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The DOI matches its Crossref record; 12 of the 12 references it cites were found in a registry or an index.

Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems

Shmakov, Sergey, Abudayyeh, Omar O., Makarova, Kira S., Wolf, Yuri I., Gootenberg, Jonathan S., Semenova, Ekaterina, Minakhin, Leonid, Joung, Julia, Konermann, Silvana, Severinov, Konstantin, Zhang, Feng, Koonin, Eugene V.·2015·Molecular Cell
DOI 10.1016/j.molcel.2015.10.008PMC PMC4660269
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Crossref · 10.1016/j.molcel.2015.10.008

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  • In type V and type VI, Cas12 and Cas13, respectively, are the proteins that process pre-crRNA into a mature crRNA, without need for tracrRNA molecules.

    “In type V and type VI, Cas12 and Cas13, respectively, are the proteins that process pre-crRNA into a mature crRNA, without need for tracrRNA molecules [18,38].”

    From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [18]

    The Results section on type VI C2c2 reports mature crRNAs without detectable tracrRNA, but does not establish that the C2c2 protein itself processes pre-crRNA. The Discussion says type V C2c1 requires tracrRNA for DNA cleavage, so the paper does not support a blanket claim that type V systems need no tracrRNA. Page numbers are unavailable in our copy. (LLM, conf=0.88)

    Experimental — accuracy not yet measured

  • Some type I, II and V systems also rely on Cas4 nuclease activity for the adaptation step.

    “Some type I, II and V systems also rely on Cas4 nuclease activity for the adaptation step [14,18].”

    From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [18]

    The Results sections on candidate loci and adaptation modules report a Cas1–Cas4 fusion in type V-B (C2c1) and type I-U systems, linking Cas4 to their adaptation modules. They do not establish that these systems rely on Cas4 nuclease activity for adaptation, or report such a role in type II systems. Page numbers are unavailable in our copy. (LLM, conf=0.85)

    Experimental — accuracy not yet measured

  • Type VI is defined by the presence of the Cas13 protein (formerly C2c2).

    “The recently characterised type VI is defined by the presence of the Cas13 protein (formerly C2c2).”

    From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [18]

    The Results section (‘C2c2 contains two HEPN domains’; page unavailable) says C2c2 systems qualify as a putative type VI CRISPR-Cas system. This supports the link between type VI and C2c2, but our copy does not identify C2c2 as Cas13, and it calls the classification putative rather than definitive. (LLM, conf=0.87)

    Experimental — accuracy not yet measured

  • Cas13 contains higher eukaryotes and prokaryotes nucleotide (HEPN)-binding domains, which are ubiquitous in RNases.

    “This protein contains higher eukaryotes and prokaryotes nucleotide (HEPN)-binding domains, which are ubiquitous in RNases [16,18].”

    From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [18]

    The Results section, under “C2c2 contains two HEPN domains and is predicted to possess RNase activity” (page unavailable), identifies two HEPN domains in C2c2 and associates the HEPN superfamily with RNase activity. It does not say HEPN domains are ubiquitous in RNases; that prevalence claim is unsupported by our copy. (LLM, conf=0.87)

    Experimental — accuracy not yet measured

  • Cas12 proteins bear some degree of similarity to Cas9, as noted by phylogenetic analysis and the bilobed structure they share in common.

    “These proteins bear some degree of similarity to Cas9, as noted by phylogenetic analysis and the bilobed structure they share in common [18,55,56].”

    From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [18]

    The Results section on C2c1 and C2c3 reports shared RuvC-like nuclease motifs and a region corresponding to the bridge helix involved in Cas9 crRNA binding, supporting a limited degree of similarity. It does not describe a shared bilobed structure; instead, it says their overall domain architectures are distinct from Cas9. Its phylogenetic analysis concerns Cas1, not a demonstrated phylogenetic similarity between these effectors and Cas9. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

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Citations

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Research works printed but not linked: 50

