Murtazalieva, K., Mu, A., Petrovskaya, A. & Finn, R. D. The growing repertoire of phage anti-defence systems. Trends Microbiol. 32, 1212–1228 (2024).
Mayo-Muñoz, D., Pinilla-Redondo, R., Camara-Wilpert, S., Birkholz, N. & Fineran, P. C. Inhibitors of bacterial immune systems: discovery, mechanisms and applications. Nat. Rev. Genet. 25, 237–254 (2024).
Davidson, A. R. et al. Anti-CRISPRs: protein inhibitors of CRISPR-Cas systems. Annu. Rev. Biochem. 89, 309–332 (2020).
Marino, N. D. Phage against the machine: discovery and mechanism of type V anti-CRISPRs. J. Mol. Biol. 435, 168054 (2023).
Knott, G. J. et al. Broad-spectrum enzymatic inhibition of CRISPR-Cas12a. Nat. Struct. Mol. Biol. 26, 315–321 (2019).
Zhang, H. et al. Structural basis for the inhibition of CRISPR-Cas12a by anti-CRISPR proteins. Cell Host Microbe 25, 815–826.e4 (2019).
Marino, N. D. et al. Discovery of widespread type I and type V CRISPR-Cas inhibitors. Science 362, 240–242 (2018).
Varadi, M. et al. AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Res. 50, D439–D444 (2022).
Varadi, M. et al. AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences. Nucleic Acids Res. 52, D368–D375 (2024).
Abramson, J. et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630, 493–500 (2024).
Peng, C. et al. Structural study on anti-CRISPR protein AcrVA2. Prog. Biochem. Biophys. 48, 77–87 (2021).
Swarts, D. C., van der Oost, J. & Jinek, M. Structural basis for guide RNA processing and seed-dependent DNA targeting by CRISPR-Cas12a. Mol. Cell 66, 221–233.e4 (2017).
Gersteuer, F. et al. The SecM arrest peptide traps a pre-peptide bond formation state of the ribosome. Nat. Commun. 15, 2431 (2024).
Gerovac, M. et al. Phage proteins target and co-opt host ribosomes immediately upon infection. Nat. Microbiol. 9, 787–800 (2024).
Shimizu, Y. et al. Cell-free translation reconstituted with purified components. Nat. Biotechnol. 19, 751–755 (2001).
Mackie, G. A. RNase E: at the interface of bacterial RNA processing and decay. Nat. Rev. Microbiol. 11, 45–57 (2013).
Geslain, S. A. M. et al. Critical functions and key interactions mediated by the RNase E scaffolding domain in Pseudomonas aeruginosa. PLoS Genet. 21, e1011618 (2025).
Gasson, M. & Willetts, N. Transfer gene expression during fertility inhibition of the Escherichia coli K12 sex factor F by the I-like plasmid R62. Mol. Gen. Genet. 149, 329–333 (1976).
Gasson, M. J. & Willetts, N. S. Further characterization of the F fertility inhibition systems of “unusual” Fin+ plasmids. J. Bacteriol. 131, 413–420 (1977).
Gaffney, D., Skurray, R. & Willetts, N. Regulation of the F conjugation genes studied by hybridization and tra-lacZ fusion. J. Mol. Biol. 168, 103–122 (1983).
Osuna, B. A. et al. Listeria phages induce Cas9 degradation to protect lysogenic genomes. Cell Host Microbe 28, 31–40.e9 (2020).
Osuna, B. A. et al. Critical anti-CRISPR locus repression by a bi-functional Cas9 inhibitor. Cell Host Microbe 28, 23–30.e5 (2020).
Leroy, M. et al. Rae1/YacP, a new endoribonuclease involved in ribosome-dependent mRNA decay in Bacillus subtilis. EMBO J. 36, 1167–1181 (2017).
Goeders, N., Drèze, P.-L. & Van Melderen, L. Relaxed cleavage specificity within the RelE toxin family. J. Bacteriol. 195, 2541–2549 (2013).
Lalaouna, D. & Massé, E. Cut in translation: ribosome-dependent mRNA decay. EMBO J. 36, 1120–1122 (2017).
Felletti, M., Romilly, C., Wagner, E. G. H. & Jonas, K. A nascent polypeptide sequence modulates DnaA translation elongation in response to nutrient availability. eLife 10, e71611 (2021).
Lin, Z. et al. TTC5 mediates autoregulation of tubulin via mRNA degradation. Science 367, 100–104 (2020).
Höpfler, M. et al. Mechanism of ribosome-associated mRNA degradation during tubulin autoregulation. Mol. Cell 83, 2290–2302.e13 (2023).
Watters, K. E., Fellmann, C., Bai, H. B., Ren, S. M. & Doudna, J. A. Systematic discovery of natural CRISPR-Cas12a inhibitors. Science 362, 236–239 (2018).
Hoang, T. T., Kutchma, A. J., Becher, A. & Schweizer, H. P. Integration-proficient plasmids for Pseudomonas aeruginosa: site-specific integration and use for engineering of reporter and expression strains. Plasmid 43, 59–72 (2000).
Choi, K.-H. & Schweizer, H. P. mini-Tn7 insertion in bacteria with single attTn7 sites: example Pseudomonas aeruginosa. Nat. Protoc. 1, 153–161 (2006).
Choi, K.-H., Kumar, A. & Schweizer, H. P. A 10-min method for preparation of highly electrocompetent Pseudomonas aeruginosa cells: application for DNA fragment transfer between chromosomes and plasmid transformation. J. Microbiol. Methods 64, 391–397 (2006).
Peters, J. M. et al. Enabling genetic analysis of diverse bacteria with Mobile-CRISPRi. Nat. Microbiol. 4, 244–250 (2019).
Sambrook, J. & Russell, D. Molecular Cloning: A Laboratory Manual 3rd edn (Cold Spring Harbor Laboratory, 2000).
Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367–1372 (2008).
Teo, G. et al. SAINTexpress: improvements and additional features in Significance Analysis of INTeractome software. J. Proteomics 100, 37–43 (2014).
Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).
Katoh, K., Kuma, K.-I., Toh, H. & Miyata, T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33, 511–518 (2005).
Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49, W293–W296 (2021).
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
Marino, N. Proteins — phylogenetic free. Figshare https://doi.org/10.6084/m9.figshare.31680328.v1 (2026).
Marino, N. Mass spectrometry results for AcrVA2 immunoprecipitation. Figshare https://doi.org/10.6084/m9.figshare.31680478.v1 (2026).
Marino, N. Alignment of AcrVA2 homologs. Figshare https://doi.org/10.6084/m9.figshare.31684630.v1 (2026).
Marino, N. Alignment of cas12a nucleotide sequences downregulated by AcrVA2. Figshare https://doi.org/10.6084/m9.figshare.31684813.v1 (2026).
