CRISPR-Cas - introduction. John van der Oost

Transcription

1 CRISPR-Cas - introduction John van der Oost

2 CRISPR-Cas 2 classes cas operon leader CRISPR CRISPR clustered regularly interspaced palindromic repeats Cas CRISPR-associated genes & proteins present in genomes of 40% of bacteria and 85% of archaea Jansen (2002) Mol Microbiol, Makarova (2015) Nat Rev Microbiol

3 CRISPR-Cas 2 classes Class 1 cas operon leader CRISPR Cas3 Cascade-like Cas1/Cas2 crrna Class 2 cas operon leader CRISPR Cas9-like Cas1/Cas2 crrna Jansen (2002) Mol Microbiol, Makarova (2015) Nat Rev Microbiol

4 CRISPR-Cas mechanism Spacer acquisition Guide expression many CRISPR spacers are homologous to viruses or plasmids experimental evidence: adaptive & heritable immunity Target interference Mojica (2005), Pourcel (2005), Bolotin (2005), Barrangou (2007) Science

5 CRISPR-Cas class 1 Class 1 cas operon leader CRISPR Cascade-like Cas1/Cas2 crrna first insights in molecular basis of CRISPR interference immunity control (no phage) sensitivity Natural defense & Engineering - maturation pre-crrna > crrna - RNP complex (Cascade/crRNA) - DNA nuclease (Cas3) - RNA-guide DNA interference - crrna design & spec. targeting Brouns et al. (2008) Science

6 CRISPR-Cas mechanism 3 stages Spacer acquisition Guide expression Target interference Van der Oost (2014) Nat Rev Microbiol

7 CRISPR-Cas mechanism auto-immunity? Van der Oost (2014) Nat Rev Microbiol

8 CRISPR-Cas self / non-self discrimination self non-self Van der Oost (2014) Nat Rev Microbiol

9 CRISPR-Cas self / non-self discrimination Spacer acquisition Target interference non-self Target interference

10 CRISPR-Cas self / non-self discrimination Seed Protospacer Adjacent Motif (PAM) Target interference Jore et al. (2011) NSMB, Semanova et al. (2011) PNAS, Westra et al. (2012) PLoS Gen.

11 E.coli Cascade & Cas3 target interference Richard van der Oost ( Jackson (2014) Science, Gong (2015) PNAS

12 CRISPR Application genome editing Fusion of a Nuclease domain (FokI) with DNA-binding domain (ZF, TALE Cascade)

13 CRISPR Application genome editing Fusion of a Nuclease domain (FokI) with DNA-binding domain (ZF, TALE, Cascade) Brouns & Van der Oost (2011) patent

14 CRISPR-Cas 2 classes Class 1 cas operon leader CRISPR Cascade-like Cas1/Cas2 crrna Class 2 cas operon leader CRISPR Cas9-like Cas1/Cas2 crrna Jansen (2002) Mol Microbiol, Makarova (2015) Nat Rev Microbiol

15 Class 2 / Type II Cas9 Type II unique features single subunit (Cas9) two DNase domains PAM at 3 side crrna & tracrrna RNase-III (non-cas) dsdna break, blunt ends Garneau (2010), Deltcheva (2011), Jinek (2012), Gasiunas (2012)

16 Class 2 / Type II Cas9 Cong (2013) Science, Mali (2013) Science, Jinek (2013) elife, Kim (2013) Nat Biotech

17 CRISPR Application genome editing Hsu & Zhang (2014) Cell

18 Class 2 Cas9 & Cpf1 5 5 PAM Type II Cas9 Zetsche (2015) Cell, Mohanraju et al. (2016) Science

19 Class 2 Cas9 & Cpf1 5 5 PAM Type II Cas9 5 PAM Type V Cpf1 5 Zetsche (2015) Cell, Mohanraju et al. (2016) Science

20 Class 2 Cas9 & Cpf1 AsCpf1 LbCpf1 SpCas9 comparable efficiency of Cas9 and Cpf1 to generate knockouts in human cells Zetsche (2015) Cell, Mohanraju et al. (2016) Science

21 Genome editing systems Peptide-guided: Restriction & Homing enzymes Peptide-guided / engineered: TALEN & ZFN nucleases Oligo DNA/RNA-guided: Argonaute & CRISPR-Cas beat their swords into ploughshares

22 Collaborators Wageningen Stan Brouns* Matthijs Jore* Edze Westra* Magnus Lundgren* Daan Swarts* Raymond Staals Yifan Zhu Jorrit Hegge Prarthana Mohanraju Wen Wu Sjoerd Creutzburg Utrecht Albert Heck Rotterdam Rogier Louwen Bethesda Kira Makarova Eugene Koonin Boston Feng Zhang New York Dinshaw Patel Beijing Yanli Wang Berkeley Jennifer Doudna Bozeman Blake Wiedenheft

