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Amlinger, Lina
Publications (5 of 5) Show all publications
Amlinger, L., Hoekzema, M., Wagner, G. E. H., Koskiniemi, S. & Lundgren, M. (2017). Fluorescent CRISPR Adaptation Reporter for rapid quantification of spacer acquisition. Scientific Reports, 7, Article ID 10392.
Open this publication in new window or tab >>Fluorescent CRISPR Adaptation Reporter for rapid quantification of spacer acquisition
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2017 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 10392Article in journal (Refereed) Published
Abstract [en]

CRISPR-Cas systems are adaptive prokaryotic immune systems protecting against horizontally transferred DNA or RNA such as viruses and other mobile genetic elements. Memory of past invaders is stored as spacers in CRISPR loci in a process called adaptation. Here we developed a novel assay where spacer integration results in fluorescence, enabling detection of memory formation in single cells and quantification of as few as 0.05% cells with expanded CRISPR arrays in a bacterial population. Using this fluorescent CRISPR Adaptation Reporter (f-CAR), we quantified adaptation of the two CRISPR arrays of the type I-E CRISPR-Cas system in Escherichia coli, and confirmed that more integration events are targeted to CRISPR-II than to CRISPR-I. The f-CAR conveniently analyzes and compares many samples, allowing new insights into adaptation. For instance, we show that in an E. coli culture the majority of acquisition events occur in late exponential phase.

Keywords
quorum sensing controls, escherichia-coli, cas adaptation, immune-system, host factor, dna, resistance, elements, repeats, bacteriophage
National Category
Microbiology
Identifiers
urn:nbn:se:uu:diva-334399 (URN)10.1038/s41598-017-10876-z (DOI)000408997700091 ()
Available from: 2017-12-08 Created: 2017-12-08 Last updated: 2017-12-08Bibliographically approved
Amlinger, L., Hoekzema, M., Wagner, G. E. H., Koskiniemi, S. & Lundgren, M. (2017). Fluorescent CRISPR Adaptation Reporter for rapid quantification of spacer acquisition. Scientific Reports, 7, Article ID 10392.
Open this publication in new window or tab >>Fluorescent CRISPR Adaptation Reporter for rapid quantification of spacer acquisition
Show others...
2017 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 10392Article in journal (Refereed) Published
Abstract [en]

CRISPR-Cas systems are adaptive prokaryotic immune systems protecting against horizontally transferred DNA or RNA such as viruses and other mobile genetic elements. Memory of past invaders is stored as spacers in CRISPR loci in a process called adaptation. Here we developed a novel assay where spacer integration results in fluorescence, enabling detection of memory formation in single cells and quantification of as few as 0.05% cells with expanded CRISPR arrays in a bacterial population. Using this fluorescent CRISPR Adaptation Reporter (f-CAR), we quantified adaptation of the two CRISPR arrays of the type I-E CRISPR-Cas system in Escherichia coli, and confirmed that more integration events are targeted to CRISPR-II than to CRISPR-I. The f-CAR conveniently analyzes and compares many samples, allowing new insights into adaptation. For instance, we show that in an E. coli culture the majority of acquisition events occur in late exponential phase.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 2017
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-335401 (URN)10.1038/s41598-017-10876-z (DOI)000408997700091 ()28871175 (PubMedID)
Funder
Swedish Research CouncilWenner-Gren FoundationsThe Royal Swedish Academy of SciencesScience for Life Laboratory - a national resource center for high-throughput molecular bioscience
Available from: 2017-12-05 Created: 2017-12-05 Last updated: 2018-02-28Bibliographically approved
Amlinger, L. (2017). The type I-E CRISPR-Cas system: Biology and applications of an adaptive immune system in bacteria. (Doctoral dissertation). Uppsala: Acta Universitatis Upsaliensis
Open this publication in new window or tab >>The type I-E CRISPR-Cas system: Biology and applications of an adaptive immune system in bacteria
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
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:nbn:se:uu:diva-312234 (URN)978-91-554-9787-3 (ISBN)
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
Rath, D., Amlinger, L., Hoekzema, M., Devulapally, P. R. & Lundgren, M. (2015). Efficient programmable gene silencing by Cascade. Nucleic Acids Research, 43(1), 237-246
Open this publication in new window or tab >>Efficient programmable gene silencing by Cascade
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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
Rath, D., Amlinger, L., Rath, A. & Lundgren, M. (2015). The CRISPR-Cas immune system: Biology, mechanisms and applications. Biochimie, 117, 119-128
Open this publication in new window or tab >>The CRISPR-Cas immune system: Biology, mechanisms and applications
2015 (English)In: Biochimie, ISSN 0300-9084, E-ISSN 1638-6183, Vol. 117, p. 119-128Article, review/survey (Refereed) Published
Abstract [en]

Viruses are a common threat to cellular life, not the least to bacteria and archaea who constitute the majority of life on Earth. Consequently, a variety of mechanisms to resist virus infection has evolved. A recent discovery is the adaptive immune system in prokaryotes, a type of system previously thought to be present only in vertebrates. The system, called CRISPR-Cas, provide sequence-specific adaptive immunity and fundamentally affect our understanding of virus host interaction. CRISPR-based immunity acts by integrating short virus sequences in the cell's CRISPR locus, allowing the cell to remember, recognize and clear infections. There has been rapid advancement in our understanding of this immune system and its applications, but there are many aspects that await elucidation making the field an exciting area of research. This review provides an overview of the field and highlights unresolved issues.

Keywords
CRISPR, Cascade, Cas9, Cas3, Cmr/Csm
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-266137 (URN)10.1016/j.biochi.2015.03.025 (DOI)000361864900013 ()25868999 (PubMedID)
Funder
Swedish Research CouncilWenner-Gren Foundations
Available from: 2015-11-17 Created: 2015-11-05 Last updated: 2017-12-01Bibliographically approved
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