Thursday, March 5, 2026
No menu items!
HomeNatureExapted CRISPR–Cas12f homologues drive RNA-guided transcription

Exapted CRISPR–Cas12f homologues drive RNA-guided transcription

  • Feklistov, A., Sharon, B. D., Darst, S. A. & Gross, C. A. Bacterial sigma factors: a historical, structural, and genomic perspective. Annu. Rev. Microbiol. 68, 357–376 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Sharma, U. K. & Chatterji, D. Transcriptional switching in Escherichia coli during stress and starvation by modulation of σ70 activity. FEMS Microbiol. Rev. 34, 646–657 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Casas-Pastor, D. et al. Expansion and re-classification of the extracytoplasmic function (ECF) σ factor family. Nucleic Acids Res. 49, 986–1005 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bikard, D. et al. Programmable repression and activation of bacterial gene expression using an engineered CRISPR–Cas system. Nucleic Acids Res. 41, 7429–7437 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gilbert, L. A. et al. Genome-scale CRISPR-mediated control of gene repression and activation. Cell 159, 647–661 (2014).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Makarova, K. S. et al. Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants. Nat. Rev. Microbiol. 18, 67–83 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zetsche, B. et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR–Cas system. Cell 163, 759–771 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shmakov, S. et al. Diversity and evolution of class 2 CRISPR–Cas systems. Nat. Rev. Microbiol. 15, 169–182 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Altae-Tran, H. et al. The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases. Science 374, 57–65 (2021).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sasnauskas, G. et al. TnpB structure reveals minimal functional core of Cas12 nuclease family. Nature 616, 384–389 (2023).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Meers, C. et al. Transposon-encoded nucleases use guide RNAs to promote their selfish spread. Nature 622, 863–871 (2023).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Durrant, M. G. et al. Bridge RNAs direct programmable recombination of target and donor DNA. Nature 630, 984–993 (2024).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Siddiquee, R., Pong, C. H., Hall, R. M. & Ataide, S. F. A programmable seekRNA guides target selection by IS1111 and IS110 type insertion sequences. Nat. Commun. 15, 5235 (2024).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Vaysset, H., Meers, C., Cury, J., Bernheim, A. & Sternberg, S. H. Evolutionary origins of archaeal and eukaryotic RNA-guided RNA modification in bacterial IS110 transposons. Nat. Microbiol. 10, 20–27 (2025).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Saito, M. et al. Fanzor is a eukaryotic programmable RNA-guided endonuclease. Nature 620, 660–668 (2023).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Altae-Tran, H. et al. Diversity, evolution, and classification of the RNA-guided nucleases TnpB and Cas12. Proc. Natl Acad. Sci. USA 120, e2308224120 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wiegand, T. et al. TnpB homologues exapted from transposons are RNA-guided transcription factors. Nature 631, 439–448 (2024).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Workman, R. E. et al. A natural single-guide RNA repurposes Cas9 to autoregulate CRISPR–Cas expression. Cell 184, 675–688.e19 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Sampson, T. R., Saroj, S. D., Llewellyn, A. C., Tzeng, Y.-L. & Weiss, D. S. A CRISPR/Cas system mediates bacterial innate immune evasion and virulence. Nature 497, 254–257 (2013).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ratner, H. K. et al. Catalytically active Cas9 mediates transcriptional interference to facilitate bacterial virulence. Mol. Cell 75, 498–510.e5 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wu, W. Y. et al. The miniature CRISPR–Cas12m effector binds DNA to block transcription. Mol. Cell 82, 4487–4502.e7 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Huang, C. J., Adler, B. A. & Doudna, J. A. A naturally DNase-free CRISPR–Cas12c enzyme silences gene expression. Mol. Cell 82, 2148–2160.e4 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Li, M. et al. Toxin-antitoxin RNA pairs safeguard CRISPR–Cas systems. Science 372, eabe5601 (2021).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Qi, L. S. et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152, 1173–1183 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gilbert, L. A. et al. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154, 442–451 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang, X. et al. Multiplex gene regulation by CRISPR–ddCpf1. Cell Discov. 3, 17018 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zalatan, J. G. et al. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 160, 339–350 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Fontana, J. et al. Effective CRISPRa-mediated control of gene expression in bacteria must overcome strict target site requirements. Nat. Commun. 11, 1618 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Burgess, R. R., Travers, A. A., Dunn, J. J. & Bautz, E. K. F. Factor stimulating transcription by RNA polymerase. Nature 221, 43–46 (1969).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Ross, W. et al. A third recognition element in bacterial promoters: DNA binding by the α subunit of RNA polymerase. Science 262, 1407–1413 (1993).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Ishihama, A. Functional modulation of Escherichia coli RNA polymerase. Annu. Rev. Microbiol. 54, 499–518 (2000).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Paget, M. S. Bacterial sigma factors and anti-sigma factors: structure, function and distribution. Biomolecules 5, 1245–1265 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Erickson, J. W. & Gross, C. A. Identification of the sigma E subunit of Escherichia coli RNA polymerase: a second alternate sigma factor involved in high-temperature gene expression. Genes Dev. 3, 1462–1471 (1989).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Mecsas, J., Rouviere, P. E., Erickson, J. W., Donohue, T. J. & Gross, C. A. The activity of sigma E, an Escherichia coli heat-inducible sigma-factor, is modulated by expression of outer membrane proteins. Genes Dev. 7, 2618–2628 (1993).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Hove, B. V., Staudenmaier, H. & Braun, V. Novel two-component transmembrane transcription control: regulation of iron dicitrate transport in Escherichia coli K-12. J. Bacteriol. 172, 6749–6758 (1990).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Pinto, D. & da Fonseca, R. R. Evolution of the extracytoplasmic function σ factor protein family. NAR Genom. Bioinformatics 2, lqz026 (2020).

