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The type I-E CRISPR-Cas system: Biology and applications of an adaptive immune system in bacteria
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Microbiology.
2017 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

CRISPR-Cas systems are adaptive immune systems in bacteria and archaea, consisting of a clustered regularly interspaced short palindromic repeats (CRISPR) array and CRISPR associated (Cas) proteins. In this work, the type I-E CRISPR-Cas system of Escherichia coli was studied.

CRISPR-Cas immunity is divided into three stages. In the first stage, adaptation, Cas1 and Cas2 store memory of invaders in the CRISPR array as short intervening sequences, called spacers. During the expression stage, the array is transcribed, and subsequently processed into small CRISPR RNAs (crRNA), each consisting of one spacer and one repeat. The crRNAs are bound by the Cascade multi-protein complex. During the interference step, Cascade searches for DNA molecules complementary to the crRNA spacer. When a match is found, the target DNA is degraded by the recruited Cas3 nuclease.

Host factors required for integration of new spacers into the CRISPR array were first investigated. Deleting recD, involved in DNA repair, abolished memory formation by reducing the concentration of the Cas1-Cas2 expression plasmid, leading to decreased amounts of Cas1 to levels likely insufficient for spacer integration. Deletion of RecD has an indirect effect on adaptation. To facilitate detection of adaptation, a sensitive fluorescent reporter was developed where an out-of-frame yfp reporter gene is moved into frame when a new spacer is integrated, enabling fluorescent detection of adaptation. Integration can be detected in single cells by a variety of fluorescence-based methods. A second aspect of this thesis aimed at investigating spacer elements affecting target interference. Spacers with predicted secondary structures in the crRNA impaired the ability of the CRISPR-Cas system to prevent transformation of targeted plasmids. Lastly, in absence of Cas3, Cascade was successfully used to inhibit transcription of specific genes by preventing RNA polymerase access to the promoter.

The CRISPR-Cas field has seen rapid development since the first demonstration of immunity almost ten years ago. However, much research remains to fully understand these interesting adaptive immune systems and the research presented here increases our understanding of the type I-E CRISPR-Cas system. 

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2017. , p. 61
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1466
Keywords [en]
CRISPR, CRISPR-Cas, virus defense, bacteria, bacteriophage, adaptation, spacer integration, interference, gene silencing, fluorescent reporter, Escherichia coli
National Category
Microbiology
Research subject
Microbiology
Identifiers
URN: urn:nbn:se:uu:diva-312234ISBN: 978-91-554-9787-3 (print)OAI: oai:DiVA.org:uu-312234DiVA, id: diva2:1062815
Public defence
2017-02-24, A1:111a, BMC, Husargatan 3, Uppsala, 09:00 (English)
Opponent
Supervisors
Available from: 2017-02-02 Created: 2017-01-08 Last updated: 2017-02-07
List of papers
1. Deletion of recD indirectly reduce adaptation in the type I-E CRISPR-Cas system
Open this publication in new window or tab >>Deletion of recD indirectly reduce adaptation in the type I-E CRISPR-Cas system
(English)Manuscript (preprint) (Other academic)
National Category
Microbiology
Identifiers
urn:nbn:se:uu:diva-312230 (URN)
Available from: 2017-01-08 Created: 2017-01-08 Last updated: 2017-01-09
2. Quantification of CRISPR-Cas spacer integration using a fluorescent reporter
Open this publication in new window or tab >>Quantification of CRISPR-Cas spacer integration using a fluorescent reporter
Show others...
(English)Manuscript (preprint) (Other academic)
National Category
Microbiology
Identifiers
urn:nbn:se:uu:diva-312231 (URN)
Available from: 2017-01-08 Created: 2017-01-08 Last updated: 2017-01-09
3. Effect of spacer sequence on efficiency of Type I-E CRISPR-Cas systems
Open this publication in new window or tab >>Effect of spacer sequence on efficiency of Type I-E CRISPR-Cas systems
(English)Manuscript (preprint) (Other academic)
National Category
Microbiology
Identifiers
urn:nbn:se:uu:diva-312233 (URN)
Available from: 2017-01-08 Created: 2017-01-08 Last updated: 2017-01-09
4. Efficient programmable gene silencing by Cascade
Open this publication in new window or tab >>Efficient programmable gene silencing by Cascade
Show others...
2015 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 43, no 1, p. 237-246Article in journal (Refereed) Published
Abstract [en]

Methods that permit controlled changes in the expression of genes are important tools for biological and medical research, and for biotechnological applications. Conventional methods are directed at individually changing each gene, its regulatory elements or its mRNA's translation rate. We demonstrate that the CRISPR-associated DNA-binding Cascade complex can be used for efficient, long-lasting and programmable gene silencing. When Cascade is targeted to a promoter sequence the transcription of the downstream gene is inhibited, resulting in dramatically reduced expression. The specificity of Cascade binding is provided by the integral crRNA component, which is easily designed to target virtually any stretch of DNA. Cascade targeted to the ORF sequence of the gene can also silence expression, albeit at lower efficiency. The system can be used to silence plasmid and chromosome targets, simultaneously target several genes and is active in different bacterial species and strains. The findings described here are an addition to the expanding range of CRISPR-based technologies and may be adapted to additional organisms and cell systems.

National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-249042 (URN)10.1093/nar/gku1257 (DOI)000350207100026 ()25435544 (PubMedID)
Available from: 2015-04-23 Created: 2015-04-10 Last updated: 2018-02-28Bibliographically approved

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