  1. Anantharaman, 2013, Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing, Biol. Direct, 8, 15, 10.1186/1745-6150-8-15 · DOI
  2. Anders, 2014, Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease, Nature, 513, 569, 10.1038/nature13579 · DOI · Paper page
  3. Aravind, 2000, SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories, Nucleic Acids Res., 28, 3417, 10.1093/nar/28.18.3417 · DOI
  4. Barrangou, 2014, CRISPR-Cas systems: Prokaryotes upgrade to adaptive immunity, Mol. Cell, 54, 234, 10.1016/j.molcel.2014.03.011 · DOI · Paper page
  5. Barrangou, 2007, CRISPR provides acquired resistance against viruses in prokaryotes, Science, 315, 1709, 10.1126/science.1138140 · DOI · Paper page
  6. Besemer, 2001, GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions, Nucleic Acids Res., 29, 2607, 10.1093/nar/29.12.2607 · DOI
  7. Biswas, 2014, Accurate computational prediction of the transcribed strand of CRISPR non-coding RNAs, Bioinformatics, 30, 1805, 10.1093/bioinformatics/btu114 · DOI
  8. Chang, 2004, Alicyclobacillus spp. in the fruit juice industry: history, characteristics, and current isolation/detection procedures, Crit. Rev. Microbiol., 30, 55, 10.1080/10408410490435089 · DOI
  9. Cho, 2013, Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease, Nat. Biotechnol., 31, 230, 10.1038/nbt.2507 · DOI · Paper page
  10. Chylinski, 2013, The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems, RNA Biol., 10, 726, 10.4161/rna.24321 · DOI · Paper page
  11. Chylinski, 2014, Classification and evolution of type II CRISPR-Cas systems, Nucleic Acids Res., 42, 6091, 10.1093/nar/gku241 · DOI · Paper page
  12. Drozdetskiy, 2015, JPred4: a protein secondary structure prediction server, Nucleic Acids Res., 43, 10.1093/nar/gkv332 · DOI
  13. Edgar, 2004, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res., 32, 1792, 10.1093/nar/gkh340 · DOI · Paper page
  14. Edgar, 2007, PILER-CR: fast and accurate identification of CRISPR repeats, BMC Bioinformatics, 8, 18, 10.1186/1471-2105-8-18 · DOI
  15. Fonfara, 2014, Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems, Nucleic Acids Res., 42, 2577, 10.1093/nar/gkt1074 · DOI · Paper page
  16. Garneau, 2010, The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA, Nature, 468, 67, 10.1038/nature09523 · DOI
  17. Gasiunas, 2012, Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria, Proc. Natl. Acad. Sci. USA, 109, E2579, 10.1073/pnas.1208507109 · DOI · Paper page
  18. Geissmann, 2013, OpenCFU, a new free and open-source software to count cell colonies and other circular objects, PLoS One, 8, 10.1371/journal.pone.0054072 · DOI
  19. Grissa, 2007, CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats, Nucleic Acids Res., 35, W52, 10.1093/nar/gkm360 · DOI
  20. Grynberg, 2003, HEPN: a common domain in bacterial drug resistance and human neurodegenerative proteins, Trends Biochem. Sci., 28, 224, 10.1016/S0968-0004(03)00060-4 · DOI
  21. Hale, 2009, RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex, Cell, 139, 945, 10.1016/j.cell.2009.07.040 · DOI · Paper page
  22. Hale, 2014, Target RNA capture and cleavage by the Cmr type III-B CRISPR-Cas effector complex, Genes Dev., 28, 2432, 10.1101/gad.250712.114 · DOI
  23. Heidrich, 2015, Investigating CRISPR RNA Biogenesis and Function Using RNA-seq, Methods Mol. Biol., 1311, 1, 10.1007/978-1-4939-2687-9_1 · DOI
  24. Koonin, 2015, Evolution of adaptive immunity from transposable elements combined with innate immune systems, Nat. Rev. Genet., 16, 184, 10.1038/nrg3859 · DOI
  25. Koonin, 2013, CRISPR-Cas: evolution of an RNA-based adaptive immunity system in prokaryotes, RNA Biol., 10, 679, 10.4161/rna.24022 · DOI
  26. Krupovic, 2014, Casposons: a new superfamily of self-synthesizing DNA transposons at the origin of prokaryotic CRISPR-Cas immunity, BMC Biol., 12, 36, 10.1186/1741-7007-12-36 · DOI
  27. Lange, 2013, CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems, Nucleic Acids Res., 41, 8034, 10.1093/nar/gkt606 · DOI