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24 CRISPR Application genome editing AsCpf1 LbCpf1 SpCas9 comparable efficiency of Cas9 and Cpf1 to generate knockouts Makarova (2015) Nat Rev Microbiol., Zetsche et al. (2015) Cell

25 Class 1 & 2 - summary 5 PAM 5 Type I Cascade + Cas3 Class 1 5 Type III Csm / Cmr PAM Type II Cas9 Class 2 5 PAM Type V Cpf1 5

26 CRISPR-Cas CRISPR-Cas is more than Cas9 Cas9

27 CRISPR-Cas CRISPR-Cas is an anti-virus system of bacteria and archaea... Cas9 - operon... and there is a huge diversity of CRISPR-Cas systems

28 CRISPR-Cas diversity Class 1 E. coli Cascade & Cas3 Makarova (2015) Nat Rev Microbiol

29 CRISPR-Cas diversity Class 2 Streptococcus Cas9 Makarova (2015) Nat Rev Microbiol Francisella Cpf1

30 Makarova (2015) Nat Rev Microbiol CRISPR-Cas diversity

31 CRISPR Application (3) genome editing guided RNP complex Richard van der Oost ( Brouns & Van der Oost (unpubl.)

32 CRISPR-Cas self / non-self discrimination Scanning for PAM Seed nucleation Complete R-loop formation Interference 5 3 seed PAM protospacer Jore et al. (2011) NSMB, Semanova et al. (2011) PNAS, Westra et al. (2012) PLoS Gen.

33 CRISPR-Cas diversity 2 classes???? Mohanraju, Zhang, Koonin, Van der Oost (2016) Science

34 CRISPR-Cas diversity Class 1 Cascade Class 2 Cas9 Mohanraju, Zhang, Koonin, Van der Oost (2016) Science

35 CRISPR-Cas diversity???? Class 2 Cas effector proteins (Cas9 / Cpf1) are multi-functional Mohanraju, Zhang, Koonin, Van der Oost (2016) submitted

36 Class 2 Cas9 & Cpf1? in silico prediction of structural differences Makarova (2015) Nat Rev Microbiol.

37 Class 2 Cas9 & Cpf1 Francisella novicida Cas9 5 side 3 side Francisella novicida Cpf1 5 side 3 side in silico prediction of functional differences experimental confirmation Makarova (2015) Nat Rev Microbiol., Zetsche et al. (2015) Cell

38 Class 2 Cas9 & Cpf1 unlike Cas9, Cpf1 can process its own guides this may facilitate multiplex knockouts by Cpf1 with CRISPR array efficiency of homologous recombination is under investigation Makarova (2015) Nat Rev Microbiol., Zetsche & Mohanraju (2016) unpubl.

39 CRISPR Application (1) Flu Shot Protect good bacteria from bad viruses control (no phage) engineering of anti-virus immunity of E. coli BL21 immunity sensitivity requires: - Cas3 - nuclease - Cascade - complex - (design) anti-virus crrna Brouns et al. (2008) Science

40 CRISPR Application (2) Phage therapy 2.0 Engineer good viruses (with Cas9) to target bad bacteria Bacteriophage-based delivery of Cas9 that specifically targets virulence genes, and as such only kills virulent bacteria Bikard et al. (2014) Nat Biotech

41 CRISPR Application (3) genome editing Hsu & Zhang (2014) Cell

42 CRISPR-Cas mechanism adaptive immunity Van der Oost (2014) Nat Rev Microbiol

43 virus infection in prokaryotes DNA RNA protein

44 prokaryotic defence systems Restriction Enzymes Prokaryotic Argonautes CRISPR-Cas systems Van der Oost et al. (2014) Nat. Rev. Microbiol., Swarts et al. (2014) NSMB

45 RNA-guided DNA interference by CRISPR-Cas from exploration to exploitation CRISPR-Cas discovery & mechanism Cas9-like complexes & applications

46 CRISPR-Cas system CRISPR = clustered regularly interspaced palindromic repeats Cas-CRISPR-associated genes & proteins present in genomes of 40% of bacteria and 85% of archaea cas operon leader CRISPR Makarova (2015) Nat Rev Microbiol

47 RNA-guided DNA interference by CRISPR-Cas from exploration to exploitation CRISPR-Cas discovery & mechanism Cas9-like complexes & applications

