e01467–e01418. https://doi.org/10.1128/
mBio.01467-18
15. Johnson EO, LaVerriere E, Office E et al
(2019) Large-scale chemical-genetics yields
new M. tuberculosis inhibitor classes. Nature
571(7763):72–78. https://doi.org/10.1038/
s41586-019-1315-z
16. Tufariello JM, Malek AA, Vilcheze C et al
(2014) Enhanced specialized transduction
using recombineering in Mycobacterium tuberculosis. mBio 5(3):e01179–e01114. https://
doi.org/10.1128/mBio.01179-14
17. van Kessel JC, Hatfull GF (2008) Efficient
point mutagenesis in mycobacteria using
single-stranded DNA recombineering: characterization of antimycobacterial drug targets.
Mol Microbiol 67(5):1094–1107. https://
doi.org/10.1111/j.1365-2958.2008.
06109.x
18. Ioerger TR, O’Malley T, Liao R et al (2013)
Identification of new drug targets and resistance mechanisms in Mycobacterium tuberculosis. PLoS One 8(9):e75245. https://doi.org/
10.1371/journal.pone.0075245
19. Jiang W, Bikard D, Cox D et al (2013)
RNA-guided editing of bacterial genomes
using CRISPR-Cas systems. Nat Biotechnol
31(3):233–239. https://doi.org/10.1038/
nbt.2508
20. Yan MY, Yan HQ, Ren GX et al (2017)
CRISPR-Cas12a-assisted Recombineering in
bacteria. Appl Environ Microbiol 83(17):
e00947-17. https://doi.org/10.1128/AEM.
00947-17
21. Papaioannou I, Disterer P, Owen JS (2009)
Use of internally nuclease-protected singlestrand DNA oligonucleotides and silencing of
the mismatch repair protein, MSH2, enhances
the replication of corrected cells following gene
editing. J Gene Med 11(3):267–274. https://
doi.org/10.1002/jgm.1296
22. Dekker M, Brouwers C, te Riele H (2003)
Targeted gene modification in mismatchrepair-deficient embryonic stem cells by
single-stranded
DNA
oligonucleotides.
Nucleic Acids Res 31(6):e27. https://doi.
org/10.1093/nar/gng027
23. Costantino N, Court DL (2003) Enhanced
levels of lambda red-mediated recombinants
in mismatch repair mutants. Proc Natl Acad
Sci U S A 100(26):15748–15753. https://
doi.org/10.1073/pnas.2434959100
24. Castaneda-Garcia A, Prieto AI, RodriguezBeltran J et al (2017) A non-canonical mismatch repair pathway in prokaryotes. Nat
Commun
8:14246.
https://doi.org/10.
1038/ncomms14246
25. Takemoto N, Numata I, Su’etsugu M et al
(2018) Bacterial EndoMS/NucS acts as a
clamp-mediated mismatch endonuclease to
prevent asymmetric accumulation of replication errors. Nucleic Acids Res 46
(12):6152–6165. https://doi.org/10.1093/
nar/gky481
26. Ishino S, Skouloubris S, Kudo H et al (2018)
Activation of the mismatch-specific endonuclease EndoMS/NucS by the replication clamp is
required for high fidelity DNA replication.
Nucleic Acids Res 46(12):6206–6217.
https://doi.org/10.1093/nar/gky460
27. Singh S, Ghosh P, Hatfull GF (2013) Attachment site selection and identity in Bxb1 serine
integrase-mediated site-specific recombination.
