Sockett, R. E. Predatory lifestyle of Bdellovibrio bacteriovorus. Annu. Rev. Microbiol. 63, 523–539 (2009).
Lai, T. F., Ford, R. M. & Huwiler, S. G. Advances in cellular and molecular predatory biology of Bdellovibrio bacteriovorus six decades after discovery. Front. Microbiol. 14, 1168709 (2023).
Evans, M. L. & Chapman, M. R. Curli biogenesis: order out of disorder. Biochim. Biophys. Acta 1843, 1551–1558 (2014).
Santin, Y. G., Lamot, T., Van Raaphorst, R., Kaljević, J. & Laloux, G. Modulation of prey size reveals adaptability and robustness in the cell cycle of an intracellular predator. Curr. Biol. 33, 2213–2222.e4 (2023).
Georjon, H. & Bernheim, A. The highly diverse antiphage defence systems of bacteria. Nat. Rev. Microbiol. 21, 686–700 (2023).
Aharon, E. et al. Secretion systems play a critical role in resistance to predation by Bdellovibrio bacteriovorus. Res. Microbiol. 172, 103878 (2021).
Koval, S. F. & Hynes, S. H. Effect of paracrystalline protein surface layers on predation by Bdellovibrio bacteriovorus. J. Bacteriol. 173, 2244–2249 (1991).
Duncan, M. C. et al. High-throughput analysis of gene function in the bacterial predator Bdellovibrio bacteriovorus. mBio 10, e01040–19 (2019).
Shemesh, Y. & Jurkevitch, E. Plastic phenotypic resistance to predation by Bdellovibrio and like organisms in bacterial prey. Environ. Microbiol. 6, 12–18 (2004).
Mitchell, R. J., Mun, W., Mabekou, S. S., Jang, H. & Choi, S. Y. Compounds affecting predation by and viability of predatory bacteria. Appl. Microbiol. Biotechnol. 104, 3705–3713 (2020).
Mun, W. et al. Cyanide production by Chromobacterium piscinae shields it from Bdellovibrio bacteriovorus HD100 predation. mBio 8, e01370–17 (2017).
Dwidar, M., Nam, D. & Mitchell, R. J. Indole negatively impacts predation by Bdellovibrio bacteriovorus and its release from the bdelloplast. Environ. Microbiol. 17, 1009–1022 (2015).
Hoshiko, Y. et al. Quinolone signals related to Pseudomonas quinolone signal-quorum sensing inhibits the predatory activity of Bdellovibrio bacteriovorus. Front. Microbiol. 12, 722579 (2021).
Dwidar, M. et al. Diffusible signaling factor, a quorum-sensing molecule, interferes with and is toxic towards Bdellovibrio bacteriovorus 109J. Microb. Ecol. 81, 347–356 (2021).
Fagan, R. P. & Fairweather, N. F. Biogenesis and functions of bacterial S-layers. Nat. Rev. Microbiol. 12, 211–222 (2014).
Ochman, H. & Selander, R. K. Standard reference strains of Escherichia coli from natural populations. J. Bacteriol. 157, 690–693 (1984).
Patel, I. R. et al. Draft genome sequences of the Escherichia coli Reference (ECOR) collection. Microbiol. Resour. Announc. https://doi.org/10.1128/mra.01133-18 (2018).
Hoshiko, Y., Okuno, M., Yamamoto, T., Maeda, T. & Ogura, Y. Improved complete genome sequence of Bdellovibrio bacteriovorus 109J, a widely studied laboratory strain of predatory bacteria. Microbiol. Resour. Announc. https://doi.org/10.1128/mra.01296-23 (2024).
Ogasawara, H., Yamamoto, K. & Ishihama, A. Regulatory role of MlrA in transcription activation of csgD, the master regulator of biofilm formation in Escherichia coli. FEMS Microbiol. Lett. 312, 160–168 (2010).
Ogasawara, H., Yamada, K., Kori, A., Yamamoto, K. & Ishihama, A. Regulation of the Escherichia coli csgD promoter: interplay between five transcription factors. Microbiology 156, 2470–2483 (2010).
Brown, P. K. et al. MlrA, a novel regulator of curli (AgF) and extracellular matrix synthesis by Escherichia coli and Salmonella enterica serovar Typhimurium. Mol. Microbiol. 41, 349–363 (2001).
Serra, D. O., Richter, A. M. & Hengge, R. Cellulose as an architectural element in spatially structured Escherichia coli biofilms. J. Bacteriol. 195, 5540–5554 (2013).