48 CRISPR-Cas9 Type II unique features single subunit (Cas9) crrna & tracrrna PAM at 3 side two DNase domains dsdna break, blunt ends Jinek et al. (2014) Science, Nishimasu et al. (2014) Cell, Anders et al. (2014) Nature

49 CRISPR-Cpf1 5 5 PAM Type II Cas9 Class 2 5 PAM Type V Cpf1 5 va (2015) Nat Rev Microbiol., Zhang et al. (2015) Cell, Charpentier et al (2016) Nature

50 CRISPR Application genome editing Hsu & Zhang (2014) Cell

51 RNAi and DNAi systems - applications Bacterial Defence systems Restriction Enzymes Prokaryotic Argonautes CRISPR-Cas systems beat their swords into ploughshares

52 Collaborators Wageningen Prarthana Mohanraju Yifan Zhu Wen Wu Jorrit Hegge Raymond Staals* Daan Swarts* Matthijs Jore* Edze Westra* Stan Brouns* Beijing Yanli Wang Bethesda Kira Makarova Eugene Koonin Boston Bernd Zetsche Feng Zhang Bozeman Blake Wiedenheft Rotterdam Hans van Leeuwen Irene Mathijssen Utrecht Niels Geijsen Berkeley David Taylor Jennifer Doudna

53 CRISPR Application genome editing multiplex knockouts by Cpf1 with CRISPR array efficiency of homologous recombination is under investigation Makarova (2015) Nat Rev Microbiol., Zetsche & Mohanraju (2016) submitted

54 CRISPR-Cas diversity???? Class 2 Cas effector proteins (Cas9 / Cpf1) are multi-functional Mohanraju, Zhang, Koonin, Van der Oost (2016) submitted

55 CRISPR Application (1) Flu Shot Protect good bacteria from bad viruses control (no phage) engineering of anti-virus immunity of E. coli BL21 immunity sensitivity requires: - Cas3 - nuclease - Cascade - complex - (design) anti-virus crrna Brouns et al. (2008) Science

56 CRISPR Application (2) Phage therapy 2.0 Engineer good viruses (with Cas9) to target bad bacteria Bacteriophage-based delivery of Cas9 that specifically targets virulence genes, and as such only kills virulent bacteria Bikard et al. (2014) Nat Biotech

57 CRISPR-Cas diversity Class 1 Cascade Class 2 Cas9 Mohanraju, Zhang, Koonin, Van der Oost (2016) submitted

58 RNA-guided DNA interference by CRISPR-Cas from exploration to exploitation CRISPR-Cas discovery & mechanism class 1 Cascade-like complexes class 2 Cas9-like complexes applications

59 CRISPR Application (3) genome editing Hsu & Zhang (2014) Cell

60 Class 2 / Type V Cpf1 Type II unique features single subunit (Cas9) two DNase domains PAM at 3 side crrna & tracrrna? RNase-III (non-cas) dsdna break, blunt ends Type V unique features single subunit (Cpf1) PAM at 5 side RNase? crrna, no tracrrna dsdna break, sticky ends Makarova (2015) Nat Rev Microbiol., Zetsche et al. (2015) Cell

61 Class 2 / Type V Cpf1 Type II unique features single subunit (Cas9) two DNase domains PAM at 3 side crrna & tracrrna? RNase-III (non-cas) dsdna break, blunt ends Type V unique features single subunit (Cpf1) single DNase domain (RuvC) PAM at 5 side RNase? crrna, no tracrrna dsdna break, sticky ends Makarova (2015) Nat Rev Microbiol., Zetsche et al. (2015) Cell

62 Class 2 / Type V Cpf1 Type II unique features Francisella novicida Cas9 single subunit (Cas9) two DNase domains 5 side 3 side PAM at 3 side crrna & tracrrna RNase-III (non-cas) in silico prediction dsdna break, blunt ends experimental confirmation Francisella novicida Cpf1 Type V unique features single subunit (Cpf1) single DNase domain (RuvC) PAM at 5 side 5 side 3 side Makarova (2015) Nat Rev Microbiol., Zetsche et al. (2015) Cell

63 Class 2 / Type V Cpf1 Type II unique features single subunit (Cas9) functional expression of two DNase domains cpf1 locus (variants) in E.coli: PAM at 3 side RNA-guided DNA interference crrna & tracrrna RNase-III (non-cas) dsdna break, blunt ends Type V unique features single subunit (Cpf1) single DNase domain (RuvC) PAM at 5 side crrna, no tracrrna Makarova (2015) Nat Rev Microbiol., Zetsche et al. (2015) Cell

