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Volume 6, Issue 11

Functional genomics reveals the toxin–antitoxin repertoire and AbiE activity in Open Access

Abstract

Bacteriophage defences are divided into innate and adaptive systems. sp. ATCC 39006 has three CRISPR-Cas adaptive immune systems, but its innate immune repertoire is unknown. Here, we re-sequenced and annotated the genome and predicted its toxin–antitoxin (TA) systems. TA systems can provide innate phage defence through abortive infection by causing infected cells to ‘shut down’, limiting phage propagation. To assess TA system function on a genome-wide scale, we utilized transposon insertion and RNA sequencing. Of the 32 TA systems predicted bioinformatically, 4 resembled pseudogenes and 11 were demonstrated to be functional based on transposon mutagenesis. Three functional systems belonged to the poorly characterized but widespread, AbiE, abortive infection/TA family. AbiE is a type IV TA system with a predicted nucleotidyltransferase toxin. To investigate the mode of action of this toxin, we measured the transcriptional response to AbiEii expression. We observed dysregulated levels of tRNAs and propose that the toxin targets tRNAs resulting in bacteriostasis. A recent report on a related toxin shows this occurs through addition of nucleotides to tRNA(s). This study has demonstrated the utility of functional genomics for probing TA function in a high-throughput manner, defined the TA repertoire in and shown the consequences of AbiE induction.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): AbiE , abortive infection , toxin–antitoxin and transposon mutagenesis
Funding
This study was supported by the:
  • University of Otago Doctoral Scholarship
    • Principle Award Recipient: Leah M. Smith
  • University of Otago Doctoral Scholarship
    • Principle Award Recipient: Hannah G. Hampton
  • Tertiary Education Commission
    • Principle Award Recipient: Peter C Fineran
  • H2020 Marie Skłodowska-Curie Actions (Award MSCA - 842656)
    • Principle Award Recipient: Sean Meaden
  • Ministry for Business Innovation and Employment (Award C10X1308)
    • Principle Award Recipient: Shaun Ferguson
  • University of Otago
    • Principle Award Recipient: Peter C Fineran
  • Marsden Fund
    • Principle Award Recipient: Peter C Fineran
© 2020 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2024-04-23
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Functional genomics reveals the toxin–antitoxin repertoire and AbiE activity in Serratia
M Gen 6, e000458 (2020); https://doi.org/10.1099/mgen.0.000458
/content/journal/mgen/10.1099/mgen.0.000458
/content/journal/mgen/10.1099/mgen.0.000458
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