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Single cell variability of CRISPR‐Cas interference and adaptation
While CRISPR‐Cas defence mechanisms have been studied on a population level, their temporal dynamics and variability in individual cells have remained unknown. Using a microfluidic device, time‐lapse microscopy and mathematical modelling, we studied invader clearance in Escherichia coli across multi...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10561596/ https://www.ncbi.nlm.nih.gov/pubmed/35467080 http://dx.doi.org/10.15252/msb.202110680 |
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author | McKenzie, Rebecca E Keizer, Emma M Vink, Jochem N A van Lopik, Jasper Büke, Ferhat Kalkman, Vera Fleck, Christian Tans, Sander J Brouns, Stan J J |
author_facet | McKenzie, Rebecca E Keizer, Emma M Vink, Jochem N A van Lopik, Jasper Büke, Ferhat Kalkman, Vera Fleck, Christian Tans, Sander J Brouns, Stan J J |
author_sort | McKenzie, Rebecca E |
collection | PubMed |
description | While CRISPR‐Cas defence mechanisms have been studied on a population level, their temporal dynamics and variability in individual cells have remained unknown. Using a microfluidic device, time‐lapse microscopy and mathematical modelling, we studied invader clearance in Escherichia coli across multiple generations. We observed that CRISPR interference is fast with a narrow distribution of clearance times. In contrast, for invaders with escaping PAM mutations we found large cell‐to‐cell variability, which originates from primed CRISPR adaptation. Faster growth and cell division and higher levels of Cascade increase the chance of clearance by interference, while slower growth is associated with increased chances of clearance by priming. Our findings suggest that Cascade binding to the mutated invader DNA, rather than spacer integration, is the main source of priming heterogeneity. The highly stochastic nature of primed CRISPR adaptation implies that only subpopulations of bacteria are able to respond quickly to invading threats. We conjecture that CRISPR‐Cas dynamics and heterogeneity at the cellular level are crucial to understanding the strategy of bacteria in their competition with other species and phages. |
format | Online Article Text |
id | pubmed-10561596 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-105615962023-10-10 Single cell variability of CRISPR‐Cas interference and adaptation McKenzie, Rebecca E Keizer, Emma M Vink, Jochem N A van Lopik, Jasper Büke, Ferhat Kalkman, Vera Fleck, Christian Tans, Sander J Brouns, Stan J J Mol Syst Biol Articles While CRISPR‐Cas defence mechanisms have been studied on a population level, their temporal dynamics and variability in individual cells have remained unknown. Using a microfluidic device, time‐lapse microscopy and mathematical modelling, we studied invader clearance in Escherichia coli across multiple generations. We observed that CRISPR interference is fast with a narrow distribution of clearance times. In contrast, for invaders with escaping PAM mutations we found large cell‐to‐cell variability, which originates from primed CRISPR adaptation. Faster growth and cell division and higher levels of Cascade increase the chance of clearance by interference, while slower growth is associated with increased chances of clearance by priming. Our findings suggest that Cascade binding to the mutated invader DNA, rather than spacer integration, is the main source of priming heterogeneity. The highly stochastic nature of primed CRISPR adaptation implies that only subpopulations of bacteria are able to respond quickly to invading threats. We conjecture that CRISPR‐Cas dynamics and heterogeneity at the cellular level are crucial to understanding the strategy of bacteria in their competition with other species and phages. John Wiley and Sons Inc. 2022-04-25 /pmc/articles/PMC10561596/ /pubmed/35467080 http://dx.doi.org/10.15252/msb.202110680 Text en © 2022 The Authors. Published under the terms of the CC BY 4.0 license https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Articles McKenzie, Rebecca E Keizer, Emma M Vink, Jochem N A van Lopik, Jasper Büke, Ferhat Kalkman, Vera Fleck, Christian Tans, Sander J Brouns, Stan J J Single cell variability of CRISPR‐Cas interference and adaptation |
title | Single cell variability of CRISPR‐Cas interference and adaptation |
title_full | Single cell variability of CRISPR‐Cas interference and adaptation |
title_fullStr | Single cell variability of CRISPR‐Cas interference and adaptation |
title_full_unstemmed | Single cell variability of CRISPR‐Cas interference and adaptation |
title_short | Single cell variability of CRISPR‐Cas interference and adaptation |
title_sort | single cell variability of crispr‐cas interference and adaptation |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10561596/ https://www.ncbi.nlm.nih.gov/pubmed/35467080 http://dx.doi.org/10.15252/msb.202110680 |
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