  28. Majumdar, 2015, Three CRISPR-Cas immune effector complexes coexist in Pyrococcus furiosus, RNA, 21, 1147, 10.1261/rna.049130.114 · DOI
  29. Makarova, 2015, Annotation and Classification of CRISPR-Cas Systems, Methods Mol. Biol., 1311, 47, 10.1007/978-1-4939-2687-9_4 · DOI
  30. Makarova, 2006, A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action, Biol. Direct, 1, 7, 10.1186/1745-6150-1-7 · DOI · Paper page
  31. Makarova, 2011, Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems, Biol. Direct, 6, 38, 10.1186/1745-6150-6-38 · DOI
  32. Makarova, 2011, Evolution and classification of the CRISPR-Cas systems, Nat. Rev. Microbiol., 9, 467, 10.1038/nrmicro2577 · DOI · Paper page
  33. Makarova, 2013, The basic building blocks and evolution of CRISPR-CAS systems, Biochem. Soc. Trans., 41, 1392, 10.1042/BST20130038 · DOI · Paper page
  34. Makarova, 2015, An updated evolutionary classification of CRISPR-Cas systems, Nat. Rev. Microbiol., 10.1038/nrmicro3569 · DOI · Paper page
  35. Marchler-Bauer, 2002, CDD: a database of conserved domain alignments with links to domain three-dimensional structure, Nucleic Acids Res., 30, 281, 10.1093/nar/30.1.281 · DOI
  36. Marchler-Bauer, 2013, CDD: conserved domains and protein three-dimensional structure, Nucleic Acids Res., 41, D348, 10.1093/nar/gks1243 · DOI
  37. Marraffini, 2010, CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea, Nat. Rev. Genet., 11, 181, 10.1038/nrg2749 · DOI · Paper page
  38. Mojica, 2009, Short motif sequences determine the targets of the prokaryotic CRISPR defence system, Microbiology, 155, 733, 10.1099/mic.0.023960-0 · DOI · Paper page
  39. Morgulis, 2008, Database indexing for production MegaBLAST searches, Bioinformatics, 24, 1757, 10.1093/bioinformatics/btn322 · DOI
  40. Norais, 2013, Diversity of CRISPR systems in the euryarchaeal Pyrococcales, RNA Biol., 10, 659, 10.4161/rna.23927 · DOI
  41. Peng, 2015, An archaeal CRISPR type III-B system exhibiting distinctive RNA targeting features and mediating dual RNA and DNA interference, Nucleic Acids Res., 43, 406, 10.1093/nar/gku1302 · DOI
  42. Price, 2010, FastTree 2--approximately maximum-likelihood trees for large alignments, PLoS ONE, 5, e9490, 10.1371/journal.pone.0009490 · DOI · Paper page
  43. Sampson, 2013, A CRISPR/Cas system mediates bacterial innate immune evasion and virulence, Nature, 497, 254, 10.1038/nature12048 · DOI
  44. Sapranauskas, 2011, The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli, Nucleic Acids Res., 39, 9275, 10.1093/nar/gkr606 · DOI
  45. Schunder, 2013, First indication for a functional CRISPR/Cas system in Francisella tularensis, Int. J. Med. Microbiol., 303, 51, 10.1016/j.ijmm.2012.11.004 · DOI
  46. Söding, 2006, HHsenser: exhaustive transitive profile search using HMM-HMM comparison, Nucleic Acids Res., 34, W374, 10.1093/nar/gkl195 · DOI
  47. Stoddard, 2005, Homing endonuclease structure and function, Q. Rev. Biophys., 38, 49, 10.1017/S0033583505004063 · DOI
  48. Takeuchi, 2012, Nature and intensity of selection pressure on CRISPR-associated genes, J. Bacteriol., 194, 1216, 10.1128/JB.06521-11 · DOI
  49. Zetsche, 2015, Cpf1 is a single RNA-guided endonuclease of a novel Class 2 CRISPR-Cas system, Cell, 10.1016/j.cell.2015.09.038 · DOI · Paper page
  50. Zhang, 2013, Processing-independent CRISPR RNAs limit natural transformation in Neisseria meningitidis, Mol. Cell, 50, 488, 10.1016/j.molcel.2013.05.001 · DOI

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Metadata

Authors
Shmakov, S., Abudayyeh, O. O., Makarova, K. S., Wolf, Y. I., Gootenberg, J. S., Semenova, E., Minakhin, L., Joung, J., Konermann, S., Severinov, K., Zhang, F., & Koonin, E. V.
Venue
Molecular Cell
Publisher
Elsevier BV
Published
2015-11
Volume
60
Issue
3
Pages
385-397
ISSN
1097-2765
DOI
10.1016/j.molcel.2015.10.008
PMC
PMC4660269
Cited by
1,209
References
12
Language
en
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