    Article 

    Google Scholar
     

  • Martens, E. C., Roth, R., Heuser, J. E. & Gordon, J. I. Coordinate regulation of glycan degradation and polysaccharide capsule biosynthesis by a prominent human gut symbiont. J. Biol. Chem. 284, 18445–18457 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ades, S. E. Regulation by destruction: design of the σE envelope stress response. Curr. Opin. Microbiol. 11, 535–540 (2008).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Xiao, R., Li, Z., Wang, S., Han, R. & Chang, L. Structural basis for substrate recognition and cleavage by the dimerization-dependent CRISPR–Cas12f nuclease. Nucleic Acids Res. 49, 4120–4128 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Aravind, L., Anantharaman, V., Balaji, S., Babu, M. & Iyer, L. The many faces of the helix-turn-helix domain: transcription regulation and beyond. FEMS Microbiol. Rev. 29, 231–262 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Yokoyama, T. et al. The Escherichia coli S2P intramembrane protease RseP regulates ferric citrate uptake by cleaving the sigma factor regulator FecR. J. Biol. Chem. 296, 100673 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hoffmann, F. T. et al. Selective TnsC recruitment enhances the fidelity of RNA-guided transposition. Nature 609, 384–393 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Harrington, L. B. et al. Programmed DNA destruction by miniature CRISPR–Cas14 enzymes. Science 362, 839–842 (2018).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Karvelis, T. et al. PAM recognition by miniature CRISPR–Cas12f nucleases triggers programmable double-stranded DNA target cleavage. Nucleic Acids Res. 48, 5016–5023 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Karvelis, T. et al. Transposon-associated TnpB is a programmable RNA-guided DNA endonuclease. Nature 599, 692–696 (2021).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Brooks, B. E. & Buchanan, S. K. Signaling mechanisms for activation of extracytoplasmic function (ECF) sigma factors. Biochim. Biophys. Acta 1778, 1930–1945 (2008).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Noinaj, N., Guillier, M., Barnard, T. J. & Buchanan, S. K. TonB-dependent transporters: regulation, structure, and function. Microbiology 64, 43–60 (2010).

