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CRISPR and RNA interference: similarities across immune systems
Available online at www.sciencedirect.com
ScienceDirect Physics of Life Reviews 11 (2014) 135–136 www.elsevier.com/locate/plrev
Comment
CRISPR and RNA interference: similarities across immune systems Comment on “Diversity, evolution, and therapeutic applications of small RNAs in prokaryotic and eukaryotic immune systems” by Edwin L. Cooper and Nicola Overstreet Adi Stern a,b a Department of Microbiology and Immunology, University of California, San Francisco, CA, USA b Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
Received 7 November 2013; accepted 11 November 2013 Available online 13 November 2013 Communicated by M. Frank-Kamenetskii
Since the confirmation of CRISPR as a prokaryotic immune system, interest in this fascinating system has soared. The review of Cooper and Overstreet [1] surveys the CRISPR system first from a mechanistic approach, and then from an evolutionary perspective. The review raises the analogy with the adaptive immune system, previously thought to exist only in vertebrates. This leads to more analogies with various small RNA interference systems. Finally, therapeutic applications of small RNAs are discussed. In line with many other prokaryotic systems that were co-opted into biotechnological applications (e.g., restriction enzymes), a recent explosion of research papers have used CRISPR for manipulation of cellular DNA across a broad range of organisms, ranging from rat to human to zebrafish (e.g., [2–4]). While the road from basic to therapeutic applications may still be long, the authors [1] aptly note that augmenting the human immune system with the broadly used mechanisms of RNA interference could be a powerful and useful approach. The interesting comparison between CRISPR and small RNAs delineates the diversity of immune defense mechanisms found today in nature, yet also underscores the similarities among them. Not long ago, a clear-cut distinction was made between innate and adaptive immunity, and the latter was assumed to be exclusive to vertebrates. Yet the prokaryotic CRISPR system is by all means a system, which allows memory of previous infections, and further even allows inheritance of this memory. Interestingly, the discoveries on CRISPR come at a time when more and more revelations are made on the mammalian innate system. In the previous decade an array of different mammalian “intrinsic immunity” factors (e.g., TRIM5a, APOBEC, and Tetherin) have been discovered, which block viral replication from within the infected cell [5]. Furthermore, it has recently been discovered that antiviral RNA interference operates in mammals and not only in plants and invertebrates [6]. Cooper and Overstreet [1] go on to discuss the similarities between defense mechanisms based on small RNAs. Indeed the similarity between CRISPRs and piRNAs are striking. Are these similarities due to shared ancestry, or are they a case of convergent evolution? While the former argument is impelling, it may be likely that the constraints imposed by parasites have led to the independent emergence of many immune systems with similar properties. This suggests that there may be a few “general solutions” to the problem of parasites: recognition of foreign patterns and DOI of original article: http://dx.doi.org/10.1016/j.plrev.2013.11.002. 1571-0645/$ – see front matter © 2013 Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.plrev.2013.11.004
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A. Stern / Physics of Life Reviews 11 (2014) 135–136
motifs (e.g., restriction modification systems, siRNAs, and toll-like receptors), infected cell death to prevent spread of infection (abortive infection, and apoptosis), and memory of previous infection (CRISPRs, piRNAs, and adaptive immunity). While these similarities are broad, they serve to illustrate that it is possible for similar solutions to arise independently multiple times, suggesting that parallel evolution may be abundant across different immune systems. In fact, it may be reasonable to assume that all organisms that face attack from parasites and/or selfish elements must defend their genomic integrity by similar means of both adaptive and innate immunity. It is likely that we have yet to learn much about the breadth and diversity of immune systems across the three domains of life. References [1] Cooper EL, Overstreet N. Diversity, evolution, and therapeutic applications of small RNAs in prokaryotic and eukaryotic immune systems. Phys Life Rev 2014;11(1):113–34 [in this issue]. [2] Hwang WY, et al. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol 2013;31:227–9. [3] Li D, et al. Heritable gene targeting in the mouse and rat using a CRISPR-Cas system. Nat Biotechnol 2013;31:681–3. [4] Maeder M, et al. CRISPR RNA-guided activation of endogenous human genes. Nat Methods 2013;10:977–9. [5] Bieniasz PD. Intrinsic immunity: a front-line defense against viral attack. Nat Immunol 2004;5:1109–15. [6] Maillard PV, et al. Antiviral RNA interference in mammalian cells. Science 2013;342:235–8.
