Recruitment of CRISPR-Cas systems by Tn7-like transposons

Abstract

A survey of bacterial and archaeal genomes shows that many Tn7-like transposons contain minimal type I-F CRISPR-Cas systems that consist of fused cas8f and cas5f, cas7f, and cas6f genes and a short CRISPR array. Several small groups of Tn7-like transposons encompass similarly truncated type I-B CRISPR-Cas. This minimal gene complement of the transposon-associated CRISPR-Cas systems implies that they are competent for pre-CRISPR RNA (precrRNA) processing yielding mature crRNAs and target binding but not target cleavage that is required for interference. Phylogenetic analysis demonstrates that evolution of the CRISPR-Cas-containing transposons included a single, ancestral capture of a type I-F locus and two independent instances of type I-B loci capture. We show that the transposon-associated CRISPR arrays contain spacers homologous to plasmid and temperate phage sequences and, in some cases, chromosomal sequences adjacent to the transposon. We hypothesize that the transposon-encoded CRISPR-Cas systems generate displacement (R-loops) in the cognate DNA sites, targeting the transposon to these sites and thus facilitating their spread via plasmids and phages. These findings suggest the existence of RNAguided transposition and fit the guns-for-hire concept whereby mobile genetic elements capture host defense systems and repurpose them for different stages in the life cycle of the element.CRISPR-Cas systems | Tn7 transposon | transposition strategy | crRNA guide | target-site selection

Targeted transposition with Tn7 elements: safe sites, mobile plasmids, CRISPR/Cas and beyond

“…While bioinformatics analysis of these elements supported the hypothesis that the CRISPR/Cas systems were being used for guide RNA targeted transposition (Peters et al, 2017) the final proof came from experiments in a heterologous Escherichia coli system. Remarkably, by expressing the transposition and CRISPR/Cas guide RNA systems in E. coli, targeting could be specifically directed with the I-F variant (Klompe et al, 2019) and Cas12k (Strecker et al, 2019) systems.…”

“…A B C these transposons appear to encode TnsA, TnsB, TnsC and TnsD(TniQ) (Peters et al, 2017;Fig. 3).…”

“…3). Tn6230 and related elements insert into the very C-terminal encoding region of the yhiN gene (Moreno Switt et al, 2012;Peters et al, 2014) and one sub-family of elements inserts adjacent to the yciA gene (Peters et al, 2017). Tn6022 and related elements insert well within the comM gene, presumably inactivating the normal gene Tn7-like elements as situated with the attachment site(s) used within each family (bright yellow block arrow; named where known or indicated with a ?).…”

“…Two slashes indicate where cargo genes have been omitted to simplify the figure. An artistic representation of the TnsA phylogenetic tree is shown (Blue), but is available in Peters et al (2017) along with information for downloading via ftp. See text for details.…”

Strategies for Developing CRISPR‐Based Gene Editing Methods in Bacteria

“…The randomized pathway is prone to target other mobile genetic elements, such as exogenous plasmids, maximizing its ability to horizontally transfer. Recent bioinformatics analyses uncovered that a set of Tn7‐like transposons contain CRISPR‐Cas systems . These CRISPR‐Cas systems are seemed to be “minimal,” i.e., neither do they have the Cas proteins for acquiring new spacers into their CRISPR array nor the effector complex to cleave a target, implying these “minimal” CRISPR‐Cas system may function as a guide for the Tn7‐like transposon .…”