• von Wintersdorff, C. J. H. et al. Dissemination of antimicrobial resistance in microbial ecosystems through horizontal gene transfer. Front. Microbiol. 7, 173 (2016).


    Google Scholar
     

  • Carattoli, A. Plasmids and the spread of resistance. Int. J. Med. Microbiol. 303, 298–304 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Doron, S. et al. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359, eaar4120 (2018).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Getino, M. & de la Cruz, F. Natural and artificial strategies to control the conjugative transmission of plasmids. Microbiol. Spectr. https://doi.org/10.1128/microbiolspec.mtbp-0015-2016 (2018).

  • Gophna, U. et al. No evidence of inhibition of horizontal gene transfer by CRISPR–Cas on evolutionary timescales. ISME J. 9, 2021–2027 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Masai, H. & Arai, K. Frpo: a novel single-stranded DNA promoter for transcription and for primer RNA synthesis of DNA replication. Cell 89, 897–907 (1997).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Rodríguez-Beltrán, J., DelaFuente, J., León-Sampedro, R., MacLean, R. C. & San Millán, Á. Beyond horizontal gene transfer: the role of plasmids in bacterial evolution. Nat. Rev. Microbiol. https://doi.org/10.1038/s41579-020-00497-1 (2021).

  • Guglielmini, J., de la Cruz, F. & Rocha, E. P. C. Evolution of conjugation and type IV secretion systems. Mol. Biol. Evol. 30, 315–331 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Smillie, C., Garcillán-Barcia, M. P., Francia, M. V., Rocha, E. P. C. & de la Cruz, F. Mobility of plasmids. Microbiol. Mol. Biol. Rev. 74, 434–452 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ares-Arroyo, M., Nucci, A. & Rocha, E. P. C. Identification of novel origins of transfer across bacterial plasmids. Preprint at https://doi.org/10.1101/2024.01.30.577996 (2024).

  • Ramsay, J. P. & Firth, N. Diverse mobilization strategies facilitate transfer of non-conjugative mobile genetic elements. Curr. Opin. Microbiol. 38, 1–9 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ares-Arroyo, M., Coluzzi, C. & Rocha, E. P. C. Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation. Nucleic Acids Res. https://doi.org/10.1093/nar/gkac1079 (2022).

  • De La Cruz, F., Frost, L. S., Meyer, R. J. & Zechner, E. L. Conjugative DNA metabolism in Gram-negative bacteria. FEMS Microbiol. Rev. 34, 18–40 (2010).

    Article 
    PubMed 

    Google Scholar
     

  • Westra, E. R. et al. CRISPR-Cas systems preferentially target the leading regions of MOBF conjugative plasmids. RNA Biol. 10, 749–761 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Venturini, C. et al. Sequences of two related multiple antibiotic resistance virulence plasmids sharing a unique IS26-related molecular signature isolated from different Escherichia coli pathotypes from different hosts. PLoS ONE 8, e78862 (2013).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Takahashi, H., Shao, M., Furuya, N. & Komano, T. The genome sequence of the incompatibility group Iγ plasmid R621a: evolution of IncI plasmids. Plasmid 66, 112–121 (2011).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bates, S., Roscoe, R. A., Althorpe, N. J., Brammar, W. J. & Wilkins, B. M. Y. Expression of leading region genes on IncI1 plasmid ColIb-P9: genetic evidence for single-stranded DNA transcription. Microbiology 145, 2655–2662 (1999).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Althorpe, N. J., Chilley, P. M., Thomas, A. T., Brammar, W. J. & Wilkins, B. M. Transient transcriptional activation of the IncI1 plasmid anti-restriction gene (ardA) and SOS inhibition gene (psiB) early in conjugating recipient bacteria. Mol. Microbiol. 31, 133–142 (1999).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Miyakoshi, M., Ohtsubo, Y., Nagata, Y. & Tsuda, M. Transcriptome analysis of zygotic induction during conjugative transfer of plasmid RP4. Front. Microbiol. 11, 1125 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Couturier, A. et al. Real-time visualisation of the intracellular dynamics of conjugative plasmid transfer. Nat. Commun. 14, 294 (2023).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bernheim, A. & Sorek, R. The pan-immune system of bacteria: antiviral defence as a community resource. Nat. Rev. Microbiol. 18, 113–119 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Borges, A. L., Davidson, A. R. & Bondy-Denomy, J. The discovery, mechanisms, and evolutionary impact of anti-CRISPRs. Annu. Rev. Virol. 4, 37–59 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Goryanin, I. I. et al. Antirestriction activities of KlcA (RP4) and ArdB (R64) proteins. FEMS Microbiol. Lett. https://doi.org/10.1093/femsle/fny227 (2018).

