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Volumn 116, Issue 41, 2019, Pages 20366-20375

Highly efficient DSB-free base editing for streptomycetes with CRISPR-BEST

Author keywords

Adenosine deaminase; CRISPR base editor; Cytidine deaminase; Genome editing; Streptomycetes

Indexed keywords

ADENOSINE; ADENOSINE DEAMINASE; CYTIDINE; CYTIDINE DEAMINASE; GUANOSINE; GUIDE RNA; MOCIMYCIN; NUCLEOTIDE; THYMIDINE; BACTERIAL DNA;

EID: 85073071217     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1913493116     Document Type: Article
Times cited : (133)

References (50)
  • 1
    • 84969206734 scopus 로고    scopus 로고
    • Solving the antibiotic crisis
    • G. D. Wright, Solving the antibiotic crisis. ACS Infect. Dis. 1, 80–84 (2015).
    • (2015) ACS Infect. Dis. , vol.1 , pp. 80-84
    • Wright, G.D.1
  • 2
    • 85020822860 scopus 로고    scopus 로고
    • AntiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification
    • K. Blin et al., antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res. 45, W36–W41 (2017).
    • (2017) Nucleic Acids Res , vol.45 , pp. W36-W41
    • Blin, K.1
  • 3
    • 84918813440 scopus 로고    scopus 로고
    • Metabolic engineering of antibiotic factories: New tools for antibiotic production in actinomycetes
    • T. Weber et al., Metabolic engineering of antibiotic factories: New tools for antibiotic production in actinomycetes. Trends Biotechnol. 33, 15–26 (2015).
    • (2015) Trends Biotechnol , vol.33 , pp. 15-26
    • Weber, T.1
  • 4
    • 84895453461 scopus 로고    scopus 로고
    • Systems biology and biotechnology of Streptomyces species for the production of secondary metabolites
    • K. S. Hwang, H. U. Kim, P. Charusanti, B. O. Palsson, S. Y. Lee, Systems biology and biotechnology of Streptomyces species for the production of secondary metabolites. Biotechnol. Adv. 32, 255–268 (2014).
    • (2014) Biotechnol. Adv. , vol.32 , pp. 255-268
    • Hwang, K.S.1    Kim, H.U.2    Charusanti, P.3    Palsson, B.O.4    Lee, S.Y.5
  • 5
    • 0037452723 scopus 로고    scopus 로고
    • PCR-targeted Streptomyces gene replacement identifies a protein domain needed for biosynthesis of the sesquiterpene soil odor geosmin
    • B. Gust, G. L. Challis, K. Fowler, T. Kieser, K. F. Chater, PCR-targeted Streptomyces gene replacement identifies a protein domain needed for biosynthesis of the sesquiterpene soil odor geosmin. Proc. Natl. Acad. Sci. U.S.A. 100, 1541–1546 (2003).
    • (2003) Proc. Natl. Acad. Sci. U.S.A. , vol.100 , pp. 1541-1546
    • Gust, B.1    Challis, G.L.2    Fowler, K.3    Kieser, T.4    Chater, K.F.5
  • 7
    • 84900314611 scopus 로고    scopus 로고
    • CRISPR-Cas systems for editing, regulating and targeting genomes
    • J. D. Sander, J. K. Joung, CRISPR-Cas systems for editing, regulating and targeting genomes. Nat. Biotechnol. 32, 347–355 (2014).
    • (2014) Nat. Biotechnol. , vol.32 , pp. 347-355
    • Sander, J.D.1    Joung, J.K.2
  • 8
    • 84934947770 scopus 로고    scopus 로고
    • High-efficiency multiplex genome editing of Streptomyces species using an engineered CRISPR/Cas system
    • R. E. Cobb, Y. Wang, H. Zhao, High-efficiency multiplex genome editing of Streptomyces species using an engineered CRISPR/Cas system. ACS Synth. Biol. 4, 723–728 (2015).
    • (2015) ACS Synth. Biol. , vol.4 , pp. 723-728
    • Cobb, R.E.1    Wang, Y.2    Zhao, H.3
  • 11
    • 85072344046 scopus 로고    scopus 로고
    • CRISPR/Cas-based genome engineering in natural product discovery
    • Y. Tong, T. Weber, S. Y. Lee, CRISPR/Cas-based genome engineering in natural product discovery. Nat. Prod. Rep., 10.1039/c8np00089a (2018).