64 Class 2 / Type V Cpf1 Type II unique features single subunit (Cas9) two DNase domains PAM at 3 side crrna & tracrrna RNase-III (non-cas) dsdna break, blunt ends Type V unique features single subunit (Cpf1) single DNase domain (RuvC) PAM at 5 side crrna, no tracrrna no RNase, cleavage by Cpf1 Makarova (2015) Nat Rev Microbiol., Zetsche & Mohanraju (2016) submitted

65 Class 2 / Type V Cpf1 Type II unique features single subunit (Cas9) two DNase domains PAM at 3 side crrna & tracrrna RNase-III (non-cas) dsdna break, blunt ends Type V unique features single subunit (Cpf1) single DNase domain (RuvC) PAM at 5 side crrna, no tracrrna no RNase, cleavage by Cpf1 dsdna break, sticky ends Makarova (2015) Nat Rev Microbiol., Zetsche et al. (2015) Cell

66 CRISPR-Cas system - discovery GAGTTCCCCGCGCCAGCGGGGATAAACCGCTTTCGCAGACGCGCGGCGA TACGCTCACGCAGAGTTCCCCGCGCCAGCGGGGATAAACCGCAGCCGAA GCCAAAGGTGATGCCGAACACGCTGAGTTCCCCGCGCCAGCGGGGATAA ACCGGGCTCCCTGTCGGTTGTAATTGATAATGTTGAGAGTTCCCCGCGC CAGCGGGGATAAACCGTTTGGATCGGGTCTGGAATTTCTGAGCGGTCGC GAGTTCCCCGCGCCAGCGGGGATAAACCGCGAATCGCGCATACCCTGCG CGTCGCCGCCTGCGAGTTCCCCGCGCCAGCGGGGATAAACCGTCAGCTT TATAAATCCGGAGATACGGAAACTAGAGTTCCCCGCGCCAGCGGGGATA CRISPR clustered regularly interspaced palindromic repeats Cas CRISPR-associated genes & proteins present in genomes of 40% of bacteria and 85% of archaea Oshino (1987), She (2001), Jansen (2002)

67 CRISPR-Cas system - discovery GAGTTCCCCGCGCCAGCGGGGATAAACCGCTTTCGCAGACGCGCGGCGA TACGCTCACGCAGAGTTCCCCGCGCCAGCGGGGATAAACCGCAGCCGAA GCCAAAGGTGATGCCGAACACGCTGAGTTCCCCGCGCCAGCGGGGATAA ACCGGGCTCCCTGTCGGTTGTAATTGATAATGTTGAGAGTTCCCCGCGC CAGCGGGGATAAACCGTTTGGATCGGGTCTGGAATTTCTGAGCGGTCGC GAGTTCCCCGCGCCAGCGGGGATAAACCGCGAATCGCGCATACCCTGCG CGTCGCCGCCTGCGAGTTCCCCGCGCCAGCGGGGATAAACCGTCAGCTT TATAAATCCGGAGATACGGAAACTAGAGTTCCCCGCGCCAGCGGGGATA CRISPR clustered regularly interspaced palindromic repeats Cas CRISPR-associated genes & proteins present in genomes of 40% of bacteria and 85% of archaea Oshino (1987), She (2001)

68 CRISPR-Cas system - discovery GAGTTCCCCGCGCCAGCGGGGATAAACCGCTTTCGCAGACGCGCGGCGA TACGCTCACGCAGAGTTCCCCGCGCCAGCGGGGATAAACCGCAGCCGAA GCCAAAGGTGATGCCGAACACGCTGAGTTCCCCGCGCCAGCGGGGATAA ACCGGGCTCCCTGTCGGTTGTAATTGATAATGTTGAGAGTTCCCCGCGC CAGCGGGGATAAACCGTTTGGATCGGGTCTGGAATTTCTGAGCGGTCGC GAGTTCCCCGCGCCAGCGGGGATAAACCGCGAATCGCGCATACCCTGCG CGTCGCCGCCTGCGAGTTCCCCGCGCCAGCGGGGATAAACCGTCAGCTT TATAAATCCGGAGATACGGAAACTAGAGTTCCCCGCGCCAGCGGGGATA CRISPR clustered regularly interspaced palindromic repeats Cas CRISPR-associated genes & proteins present in genomes of 40% of bacteria and 85% of archaea Oshino (1987), She (2001), Jansen (2002)