  • Read, T. D., Thomas, A. T. & Wilkins, B. M. Evasion of type I and type II DNA restriction systems by Incl1 plasmid Collb-P9 during transfer by bacterial conjugation. Mol. Microbiol. 6, 1933–1941 (1992).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Jones, A. L., Barth, P. T. & Wilkins, B. M. Zygotic induction of plasmid ssb and psiB genes following conjugative transfer of Incl1 plasmid Collb-P9. Mol. Microbiol. 6, 605–613 (1992).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Virolle, C., Goldlust, K., Djermoun, S., Bigot, S. & Lesterlin, C. Plasmid transfer by conjugation in Gram-negative bacteria: from the cellular to the community level. Genes 11, 1239 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Garcillán-Barcia, M. P., Alvarado, A. & de la Cruz, F. Identification of bacterial plasmids based on mobility and plasmid population biology. FEMS Microbiol. Rev. 35, 936–956 (2011).

    Article 
    PubMed 

    Google Scholar
     

  • Fraikin, N., Couturier, A. & Lesterlin, C. The winding journey of conjugative plasmids toward a novel host cell. Curr. Opin. Microbiol. 78, 102449 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Stanley, S. Y. et al. Anti-CRISPR-associated proteins are crucial repressors of anti-CRISPR transcription. Cell 178, 1452–1464.e13 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Studier, F. W. Gene 0.3 of bacteriophage T7 acts to overcome the DNA restriction system of the host. J. Mol. Biol. 94, 283–295 (1975).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zavilgelsky, G. B., Kotova, V. Y. & Rastorguev, S. M. Antimodification activity of the ArdA and Ocr proteins. Russ. J. Genet. 47, 139–146 (2011).

    Article 
    CAS 

    Google Scholar
     

  • Fernández-López, C. et al. Mobilizable rolling-circle replicating plasmids from Gram-positive bacteria: a low-cost conjugative transfer. Microbiol. Spectr. https://doi.org/10.1128/microbiolspec.plas-0008-2013 (2014).

  • Soler, N. et al. Characterization of a relaxase belonging to the MOBT family, a widespread family in Firmicutes mediating the transfer of ICEs. Mob. DNA 10, 18 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Heilers, J.-H. et al. DNA processing by the MOBH family relaxase TraI encoded within the gonococcal genetic island. Nucleic Acids Res. 47, 8136–8153 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Murphy, J., Mahony, J., Ainsworth, S., Nauta, A. & Sinderen, D. Bacteriophage orphan DNA methyltransferases: insights from their bacterial origin, function, and occurrence. Appl. Environ. Microbiol. 79, 7547–7555 (2013).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Günthert, U. & Reiners, L. Bacillus subtilis phage SPR codes for a DNA methyltransferase with triple sequence specificity. Nucleic Acids Res. 15, 3689–3702 (1987).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Takahashi, N., Naito, Y., Handa, N. & Kobayashi, I. A DNA methyltransferase can protect the genome from postdisturbance attack by a restriction-modification gene complex. J. Bacteriol. 184, 6100–6108 (2002).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fomenkov, A. et al. Plasmid replication-associated single-strand-specific methyltransferases. Nucleic Acids Res. 48, 12858–12873 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Petrova, V., Chitteni-Pattu, S., Drees, J. C., Inman, R. B. & Cox, M. M. An SOS inhibitor that binds to free RecA protein: the PsiB protein. Mol. Cell 36, 121–130 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Al Mamun, A. A. M., Kishida, K. & Christie, P. J. Protein transfer through an F plasmid-encoded type IV secretion system suppresses the mating-induced SOS response. mBio 12, e01629-21 (2021).