    • (2018) Nat. Prod. Rep.
    • Tong, Y.1    Weber, T.2    Lee, S.Y.3
  • 12
    • 85063233714 scopus 로고    scopus 로고
    • Editing streptomycete genomes in the CRISPR/Cas9 age
    • F. Alberti, C. Corre, Editing streptomycete genomes in the CRISPR/Cas9 age. Nat. Prod. Rep., 10.1039/c8np00081f (2019).
    • (2019) Nat. Prod. Rep.
    • Alberti, F.1    Corre, C.2
  • 13
    • 0031973808 scopus 로고    scopus 로고
    • Genetic instability of the Streptomyces chromosome
    • J. N. Volff, J. Altenbuchner, Genetic instability of the Streptomyces chromosome. Mol. Microbiol. 27, 239–246 (1998).
    • (1998) Mol. Microbiol. , vol.27 , pp. 239-246
    • Volff, J.N.1    Altenbuchner, J.2
  • 14
    • 85044583181 scopus 로고    scopus 로고
    • Genome plasticity is governed by double strand break DNA repair in Streptomyces
    • G. Hoff, C. Bertrand, E. Piotrowski, A. Thibessard, P. Leblond, Genome plasticity is governed by double strand break DNA repair in Streptomyces. Sci. Rep. 8, 5272 (2018).
    • (2018) Sci. Rep. , vol.8 , pp. 5272
    • Hoff, G.1    Bertrand, C.2    Piotrowski, E.3    Thibessard, A.4    Leblond, P.5
  • 15
    • 85044579211 scopus 로고    scopus 로고
    • Macbeth: Multiplex automated Corynebacterium glutamicum base editing method
    • Y. Wang et al., MACBETH: Multiplex automated Corynebacterium glutamicum base editing method. Metab. Eng. 47, 200–210 (2018).
    • (2018) Metab. Eng. , vol.47 , pp. 200-210
    • Wang, Y.1
  • 16
    • 85027502168 scopus 로고    scopus 로고
    • CRISPR-stop: Gene silencing through base-editing-induced nonsense mutations
    • C. Kuscu et al., CRISPR-STOP: Gene silencing through base-editing-induced nonsense mutations. Nat. Methods 14, 710–712 (2017).
    • (2017) Nat. Methods , vol.14 , pp. 710-712
    • Kuscu, C.1
  • 17
    • 85030254880 scopus 로고    scopus 로고
    • CRISPR-mediated base editing enables efficient disruption of eukaryotic genes through induction of STOP codons
    • e4
    • P. Billon et al., CRISPR-mediated base editing enables efficient disruption of eukaryotic genes through induction of STOP codons. Mol. Cell 67, 1068–1079.e4 (2017).
    • (2017) Mol. Cell , vol.67 , pp. 1068-1079
    • Billon, P.1
  • 18
  • 19
    • 84971006562 scopus 로고    scopus 로고
    • Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage
    • A. C. Komor, Y. B. Kim, M. S. Packer, J. A. Zuris, D. R. Liu, Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533, 420–424 (2016).
    • (2016) Nature , vol.533 , pp. 420-424
    • Komor, A.C.1    Kim, Y.B.2    Packer, M.S.3    Zuris, J.A.4    Liu, D.R.5
  • 20
    • 85034861903 scopus 로고    scopus 로고
    • Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage
    • N. M. Gaudelli et al., Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature 551, 464–471 (2017).
    • (2017) Nature , vol.551 , pp. 464-471
    • Gaudelli, N.M.1
  • 21
    • 84958953000 scopus 로고    scopus 로고
    • Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage
    • F. Jiang et al., Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage. Science 351, 867–871 (2016).
    • (2016) Science , vol.351 , pp. 867-871
    • Jiang, F.1
  • 22
    • 85053441028 scopus 로고    scopus 로고
    • The pSG5-based thermosensitive vector family for genome editing and gene expression in actinomycetes
    • G. Muth, The pSG5-based thermosensitive vector family for genome editing and gene expression in actinomycetes. Appl. Microbiol. Biotechnol. 102, 9067–9080 (2018).
