CRISPR-Cas Part II

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 2: Line 2:
SEE [[CRISPR-Cas|CRISPR-Cas Part I]]
SEE [[CRISPR-Cas|CRISPR-Cas Part I]]
==CRISPR adaptation (continuation CRISPR adaptation from [[CRISPR-Cas|CRISPR-Cas Part I]])==
==CRISPR adaptation (continuation CRISPR adaptation from [[CRISPR-Cas|CRISPR-Cas Part I]])==
-
Primed spacer adaptation so far has been demonstrated only in type I systems <ref name="Rev450">doi:10.1038/ncomms1937</ref><ref name="Rev465">doi:10.1093/nar/gkt1154</ref><ref name="Rev466">doi:10.1093/nar/gku527</ref>. This priming mechanism constitutes a positive feedback loop that facilitates the acquisition of new spacers from formerly encountered genetic elements (67). Priming can occur even with spacers that contain several mismatches, making them incompetent as guides for targeting the cognate foreign DNA (67). Based on PAM selection, functional spacers are preferentially acquired during naïve adaptation. This initial acquisition event triggers a rapid priming response after subsequent infections. Priming appears to be a major pathway of CRISPR adaptation, at least for some type I systems (65). Primed adaptation strongly depends on the spacer sequence (68), and the acquisition efficiency is highest in close proximity to the priming site. In addition, the orientation of newly inserted spacers indicates a strand bias, which is consistentwith the involvement of singlestranded adaption intermediates (69). According to one proposed model (70), replication forks in the invader’s DNA are blocked by the Cascade complex bound to the priming crRNA, enabling the RecG helicase and the Cas3 helicase/nuclease proteins to attack the DNA. The ends at the collapsed forks then could be targeted by RecBCD, which provides DNA fragments for new spacer generation (70). Given that the use of crRNA for priming has much less strict sequence requirements than direct targeting of the invading DNA, priming is a powerful strategy that might have evolved in the course of the host-parasite arms race to reduce the escape by viral mutants, to provide robust resistance against invading DNA, and to enhance self/nonself discrimination. Naïve as well as primed adaptation in the subtype I-F system of Pseudomonas aeruginosa CRISPR-Cas require both the adaptation and the effector module (69).
+
Primed spacer adaptation so far has been demonstrated only in type I systems <ref name="Rev450">doi:10.1038/ncomms1937</ref><ref name="Rev465">doi:10.1093/nar/gkt1154</ref><ref name="Rev466">doi:10.1093/nar/gku527</ref>. This priming mechanism constitutes a positive feedback loop that facilitates the acquisition of new spacers from formerly encountered genetic elements <ref name="Rev467">doi:10.1073/pnas.1400071111</ref>. Priming can occur even with spacers that contain several mismatches, making them incompetent as guides for targeting the cognate foreign DNA <ref name="Rev467">doi:10.1073/pnas.1400071111</ref>. Based on PAM selection, functional spacers are preferentially acquired during naïve adaptation. This initial acquisition event triggers a rapid priming response after subsequent infections. Priming appears to be a major pathway of CRISPR adaptation, at least for some type I systems <ref name="Rev465">doi:10.1093/nar/gkt1154</ref>. Primed adaptation strongly depends on the spacer sequence <ref name="Rev468">doi:10.1093/nar/gkv1259</ref>, and the acquisition efficiency is highest in close proximity to the priming site. In addition, the orientation of newly inserted spacers indicates a strand bias, which is consistentwith the involvement of singlestranded adaption intermediates <ref name="Rev469">doi:10.1093/nar/gkv1261</ref>. According to one proposed model <ref name="Rev470">doi:10.1093/nar/gkv1213</ref>, replication forks in the invader’s DNA are blocked by the Cascade complex bound to the priming crRNA, enabling the RecG helicase and the Cas3 helicase/nuclease proteins to attack the DNA. The ends at the collapsed forks then could be targeted by RecBCD, which provides DNA fragments for new spacer generation <ref name="Rev470">doi:10.1093/nar/gkv1213</ref>. Given that the use of crRNA for priming has much less strict sequence requirements than direct targeting of the invading DNA, priming is a powerful strategy that might have evolved in the course of the host-parasite arms race to reduce the escape by viral mutants, to provide robust resistance against invading DNA, and to enhance self/nonself discrimination. Naïve as well as primed adaptation in the subtype I-F system of Pseudomonas aeruginosa CRISPR-Cas require both the adaptation and the effector module <ref name="Rev469">doi:10.1093/nar/gkv1261</ref>.<ref name="Rev4">doi:10.1126/science.aad5147</ref>