Acheson, J. F., Derewenda, Z. S. & Zimmer, J. Architecture of the cellulose synthase outer membrane channel and its association with the periplasmic TPR domain. Structure 27, 1855–1861.e3 (2019).
Olsén, A., Arnqvist, A., Hammar, M., Sukupolvi, S. & Normark, S. The RpoS Sigma factor relieves H-NS-mediated transcriptional repression of csgA, the subunit gene of fibronectin-binding curli in Escherichia coli. Mol. Microbiol. 7, 523–536 (1993).
Reshamwala, S. M. S. & Noronha, S. B. Biofilm formation in Escherichia coli cra mutants is impaired due to down-regulation of curli biosynthesis. Arch. Microbiol. 193, 711–722 (2011).
Jubelin, G. et al. CpxR/OmpR interplay regulates curli gene expression in response to osmolarity in Escherichia coli. J. Bacteriol. 187, 2038–2049 (2005).
Mun, W., Upatissa, S., Lim, S., Dwidar, M. & Mitchell, R. J. Outer membrane porin F in E. coli is critical for effective predation by Bdellovibrio. Microbiol. Spectr. 10, e03094–22 (2022).
Dueholm, M. S., Albertsen, M., Otzen, D. & Nielsen, P. H. Curli functional amyloid systems are phylogenetically widespread and display large diversity in operon and protein structure. PLoS ONE 7, e51274 (2012).
Smith, D. R. et al. The production of curli amyloid fibers is deeply integrated into the biology of Escherichia coli. Biomolecules 7, 75 (2017).
Sawaya, M. R., Hughes, M. P., Rodriguez, J. A., Riek, R. & Eisenberg, D. S. The expanding amyloid family: structure, stability, function, and pathogenesis. Cell 184, 4857–4873 (2021).
Olsén, A., Jonsson, A. & Normark, S. Fibronectin binding mediated by a novel class of surface organelles on Escherichia coli. Nature 338, 652–655 (1989).
Barnhart, M. M. & Chapman, M. R. Curli biogenesis and function. Annu. Rev. Microbiol. 60, 131–147 (2006).
Tursi, S. A. & Tükel, Ç. Curli-containing enteric biofilms inside and out: matrix composition, immune recognition, and disease implications. Microbiol. Mol. Biol. Rev. https://doi.org/10.1128/mmbr.00028-18 (2018).
Maury, C. P. J. The emerging concept of functional amyloid. J. Intern. Med. 265, 329–334 (2009).
Evans, M. L. et al. The bacterial curli system possesses a potent and selective inhibitor of amyloid formation. Mol. Cell 57, 445–455 (2015).
Gualdi, L. et al. Cellulose modulates biofilm formation by counteracting curli-mediated colonization of solid surfaces in Escherichia coli. Microbiology 154, 2017–2024 (2008).
Bian, Z. & Normark, S. Nucleator function of CsgB for the assembly of adhesive surface organelles in Escherichia coli. EMBO J. 16, 5827–5836 (1997).
Arnqvist, A., Olsén, A. & Normark, S. σS-dependent growth-phase induction of the csgBA promoter in Escherichia coli can be achieved in vivo by σ70 in the absence of the nucleoid-associated protein H-NS. Mol. Microbiol. 13, 1021–1032 (1994).
Weber, H., Pesavento, C., Possling, A., Tischendorf, G. & Hengge, R. Cyclic-di-GMP-mediated signalling within the σS network of Escherichia coli. Mol. Microbiol. 62, 1014–1034 (2006).
Pesavento, C. et al. Inverse regulatory coordination of motility and curli-mediated adhesion in Escherichia coli. Genes Dev. 22, 2434–2446 (2008).
Lindenberg, S., Klauck, G., Pesavento, C., Klauck, E. & Hengge, R. The EAL domain protein YciR acts as a trigger enzyme in a c-di-GMP signalling cascade in E. coli biofilm control. EMBO J. 32, 2001–2014 (2013).
Ahmad, I., Cimdins, A., Beske, T. & Römling, U. Detailed analysis of c-di-GMP mediated regulation of csgD expression in Salmonella typhimurium. BMC Microbiol. 17, 27 (2017).
Serra, D. O. & Hengge, R. A c-di-GMP-based switch controls local heterogeneity of extracellular matrix synthesis which is crucial for integrity and morphogenesis of Escherichia coli macrocolony biofilms. J. Mol. Biol. 431, 4775–4793 (2019).
