Rapid and Scalable Characterization of CRISPR Technologies Using an E. coli Cell-Free Transcription-Translation System

Abstract

CRISPR-Cas systems offer versatile technologies for genome engineering, yet their implementation has been outpaced by ongoing discoveries of new Cas nucleases and anti-CRISPR proteins. Here, we present the use of E. coli cell-free transcription-translation (TXTL) systems to vastly improve the speed and scalability of CRISPR characterization and validation. TXTL can express active CRISPR machinery from added plasmids and linear DNA, and TXTL can output quantitative dynamics of DNA cleavage and gene repression-all without protein purification or live cells. We used TXTL to measure the dynamics of DNA cleavage and gene repression for single- and multi-effector CRISPR nucleases, predict gene repression strength in E. coli, determine the specificities of 24 diverse anti-CRISPR proteins, and develop a fast and scalable screen for protospacer-adjacent motifs that was successfully applied to five uncharacterized Cpf1 nucleases. These examples underscore how TXTL can facilitate the characterization and application of CRISPR technologies across their many uses.

Keywords: Cas9; Cascade; Cpf1; PAM; TXTL; prototyping; synthetic biology.

Figure 1. S. pyogenes Cas9 Functions Efficiently in TXTL

(A) Schematic of using TXTL to dynamically and quantitatively measure the activity of Cas9 and dCas9. (B) Time series showing deGFP concentration for cell-free reactions expressing (d)Cas9 and a non-targeting sgRNA (green) or targeting sgRNAs (blue). Target locations include the sequence matching the guide (blue line) and the PAM (yellow circle). Error bars represent the SEM from at least six repeats. (C) Alternative sigma factors σ²⁸, σ³⁸, and σ⁵⁴ and the T7 polymerase can be expressed in TXTL from the P_70a promoter and activate their cognate promoters P_28a, P_38a, P_54a, and P_T7, respectively. A matrix showing dSpyCas9-based repression of promoters dependent on σ²⁸, σ³⁸, σ⁵⁴, and the T7 polymerase is shown. An sgRNA targeting each promoter or the gfp gene body was expressed along with each sigma factor or polymerase and a reporter gene driven by the sigma factor of its cognate promoter. Values represent the mean of at least three repeats.

Figure 2. Multiple Factors Affect dSpyCas9-Based Repression of Reporter Gene Expression in TXTL

(A) Fold repression produced by a TXTL reaction when deGFP is expressed from either a targeted plasmid (dark) or linear (light) construct. Error bars represent the SEM from at least three repeats. (B) Time series showing deGFP concentration in TXTL for cell-free reactions expressing dSpyCas9 and a targeting sgRNA. The reporter plasmid is added to the reaction either at the same time as dSpyCas9 and the sgRNA (top row) or after 3 hr (bottom row). Error bars represent the SEM from at least five repeats. (C) Time to repression for the curves from (B), as well as for “dSpyCas9 pre-pack.” Error bars represent the SEM from at least five repeats.

Figure 3. TXTL Can Be Used to Assess the Activity of sgRNAs

(A) A schematic of where each guide binds in the gfp promoter and gene body (top). The location of the target and PAM is indicated by a blue line and a yellow or orange dot, respectively. The fold repression of GFP production by dCas9-based repression for each sgRNA in vivo and in vitro (bottom). Points are colored by whether the guide is adjacent to an NGG (yellow) or NAG (orange) PAM, and whether the sgRNA targets the non-template strand (black ring) or template strand (gray ring). Error bars represent the SEM from at least three repeats. (B) Assessing non-gfp targeting sgRNAs used by dCas9. The sequence or gene of interest is transcriptionally or translationally fused upstream of degfp. Fold repression was measured in TXTL for four targeting sgRNAs when degfp is fused to mscL or hla. Error bars represent the SEM from at least three repeats. (C) Assessing non-gfp targeting sgRNAs used by Cas9. The sequence or gene of interest was inserted upstream of the promoter driving expression of deGFP. In the absence of a RecBCD inhibitor, cleavage by Cas9 leads to rapid degradation of the plasmid and loss of GFP expression. Fold repression was measured in TXTL when targeting in the gfp coding sequence (sg8) or upstream of the promoter (sg8) with Cas9 or dCas9, and in the presence or absence of the RecBCD inhibitor Chi site containing DNA. Error bars represent the SEM from at least three repeats.

Figure 4. Single Effector and Multi-protein Effector Cas Proteins Function Efficiently in TXTL

(A and B) Time series of reporter gene expression in TXTL for cell-free reactions expressing (A) a catalytically inactive version of the Type V-A Cpf1 nuclease from Francisella novicida or (B) the Type I-E Cascade complex from E. coli. The protein or set of proteins was expressed along with a non-targeting gRNA (green) or one of three gRNAs (blue) designed to target the promoter of the deGFP reporter construct. The reporter plasmid is added to the reaction either at the same time as the constructs expressing the Cas protein(s) and the gRNA (top row) or after 3 hr (bottom row). Error bars represent the SEM from six repeats. (C) Time to repression for the curves from (A), as well as for “dFnCpf1 pre-pack.” Error bars represent the SEM from at least five repeats. (D) Time to repression for the curves from (B). Error bars represent the SEM from at least four repeats.

Figure 5. TXTL Can Be Used to Rapidly Characterize Anti-CRISPR Proteins

(A) Time series of deGFP-ssrA expression in TXTL for cell-free reactions also expressing dSpyCas9, an sgRNA, and one of two anti-CRISPR proteins, AcrIIA2 and AcrIIA4, shown to inhibit SpyCas9 activity. Each reaction was performed with a targeting sgRNA (blue) or a non-targeting sgRNA (green). Error bars represent the SEM from at least three repeats. (B) A matrix showing the percentage inhibition for 24 different anti-CRISPR proteins on five different Cas9. Samples with no appreciable GFP expression in the presence of the anti-CRISPR protein are designated with light red. Values represent the mean of at least three technical replicates.

Figure 6. TXTL Can Be Used to Determine CRISPR PAMs

(A) Schematic of a TXTL-based cleavage assay to determine the PAM sequences recognized by Cas nucleases. (B) Plots showing the fold change in the representation of a nucleotide at each variable position in the PAM library as a result of FnCpf1 activity in comparison to the original PAM library. Note that the y axis is inverted to highlight nucleotides that are depleted. (C) Time series showing the depletion of selected motifs by FnCpf1 matching the consensus sequence in the sequencing libraries is shown. Error bars show the SD of the fold change. (D) A PAM wheel showing the determined PAM sequences recognized by FnCpf1. PAM sequences are read proceeding from the outside to the inside of the circle, and the arc length directly correlates with the extent of PAM depletion. The −5 position was not shown for clarity. (E) Plots showing the fold change in the representation of a nucleotide at each variable position in the PAM library in comparison to the original PAM library (top) and PAM wheels showing the determined PAM sequences (bottom) for five uncharacterized Cpf1 nucleases. A sixth Cpf1 nuclease (MbCpf1) previously characterized in Zetsche et al. (2015) is also reported in Figure S5.