Defining the ABC of gene essentiality in streptococci
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 unc...
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| Format: | Article |
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BioMed Central
2017
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| Online Access: | https://eprints.nottingham.ac.uk/43394/ |
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| author | 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. |
| author_facet | 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. |
| author_sort | Charbonneau, Amelia R. L. |
| building | Nottingham Research Data Repository |
| collection | Online Access |
| description | 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. |
| first_indexed | 2025-11-14T19:51:47Z |
| format | Article |
| id | nottingham-43394 |
| institution | University of Nottingham Malaysia Campus |
| institution_category | Local University |
| last_indexed | 2025-11-14T19:51:47Z |
| publishDate | 2017 |
| publisher | BioMed Central |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | nottingham-433942020-05-04T18:48:24Z https://eprints.nottingham.ac.uk/43394/ 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. 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. BioMed Central 2017-05-31 Article PeerReviewed Charbonneau, Amelia R. L., Forman, Oliver P., Cain, Amy K., Newland, Graham, Robinson, Carl, Boursnell, Mike, Parkhill, Julian, Leigh, James A., Maskell, Duncan J. and Waller, Andrew S. (2017) Defining the ABC of gene essentiality in streptococci. BMC Genomics, 18 (1). 426/1-426/11. ISSN 1471-2164 Transposon Sequencing Essentiality Barcode http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3794-3 doi:10.1186/s12864-017-3794-3 doi:10.1186/s12864-017-3794-3 |
| spellingShingle | Transposon Sequencing Essentiality Barcode 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. Defining the ABC of gene essentiality in streptococci |
| title | Defining the ABC of gene essentiality in streptococci |
| title_full | Defining the ABC of gene essentiality in streptococci |
| title_fullStr | Defining the ABC of gene essentiality in streptococci |
| title_full_unstemmed | Defining the ABC of gene essentiality in streptococci |
| title_short | Defining the ABC of gene essentiality in streptococci |
| title_sort | defining the abc of gene essentiality in streptococci |
| topic | Transposon Sequencing Essentiality Barcode |
| url | https://eprints.nottingham.ac.uk/43394/ https://eprints.nottingham.ac.uk/43394/ https://eprints.nottingham.ac.uk/43394/ |