    • (2018) Appl. Microbiol. Biotechnol. , vol.102 , pp. 9067-9080
    • Muth, G.1
  • 23
    • 0024515525 scopus 로고
    • Thiostrepton-induced gene expression in Streptomyces lividans
    • T. Murakami, T. G. Holt, C. J. Thompson, Thiostrepton-induced gene expression in Streptomyces lividans. J. Bacteriol. 171, 1459–1466 (1989).
    • (1989) J. Bacteriol. , vol.171 , pp. 1459-1466
    • Murakami, T.1    Holt, T.G.2    Thompson, C.J.3
  • 24
    • 0035002129 scopus 로고    scopus 로고
    • Thiopeptide non-producing Streptomyces species carry the tipA gene: A clue to its function
    • B. S. Yun, T. Hidaka, T. Kuzuyama, H. Seto, Thiopeptide non-producing Streptomyces species carry the tipA gene: A clue to its function. J. Antibiot. (Tokyo) 54, 375–378 (2001).
    • (2001) J. Antibiot. (Tokyo) , vol.54 , pp. 375-378
    • Yun, B.S.1    Hidaka, T.2    Kuzuyama, T.3    Seto, H.4
  • 25
    • 84923674774 scopus 로고    scopus 로고
    • Uracil-DNA glycosylases-structural and functional perspectives on an essential family of DNA repair enzymes
    • N. Schormann, R. Ricciardi, D. Chattopadhyay, Uracil-DNA glycosylases-structural and functional perspectives on an essential family of DNA repair enzymes. Protein Sci. 23, 1667–1685 (2014).
    • (2014) Protein Sci , vol.23 , pp. 1667-1685
    • Schormann, N.1    Ricciardi, R.2    Chattopadhyay, D.3
  • 26
    • 24044438506 scopus 로고    scopus 로고
    • Close-fitting sleeves’: DNA damage recognition by the UvrABC nuclease system
    • B. Van Houten, D. L. Croteau, M. J. DellaVecchia, H. Wang, C. Kisker, ‘Close-fitting sleeves’: DNA damage recognition by the UvrABC nuclease system. Mutat. Res. 577, 92–117 (2005).
    • (2005) Mutat. Res. , vol.577 , pp. 92-117
    • van Houten, B.1    Croteau, D.L.2    DellaVecchia, M.J.3    Wang, H.4    Kisker, C.5
  • 27
    • 0032786233 scopus 로고    scopus 로고
    • A phylogenomic study of DNA repair genes, proteins, and processes
    • J. A. Eisen, P. C. Hanawalt, A phylogenomic study of DNA repair genes, proteins, and processes. Mutat. Res. 435, 171–213 (1999).
    • (1999) Mutat. Res. , vol.435 , pp. 171-213
    • Eisen, J.A.1    Hanawalt, P.C.2
  • 28
    • 84983290764 scopus 로고    scopus 로고
    • CRISPY-Web: An online resource to design sgRNAs for CRISPR applications
    • K. Blin, L. E. Pedersen, T. Weber, S. Y. Lee, CRISPy-web: An online resource to design sgRNAs for CRISPR applications. Synth. Syst. Biotechnol. 1, 118–121 (2016).
    • (2016) Synth. Syst. Biotechnol. , vol.1 , pp. 118-121
    • Blin, K.1    Pedersen, L.E.2    Weber, T.3    Lee, S.Y.4
  • 29
    • 84981516964 scopus 로고    scopus 로고
    • Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems
    • K. Nishida et al., Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems. Science 353, aaf8729 (2016).
    • (2016) Science , vol.353 , pp. aaf8729
    • Nishida, K.1
  • 30
    • 85050878241 scopus 로고    scopus 로고
    • Patscanui: An intuitive web interface for searching patterns in DNA and protein data
    • K. Blin, W. Wohlleben, T. Weber, Patscanui: An intuitive web interface for searching patterns in DNA and protein data. Nucleic Acids Res. 46, W205–W208 (2018).