  • Roy, D., Huguet, K. T., Grenier, F. & Burrus, V. IncC conjugative plasmids and SXT/R391 elements repair double-strand breaks caused by CRISPR–Cas during conjugation. Nucleic Acids Res. 48, 8815–8827 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shereda, R. D., Kozlov, A. G., Lohman, T. M., Cox, M. M. & Keck, J. L. SSB as an organizer/mobilizer of genome maintenance complexes. Crit. Rev. Biochem. Mol. Biol. 43, 289–318 (2008).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Pinilla-Redondo, R. et al. Discovery of multiple anti-CRISPRs highlights anti-defense gene clustering in mobile genetic elements. Nat. Commun. 11, 5652 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gerdes, K., Christensen, S. K. & Løbner-Olesen, A. Prokaryotic toxin–antitoxin stress response loci. Nat. Rev. Microbiol. 3, 371–382 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Sutton, M. D., Smith, B. T., Godoy, V. G. & Walker, G. C. The SOS response: recent insights into umuDC-dependent mutagenesis and DNA damage tolerance. Ann. Rev. Genet. 34, 479–497 (2000).

  • Lodwick, D., Owen, D. & Strike, P. DNA sequence analysis of the IMP UV protection and mutation operon of the plasmid TP110: identification of a third gene. Nucleic Acids Res. 18, 5045–5050 (1990).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kulaeva, O. I., Wootton, J. C., Levine, A. S. & Woodgate, R. Characterization of the umu-complementing operon from R391. J. Bacteriol. 177, 2737–2743 (1995).

  • Munoz-Najar, U. & Vijayakumar, M. N. An operon that confers UV resistance by evoking the SOS mutagenic response in streptococcal conjugative transposon Tn5252. J. Bacteriol. 181, 2782–2788 (1999).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Permina, E. A., Mironov, A. A. & Gelfand, M. S. Damage-repair error-prone polymerases of eubacteria: association with mobile genome elements. Gene 293, 133–140 (2002).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • McLenigan, M. P., Kulaeva, O. I., Ennis, D. G., Levine, A. S. & Woodgate, R. The bacteriophage P1 HumD protein is a functional homolog of the prokaryotic UmuD′-like proteins and facilitates SOS mutagenesis in Escherichia coli. J. Bacteriol. 181, 7005–7013 (1999).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Goldsmith, M., Sarov-Blat, L. & Livneh, Z. Plasmid-encoded MucB protein is a DNA polymerase (pol RI) specialized for lesion bypass in the presence of MucA′, RecA, and SSB. Proc. Natl Acad. Sci. USA 97, 11227–11231 (2000).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Turlan, C., Prudhomme, M., Fichant, G., Martin, B. & Gutierrez, C. SpxA1, a novel transcriptional regulator involved in X-state (competence) development in Streptococcus pneumoniae. Mol. Microbiol. 73, 492–506 (2009).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Garriss, G. & Henriques-Normark, B. Lysogeny in Streptococcus pneumoniae. Microorganisms 8, 1546 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Del Grosso, M. et al. Macrolide efflux genes mef(A) and mef(E) are carried by different genetic elements in Streptococcus pneumoniae. J. Clin. Microbiol. 40, 774–778 (2002).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Croucher, N. J. et al. Horizontal DNA transfer mechanisms of bacteria as weapons of intragenomic conflict. PLoS Biol. 14, e1002394 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Norman, A., Hansen, L. H. & Sørensen, S. J. Conjugative plasmids: vessels of the communal gene pool. Philos. Trans. R. Soc. B. Biol. Sci. 364, 2275–2289 (2009).

