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CRISPR Interference (CRISPRi) Mediated Suppression of OmpR Gene in E. coli: An Alternative Approach to Inhibit Biofilm

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Abstract

Biofilm plays an important role in the community and hospital-acquired infections. Especially E. coli biofilm that contributes towards the significant part of medical devices associated with microbial infections. OmpR/EnvZ, a two-component system, is one of the regulatory mechanisms involved in transcription regulation in response to environmental osmolarity changes. The main objective of this study was to elucidate the role of the OmpR/EnvZ two-component system in regulating the biofilm through curli and fimbriae (FimH gene), a contrary approach towards biofilm inhibition. In this study, the CRISPRi technique was used to suppress the expression of the OmpR gene. The RT-PCR assay was performed to quantify mRNA gene expression of curli and biofilm producing genes, and the data were further confirmed by different microscopic, spectroscopic and biofilm quantification assay (Crystal Violet). It is the first time we have shown downregulation of the OmpR gene in biofilm causing clinical isolates of E. coli, which further suppressed the FimH gene, leading to biofilm reduction. The crystal violet assay and microscopic studies also confirmed the biofilm reduction. We conclude that the OmpR gene of the OmpR/EnvZ two-component system could be one of the targets for biofilm mediated infection intervention. Our findings open new vistas to explore the pathways and targets to control biofilm mediated infections.

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Acknowledgements

DST-PURSE Phase-II created facilities are highly acknowledged.

Funding

This work was supported by internal funds of the Interdisciplinary Biotechnology Unit, AMU, Aligarh, India.

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  1. Azna Zuberi and Mohd W. Azam have contributed equally to this work.

Authors and Affiliations

  1. Medical Microbiology and Molecular Biology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, Uttar Pradesh, India

    Azna Zuberi, Mohd W. Azam & Asad U. Khan

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  1. Azna Zuberi
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  2. Mohd W. Azam
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  3. Asad U. Khan
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Contributions

AZ designed problem, performed experiments, analyzed data and wrote the manuscript, MWA performed experiments and wrote part of the manuscript, AUK designed problem, analyzed data and edited the draft manuscript.

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Correspondence to Asad U. Khan.

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All the strains used in this study are already published strains which has already been approved from institutional ethical committee before these were published.

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Zuberi, A., Azam, M.W. & Khan, A.U. CRISPR Interference (CRISPRi) Mediated Suppression of OmpR Gene in E. coli: An Alternative Approach to Inhibit Biofilm. Curr Microbiol 79, 78 (2022). https://doi.org/10.1007/s00284-021-02760-x

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