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Enright AL, Heelan WJ, Ward RD, Peters JM. CRISPRi functional genomics in bacteria and its application to medical and industrial research. Microbiol Mol Biol Rev 2024:e0017022. [PMID: 38809084 DOI: 10.1128/mmbr.00170-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024] Open
Abstract
SUMMARYFunctional genomics is the use of systematic gene perturbation approaches to determine the contributions of genes under conditions of interest. Although functional genomic strategies have been used in bacteria for decades, recent studies have taken advantage of CRISPR (clustered regularly interspaced short palindromic repeats) technologies, such as CRISPRi (CRISPR interference), that are capable of precisely modulating expression of all genes in the genome. Here, we discuss and review the use of CRISPRi and related technologies for bacterial functional genomics. We discuss the strengths and weaknesses of CRISPRi as well as design considerations for CRISPRi genetic screens. We also review examples of how CRISPRi screens have defined relevant genetic targets for medical and industrial applications. Finally, we outline a few of the many possible directions that could be pursued using CRISPR-based functional genomics in bacteria. Our view is that the most exciting screens and discoveries are yet to come.
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Affiliation(s)
- Amy L Enright
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
- DOE Great Lakes Bioenergy Research Center University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - William J Heelan
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ryan D Ward
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- DOE Great Lakes Bioenergy Research Center University of Wisconsin-Madison, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jason M Peters
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- DOE Great Lakes Bioenergy Research Center University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Yin Z, Zhu Y, Shi J, He Y, Zhang F. The role of the Notch signaling pathway in bacterial infectious diseases. Microb Pathog 2024; 188:106557. [PMID: 38272330 DOI: 10.1016/j.micpath.2024.106557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 01/27/2024]
Abstract
The Notch signaling pathway is the most crucial link in the normal operation and maintenance of physiological functions of mammalian life processes. Notch receptors interact with ligands and this leads to three cleavages and goes on to enter the nucleus to initiate the transcription of target genes. The Notch signaling pathway deeply participates in the differentiation and function of various cells, including immune cells. Recent studies indicate that the outcomes of Notch signaling are changeable and highly dependent on different bacterial infection. The Notch signaling pathway plays a different role in promoting and inhibiting bacterial infection. In this review, we focus on the latest research findings of the Notch signaling pathway in bacterial infectious diseases. The Notch signaling pathway is critically involved in a variety of development processes of immunosuppression of different APCs. The Notch signaling pathway leads to functional changes in epithelial cells to aggravate tissue damage. Specifically, we illustrate the regulatory mechanism of the Notch signaling pathway in various bacterial infections, such as Mycobacterium tuberculosis, Mycobacterium avium paratuberculosis, Mycobacterium leprae, Helicobacter pylori, Klebsiella pneumoniae, Bacillus subtilis, Staphylococcus aureus, Ehrlichia chaffeensis and sepsis. Collectively, this review will not only help beginners intuitively and systematically understand the Notch signaling pathway in bacterial infectious diseases but also help experts to generate fresh insight in this field.
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Affiliation(s)
- Zhengwei Yin
- The First Affiliated Hospital of Xinjiang Medical University, No. 393, Xinyi Road, Urumqi, 830011, Xinjiang, China
| | - Yuejie Zhu
- Reproductive Fertility Assistance Center, First Affiliated Hospital of Xinjiang Medical University, China
| | - Juan Shi
- The First Affiliated Hospital of Xinjiang Medical University, No. 393, Xinyi Road, Urumqi, 830011, Xinjiang, China
| | - Yueyue He
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, No. 393, Xinyi Road, Urumqi, 830011, Xinjiang, China
| | - Fengbo Zhang
- The First Affiliated Hospital of Xinjiang Medical University, No. 393, Xinyi Road, Urumqi, 830011, Xinjiang, China.
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Geissler AS, Fehler AO, Poulsen LD, González-Tortuero E, Kallehauge TB, Alkan F, Anthon C, Seemann SE, Rasmussen MD, Breüner A, Hjort C, Vinther J, Gorodkin J. CRISPRi screen for enhancing heterologous α-amylase yield in Bacillus subtilis. J Ind Microbiol Biotechnol 2023; 50:kuac028. [PMID: 36564025 PMCID: PMC9936203 DOI: 10.1093/jimb/kuac028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 12/19/2022] [Indexed: 12/25/2022]
Abstract
Yield improvements in cell factories can potentially be obtained by fine-tuning the regulatory mechanisms for gene candidates. In pursuit of such candidates, we performed RNA-sequencing of two α-amylase producing Bacillus strains and predict hundreds of putative novel non-coding transcribed regions. Surprisingly, we found among hundreds of non-coding and structured RNA candidates that non-coding genomic regions are proportionally undergoing the highest changes in expression during fermentation. Since these classes of RNA are also understudied, we targeted the corresponding genomic regions with CRIPSRi knockdown to test for any potential impact on the yield. From differentially expression analysis, we selected 53 non-coding candidates. Although CRISPRi knockdowns target both the sense and the antisense strand, the CRISPRi experiment cannot link causes for yield changes to the sense or antisense disruption. Nevertheless, we observed on several instances with strong changes in enzyme yield. The knockdown targeting the genomic region for a putative antisense RNA of the 3' UTR of the skfA-skfH operon led to a 21% increase in yield. In contrast, the knockdown targeting the genomic regions of putative antisense RNAs of the cytochrome c oxidase subunit 1 (ctaD), the sigma factor sigH, and the uncharacterized gene yhfT decreased yields by 31 to 43%.
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Affiliation(s)
- Adrian Sven Geissler
- Center for non-coding RNA in Technology and Health, Department of
Veterinary and Animal Sciences, University of Copenhagen, 1870
Frederiksberg,Denmark
| | - Annaleigh Ohrt Fehler
- Section for Computational and RNA Biology, Department of Biology,
University of Copenhagen, 2200 Copenhagen,Denmark
| | - Line Dahl Poulsen
- Section for Computational and RNA Biology, Department of Biology,
University of Copenhagen, 2200 Copenhagen,Denmark
| | - Enrique González-Tortuero
- Center for non-coding RNA in Technology and Health, Department of
Veterinary and Animal Sciences, University of Copenhagen, 1870
Frederiksberg,Denmark
| | | | - Ferhat Alkan
- Center for non-coding RNA in Technology and Health, Department of
Veterinary and Animal Sciences, University of Copenhagen, 1870
Frederiksberg,Denmark
| | - Christian Anthon
- Center for non-coding RNA in Technology and Health, Department of
Veterinary and Animal Sciences, University of Copenhagen, 1870
Frederiksberg,Denmark
| | - Stefan Ernst Seemann
- Center for non-coding RNA in Technology and Health, Department of
Veterinary and Animal Sciences, University of Copenhagen, 1870
Frederiksberg,Denmark
| | | | | | | | - Jeppe Vinther
- Section for Computational and RNA Biology, Department of Biology,
University of Copenhagen, 2200 Copenhagen,Denmark
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health, Department of
Veterinary and Animal Sciences, University of Copenhagen, 1870
Frederiksberg,Denmark
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