Computationally Designed Anti-LuxP DNA Aptamer Suppressed Flagellar Assembly- and Quorum Sensing-Related Gene Expression in <i>Vibrio parahaemolyticus</i>
(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...
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2022-11-01
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| author | 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 |
| author_facet | 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 |
| author_sort | Nur Afiqah Md Yusof |
| collection | DOAJ |
| description | (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 (K<sub>d</sub>) of 0.2 and 0.5 micromolar. The aptamer with the lowest K<sub>d</sub> 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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| issn | 2079-7737 |
| language | English |
| last_indexed | 2024-03-09T19:15:40Z |
| publishDate | 2022-11-01 |
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| series | Biology |
| spelling | doaj.art-ead36ec4965f495d82f708ad38500a362023-11-24T03:48:05ZengMDPI AGBiology2079-77372022-11-011111160010.3390/biology11111600Computationally Designed Anti-LuxP DNA Aptamer Suppressed Flagellar Assembly- and Quorum Sensing-Related Gene Expression in <i>Vibrio parahaemolyticus</i>Nur Afiqah Md Yusof0Siti Aisyah Razali1Azyyati Mohd Padzil2Benjamin Yii Chung Lau3Syarul Nataqain Baharum4Nor Azlan Nor Muhammad5Nurul Hanun Ahmad Raston6Chou Min Chong7Natrah Fatin Mohd Ikhsan8Magdalena Lenny Situmorang9Low Chen Fei10Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, MalaysiaFaculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Nerus 21030, Terengganu, MalaysiaMalaysia Genome and Vaccine Institute (MGVI), National Institute of Biotechnology Malaysia (NIBM), Jalan Bangi, Kajang 43000, Selangor, MalaysiaMalaysian Palm Oil Board, Persiaran Institusi, Bandar Baru Bangi, Kajang 43000, Selangor, MalaysiaInstitute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, MalaysiaInstitute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, MalaysiaDepartment of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, MalaysiaDepartment of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, MalaysiaSchool of Life Sciences and Technology, Institut Teknologi Bandung, Bandung 40132, IndonesiaInstitute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia(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 (K<sub>d</sub>) of 0.2 and 0.5 micromolar. The aptamer with the lowest K<sub>d</sub> 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.https://www.mdpi.com/2079-7737/11/11/1600single-stranded DNA aptamerquorum sensingLuxPin silico modelingmolecular dynamics simulationisothermal titration calorimetry |
| spellingShingle | 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 Computationally Designed Anti-LuxP DNA Aptamer Suppressed Flagellar Assembly- and Quorum Sensing-Related Gene Expression in <i>Vibrio parahaemolyticus</i> Biology single-stranded DNA aptamer quorum sensing LuxP in silico modeling molecular dynamics simulation isothermal titration calorimetry |
| title | Computationally Designed Anti-LuxP DNA Aptamer Suppressed Flagellar Assembly- and Quorum Sensing-Related Gene Expression in <i>Vibrio parahaemolyticus</i> |
| title_full | Computationally Designed Anti-LuxP DNA Aptamer Suppressed Flagellar Assembly- and Quorum Sensing-Related Gene Expression in <i>Vibrio parahaemolyticus</i> |
| title_fullStr | Computationally Designed Anti-LuxP DNA Aptamer Suppressed Flagellar Assembly- and Quorum Sensing-Related Gene Expression in <i>Vibrio parahaemolyticus</i> |
| title_full_unstemmed | Computationally Designed Anti-LuxP DNA Aptamer Suppressed Flagellar Assembly- and Quorum Sensing-Related Gene Expression in <i>Vibrio parahaemolyticus</i> |
| title_short | Computationally Designed Anti-LuxP DNA Aptamer Suppressed Flagellar Assembly- and Quorum Sensing-Related Gene Expression in <i>Vibrio parahaemolyticus</i> |
| title_sort | computationally designed anti luxp dna aptamer suppressed flagellar assembly and quorum sensing related gene expression in i vibrio parahaemolyticus i |
| topic | single-stranded DNA aptamer quorum sensing LuxP in silico modeling molecular dynamics simulation isothermal titration calorimetry |
| url | https://www.mdpi.com/2079-7737/11/11/1600 |
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