    Article 
    CAS 

    Google Scholar
     

  • Rubin, B. E. et al. Species- and site-specific genome editing in complex bacterial communities. Nat. Microbiol. 7, 34–47 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Araya, D. P. et al. Efficacy of plasmid-encoded CRISPR-Cas antimicrobial is affected by competitive factors found in wild Enterococcus faecalis isolates. Preprint at bioRxiv https://doi.org/10.1101/2022.03.08.483478 (2022).

  • Citorik, R. J., Mimee, M. & Lu, T. K. Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases. Nat. Biotechnol. 32, 1141–1145 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rodrigues, M., McBride, S. W., Hullahalli, K.,Palmer, K. L. & Duerkop, B. A. Conjugative Delivery of CRISPR-Cas9 for the Selective Depletion of Antibiotic-Resistant Enterococci. Antimicrobial Agents and Chemotherapy 63, 10.1128/aac.01454-19 (2019).

  • Benson, D. A. et al. GenBank. Nucleic Acids Res. 41, D36–D42 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Mitchell, A. L. et al. MGnify: the microbiome analysis resource in 2020. Nucleic Acids Res. 48, D570–D578 (2020).

    CAS 
    PubMed 

    Google Scholar
     

  • Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinf. 11, 119 (2010).

    Article 

    Google Scholar
     

  • Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Miller, D., Stern, A. & Burstein, D. Deciphering microbial gene function using natural language processing. Nat. Commun. 13, 5731 (2022).

    Article 
    ADS 
    CAS 
    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
     

  • Katoh, K., Misawa, K., Kuma, K. & Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059–3066 (2002).

    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
     

  • Garcillán-Barcia, M. P., Redondo-Salvo, S., Vielva, L. & de la Cruz, F. in Horizontal Gene Transfer: Methods and Protocols. Methods in Molecular Biology vol. 2075 (ed. de la Cruz, F.) 295–308 (Humana, New York, 2020).

  • Mistry, J. et al. Pfam: the protein families database in 2021. Nucleic Acids Res. 49, D412–D419 (2020).

    Article 
    PubMed Central 

    Google Scholar
     

  • Li, X. et al. oriTfinder: a web-based tool for the identification of origin of transfers in DNA sequences of bacterial mobile genetic elements. Nucleic Acids Res. 46, W229–W234 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zrimec, J. Multiple plasmid origin-of-transfer regions might aid the spread of antimicrobial resistance to human pathogens. MicrobiologyOpen 9, e1129 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

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

    Article 

    Google Scholar
     

  • Li, W. & Godzik, A. CD-HIT: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658–1659 (2006).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • 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).

  • Ciccarelli, F. D. et al. Toward automatic reconstruction of a highly resolved tree of life. Science 311, 1283–1287 (2006).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • ggtreeExtra: an R package to add geom layers on circular or other layout tree of ‘ggtree’ (Bioconductor, 2022).

  • Kanehisa, M. & Goto, S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27–30 (2000).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Riadi, G., Medina-Moenne, C. & Holmes, D. S. TnpPred: a web service for the robust prediction of prokaryotic transposases. Int. J. Genomics 2012, 678761 (2012).

  • Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • The UniProt Consortium. UniProt: the Universal Protein Knowledgebase in 2023. Nucleic Acids Res. 51, D523–D531 (2023).

    Article 

    Google Scholar
     

  • Wang, J. et al. The conserved domain database in 2023. Nucleic Acids Res. 51, D384–D388 (2023).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Sayers, E. W. et al. Database resources of the National Center for Biotechnology Information in 2023. Nucleic Acids Res. 51, D29–D38 (2023).