In the type II-A system, the Cas9-tracrRNA complex and Csn2 are involved in spacer acquisition along with the Cas1-Cas2 complex (53, 71); the involvement of Cas9 in adaptation is likely to be a general feature of type II systems. Although the key residues of Cas9 involved in PAM recognition are dispensable for spacer acquisition, they are essential for the incorporation of new spacers with the correct PAM sequence (71).
In the type II-A system, the Cas9-tracrRNA complex and Csn2 are involved in spacer acquisition along with the Cas1-Cas2 complex (53, 71); the involvement of Cas9 in adaptation is likely to be a general feature of type II systems. Although the key residues of Cas9 involved in PAM recognition are dispensable for spacer acquisition, they are essential for the incorporation of new spacers with the correct PAM sequence (71).
-
The involvement of Cas9 in PAM recognition and protospacer selection (71) suggests that in type II systems Cas1 may have lost this role. Similarly, Cas4 that is present in subtypes IA-D and II-B has been proposed to be involved in the CRISPR adaptation process, and this prediction has been validated experimentally for type I-B (65). Cas4 is absent in the subtype II-C system of Campylobacter jejuni. Nonetheless, a conserved Cas4-like protein found in Campylobacter bacteriophages can activate spacer acquisition to use host DNA as an effective decoy to bacteriophage
+
The involvement of Cas9 in PAM recognition and protospacer selection (71) suggests that in type II systems Cas1 may have lost this role. Similarly, Cas4 that is present in subtypes IA-D and II-B has been proposed to be involved in the CRISPR adaptation process, and this prediction has been validated experimentally for type I-B <ref name="Rev465">doi:10.1093/nar/gkt1154</ref>. Cas4 is absent in the subtype II-C system of Campylobacter jejuni. Nonetheless, a conserved Cas4-like protein found in Campylobacter bacteriophages can activate spacer acquisition to use host DNA as an effective decoy to bacteriophage DNA. Bacteria that acquire self-spacers and escape phage infection must either overcome CRISPR-mediated autoimmunity by loss of the interference functions, leaving them susceptible to foreign DNA invasions, or tolerate changes in gene regulation (72). Furthermore, in subtypes I-U and V-B, Cas4 is fused to Cas1, which implies cooperation between these proteins during adaptation. In type I-F systems, Cas2 is fused to Cas3 (19), which suggests a dual role for Cas3 (20): involvement in adaptation as well as in interference. These findings support the coupling between the adaptation and interference stages of CRISPR-Cas defense during priming.<ref name="Rev4">doi:10.1126/science.aad5147</ref>
-
DNA. Bacteria that acquire self-spacers and escape phage infection must either overcome CRISPR-mediated autoimmunity by loss of the interference
+
-
functions, leaving them susceptible to foreign DNA invasions, or tolerate changes in gene regulation (72). Furthermore, in subtypes I-U and V-B,
+
-
Cas4 is fused to Cas1, which implies cooperation between these proteins during adaptation. In type I-F systems, Cas2 is fused to Cas3 (19), which suggests a dual role for Cas3 (20): involvement in adaptation as well as in interference. These findings support the coupling between the
+
-
adaptation and interference stages of CRISPR-Cas defense during priming.
+
=Summary of the most extensively characterized CRISPR endoribonucleases<ref name="Rev3">PMID:25468820</ref><ref name="Rev4">doi:10.1126/science.aad5147</ref>=
=Summary of the most extensively characterized CRISPR endoribonucleases<ref name="Rev3">PMID:25468820</ref><ref name="Rev4">doi:10.1126/science.aad5147</ref>=

