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In silico prediction and qPCR validation of novel sRNAs in Propionibacterium acnes KPA171202

Praveen P Balgir1, Shobha R Dhiman2, Puneet Kaur1

  • 1Department of Biotechnology, Punjabi University, Patiala, Punjab 147 002, India.

Journal, Genetic Engineering & Biotechnology
|January 17, 2019
PubMed

Insights

This study identified novel small non-coding RNAs (sRNAs) in Propionibacterium acnes, a pathogen linked to acne and cancer. Five new sRNAs were validated, showing peak expression during the stationary growth phase, suggesting a regulatory role.

Area of Science:

  • Microbiology
  • Molecular Biology
  • Genomics

Background:

  • Propionibacterium acnes is an opportunistic pathogen implicated in diseases from acne to prostate cancer.
  • Bacterial small non-coding RNAs (sRNAs) are crucial regulators of gene expression, influencing virulence and adaptation.
  • No sRNAs were previously predicted for P. acnes KPA171202 in existing databases.

Purpose of the Study:

  • To identify and characterize small non-coding RNAs (sRNAs) in Propionibacterium acnes KPA171202.
  • To validate predicted sRNAs and investigate their expression patterns during bacterial growth.
  • To lay the groundwork for understanding sRNA-mediated gene regulation in P. acnes.

Main Methods:

  • Bioinformatic prediction of sRNAs using SIPHT.
  • Homology searches against Rfam database.
  • Validation of candidate sRNAs via reverse transcriptase-polymerase chain reaction (RT-PCR) and sequencing.
  • Quantitative PCR (qPCR) to determine sRNA expression levels across different growth phases.

Main Results:

  • Eight potential candidate sRNAs were predicted in P. acnes KPA171202.
  • One predicted sRNA had a known homolog, while seven were identified as novel.
  • Five novel sRNAs were successfully validated through RT-PCR and sequencing.
  • Validated sRNAs were expressed in both exponential and stationary growth phases, with highest expression in the stationary phase.

Conclusions:

  • This study represents the first identification of sRNAs in P. acnes KPA171202.
  • The validated sRNAs are expressed differentially across growth phases, indicating a potential regulatory role.
  • Further research is warranted to elucidate the specific targets and regulatory functions of these novel sRNAs in P. acnes pathogenesis.
Keywords:
PathogenesisPropionibacterium acnesSmall non-coding RNAsncRNAssRNA

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