Faith, J. J. et al. The long-term stability of the human gut microbiota. Science 341, 1237439 (2013).
Article PubMed PubMed Central Google Scholar
Peterson, S. B., Bertolli, S. K. & Mougous, J. D. The central role of interbacterial antagonism in bacterial life. Curr. Biol. 30, R1203–r1214 (2020).
Article CAS PubMed PubMed Central Google Scholar
García-Bayona, L. & Comstock, L. E. Bacterial antagonism in host-associated microbial communities. Science https://doi.org/10.1126/science.aat2456 (2018).
Wexler, A. G. & Goodman, A. L. An insider’s perspective: Bacteroides as a window into the microbiome. Nat. Microbiol. 2, 17026 (2017).
Article CAS PubMed PubMed Central Google Scholar
Chatzidaki-Livanis, M. et al. Gut symbiont Bacteroides fragilis secretes a eukaryotic-like ubiquitin protein that mediates intraspecies antagonism. mBio https://doi.org/10.1128/mBio.01902-17 (2017).
Shumaker, A. M., Laclare McEneany, V., Coyne, M. J., Silver, P. A. & Comstock, L. E. Identification of a fifth antibacterial toxin produced by a single Bacteroides fragilis strain. J. Bacteriol. https://doi.org/10.1128/jb.00577-18 (2019).
McEneany, V. L., Coyne, M. J., Chatzidaki-Livanis, M. & Comstock, L. E. Acquisition of MACPF domain-encoding genes is the main contributor to LPS glycan diversity in gut Bacteroides species. ISME J. 12, 2919–2928 (2018).
Article CAS PubMed PubMed Central Google Scholar
Roelofs, K. G., Coyne, M. J., Gentyala, R. R., Chatzidaki-Livanis, M. & Comstock, L. E. Bacteroidales secreted antimicrobial proteins target surface molecules necessary for gut colonization and mediate competition in vivo. mBio https://doi.org/10.1128/mBio.01055-16 (2016).
Chatzidaki-Livanis, M., Coyne, M. J. & Comstock, L. E. An antimicrobial protein of the gut symbiont Bacteroides fragilis with a MACPF domain of host immune proteins. Mol. Microbiol. 94, 1361–1374 (2014).
Article CAS PubMed PubMed Central Google Scholar
Bao, Y. et al. A common pathway for activation of host-targeting and bacteria-targeting toxins in human intestinal bacteria. mBio 12, e0065621 (2021).
Evans, J. C. et al. A proteolytically activated antimicrobial toxin encoded on a mobile plasmid of Bacteroidales induces a protective response. Nat. Commun. 13, 4258 (2022).
Article CAS PubMed PubMed Central Google Scholar
Matano, L. M., Coyne, M. J., García-Bayona, L. & Comstock, L. E. Bacteroidetocins target the essential outer membrane protein BamA of Bacteroidales symbionts and pathogens. mBio 12, e0228521 (2021).
Patrick, S. et al. A unique homologue of the eukaryotic protein-modifier ubiquitin present in the bacterium Bacteroides fragilis, a predominant resident of the human gastrointestinal tract. Microbiology 157, 3071–3078 (2011).
Article CAS PubMed PubMed Central Google Scholar
Bitto, E. & McKay, D. B. Crystallographic structure of SurA, a molecular chaperone that facilitates folding of outer membrane porins. Structure 10, 1489–1498 (2002).
Article CAS PubMed Google Scholar
Calabrese, A. N. et al. Inter-domain dynamics in the chaperone SurA and multi-site binding to its outer membrane protein clients. Nat. Commun. 11, 2155 (2020).
Article CAS PubMed PubMed Central Google Scholar
Jakob, R. P. et al. Dimeric structure of the bacterial extracellular foldase PrsA. J. Biol. Chem. 290, 3278–3292 (2015).
Article CAS PubMed Google Scholar
Stull, F., Betton, J.-M. & Bardwell, J. C. A. Periplasmic chaperones and prolyl isomerases. EcoSal Plus https://doi.org/10.1128/ecosalplus.ESP-0005-2018 (2018).
Rouviere, P. E. & Gross, C. A. SurA, a periplasmic protein with peptidyl-prolyl isomerase activity, participates in the assembly of outer membrane porins. Genes Dev. 10, 3170–3182 (1996).
Article CAS PubMed Google Scholar
Xu, X., Wang, S., Hu, Y.-X. & McKay, D. B. The periplasmic bacterial molecular chaperone SurA adapts its structure to bind peptides in different conformations to assert a sequence preference for aromatic residues. J. Mol. Biol. 373, 367–381 (2007).
