title: Architecture of Burkholderia cepacia complex sigma70 gene family: evidence of alternative primary and clade-specific factors, and genomic instability.
abstract: 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 sigma70 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 sigma70 family of these bacteria.
  
  
  RESULTS
  Twenty sigma70 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 sigma70 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 sigma70 family architectures, with only three ECF paralogs in common (fecI-like, pvdS and algU). Bcen-J2315 sigma70 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).
  
  
  CONCLUSIONS
  The Bcc sigma70 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 sigma70 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.
authors.affiliation: Université de Lyon, Lyon, France. menard@biomserv.univ-lyon1.fr
authors.forename: Aymeric
authors.initials: A
authors.lastname: Menard
authors.forename: Paulina Estrada
authors.initials: PE
authors.lastname: de Los Santos
authors.forename: Arnault
authors.initials: A
authors.lastname: Graindorge
authors.forename: Benoit
authors.initials: B
authors.lastname: Cournoyer
mesh_terms: D016956:Burkholderia cepacia / Q000145:classification / Q000235:genetics*; D012321:DNA-Directed RNA Polymerases / Q000235:genetics*; D019143:Evolution, Molecular; D005798:Genes, Bacterial; D042822:Genomic Instability; D010802:Phylogeny; D012808:Sigma Factor / Q000235:genetics*; D013045:Species Specificity