ), recent duplication events ( ecfA  and  RpoD ), localized ( ecfG ) and large scale deletions ( sigI ,  sigJ ,  ecfC ,  ecfH , and  ecfK ), and a phage integration event ( ecfE ).    Conclusion  The Bcc σ 70  gene family was found to be under strong selective pressures that could lead to acquisition/deletion, and duplication events modifying its architecture. Comparative analysis of Bcc and  Pseudomonas aeruginosa  σ 70  gene families revealed distinct evolutionary strategies, with the Bcc having selected several alternative primary factors, something not recorded among  P. aeruginosa  and only previously reported to occur among the actinobacteria.

Architecture of Burkholderia cepacia complex σ70 gene family: evidence of alternative primary and clade-specific factors, and genomic instability