Article CAS PubMed PubMed Central Google Scholar
Hyyrylainen, H.-L. et al. Penicillin-binding protein folding is dependent on the PrsA peptidyl-prolyl cis–trans isomerase in Bacillus subtilis. Mol. Microbiol. 77, 108–127 (2010).
Article CAS PubMed Google Scholar
Roch, M. et al. Thermosensitive PBP2a requires extracellular folding factors PrsA and HtrA1 for Staphylococcus aureus MRSA beta-lactam resistance. Commun. Biol. https://doi.org/10.1038/s42003-019-0667-0 (2019).
Walton, T. A. & Sousa, M. C. Crystal structure of Skp, a prefoldin-like chaperone that protects soluble and membrane proteins from aggregation. Mol. Cell 15, 367–374 (2004).
Article CAS PubMed Google Scholar
Scholz, C. et al. SlyD proteins from different species exhibit high prolyl isomerase and chaperone activities. Biochemistry 45, 20–33 (2006).
Article CAS PubMed Google Scholar
Almeida, A. et al. A unified catalog of 204,938 reference genomes from the human gut microbiome. Nat. Biotechnol. 39, 105–114 (2021).
Article CAS PubMed Google Scholar
Li, J. et al. An integrated catalog of reference genes in the human gut microbiome. Nat. Biotechnol. 32, 834–841 (2014).
Article CAS PubMed Google Scholar
Elhenawy, W., Debelyy, M. O. & Feldman, M. F. Preferential packing of acidic glycosidases and proteases into Bacteroides outer membrane vesicles. mBio 5, e00909–e00914 (2014).
Article PubMed PubMed Central Google Scholar
Atanaskovic, I. & Kleanthous, C. Tools and approaches for dissecting protein bacteriocin import in gram-negative bacteria. Front. Microbiol. 10, 646 (2019).
Article PubMed PubMed Central Google Scholar
Unal, C. M. & Steinert, M. Microbial peptidyl-prolyl cis/trans isomerases (PPIases): virulence factors and potential alternative drug targets. Microbiol. Mol. Biol. Rev. 78, 544–571 (2014).
Article PubMed PubMed Central Google Scholar
Scheuplein, N. J. et al. Targeting protein folding: a novel approach for the treatment of pathogenic bacteria. J. Med. Chem. 63, 13355–13388 (2020).
Article CAS PubMed Google Scholar
Bencivenga-Barry, N. A., Lim, B., Herrera, C. M., Trent, M. S. & Goodman, A. L. Genetic manipulation of wild human gut bacteroides. J. Bacteriol. https://doi.org/10.1128/jb.00544-19 (2020).
García-Bayona, L. & Comstock, L. E. Streamlined genetic manipulation of diverse bacteroides and parabacteroides isolates from the human gut microbiota. mBio https://doi.org/10.1128/mBio.01762-19 (2019).
Liu, D., Siguenza, N. E., Zarrinpar, A. & Ding, Y. Methods of DNA introduction for the engineering of commensal microbes. Eng. Microbiol. 2, 100048 (2022).
Lim, B., Zimmermann, M., Barry, N. A. & Goodman, A. L. Engineered regulatory systems modulate gene expression of human commensals in the gut. Cell 169, 547–558.e515 (2017).
Article CAS PubMed PubMed Central Google Scholar
Jiang, K. et al. Functional characterization of Vip3Aa from Bacillus thuringiensis reveals the contributions of specific domains to its insecticidal activity. J. Biol. Chem. 299, 103000 (2023).
Article CAS PubMed PubMed Central Google Scholar
Jiang, K. et al. A strategy to enhance the insecticidal potency of Vip3Aa by introducing additional cleavage sites to increase its proteolytic activation efficiency. Eng. Microbiol. 3, 100083 (2023).
Kabsch, W. XDS. Acta Crystallogr. D Biol. Crystallogr. 66, 125–132 (2010).
Article CAS PubMed PubMed Central Google Scholar
Minor, W., Cymborowski, M., Otwinowski, Z. & Chruszcz, M. HKL-3000: the integration of data reduction and structure solution - from diffraction images to an initial model in minutes. Acta Crystallogr. D Struct. Biol. 62, 859–866 (2006).
Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D Struct. Biol. 75, 861–877 (2019).
Article CAS PubMed PubMed Central Google Scholar
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Struct. Biol. 60, 2126–2132 (2004).
Camacho, C. et al. BLAST plus: architecture and applications. BMC Bioinform. https://doi.org/10.1186/1471-2105-10-421 (2009).
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
Article CAS PubMed PubMed Central Google Scholar
Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530–1534 (2020).
Article CAS PubMed PubMed Central Google Scholar
Schmid, F. X. Prolyl isomerase: enzymatic catalysis of slow protein folding reactions. Annu. Rev. Biophys. Biomol. Struct. 22, 123–143 (1993).
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