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Home / Equine Research Bank / BMC Genomics / Defining the ABC of gene essentiality in streptococci.
BMC genomics2017; 18(1); 426; doi: 10.1186/s12864-017-3794-3

Defining the ABC of gene essentiality in streptococci.

Abstract: 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. 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. 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.
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Publication Date: 2017-05-31 PubMed ID: 28569133PubMed Central: PMC5452409DOI: 10.1186/s12864-017-3794-3Google Scholar: Lookup
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  • Journal Article
  • Research Support
  • Non-U.S. Gov't

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research article details the investigation into essential genes for the group C Streptococcus, S. equi, the bacteria responsible for strangles in horses. This is achieved primarily through the use of a novel TraDIS system involving barcoded transposons, coupled with next-generation sequencing.

Methodology

  • The researchers developed a system for defining an essential gene list for S. equi. This was done by creating mutant libraries using barcoded versions of a transposon named pGh9:ISS1.
  • Six unique barcoded variants of pGh9:ISS1 were designed and used to generate mutant libraries, which contained between 33,000 and 66,000 unique mutants.
  • TraDIS (Transposon Directed Insertion-Site Sequencing), a technique that uses next-generation sequencing, was employed to analyse DNA extracted from each of these libraries.
  • The data were analyzed both separately and as a combined master pool, giving a comprehensive view of gene distribution and function within the studied genome.

Findings

  • Results determined that 19.5% of the S. equi genome was found to be essential, meaning these specific genes are vital for the survival and efficient function of the Streptococcus.
  • In order to glean broader insights, the researchers compared these identified essential genes in S. equi with those found in Group A and B streptococci.
  • There was high concordance between the three groups, with matches of 90.2% and 89.4% for Group A and B streptococci, respectively, and an overall concordance of 83.7% across the three bacterial species.

Implications and Conclusions

  • The methodology of using barcoded pGh9:ISS1 to create mutant libraries provides a powerful tool for exploring gene function in S. equi and other streptococci.
  • The high degree of commonality in essential genes across streptococci species reinforces their close genetic relationships, and this understanding can contribute to more effective treatments for diseases caused by these bacteria.
  • The results contribute to the foundational understanding, or the ‘ABC’, of gene essentiality in streptococci, which can aid future exploration into the functional genomics of these bacteria.

Cite This Article

APA
Charbonneau ARL, Forman OP, Cain AK, Newland G, Robinson C, Boursnell M, Parkhill J, Leigh JA, Maskell DJ, Waller AS. (2017). Defining the ABC of gene essentiality in streptococci. BMC Genomics, 18(1), 426. https://doi.org/10.1186/s12864-017-3794-3

Publication

BMC genomics
ISSN: 1471-2164
NlmUniqueID: 100965258
Country: England
Language: English
Volume: 18
Issue: 1
Pages: 426
PII: 426

Researcher Affiliations

Charbonneau, Amelia R L
  • Animal Health Trust, Lanwades Park, Newmarket, Suffolk, UK. amy.charbonneau@aht.org.uk.
  • Department of Veterinary Medicine, University of Cambridge, Cambridge, UK. amy.charbonneau@aht.org.uk.
Forman, Oliver P
  • Animal Health Trust, Lanwades Park, Newmarket, Suffolk, UK.
Cain, Amy K
  • The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
  • Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia.
Newland, Graham
  • Animal Health Trust, Lanwades Park, Newmarket, Suffolk, UK.
Robinson, Carl
  • Animal Health Trust, Lanwades Park, Newmarket, Suffolk, UK.
Boursnell, Mike
  • Animal Health Trust, Lanwades Park, Newmarket, Suffolk, UK.
Parkhill, Julian
  • The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
Leigh, James A
  • The School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, Nottingham, UK.
Maskell, Duncan J
  • Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
Waller, Andrew S
  • Animal Health Trust, Lanwades Park, Newmarket, Suffolk, UK.

MeSH Terms

  • Genes, Bacterial / genetics
  • Genes, Essential / genetics
  • Genomics
  • High-Throughput Nucleotide Sequencing
  • Mutation
  • Streptococcus / genetics

Grant Funding

  • G1100100 / Medical Research Council
  • 1503883 / Biotechnology and Biological Sciences Research Council

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