Mata, J., Marguerat, S. & Bähler, J. Post-transcriptional control of gene expression: a genome-wide perspective. Trends Biochem. Sci. 30, 506–514 (2005).

Article 
CAS 
PubMed 

Google Scholar
 

Fuda, N. J., Ardehali, M. B. & Lis, J. T. Defining mechanisms that regulate RNA polymerase II transcription in vivo. Nature 461, 186–192 (2009).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Browning, D. F. & Busby, S. J. W. The regulation of bacterial transcription initiation. Nat. Rev. Microbiol. 2, 57–65 (2004).

Article 
CAS 
PubMed 

Google Scholar
 

Lee, R. C., Feinbaum, R. L. & Ambros, V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843–854 (1993).

Article 
CAS 
PubMed 

Google Scholar
 

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

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 
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 
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
 

Minamino, T. & Kinoshita, M. Structure, assembly, and function of flagella responsible for bacterial locomotion. EcoSal Plus 11, eesp-0011-2023 (2023).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Waldor, M. K. & Mekalanos, J. J. Lysogenic conversion by a filamentous phage encoding cholera toxin. Science 272, 1910–1914 (1996).

Article 
CAS 
PubMed 

Google Scholar
 

Wang, X. et al. Cryptic prophages help bacteria cope with adverse environments. Nat. Commun. 1, 147 (2010).

Mirold, S. et al. Isolation of a temperate bacteriophage encoding the type III effector protein SopE from an epidemic Salmonella typhimurium strain. Proc. Natl Acad. Sci. USA 96, 9845–9850 (1999).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Bondy-Denomy, J. et al. Prophages mediate defense against phage infection through diverse mechanisms. ISME J. 10, 2854–2866 (2016).

Article 
PubMed 

Google Scholar
 

Santoriello, F. J., Michel, L., Unterweger, D. & Pukatzki, S. Pandemic Vibrio cholerae shuts down site-specific recombination to retain an interbacterial defence mechanism. Nat. Commun. 11, 6246 (2020).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Wang, J. Y. & Doudna, J. A. CRISPR technology: a decade of genome editing is only the beginning. Science 379, eadd8643 (2023).

Article 
CAS 
PubMed 

Google Scholar
 

Nishimasu, H. et al. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 156, 935–949 (2014).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

He, S. & Scheres, S. H. W. Helical reconstruction in RELION. J. Struct. Biol. 198, 163–176 (2017).

Article 
CAS 
PubMed 

Google Scholar
 

Mondino, S., Martin, F. S. & Buschiazzo, A. 3D cryo-EM imaging of bacterial flagella: novel structural and mechanistic insights into cell motility. J. Biol. Chem. 298, 102105 (2022).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Jurczak-Kurek, A. et al. Biodiversity of bacteriophages: morphological and biological properties of a large group of phages isolated from urban sewage. Sci. Rep. 6, 34338 (2016).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Meynell, E. W. A phage, øχ, which attacks motile bacteria. Microbiology 25, 253–290 (1961).

CAS 

Google Scholar
 

Griffin, B. A., Adams, S. R. & Tsien, R. Y. Specific covalent labeling of recombinant protein molecules inside live cells. Science 281, 269–272 (1998).

Article 
CAS 
PubMed 

Google Scholar
 

Fairhead, M. & Howarth, M. Site-specific biotinylation of purified proteins using BirA. Methods Mol. Biol. 1266, 171–184 (2014).

Article 

Google Scholar
 

Komano, T. SHUFFLONS: multiple inversion systems and integrons. Annu. Rev. Genet. 33, 171–191 (1999).

Article 
CAS 
PubMed 

Google Scholar
 

Braun, V. FhuA (TonA), the career of a protein. J. Bacteriol. 191, 3431–3436 (2009).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Rand, E. A. et al. Phage DisCo: targeted discovery of bacteriophages by co-culture. mSystems 10, e01644-24 (2025).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Hayashi, F. et al. The innate immune response to bacterial flagellin is mediated by Toll-like receptor 5. Nature 410, 1099–1103 (2001).

Article 
CAS 
PubMed 

Google Scholar
 

Zhao, Y. et al. The NLRC4 inflammasome receptors for bacterial flagellin and type III secretion apparatus. Nature 477, 596–600 (2011).

Article 
CAS 
PubMed 

Google Scholar
 

Yoon, S. et al. Structural basis of TLR5-flagellin recognition and signaling. Science 335, 859–864 (2012).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Clasen, S. J. et al. Silent recognition of flagellins from human gut commensal bacteria by Toll-like receptor 5. Sci. Immunol. 8, eabq7001 (2023).

Article 
CAS 
PubMed 

Google Scholar
 

Jandl, B., Dighe, S., Gasche, C., Makristathis, A. & Muttenthaler, M. Intestinal biofilms: pathophysiological relevance, host defense, and therapeutic opportunities. Clin. Microbiol. Rev. 37, e00133-23 (2024).

Article 
PubMed 
PubMed Central 

Google Scholar
 

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

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Drider, D. & Condon, C. The continuing story of endoribonuclease III. J. Mol. Microbiol. Biotechnol. 8, 195–200 (2004).

PubMed 

Google Scholar
 

Nashimoto, H. & Uchida, H. DNA sequencing of the Escherichia coli ribonuclease III gene and its mutations. Mol. Gen. Genet. 201, 25–29 (1985).