  • Soding, J., Biegert, A. & Lupas, A. HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 33, W244–W248 (2005).

  • Berman, H. M. et al. The Protein Data Bank. Nucleic Acids Res. 28, 235–242 (2000).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lin Z. et al. Evolutionary-scale prediction of atomic-level protein structure with a language model. Science 379, 1123–1130 (2023).

  • van Kempen, M. et al. Fast and accurate protein structure search with Foldseek. Nat. Biotechnol. 42, 243–246 (2024).

    Article 
    PubMed 

    Google Scholar
     

  • Meng, E. C. et al. UCSF ChimeraX: tools for structure building and analysis. Protein Sci. 32, e4792 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nomura, N. et al. Identification of eleven single-strand initiation sequences (SSI) for priming of DNA replication in the F, R6K, R100 and ColE2 plasmids. Gene 108, 15–22 (1991).

    Article 
    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
     

  • Gruber, A. R., Lorenz, R., Bernhart, S. H., Neuböck, R. & Hofacker, I. L. The Vienna RNA Websuite. Nucleic Acids Res. 36, W70–W74 (2008).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lorenz, R. et al. ViennaRNA package 2.0. Algorithms Mol. Biol. 6, 26 (2011).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Jossinet, F. RNArtistCore: a Kotlin DSL and library to create and plot RNA 2D structures. GitHub https://github.com/fjossinet/RNArtistCore (2023).

  • Yu, D. et al. An efficient recombination system for chromosome engineering in Escherichia coli. Proc. Natl Acad. Sci. USA 97, 5978–5983 (2000).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tu, Q. et al. Room temperature electrocompetent bacterial cells improve DNA transformation and recombineering efficiency. Sci. Rep. 6, 24648 (2016).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Malaka De Silva, P. et al. A tale of two plasmids: contributions of plasmid associated phenotypes to epidemiological success among Shigella. Proc. R. Soc. B. Biol. Sci. 289, 20220581 (2022).

    Article 
    CAS 

    Google Scholar
     

  • Darphorn, T. S. Antibiotic resistance plasmid composition and architecture in Escherichia coli isolates from meat. Sci. Rep. 13, 2136 (2021).

  • Thisted, T. & Gerdes, K. Mechanism of post-segregational killing by the hok/sok system of plasmid R1. J. Mol. Biol. 223, 41–54 (1992).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Gerdes, K. The parB (hok/sok) locus of plasmid R1: a general purpose plasmid stabilization system. Nat. Biotechnol. 6, 1402–1405 (1988).

    Article 
    CAS 

    Google Scholar
     

  • Le Rhun, A. et al. Profiling the intragenic toxicity determinants of toxin–antitoxin systems: revisiting hok/Sok regulation. Nucleic Acids Res. 51, e4 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Loh, S. M., Cram, D. S. & Skurray, R. A. Nucleotide sequence and transcriptional analysis of a third function (Flm) involved in F-plasmid maintenance. Gene 66, 259–268 (1988).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Birge, E. A. Bacterial and bacteriophage genetics. VDOC.pub Library https://vdoc.pub/documents/bacterial-and-bacteriophage-genetics-5rte3vvpnkt0 (2006).

  • Her, H.-L., Lin, P.-T. & Wu, Y.-W. PangenomeNet: a pan-genome-based network reveals functional modules on antimicrobial resistome for Escherichia coli strains. BMC Bioinf. 22, 548 (2021).

    Article 
    CAS 

    Google Scholar
     

  • Uribe, R. V. et al. Discovery and characterization of Cas9 inhibitors disseminated across seven bacterial Phyla. Cell Host Microbe 25, 233–241.e5 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Davidson, A. R. et al. Anti-CRISPRs: protein inhibitors of CRISPR-Cas systems. Annu. Rev. Biochem. 89, 309–332 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     



  • Source link

    Leave a Reply

    Your email address will not be published. Required fields are marked *