ScienceDirect Physics of Life Reviews 11 (2014) 135–136 www.elsevier.com/locate/plrev
Comment
CRISPR and RNA interference: similarities across immune systems Comment on “Diversity, evolution, and therapeutic applications of small RNAs in prokaryotic and eukaryotic immune systems” by Edwin L. Cooper and Nicola Overstreet Adi Stern a,b a Department of Microbiology and Immunology, University of California, San Francisco, CA, USA b Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
Received 7 November 2013; accepted 11 November 2013 Available online 13 November 2013 Communicated by M. Frank-Kamenetskii
Since the confirmation of CRISPR as a prokaryotic immune system, interest in this fascinating system has soared. The review of Cooper and Overstreet [1] surveys the CRISPR system first from a mechanistic approach, and then from an evolutionary perspective. The review raises the analogy with the adaptive immune system, previously thought to exist only in vertebrates. This leads to more analogies with various small RNA interference systems. Finally, therapeutic applications of small RNAs are discussed. In line with many other prokaryotic systems that were co-opted into biotechnological applications (e.g., restriction enzymes), a recent explosion of research papers have used CRISPR for manipulation of cellular DNA across a broad range of organisms, ranging from rat to human to zebrafish (e.g., [2–4]). While the road from basic to therapeutic applications may still be long, the authors [1] aptly note that augmenting the human immune system with the broadly used mechanisms of RNA interference could be a powerful and useful approach. The interesting comparison between CRISPR and small RNAs delineates the diversity of immune defense mechanisms found today in nature, yet also underscores the similarities among them. Not long ago, a clear-cut distinction was made between innate and adaptive immunity, and the latter was assumed to be exclusive to vertebrates. Yet the prokaryotic CRISPR system is by all means a system, which allows memory of previous infections, and further even allows inheritance of this memory. Interestingly, the discoveries on CRISPR come at a time when more and more revelations are made on the mammalian innate system. In the previous decade an array of different mammalian “intrinsic immunity” factors (e.g., TRIM5a, APOBEC, and Tetherin) have been discovered, which block viral replication from within the infected cell [5]. Furthermore, it has recently been discovered that antiviral RNA interference operates in mammals and not only in plants and invertebrates [6]. Cooper and Overstreet [1] go on to discuss the similarities between defense mechanisms based on small RNAs. Indeed the similarity between CRISPRs and piRNAs are striking. Are these similarities due to shared ancestry, or are they a case of convergent evolution? While the former argument is impelling, it may be likely that the constraints imposed by parasites have led to the independent emergence of many immune systems with similar properties. This suggests that there may be a few “general solutions” to the problem of parasites: recognition of foreign patterns and DOI of original article: http://dx.doi.org/10.1016/j.plrev.2013.11.002. 1571-0645/$ – see front matter © 2013 Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.plrev.2013.11.004
136
A. Stern / Physics of Life Reviews 11 (2014) 135–136
motifs (e.g., restriction modification systems, siRNAs, and toll-like receptors), infected cell death to prevent spread of infection (abortive infection, and apoptosis), and memory of previous infection (CRISPRs, piRNAs, and adaptive immunity). While these similarities are broad, they serve to illustrate that it is possible for similar solutions to arise independently multiple times, suggesting that parallel evolution may be abundant across different immune systems. In fact, it may be reasonable to assume that all organisms that face attack from parasites and/or selfish elements must defend their genomic integrity by similar means of both adaptive and innate immunity. It is likely that we have yet to learn much about the breadth and diversity of immune systems across the three domains of life. References [1] Cooper EL, Overstreet N. Diversity, evolution, and therapeutic applications of small RNAs in prokaryotic and eukaryotic immune systems. Phys Life Rev 2014;11(1):113–34 [in this issue]. [2] Hwang WY, et al. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol 2013;31:227–9. [3] Li D, et al. Heritable gene targeting in the mouse and rat using a CRISPR-Cas system. Nat Biotechnol 2013;31:681–3. [4] Maeder M, et al. CRISPR RNA-guided activation of endogenous human genes. Nat Methods 2013;10:977–9. [5] Bieniasz PD. Intrinsic immunity: a front-line defense against viral attack. Nat Immunol 2004;5:1109–15. [6] Maillard PV, et al. Antiviral RNA interference in mammalian cells. Science 2013;342:235–8.