Article 
CAS 
PubMed 

Google Scholar
 

Deltcheva, E. et al. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471, 602–607 (2011).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Shmakov, S. et al. Discovery and functional characterization of diverse class 2 CRISPR-Cas systems. Mol. Cell 60, 385–397 (2015).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Johnson, R. C. Site-specific DNA inversion by serine recombinases. Microbiol. Spectr. 3, 1–36 (2015).

Silverman, M., Zieg, J., Hilmen, M. & Simon, M. Phase variation in Salmonella: genetic analysis of a recombinational switch. Proc. Natl Acad. Sci. USA 76, 391–395 (1979).

Article 
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
 

Klompe, S. E., Vo, P. L. H., Halpin-Healy, T. S. & Sternberg, S. H. Transposon-encoded CRISPR–Cas systems direct RNA-guided DNA integration. Nature 571, 219–225 (2019).

Article 
CAS 
PubMed 

Google Scholar
 

Strecker, J. et al. RNA-guided DNA insertion with CRISPR-associated transposases. Science 365, 48–53 (2019).

Article 
CAS 
PubMed 
PubMed Central 

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
 

Sztanko, K. M. et al. A prophage-expressed type IV pilus component provides anti-phage defense. Cell Rep. 45, 116759 (2026).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Taylor, V. L. et al. Prophages block cell surface receptors to preserve their viral progeny. Nature 644, 1049–1057 (2025).

Article 
CAS 
PubMed 

Google Scholar
 

Lisevich, I., Colin, R., Yang, H. Y., Ni, B. & Sourjik, V. Physics of swimming and its fitness cost determine strategies of bacterial investment in flagellar motility. Nat. Commun. 16, 1731 (2025).

Bardoel, B. W. et al. Pseudomonas evades immune recognition of flagellin in both mammals and plants. PLoS Pathog. 7, e1002206 (2011).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Ribet, D. & Cossart, P. How bacterial pathogens colonize their hosts and invade deeper tissues. Microbes Infect. 17, 173–183 (2015).

Article 
CAS 
PubMed 

Google Scholar
 

Josenhans, C. & Suerbaum, S. The role of motility as a virulence factor in bacteria. Int. J. Med. Microbiol. 291, 605–614 (2002).

Article 
CAS 
PubMed 

Google Scholar
 

Arthur, T. D. et al. Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut. Science 363, 181–187 (2019).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Klose, K. E. & Mekalanos, J. J. Differential regulation of multiple flagellins in Vibrio cholerae. J. Bacteriol. 180, 303–316 (1998).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Reisch, C. R. & Prather, K. L. J. Scarless Cas9 assisted recombineering (no-SCAR) in Escherichia coli, an easy-to-use system for genome editing. Curr. Protoc. Mol. Biol. 117, 31.8.1–31.8.20 (2017).

Kreutzberger, M. A. B. et al. Flagellin outer domain dimerization modulates motility in pathogenic and soil bacteria from viscous environments. Nat. Commun. 13, 1422 (2022).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Lövestam, S. & Scheres, S. H. W. High-throughput cryo-EM structure determination of amyloids. Faraday Discuss. 240, 243–260 (2022).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Bepler, T. et al. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nat. Methods 16, 1153–1160 (2019).

Article 
CAS 
PubMed 

Google Scholar
 

Egelman, E. H. A robust algorithm for the reconstruction of helical filaments using single-particle methods. Ultramicroscopy 85, 225–234 (2000).

Article 
CAS 
PubMed 

Google Scholar
 

Zivanov, J., Nakane, T. & Scheres, S. H. W. A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis. IUCrJ 6, 5–17 (2019).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).

Article 
CAS 
PubMed 

Google Scholar
 

Afonine, P. V. et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr. D Struct. Biol. 74, 531–544 (2018).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Murshudov, G. N. et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D Biol. Crystallogr. 67, 355–367 (2011).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Nicholls, R. A., Fischer, M., McNicholas, S. & Murshudov, G. N. Conformation-independent structural comparison of macromolecules with ProSMART. Acta Crystallogr. D Biol. Crystallogr. 70, 2487–2499 (2014).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Zhao, Z. et al. Frequent pauses in Escherichia coli flagella elongation revealed by single cell real-time fluorescence imaging. Nat. Commun. 9, 1885 (2018).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671–675 (2012).

Article 
CAS 
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 

Google Scholar
 

Banks, D. J., Lei, B. & Musser, J. M. Prophage induction and expression of prophage-encoded virulence factors in group A Streptococcus serotype M3 strain MGAS315. Infect. Immun. 71, 7079–7086 (2003).

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
 

Li, N. et al. Characterization of phage resistance and their impacts on bacterial fitness in Pseudomonas aeruginosa. Microbiol. Spectr. 10, e02072-22 (2022).

PubMed 
PubMed Central 

Google Scholar
 

Thibeaux, R., Kainiu, M. & Goarant, C. Biofilm formation and quantification using the 96-microtiter plate. Methods Mol. Biol. 2134, 207–214 (2020).

Article 
CAS 
PubMed 

Google Scholar
 

Walker, M. Temperate phages enhance host fitness via RNA-guided flagellar remodeling [Data set]. Zenodo https://doi.org/10.5281/zenodo.15307114 (2025).