69 CRISPR-Cas system adaptive immunity GAGTTCCCCGCGCCAGCGGGGATAAACCGCTTTCGCAGACGCGCGGCGA TACGCTCACGCAGAGTTCCCCGCGCCAGCGGGGATAAACCGCAGCCGAA GCCAAAGGTGATGCCGAACACGCTGAGTTCCCCGCGCCAGCGGGGATAA ACCGGGCTCCCTGTCGGTTGTAATTGATAATGTTGAGAGTTCCCCGCGC CAGCGGGGATAAACCGTTTGGATCGGGTCTGGAATTTCTGAGCGGTCGC GAGTTCCCCGCGCCAGCGGGGATAAACCGCGAATCGCGCATACCCTGCG CGTCGCCGCCTGCGAGTTCCCCGCGCCAGCGGGGATAAACCGTCAGCTT TATAAATCCGGAGATACGGAAACTAGAGTTCCCCGCGCCAGCGGGGATA many CRISPR spacers are homologous to viruses or plasmids experimental evidence: adaptive & heritable immunity huge diversity of CRISPR-Cas systems Mojica (2005), Pourcel (2005), Bolotin (2005), Barrangou (2007), Makarova (2006)

70 CRISPR-Cas self / non-self discrimination protospacer Spacer acquisition fragmentation PAM screen integration Cas2 Guide expression Cas1 Cas1 Target interference Protospacer Adjacent Motif (PAM) Swarts (2012) PLoS One, Arslan (2014) NAR, Nuňez (2015) Nature, Wang (2015) Cell

71 Class 1 / Type I target interference Class 1 leader Cas3 Cascade Cas1/Cas2 crrna Cascade and Cas3 required for crrna-guided DNA interference crrna guide processing by Cas6 ribonuclease subunit of Cascade Functional design CRISPR allows for directed targeting Brouns & Jore (2008) Science

72 CRISPR-Cas diversity Mohanraju, Zhang, Koonin, Van der Oost (2016) submitted

73 Class 2 / Type V Cpf1 Francisella novicida Cas9 5 side 3 side Francisella novicida Cpf1 5 side 3 side BLAST search with CRISPR spacers as query hits of prophages in related strains Type II unique features single subunit (Cas9) two DNase domains PAM at 3 side crrna & tracrrna RNase-III (non-cas) dsdna break, blunt ends Type V unique features single subunit (Cpf1) single DNase domain (RuvC) PAM at 5 side - prediction RNase? crrna, no tracrrna dsdna break, sticky ends Makarova (2015) Nat Rev Microbiol., Zetsche et al. (2015) Cell

74 CRISPR Application (3) genome editing guided complex (Cas9, Cascade, Ago) with nuclease domains (FokI) Richard van der Oost ( Brouns & Van der Oost (unpubl.)

75 Class 1 / Type I target interference Class 1 leader Cas3 Cascade Cas1/Cas2 crrna Cascade and Cas3 required for crrna-guided DNA interference crrna guide processing by Cas6 ribonuclease subunit of Cascade Functional design CRISPR allows for directed targeting Brouns & Jore (2008) Science

76 Class 1 / Type I target interference Class 1 leader Cas3 Cascade Cas1/Cas2 crrna Jore (2011) NSMB, Wiedenheft (2011) Nature, Hochstrasser (2014) PNAS

77 CRISPR-Cas diversity Class 2 Cas effector proteins (Cas9 / Cpf1) are multi-functional

78 anti-virus systems in prokaryotes established mechanisms inhibition of adsorption (Omp) DNA RNA protein inhibition of DNA injection (Sie) degradation of DNA (R/M) abortive infection systems (T/AT) guided interference systems CRISPR-Cas Argonaute (pago) Van der Oost et al. (2014) Nat. Rev. Microbiol., Swarts et al. (2014) NSMB

79 CRISPR Application (3) genome editing Cpf1 as alternative for Cas9 : genome editing 2.0

80 RNAi and DNAi systems - applications guided complex of inactive Cas9 (dcas9) with nuclease domains (FokI) Guilinger (2014)

81 CRISPR-Cas9 applications Hsu & Zhang (2014) Cell

82 CRISPR-Cas / Type I Cascade & Cas3 Hochstrasser & Doudna (2014) PNAS Gong et al. (2014) PNAS

83 RNAi and DNAi systems - applications Cong et al. (2013) Science, Mali et al. (2013) Science, Van der Oost (2013) Science

84 Class 1 / Type I spacer acquisition cas operon CRISPR leader Cas3 Cascade Cas1/Cas2 crrna Swarts (2012) PLoS One, Arslan (2014) NAR, Nuňez (2015) Nature, Wang (2015) Cell

85 Class 1 / Type I target interference cas operon CRISPR leader Cas3 Cascade Cas1/Cas2 crrna Blosser (2015) Mol Cell, Rutkauskas (2015) NAR, Redding (2015) Cell