Bian, Z., Brauner, A., Li, Y. & Normark, S. Expression of and cytokine activation by Escherichia coli curli fibers in human sepsis. J. Infect. Dis. 181, 602–612 (2000).
Reichhardt, C. et al. Congo Red interactions with curli-producing E. coli and native curli amyloid fibers. PLoS ONE 10, e0140388 (2015).
Serra, D. O. & Hengge, R. in c-di-GMP Signaling (ed. Sauer, K.) Vol. 1657, 133–145 (Springer, 2017).
Lamprecht, O. et al. Regulation by cyclic di-GMP attenuates dynamics and enhances robustness of bimodal curli gene activation in Escherichia coli. PLoS Genet. 19, e1010750 (2023).
Contreras-Moreno, F. J., Pérez, J., Muñoz-Dorado, J., Moraleda-Muñoz, A. & Marcos-Torres, F. J. Myxococcus xanthus predation: an updated overview. Front. Microbiol. 15, 1339696 (2024).
DePas, W. H. et al. Biofilm formation protects Escherichia coli against killing by Caenorhabditis elegans and Myxococcus xanthus. Appl. Environ. Microbiol. 80, 7079–7087 (2014).
Bond, M. C., Vidakovic, L., Singh, P. K., Drescher, K. & Nadell, C. D. Matrix-trapped viruses can prevent invasion of bacterial biofilms by colonizing cells. eLife 10, e65355 (2021).
Gallardo, R., Ranson, N. A. & Radford, S. E. Amyloid structures: much more than just a cross-β fold. Curr. Opin. Struct. Biol. 60, 7–16 (2020).
Hammer, N. D., Schmidt, J. C. & Chapman, M. R. The curli nucleator protein, CsgB, contains an amyloidogenic domain that directs CsgA polymerization. Proc. Natl Acad. Sci. USA 104, 12494–12499 (2007).
Wittmers, F., Needham, D. M., Hehenberger, E., Giovannoni, S. J. & Worden, A. Z. Genomes from uncultivated pelagiphages reveal multiple phylogenetic clades exhibiting extensive auxiliary metabolic genes and cross-family multigene transfers. mSystems 7, e0152221 (2022).
Rouse, S. L., Matthews, S. J. & Dueholm, M. S. Ecology and biogenesis of functional amyloids in Pseudomonas. J. Mol. Biol. 430, 3685–3695 (2018).
Aravind, L., Iyer, L. M. & Burroughs, A. M. Discovering biological conflict systems through genome analysis: evolutionary principles and biochemical novelty. Annu. Rev. Biomed. Data Sci. 5, 367–391 (2022).
MacLellan, S. R., Wecke, T. & Helmann, J. D. A previously unidentified sigma factor and two accessory proteins regulate oxalate decarboxylase expression in Bacillus subtilis. Mol. Microbiol. 69, 954–967 (2008).
Papayannopoulos, V. Neutrophil extracellular traps in immunity and disease. Nat. Rev. Immunol. 18, 134–147 (2018).
Kumar, D. K. V. et al. Amyloid-β peptide protects against microbial infection in mouse and worm models of Alzheimer’s disease. Sci. Transl. Med. 8, 340ra72 (2016).
Ledvina, H. E. et al. An E1–E2 fusion protein primes antiviral immune signalling in bacteria. Nature 616, 319–325 (2023).
Kibby, E. M. et al. Bacterial NLR-related proteins protect against phage. Cell https://doi.org/10.1016/j.cell.2023.04.015 (2023).
Boyd, E. F., Hill, C. W., Rich, S. M. & Hartl, D. L. Mosaic structure of plasmids from natural populations of Escherichia coli. Genetics 143, 1091–1100 (1996).
Ferrières, L. et al. Silent mischief: bacteriophage Mu insertions contaminate products of Escherichia coli random mutagenesis performed using suicidal transposon delivery plasmids mobilized by broad-host-range RP4 conjugative machinery. J. Bacteriol. 192, 6418–6427 (2010).
Lee, P., Stopford, C. M., Svenson, A. G. & Rietsch, A. Control of effector export by the Pseudomonas aeruginosa type III secretion proteins PcrG and PcrV. Mol. Microbiol. 75, 924–941 (2010).
Datsenko, K. A. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA 97, 6640–6645 (2000).
Simon, R., Priefer, U. & Pühler, A. A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in gram negative bacteria. Bio/Technology 1, 784–791 (1983).