    Article 
    CAS 

    Google Scholar
     

  • Birkholz, N. et al. Phage anti-CRISPR control by an RNA- and DNA-binding helix–turn–helix protein. Nature 631, 670–677 (2024).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Bayley, D. P., Rocha, E. R. & Smith, C. J. Analysis of cepA and other Bacteroides fragilis genes reveals a unique promoter structure. FEMS Microbiol. Lett. 193, 149–154 (2000).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Chen, S., Bagdasarian, M., Kaufman, M. G. & Walker, E. D. Characterization of strong promoters from an environmental Flavobacterium hibernum strain by using a green fluorescent protein-based reporter system. Appl. Environ. Microbiol. 73, 1089–1100 (2007).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Xiao, R. et al. Structural basis of RNA-guided transcription by a dCas12f–σE–RNAP complex. Nature https://doi.org/10.1038/s41586-026-10178-3 (2026).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Harden, T. T. et al. Bacterial RNA polymerase can retain σ70 throughout transcription. Proc. Natl Acad. Sci. USA 113, 602–607 (2016).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Jacob, F. & Monod, J. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3, 318–356 (1961).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Balleza, E. et al. Regulation by transcription factors in bacteria: beyond description. FEMS Microbiol. Rev. 33, 133–151 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bak, G., Han, K., Kim, D. & Lee, Y. Roles of rpoS-activating small RNAs in pathways leading to acid resistance of Escherichia coli. MicrobiologyOpen 3, 15–28 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Massé, E. & Gottesman, S. A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli. Proc. Natl Acad. Sci. USA 99, 4620–4625 (2002).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Madej, M. et al. Structural and functional insights into oligopeptide acquisition by the RagAB transporter from Porphyromonas gingivalis. Nat. Microbiol. 5, 1016–1025 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Grondin, J. M., Tamura, K., Déjean, G., Abbott, D. W. & Brumer, H. Polysaccharide utilization loci: fueling microbial communities. J. Bacteriol. 199, e00860-16 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lapébie, P., Lombard, V., Drula, E., Terrapon, N. & Henrissat, B. Bacteroidetes use thousands of enzyme combinations to break down glycans. Nat. Commun. 10, 2043 (2019).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tong, M. et al. A highly conserved SusCD transporter determines the import and species-specific antagonism of Bacteroides ubiquitin homologues. Nat. Commun. 15, 8794 (2024).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Martens, E. C., Chiang, H. C. & Gordon, J. I. Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Cell Host Microbe 4, 447–457 (2008).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Feng, J. et al. Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions. Cell Host Microbe 30, 200–215.e12 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Todor, H. et al. Rewiring the specificity of extracytoplasmic function sigma factors. Proc. Natl Acad. Sci. USA 117, 33496–33506 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gray, D. A. et al. Insights into SusCD-mediated glycan import by a prominent gut symbiont. Nat. Commun. 12, 44 (2021).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Takeda, S. N. et al. Structure of the miniature type V-F CRISPR–Cas effector enzyme. Mol. Cell 81, 558–570.e3 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Katoh, K., Kuma, K., Toh, H. & Miyata, T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33, 511–518 (2005).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Steinegger, M. & Söding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol. 35, 1026–1028 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Winter, D. J. rentrez: An R package for the NCBI eUtils API. The R Journal 9, 520–526 (2017).

    Article 

    Google Scholar
     

  • Cantalapiedra, C. P., Hernández-Plaza, A., Letunic, I., Bork, P. & Huerta-Cepas, J. eggNOG-mapper v2: Functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol. Biol. Evol. 38, 5825–5829 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tang, S. et al. De novo gene synthesis by an antiviral reverse transcriptase. Science 386, eadq0876 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnetJ. 17, 10–12 (2011).

    Article 

    Google Scholar
     

  • Vasimuddin, M., Misra, S., Li, H. & Aluru, S. in 2019 IEEE International Parallel and Distributed Processing Symposium 314–324 (IEEE Computer Society, 2019).

  • Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ramírez, F. et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44, W160–W165 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24–26 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cooper, L. A., Stringer, A. M. & Wade, J. T. Determining the specificity of cascade binding, interference, and primed adaptation in vivo in the Escherichia coli Type I-E CRISPR–Cas system. mBio 9, e02100-17 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang, Y. et al. Model-based analysis of ChIP–seq (MACS). Genome Biol. 9, R137 (2008).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bailey, T. L. et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37, W202–W208 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Will, S., Joshi, T., Hofacker, I. L., Stadler, P. F. & Backofen, R. LocARNA-P: accurate boundary prediction and improved detection of structural RNAs. RNA 18, 900–914 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nawrocki, E. P. & Eddy, S. R. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29, 2933–2935 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Eddy, S. R. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195 (2011).

    Article 
    ADS 
    MathSciNet 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schwengers, O. et al. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb. Genom. 7, 000685 (2021).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rice, P., Longden, I. & Bleasby, A. EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet. 16, 276–277 (2000).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wickham, H. Ggplot2: Elegant Graphics for Data Analysis (Springer, 2016).

  • RELATED ARTICLES

    Most Popular

    Recent Comments