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Genomic and transcriptomic profiling of phoenix colonies.

Devin Sindeldecker1, Matthew Dunn2, Aubree Zimmer2,3

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Researchers explored how Pseudomonas aeruginosa forms antibiotic-tolerant phoenix colonies. A gene knockout (PA3626) prevented their emergence, suggesting a role for tRNA pseudouridine synthase in bacterial survival during antibiotic exposure.

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Area of Science:

  • Microbiology
  • Bacterial Genetics
  • Antibiotic Resistance

Background:

  • Pseudomonas aeruginosa is a significant cause of human infections.
  • Previous studies identified antibiotic-tolerant phoenix colonies and viable but non-culturable (VBNC)-like variants in P. aeruginosa exposed to aminoglycosides.

Purpose of the Study:

  • To investigate the genetic and molecular mechanisms underlying the emergence of phoenix colonies and VBNC-like variants in Pseudomonas aeruginosa.
  • To identify key genes and pathways involved in antibiotic tolerance and survival.

Main Methods:

  • Whole genome sequencing (WGS) to identify genetic mutations.
  • RNA sequencing (RNA-seq) to analyze gene expression profiles.
  • Gene knockout experiments to assess the function of specific genes.

Main Results:

  • Phoenix colonies exhibited a single nucleotide polymorphism (SNP) in the PA4673 gene, encoding a GTP-binding protein.
  • No SNPs were found in VBNC-like colonies compared to the parent strain.
  • RNA-seq identified differentially expressed genes in phoenix colonies, but not altered PA4673 expression.
  • Knocking out the PA3626 gene, which encodes a tRNA pseudouridine synthase, completely abolished phoenix colony formation.

Conclusions:

  • The PA4673 SNP may contribute to phoenix colony emergence, though its precise role requires further investigation.
  • The PA3626 gene, encoding tRNA pseudouridine synthase, is crucial for the development of antibiotic-tolerant phoenix colonies in P. aeruginosa.
  • These findings offer insights into bacterial adaptation and survival strategies under antibiotic stress.