PLoS Genet 9(5):e1003490. https://doi.org/
10.1371/journal.pgen.1003490
28. Kim AI, Ghosh P, Aaron MA et al (2003)
Mycobacteriophage Bxb1 integrates into the
mycobacterium smegmatis groEL1 gene. Mol
Microbiol 50(2):463–473
29. Jain S, Hatfull GF (2000) Transcriptional regulation and immunity in mycobacteriophage
Bxb1. Mol Microbiol 38(5):971–985
Oligo-Mediated Recombineering in Mycobacteria
321
mBio.01467-18
15. Johnson EO, LaVerriere E, Office E et al
(2019) Large-scale chemical-genetics yields
new M. tuberculosis inhibitor classes. Nature
571(7763):72–78. https://doi.org/10.1038/
s41586-019-1315-z
16. Tufariello JM, Malek AA, Vilcheze C et al
(2014) Enhanced specialized transduction
using recombineering in Mycobacterium tuberculosis. mBio 5(3):e01179–e01114. https://
doi.org/10.1128/mBio.01179-14
17. van Kessel JC, Hatfull GF (2008) Efficient
point mutagenesis in mycobacteria using
single-stranded DNA recombineering: characterization of antimycobacterial drug targets.
Mol Microbiol 67(5):1094–1107. https://
doi.org/10.1111/j.1365-2958.2008.
06109.x
18. Ioerger TR, O’Malley T, Liao R et al (2013)
Identification of new drug targets and resistance mechanisms in Mycobacterium tuberculosis. PLoS One 8(9):e75245. https://doi.org/
10.1371/journal.pone.0075245
19. Jiang W, Bikard D, Cox D et al (2013)
RNA-guided editing of bacterial genomes
using CRISPR-Cas systems. Nat Biotechnol
31(3):233–239. https://doi.org/10.1038/
nbt.2508
20. Yan MY, Yan HQ, Ren GX et al (2017)
CRISPR-Cas12a-assisted Recombineering in
bacteria. Appl Environ Microbiol 83(17):
e00947-17. https://doi.org/10.1128/AEM.
00947-17
21. Papaioannou I, Disterer P, Owen JS (2009)
Use of internally nuclease-protected singlestrand DNA oligonucleotides and silencing of
the mismatch repair protein, MSH2, enhances
the replication of corrected cells following gene
editing. J Gene Med 11(3):267–274. https://
doi.org/10.1002/jgm.1296
22. Dekker M, Brouwers C, te Riele H (2003)
Targeted gene modification in mismatchrepair-deficient embryonic stem cells by
single-stranded
DNA
oligonucleotides.
Nucleic Acids Res 31(6):e27. https://doi.
org/10.1093/nar/gng027
23. Costantino N, Court DL (2003) Enhanced
levels of lambda red-mediated recombinants
in mismatch repair mutants. Proc Natl Acad
Sci U S A 100(26):15748–15753. https://
doi.org/10.1073/pnas.2434959100
24. Castaneda-Garcia A, Prieto AI, RodriguezBeltran J et al (2017) A non-canonical mismatch repair pathway in prokaryotes. Nat
Commun
8:14246.
https://doi.org/10.
1038/ncomms14246
25. Takemoto N, Numata I, Su’etsugu M et al
(2018) Bacterial EndoMS/NucS acts as a
clamp-mediated mismatch endonuclease to
prevent asymmetric accumulation of replication errors. Nucleic Acids Res 46
(12):6152–6165. https://doi.org/10.1093/
nar/gky481
26. Ishino S, Skouloubris S, Kudo H et al (2018)
Activation of the mismatch-specific endonuclease EndoMS/NucS by the replication clamp is
required for high fidelity DNA replication.
Nucleic Acids Res 46(12):6206–6217.
https://doi.org/10.1093/nar/gky460
27. Singh S, Ghosh P, Hatfull GF (2013) Attachment site selection and identity in Bxb1 serine
integrase-mediated site-specific recombination.
PLoS Genet 9(5):e1003490. https://doi.org/
10.1371/journal.pgen.1003490
28. Kim AI, Ghosh P, Aaron MA et al (2003)
Mycobacteriophage Bxb1 integrates into the
mycobacterium smegmatis groEL1 gene. Mol
Microbiol 50(2):463–473
29. Jain S, Hatfull GF (2000) Transcriptional regulation and immunity in mycobacteriophage
Bxb1. Mol Microbiol 38(5):971–985
Oligo-Mediated Recombineering in Mycobacteria
321