Revision as of 10:19, 18 December 2016

PDB ID 4qyz

Drag the structure with the mouse to rotate

References

  1. ↑ Datsenko KA, Pougach K, Tikhonov A, Wanner BL, Severinov K, Semenova E. Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system. Nat Commun. 2012 Jul 10;3:945. doi: 10.1038/ncomms1937. PMID:22781758 doi:http://dx.doi.org/10.1038/ncomms1937
  2. ↑ 2.0 2.1 2.2 Li M, Wang R, Zhao D, Xiang H. Adaptation of the Haloarcula hispanica CRISPR-Cas system to a purified virus strictly requires a priming process. Nucleic Acids Res. 2014 Feb;42(4):2483-92. doi: 10.1093/nar/gkt1154. Epub 2013, Nov 21. PMID:24265226 doi:http://dx.doi.org/10.1093/nar/gkt1154
  3. ↑ Richter C, Dy RL, McKenzie RE, Watson BN, Taylor C, Chang JT, McNeil MB, Staals RH, Fineran PC. Priming in the Type I-F CRISPR-Cas system triggers strand-independent spacer acquisition, bi-directionally from the primed protospacer. Nucleic Acids Res. 2014 Jul;42(13):8516-26. doi: 10.1093/nar/gku527. Epub 2014, Jul 2. PMID:24990370 doi:http://dx.doi.org/10.1093/nar/gku527
  4. ↑ 4.0 4.1 Fineran PC, Gerritzen MJ, Suarez-Diez M, Kunne T, Boekhorst J, van Hijum SA, Staals RH, Brouns SJ. Degenerate target sites mediate rapid primed CRISPR adaptation. Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):E1629-38. doi:, 10.1073/pnas.1400071111. Epub 2014 Apr 7. PMID:24711427 doi:http://dx.doi.org/10.1073/pnas.1400071111
  5. ↑ Xue C, Seetharam AS, Musharova O, Severinov K, Brouns SJ, Severin AJ, Sashital DG. CRISPR interference and priming varies with individual spacer sequences. Nucleic Acids Res. 2015 Dec 15;43(22):10831-47. doi: 10.1093/nar/gkv1259. Epub, 2015 Nov 19. PMID:26586800 doi:http://dx.doi.org/10.1093/nar/gkv1259
  6. ↑ 6.0 6.1 Vorontsova D, Datsenko KA, Medvedeva S, Bondy-Denomy J, Savitskaya EE, Pougach K, Logacheva M, Wiedenheft B, Davidson AR, Severinov K, Semenova E. Foreign DNA acquisition by the I-F CRISPR-Cas system requires all components of the interference machinery. Nucleic Acids Res. 2015 Dec 15;43(22):10848-60. doi: 10.1093/nar/gkv1261. Epub, 2015 Nov 19. PMID:26586803 doi:http://dx.doi.org/10.1093/nar/gkv1261
  7. ↑ 7.0 7.1 Ivancic-Bace I, Cass SD, Wearne SJ, Bolt EL. Different genome stability proteins underpin primed and naive adaptation in E. coli CRISPR-Cas immunity. Nucleic Acids Res. 2015 Dec 15;43(22):10821-30. doi: 10.1093/nar/gkv1213. Epub, 2015 Nov 17. PMID:26578567 doi:http://dx.doi.org/10.1093/nar/gkv1213
  8. ↑ 8.0 8.1 8.2 8.3 Mohanraju P, Makarova KS, Zetsche B, Zhang F, Koonin EV, van der Oost J. Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems. Science. 2016 Aug 5;353(6299):aad5147. doi: 10.1126/science.aad5147. PMID:27493190 doi:http://dx.doi.org/10.1126/science.aad5147
  9. ↑ Hochstrasser ML, Doudna JA. Cutting it close: CRISPR-associated endoribonuclease structure and function. Trends Biochem Sci. 2015 Jan;40(1):58-66. doi: 10.1016/j.tibs.2014.10.007. Epub, 2014 Nov 18. PMID:25468820 doi:http://dx.doi.org/10.1016/j.tibs.2014.10.007

Proteopedia Page Contributors and Editors (what is this?)

Alexander Berchansky, Michal Harel

Retrieved from "http://52.214.119.220/wiki/index.php/CRISPR-Cas_Part_II"
Personal tools