    • (2018) Nucleic Acids Res , vol.46 , pp. W205-W208
    • Blin, K.1    Wohlleben, W.2    Weber, T.3
  • 31
    • 84924341659 scopus 로고    scopus 로고
    • The RNA editing enzyme APOBEC1 induces somatic mutations and a compatible mutational signature is present in esophageal adenocarcinomas
    • G. Saraconi, F. Severi, C. Sala, G. Mattiuz, S. G. Conticello, The RNA editing enzyme APOBEC1 induces somatic mutations and a compatible mutational signature is present in esophageal adenocarcinomas. Genome Biol. 15, 417 (2014).
    • (2014) Genome Biol , vol.15 , pp. 417
    • Saraconi, G.1    Severi, F.2    Sala, C.3    Mattiuz, G.4    Conticello, S.G.5
  • 32
    • 85062990961 scopus 로고    scopus 로고
    • Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos
    • E. Zuo et al., Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos. Science 364, 289–292 (2019).
    • (2019) Science , vol.364 , pp. 289-292
    • Zuo, E.1
  • 33
    • 85063014306 scopus 로고    scopus 로고
    • Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice
    • S. Jin et al., Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice. Science 364, 292–295 (2019).
    • (2019) Science , vol.364 , pp. 292-295
    • Jin, S.1
  • 34
    • 85073077320 scopus 로고    scopus 로고
    • Highly efficient DSB-free base editing for streptomycetes with CRISPR-BEST
    • Deposited 31 July 2019
    • Y. Tong et al., Highly efficient DSB-free base editing for streptomycetes with CRISPR-BEST. National Center for Biotechnology Information. https://www.ncbi.nlm.nih.gov/bioproject/557658. Deposited 31 July 2019.
    • National Center for Biotechnology Information
    • Tong, Y.1
  • 35
    • 84917686994 scopus 로고    scopus 로고
    • Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq
    • D. E. Deatherage, J. E. Barrick, Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods Mol. Biol. 1151, 165–188 (2014).
    • (2014) Methods Mol. Biol. , vol.1151 , pp. 165-188
    • Deatherage, D.E.1    Barrick, J.E.2
  • 36
    • 0037046560 scopus 로고    scopus 로고
    • Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)
    • S. D. Bentley et al., Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417, 141–147 (2002).
    • (2002) Nature , vol.417 , pp. 141-147
    • Bentley, S.D.1
  • 37
    • 0021223023 scopus 로고
    • Restriction of bacteriophage plaque formation in Streptomyces spp
    • K. L. Cox, R. H. Baltz, Restriction of bacteriophage plaque formation in Streptomyces spp. J. Bacteriol. 159, 499–504 (1984).
    • (1984) J. Bacteriol. , vol.159 , pp. 499-504
    • Cox, K.L.1    Baltz, R.H.2
  • 38
    • 0023631193 scopus 로고
    • A new shuttle cosmid vector, pKC505, for streptomycetes: Its use in the cloning of three different spiramycin-resistance genes from a Streptomyces ambofaciens library
    • M. A. Richardson, S. Kuhstoss, P. Solenberg, N. A. Schaus, R. N. Rao, A new shuttle cosmid vector, pKC505, for streptomycetes: Its use in the cloning of three different spiramycin-resistance genes from a Streptomyces ambofaciens library. Gene 61, 231–241 (1987).
    • (1987) Gene , vol.61 , pp. 231-241
    • Richardson, M.A.1    Kuhstoss, S.2    Solenberg, P.3    Schaus, N.A.4    Rao, R.N.5
  • 39
    • 0023254801 scopus 로고
    • Cloning and nucleotide sequence of a carbomycin-resistance gene from Streptomyces thermotolerans
    • J. K. Epp, S. G. Burgett, B. E. Schoner, Cloning and nucleotide sequence of a carbomycin-resistance gene from Streptomyces thermotolerans. Gene 53, 73–83 (1987).
    • (1987) Gene , vol.53 , pp. 73-83
    • Epp, J.K.1    Burgett, S.G.2    Schoner, B.E.3
  • 40
    • 0022780876 scopus 로고
    • Cloning and expression of a tylosin resistance gene from a tylosin-producing strain of Streptomyces fradiae
    • V. A. Birmingham et al., Cloning and expression of a tylosin resistance gene from a tylosin-producing strain of Streptomyces fradiae. Mol. Gen. Genet. 204, 532–539 (1986).