Blattner, F. R. et al. The complete genome sequence of Escherichia coli K-12. Science 277, 1453–1462 (1997).
Jeukens, J. et al. Comparative genomics of isolates of a Pseudomonas aeruginosa epidemic strain associated with chronic lung infections of cystic fibrosis patients. PLoS ONE 9, e87611 (2014).
Rahme, L. G. et al. Common virulence factors for bacterial pathogenicity in plants and animals. Science 268, 1899–1902 (1995).
Stover, C. K. et al. Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature 406, 959–964 (2000).
Cain, A. K. et al. Complete genome sequence of Pseudomonas aeruginosa reference strain PAK. Microbiol. Resour. Announc. 8, e00865–19 (2019).
Daligault, H. E. et al. Draft genome assembly of Klebsiella pneumoniae type strain ATCC 13883. Genome Announc. 2, e00939–14 (2014).
Rendulic, S. et al. A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspective. Science 303, 689–692 (2004).
Lambert, C. & Sockett, R. E. Laboratory maintenance of Bdellovibrio. Curr. Protoc. Microbiol. 9, 7B.2.1–7B.2.13 (2008).
Hmelo, L. R. et al. Precision-engineering the Pseudomonas aeruginosa genome with two-step allelic exchange. Nat. Protoc. 10, 1820–1841 (2015).
Fenton, A. K., El Mortaji, L., Lau, D. T. C., Rudner, D. Z. & Bernhardt, T. G. CozE is a member of the MreCD complex that directs cell elongation in Streptococcus pneumoniae. Nat. Microbiol. 2, 16237 (2016).
Chiang, S. L. & Rubin, E. J. Construction of a mariner-based transposon for epitope-tagging and genomic targeting. Gene 296, 179–185 (2002).
Cameron, D. E., Urbach, J. M. & Mekalanos, J. J. A defined transposon mutant library and its use in identifying motility genes in Vibrio cholerae. Proc. Natl Acad. Sci. USA 105, 8736–8741 (2008).
Zemansky, J. et al. Development of a mariner-based transposon and identification of Listeria monocytogenes determinants, including the peptidyl-prolyl isomerase PrsA2, that contribute to its hemolytic phenotype. J. Bacteriol. 191, 3950–3964 (2009).
Zhou, Y., Smith, D. R., Hufnagel, D. A. & Chapman, M. R. Experimental manipulation of the microbial functional amyloid called curli. Methods Mol. Biol. 966, 53–75 (2013).
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
Maffei, E. et al. Systematic exploration of Escherichia coli phage–host interactions with the BASEL phage collection. PLoS Biol. 19, e3001424 (2021).
Matsui, Y. et al. Multilocus sequence typing of Escherichia coli isolates from urinary tract infection patients and from fecal samples of healthy subjects in a college community. MicrobiologyOpen 9, e1032 (2020).
Hall, B. G. Building phylogenetic trees from molecular data with MEGA. Mol. Biol. Evol. 30, 1229–1235 (2013).
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).
Sayers, E. W. et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 52, D33–D43 (2024).
Steinegger, M. & Söding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol. 35, 1026–1028 (2017).
Wootton, J. C. & Federhen, S. Analysis of compositionally biased regions in sequence databases. Methods Enzymol. 266, 554–571 (1996).
Gabler, F. et al. Protein sequence analysis using the MPI bioinformatics toolkit. Curr. Protoc. Bioinform. 72, e108 (2020).
Deorowicz, S., Debudaj-Grabysz, A. & Gudyś, A. FAMSA: fast and accurate multiple sequence alignment of huge protein families. Sci. Rep. 6, 33964 (2016).
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
Teufel, F. et al. SignalP 6.0 predicts all five types of signal peptides using protein language models. Nat. Biotechnol. 40, 1023–1025 (2022).
Cuff, J. A. & Barton, G. J. Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins 40, 502–511 (2000).
Baek, M. et al. Accurate prediction of protein structures and interactions using a three-track neural network. Science 373, 871–876 (2021).
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
Ravi, J. et al. The phage shock protein (PSP) envelope stress response: discovery of novel partners and evolutionary history. mSystems 9, e0084723 (2024).
Kaur, G., Burroughs, A. M., Iyer, L. M. & Aravind, L. Highly regulated, diversifying NTP-dependent biological conflict systems with implications for the emergence of multicellularity. eLife 9, e52696 (2020).
Dueholm, M. S. et al. Functional amyloid in Pseudomonas. Mol. Microbiol. 77, 1009–1020 (2010).