Defining the ABC of gene essentiality in streptococci

Charbonneau, Amelia R. L.; Forman, Oliver P.; Cain, Amy K.; Newland, Graham; Robinson, Carl; Boursnell, Mike; Parkhill, Julian; Leigh, James A.; Maskell, Duncan J.; Waller, Andrew S.

Abstract

Background: Utilising next generation sequencing to interrogate saturated bacterial mutant libraries provides unprecedented information for the assignment of genome-wide gene essentiality. Exposure of saturated mutant libraries to specific conditions and subsequent sequencing can be exploited to uncover gene essentiality relevant to the condition. Here we present a barcoded transposon directed insertion-site sequencing (TraDIS) system to define an essential gene list for Streptococcus equi subsp. equi, the causative agent of strangles in horses, for the first time. The gene essentiality data for this group C Streptococcus was compared to that of group A and B streptococci.

Results: Six barcoded variants of pGh9:ISS1 were designed and used to generate mutant libraries containing between 33,000-66,000 unique mutants. TraDIS was performed on DNA extracted from each library and data were analysed separately and as a combined master pool. Gene essentiality determined that 19.5% of the S. equi genome was essential. Gene essentialities were compared to those of group A and group B streptococci, identifying concordances of 90.2% and 89.4%, respectively and an overall concordance of 83.7% between the three species.

Conclusions: The use of barcoded pGh9:ISS1 to generate mutant libraries provides a highly useful tool for the assignment of gene function in S. equi and other streptococci. The shared essential gene set of group A, B and C streptococci provides further evidence of the close genetic relationships between these important pathogenic bacteria. Therefore, the ABC of gene essentiality reported here provides a solid foundation towards reporting the functional genome of streptococci.

Citation

Charbonneau, A. R. L., Forman, O. P., Cain, A. K., Newland, G., Robinson, C., Boursnell, M., …Waller, A. S. (2017). Defining the ABC of gene essentiality in streptococci. BMC Genomics, 18(1), Article 426. https://doi.org/10.1186/s12864-017-3794-3

• Journal Article Type: Article
• Acceptance Date: May 14, 2017
• Publication Date: May 31, 2017
• Deposit Date: Jun 5, 2017
• Publicly Available Date: Jun 5, 2017
• Journal: BMC Genomics
• Electronic ISSN: 1471-2164
• Publisher: Springer Verlag
• Peer Reviewed: Peer Reviewed
• Volume: 18
• Issue: 1
• Article Number: 426
• DOI: https://doi.org/10.1186/s12864-017-3794-3
• Keywords: Transposon, Sequencing, Essentiality, Barcode
• Public URL: https://nottingham-repository.worktribe.com/output/863700
• Publisher URL: http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3794-3
• Contract Date: Jun 5, 2017