    • (1986) Mol. Gen. Genet. , vol.204 , pp. 532-539
    • Birmingham, V.A.1
  • 41
    • 85068818263 scopus 로고    scopus 로고
    • AntiSMASH 5.0: Updates to the secondary metabolite genome mining pipeline
    • K. Blin et al., antiSMASH 5.0: Updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res. 47, W81–W87 (2019).
    • (2019) Nucleic Acids Res , vol.47 , pp. W81-W87
    • Blin, K.1
  • 42
    • 84888855061 scopus 로고    scopus 로고
    • Complete genome sequence of the kirromycin producer Streptomyces collinus Tü 365 consisting of a linear chromosome and two linear plasmids
    • C. Rückert et al., Complete genome sequence of the kirromycin producer Streptomyces collinus Tü 365 consisting of a linear chromosome and two linear plasmids. J. Biotechnol. 168, 739–740 (2013).
    • (2013) J. Biotechnol. , vol.168 , pp. 739-740
    • Rückert, C.1
  • 43
    • 0017078545 scopus 로고
    • Stoffwechselprodukte von mikroorganismen. 154. Mitteilung. Nikkomycin, ein neuer hemmstoff der chitinsynthese bei pilzen
    • U. Dähn et al., Stoffwechselprodukte von mikroorganismen. 154. Mitteilung. Nikkomycin, ein neuer hemmstoff der chitinsynthese bei pilzen. Arch. Microbiol. 107, 143–160 (1976).
    • (1976) Arch. Microbiol. , vol.107 , pp. 143-160
    • Dähn, U.1
  • 44
    • 84958102110 scopus 로고    scopus 로고
    • Identification and activation of novel biosynthetic gene clusters by genome mining in the kirromycin producer Streptomyces collinus Tü 365
    • D. Iftime et al., Identification and activation of novel biosynthetic gene clusters by genome mining in the kirromycin producer Streptomyces collinus Tü 365. J. Ind. Microbiol. Biotechnol. 43, 277–291 (2016).
    • (2016) J. Ind. Microbiol. Biotechnol. , vol.43 , pp. 277-291
    • Iftime, D.1
  • 45
    • 85017588486 scopus 로고    scopus 로고
    • Polyketide bioderivatization using the promiscuous acyltransferase KirCII
    • E. M. Musiol-Kroll et al., Polyketide bioderivatization using the promiscuous acyltransferase KirCII. ACS Synth. Biol. 6, 421–427 (2017).
    • (2017) ACS Synth. Biol. , vol.6 , pp. 421-427
    • Musiol-Kroll, E.M.1
  • 46
    • 85042210154 scopus 로고    scopus 로고
    • Filling the gaps in the kirromycin biosynthesis: Deciphering the role of genes involved in ethylmalonyl-CoA supply and tailoring reactions
    • H. L. Robertsen et al., Filling the gaps in the kirromycin biosynthesis: Deciphering the role of genes involved in ethylmalonyl-CoA supply and tailoring reactions. Sci. Rep. 8, 3230 (2018).
    • (2018) Sci. Rep. , vol.8 , pp. 3230
    • Robertsen, H.L.1
  • 47
    • 77956498326 scopus 로고    scopus 로고
    • Sequence- And structure-specific RNA processing by a CRISPR endonuclease
    • R. E. Haurwitz, M. Jinek, B. Wiedenheft, K. Zhou, J. A. Doudna, Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science 329, 1355–1358 (2010).
    • (2010) Science , vol.329 , pp. 1355-1358
    • Haurwitz, R.E.1    Jinek, M.2    Wiedenheft, B.3    Zhou, K.4    Doudna, J.A.5
  • 48
    • 85055342078 scopus 로고    scopus 로고
    • Mining actinomycetes for novel antibiotics in the omics era: Are we ready to exploit this new paradigm?
    • O. Genilloud, Mining actinomycetes for novel antibiotics in the omics era: Are we ready to exploit this new paradigm? Antibiotics (Basel) 7, 85 (2018).
    • (2018) Antibiotics (Basel) , vol.7 , pp. 85
    • Genilloud, O.1
  • 50
    • 84865329141 scopus 로고    scopus 로고
    • AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation
    • C. S. Nabel et al., AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation. Nat. Chem. Biol. 8, 751–758 (2012).
    • (2012) Nat. Chem. Biol. , vol.8 , pp. 751-758
    • Nabel, C.S.1


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