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Detection of Bacteria Using Fluorogenic DNAzymes
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High-throughput detection of RNA processing in bacteria.

Erin E Gill1, Luisa S Chan1, Geoffrey L Winsor1

  • 1Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.

BMC Genomics
|March 29, 2018
PubMed
Summary

This study reveals extensive RNA processing in Pseudomonas aeruginosa using monophosphate RNA-Seq (pRNA-Seq). Researchers discovered novel RNA cleavage events and a potential new form of transcriptional regulation in this important bacterium.

Keywords:
Gene expressionGene regulationNucleasesPseudomonas aeruginosaRNA processingRNA-SeqTranscriptiondRNA-SeqpRNA-Seq

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Area of Science:

  • Microbiology
  • Molecular Biology
  • Genomics

Background:

  • Understanding RNA processing is crucial for deciphering bacterial biology.
  • Pseudomonas aeruginosa is a medically significant bacterium known for its multi-drug resistance.
  • Detailed analysis of its transcriptome is essential for biological insights.

Purpose of the Study:

  • To systematically map RNA cleavage and dephosphorylation sites in Pseudomonas aeruginosa.
  • To identify transcriptional start sites (TSS) and analyze their relationship with RNA processing.
  • To investigate novel mechanisms of RNA maturation, turnover, and transcriptional regulation.

Main Methods:

  • Monophosphate RNA-Seq (pRNA-Seq) was employed to map 5'-monophosphate terminated RNA (pRNA) sites.
  • Differential RNA-Seq (dRNA-Seq) was used to map transcriptional start sites (TSS).
  • Comparative analysis of pRNA-Seq, dRNA-Seq, and conventional RNA-Seq data across various growth conditions.

Main Results:

  • Identified known and novel RNA processing sites, including those near genes involved in oxidative phosphorylation and purine metabolism.
  • Discovered precise mRNA cleavage events at codon positions, often corresponding to RNase E motifs.
  • Predicted 3159 potential TSS and identified 105 antiparallel TSS pairs suggesting bidirectional transcription initiation from palindromic motifs.
  • Confirmed expression of small non-coding RNAs (ncRNAs), with differential expression observed during swarming and biofilm formation.

Conclusions:

  • pRNA-Seq provides a genome-wide view of RNA processing, revealing extensive transcript processing in Pseudomonas aeruginosa.
  • The study offers new insights into RNA maturation, turnover, and a potential novel mechanism for transcriptional regulation.
  • Sequence data is publicly available in the NCBI sequence read archive for further research.