Cas9 sequences were identified by Blast
42 (link) or obtained from published studies
24 (link)–26 . Cas9 nuclease activity was inactivated by making the homologous D10A and H840A (
S. pyogenes numbering) mutations in the RuvC and HNH nuclease domains for each Cas9 protein.
dcas9 alleles were then codon optimized for mycobacterial expression with Jcat
43 (link) and synthesized by Genscript. dCas9 protein sequences used in this study are listed in
Supplementary Table 1. Single-plasmid platforms were generated for all
dcas9 alleles that contained: 1) the
dcas9 allele under the control of a Tet repressor (TetR)-regulated UV15-Tet promoter
1 (link) or an optimized, synthetic TetR-regulated promoter (
Supplementary Figure 4, Supplementary Table 1); 2) the cognate sgRNA under the control of a minimal synthetic constitutive promoter or an optimized, synthetic TetR-regulated promoter (
Supplementary Figure 4, Supplementary Table 1); 3) a Tet repressor; 4) a single-copy L5-integrating backbone
44 (link); 5) a pBR322-derived
E. coli replication origin; and 6) a kanamycin-selectable marker. sgRNA scaffold sequences were obtained from published studies
25 ,26 or engineered by fusing the crRNA direct repeat to the tracrRNA in an analogous manner to the
S. pyogenes sgRNA
11 (link). We attempted to enrich for highly active dCas9
Spy sgRNAs by selecting top-scoring sgRNAs based on the algorithm described in Doench et al.
45 (link). All sgRNA scaffold sequences used in this study are listed in
Supplementary Table 1.
To clone sgRNA targeting sequences, the sgRNA scaffolds were designed with two unique BsmBI restriction sites immediately 5’ to the sgRNA scaffold sequence. Complementary sgRNA targeting oligos (N20–25) were then annealed and ligated (T4 DNA ligase, NEB) into the BsmBI-digested CRISPRi vector backbone. To clone multiple sgRNAs into the same vector, the CRISPRi vector backbones were designed with a SapI-based Golden Gate cloning site 3’ to the first sgRNA scaffold. sgRNA targeting sequences are listed in
Supplementary Table 2.
To construct the
Renilla luciferase reporter plasmid, the
Renilla gene was cloned downstream of the G13 promoter from
Mycobacterium marinum46 (link) with a synthetic 5’ untranslated region (UTR) in a single-copy Giles integrating vector
47 (link). The
Renilla 5’UTR was engineered such that the optimal PAM for each dCas9 protein could be tested with an identical sgRNA targeting sequence (UTR1) for all dCas9 proteins. The
Renilla reporter sequences used for each dCas9 protein are shown in
Supplementary Table 1.
Rock J.M., Hopkins F.F., Chavez A., Diallo M., Chase M.R., Gerrick E.R., Pritchard J.R., Church G.M., Rubin E.J., Sassetti C.M., Schnappinger D, & Fortune S.M. (2017). Programmable transcriptional repression in mycobacteria using an orthogonal CRISPR interference platform. Nature microbiology, 2, 16274.