Biology (Nov 2022)

Computationally Designed Anti-LuxP DNA Aptamer Suppressed Flagellar Assembly- and Quorum Sensing-Related Gene Expression in <i>Vibrio parahaemolyticus</i>

  • Nur Afiqah Md Yusof,
  • Siti Aisyah Razali,
  • Azyyati Mohd Padzil,
  • Benjamin Yii Chung Lau,
  • Syarul Nataqain Baharum,
  • Nor Azlan Nor Muhammad,
  • Nurul Hanun Ahmad Raston,
  • Chou Min Chong,
  • Natrah Fatin Mohd Ikhsan,
  • Magdalena Lenny Situmorang,
  • Low Chen Fei

DOI
https://doi.org/10.3390/biology11111600
Journal volume & issue
Vol. 11, no. 11
p. 1600

Abstract

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(1) Background: Quorum sensing (QS) is the chemical communication between bacteria that sense chemical signals in the bacterial population to control phenotypic changes through the regulation of gene expression. The inhibition of QS has various potential applications, particularly in the prevention of bacterial infection. QS can be inhibited by targeting the LuxP, a periplasmic receptor protein that is involved in the sensing of the QS signaling molecule known as the autoinducer 2 (AI-2). The sensing of AI-2 by LuxP transduces the chemical information through the inner membrane sensor kinase LuxQ protein and activates the QS cascade. (2) Methods: An in silico approach was applied to design DNA aptamers against LuxP in this study. A method combining molecular docking and molecular dynamics simulations was used to select the oligonucleotides that bind to LuxP, which were then further characterized using isothermal titration calorimetry. Subsequently, the bioactivity of the selected aptamer was examined through comparative transcriptome analysis. (3) Results: Two aptamer candidates were identified from the ITC, which have the lowest dissociation constants (Kd) of 0.2 and 0.5 micromolar. The aptamer with the lowest Kd demonstrated QS suppression and down-regulated the flagellar-assembly-related gene expression. (4) Conclusions: This study developed an in silico approach to design an aptamer that possesses anti-QS properties.

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