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The essential genome of Burkholderia cenocepacia H111

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Abstract
The study of the minimum set of genes required to sustain life is a fundamental question in biological research. Recent studies on bacterial essential genes suggested that between 350 and 700 genes are essential to support autonomous bacterial cell growth. Essential genes are of interest as potential new antimicrobial drug targets; hence, our aim was to identify the essential genome of the cystic fibrosis (CF) isolate Burkholderia cenocepacia H111. Using a transposon sequencing (Tn-Seq) approach, we identified essential genes required for growth in rich medium under aerobic and microoxic conditions as well as in a defined minimal medium with citrate as a sole carbon source. Our analysis suggests that 398 genes are required for autonomous growth in rich medium, a number that represents only around 5% of the predicted genes of this bacterium. Five hundred twenty-six genes were required to support growth in minimal medium, and 434 genes were essential under microoxic conditions (0.5% O-2). A comparison of these data sets identified 339 genes that represent the minimal set of essential genes required for growth under all conditions tested and can be considered the core essential genome of B. cenocepacia H111. The majority of essential genes were found to be located on chromosome 1, and few such genes were located on chromosome 2, where most of them were clustered in one region. This gene cluster is fully conserved in all Burkholderia species but is present on chromosome 1 in members of the closely related genus Ralstonia, suggesting that the transfer of these essential genes to chromosome 2 in a common ancestor contributed toward the separation of the two genera. IMPORTANCE Transposon sequencing (Tn-Seq) is a powerful method used to identify genes that are essential for autonomous growth under various conditions. In this study, we have identified a set of "core essential genes" that are required for growth under multiple conditions, and these genes represent potential antimicrobial targets. We also identified genes specifically required for growth under low-oxygen and nutrient-limited environments. We generated conditional mutants to verify the results of our Tn-Seq analysis and demonstrate that one of the identified genes was not essential per se but was an artifact of the construction of the mutant library. We also present verified examples of genes that were not truly essential but, when inactivated, showed a growth defect. These examples have identified so-far-underestimated shortcomings of this powerful method.
Keywords
Burkholderia, Tn-Seq, essential genes, minimal genome, CYSTIC-FIBROSIS, CEPACIA COMPLEX, PSEUDOMONAS-AERUGINOSA, ESSENTIAL GENES, TN-SEQ, AMINOARABINOSE, BIOSYNTHESIS, EPIDEMIOLOGY, CHROMOSOME, PROTEINS

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Chicago
Higgins, Steven, Maria Sanchez-Contreras, Stefano Gualdi, Marta Pinto-Carbó, Aurélien Carlier, and Leo Eberl. 2017. “The Essential Genome of Burkholderia Cenocepacia H111.” Journal of Bacteriology 199 (22).
APA
Higgins, S., Sanchez-Contreras, M., Gualdi, S., Pinto-Carbó, M., Carlier, A., & Eberl, L. (2017). The essential genome of Burkholderia cenocepacia H111. JOURNAL OF BACTERIOLOGY, 199(22).
Vancouver
1.
Higgins S, Sanchez-Contreras M, Gualdi S, Pinto-Carbó M, Carlier A, Eberl L. The essential genome of Burkholderia cenocepacia H111. JOURNAL OF BACTERIOLOGY. 2017;199(22).
MLA
Higgins, Steven, Maria Sanchez-Contreras, Stefano Gualdi, et al. “The Essential Genome of Burkholderia Cenocepacia H111.” JOURNAL OF BACTERIOLOGY 199.22 (2017): n. pag. Print.
@article{8529888,
  abstract     = {The study of the minimum set of genes required to sustain life is a fundamental question in biological research. Recent studies on bacterial essential genes suggested that between 350 and 700 genes are essential to support autonomous bacterial cell growth. Essential genes are of interest as potential new antimicrobial drug targets; hence, our aim was to identify the essential genome of the cystic fibrosis (CF) isolate Burkholderia cenocepacia H111. Using a transposon sequencing (Tn-Seq) approach, we identified essential genes required for growth in rich medium under aerobic and microoxic conditions as well as in a defined minimal medium with citrate as a sole carbon source. Our analysis suggests that 398 genes are required for autonomous growth in rich medium, a number that represents only around 5\% of the predicted genes of this bacterium. Five hundred twenty-six genes were required to support growth in minimal medium, and 434 genes were essential under microoxic conditions (0.5\% O-2). A comparison of these data sets identified 339 genes that represent the minimal set of essential genes required for growth under all conditions tested and can be considered the core essential genome of B. cenocepacia H111. The majority of essential genes were found to be located on chromosome 1, and few such genes were located on chromosome 2, where most of them were clustered in one region. This gene cluster is fully conserved in all Burkholderia species but is present on chromosome 1 in members of the closely related genus Ralstonia, suggesting that the transfer of these essential genes to chromosome 2 in a common ancestor contributed toward the separation of the two genera. 
IMPORTANCE Transposon sequencing (Tn-Seq) is a powerful method used to identify genes that are essential for autonomous growth under various conditions. In this study, we have identified a set of {\textacutedbl}core essential genes{\textacutedbl} that are required for growth under multiple conditions, and these genes represent potential antimicrobial targets. We also identified genes specifically required for growth under low-oxygen and nutrient-limited environments. We generated conditional mutants to verify the results of our Tn-Seq analysis and demonstrate that one of the identified genes was not essential per se but was an artifact of the construction of the mutant library. We also present verified examples of genes that were not truly essential but, when inactivated, showed a growth defect. These examples have identified so-far-underestimated shortcomings of this powerful method.},
  articleno    = {e00260-17},
  author       = {Higgins, Steven and Sanchez-Contreras, Maria and Gualdi, Stefano and Pinto-Carb{\'o}, Marta and Carlier, Aur{\'e}lien and Eberl, Leo},
  issn         = {0021-9193},
  journal      = {JOURNAL OF BACTERIOLOGY},
  keyword      = {Burkholderia,Tn-Seq,essential genes,minimal genome,CYSTIC-FIBROSIS,CEPACIA COMPLEX,PSEUDOMONAS-AERUGINOSA,ESSENTIAL GENES,TN-SEQ,AMINOARABINOSE,BIOSYNTHESIS,EPIDEMIOLOGY,CHROMOSOME,PROTEINS},
  language     = {eng},
  number       = {22},
  pages        = {14},
  title        = {The essential genome of Burkholderia cenocepacia H111},
  url          = {http://dx.doi.org/10.1128/jb.00260-17},
  volume       = {199},
  year         = {2017},
}

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