Fitness
Metabolism of l-arabinose converges with virulence regulation to promote enteric pathogen fitness – Nature Communications
Caballero-Flores, G., Pickard, J. M. & Núñez, G. Microbiota-mediated colonization resistance: mechanisms and regulation. Nat. Rev. Microbiol. 21, 347–360 (2023).
Baümler, A. J. & Sperandio, V. Interactions between the microbiota and pathogenic bacteria in the gut. Nature 535, 85–93 (2016).
Connolly, J. P. R., Brett Finlay, B. & Roe, A. J. From ingestion to colonization: the influence of the host environment on regulation of the LEE encoded type III secretion system in enterohaemorrhagic Escherichia coli. Front. Microbiol. 6, 568 (2015).
Turner, N. C. A., Connolly, J. P. R. & Roe, A. J. Control freaks—signals and cues governing the regulation of virulence in attaching and effacing pathogens. Biochem. Soc. Trans. 47, 229–238 (2018).
Wale, K. R., Cottam, C., Connolly, J. P. & Roe, A. J. Transcriptional and metabolic regulation of EHEC and Citrobacter rodentium pathogenesis. Curr. Opin. Microbiol. 63, 70–75 (2021).
Kaper, J. B., Nataro, J. P. & Mobley, H. L. Pathogenic Escherichia coli. Nat. Rev. Microbiol. 2, 123–140 (2004).
Croxen, M. A. & Finlay, B. B. Molecular mechanisms of Escherichia coli pathogenicity. Nat. Rev. Microbiol. 8, 26–38 (2010).
Moon, H. W., Whipp, S. C., Argenzio, R. A., Levine, M. M. & Giannella, R. A. Attaching and effacing activities of rabbit and human enteropathogenic Escherichia coli in pig and rabbit intestines. Infect. Immun. 41, 1340–1351 (1983).
Kenny, B. et al. Enteropathogenic E. coli (EPEC) transfers its receptor for intimate adherence into mammalian cells. Cell 91, 511–520 (1997).
Jerse, A. E., Yu, J., Tall, B. D. & Kaper, J. B. A genetic locus of enteropathogenic Escherichia coli necessary for the production of attaching and effacing lesions on tissue culture cells. Proc. Natl Acad. Sci. USA 87, 7839–7843 (1990).
Mcdaniel, T. K., Jarvis, K. G., Donnenberg, M. S. & Kaper, J. B. A genetic locus of enterocyte effacement conserved among diverse enterobacterial pathogens. Proc. Natl Acad. Sci. USA 92, 1664–1668 (1995).
Deng, W. et al. Dissecting virulence: systematic and functional analyses of a pathogenicity island. Proc. Natl Acad. Sci. USA 101, 3597–3602 (2004).
Dean, P. & Kenny, B. The effector repertoire of enteropathogenic E. coli: ganging up on the host cell. Curr. Opin. Microbiol. 12, 101–109 (2009).
Tobe, T. et al. An extensive repetoire of type III secretion effectors in Escherichia coli O157 and the role of lambdoid phages in their dissemination. Proc. Natl Acad. Sci. USA 103, 14941–14946 (2006).
Perna, N. T. et al. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409, 529–533 (2001).
Wong, A. R. C. et al. Enteropathogenic and enterohaemorrhagic Escherichia coli: Even more subversive elements. Mol. Microbiol. 80, 1420–1438 (2011).
Collins, J. W. et al. Citrobacter rodentium: Infection, inflammation and the microbiota. Nat. Rev. Microbiol. 12, 612–623 (2014).
Mullineaux-Sanders, C. et al. Citrobacter rodentium–host–microbiota interactions: immunity, bioenergetics and metabolism. Nat. Rev. Microbiol. 17, 701–715 (2019).
Crepin, V. F., Collins, J. W., Habibzay, M. & Frankel, G. Citrobacter rodentium mouse model of bacterial infection. Nat. Protoc. 11, 1851–1876 (2016).
Kamada, N. et al. Regulated virulence controls the ability of a pathogen to compete with the gut microbiota. Science 336, 1325–1329 (2012).
Connolly, J. P. R. et al. Host-associated niche metabolism controls enteric infection through fine-tuning the regulation of type 3 secretion. Nat. Commun. 9, 4187 (2018).
Njoroge, J. W., Nguyen, Y., Curtis, M. M., Moreira, C. G. & Sperandio, V. Virulence meets metabolism: Cra and KdpE gene regulation in enterohemorrhagic Escherichia coli. MBio 3, e00280–00212 (2012).
Curtis, M. M. et al. The gut commensal bacteroides thetaiotaomicron exacerbates enteric infection through modification of the metabolic landscape. Cell Host Microbe 16, 759–769 (2014).
Menezes-Garcia, Z., Kumar, A., Zhu, W., Winter, S. E. & Sperandio, V. L-Arginine sensing regulates virulence gene expression and disease progression in enteric pathogens. Proc. Natl Acad. Sci. USA 117, 12387–12393 (2020).
Connolly, J. P. R. et al. The host metabolite D-serine contributes to bacterial niche specificity through gene selection. ISME J. 9, 1039–1051 (2015).
O’Boyle, N., Connolly, J. P. R., Tucker, N. P. & Roe, A. J. Genomic plasticity of pathogenic Escherichia coli mediates D-serine tolerance via multiple adaptive mechanisms. Proc. Natl Acad. Sci. USA 117, 22484–22493 (2020).
Conway, T. & Cohen, P. S. Commensal and pathogenic Escherichia coli Metabolism in the gut. Microbiol. Spectr. 3, MBP-0006-2014 (2015).
Fabich, A. J. et al. Comparison of carbon nutrition for pathogenic and commensal Escherichia coli strains in the mouse intestine. Infect. Immun. 76, 1143–1152 (2008).
Crozier, L. et al. The role of l-arabinose metabolism for Escherichia coli o157:H7 in edible plants. Microbiology 167, 1–12 (2021).
Mayer, C. & Boos, W. Hexose/pentose and hexitol/pentitol metabolism. EcoSal Plus https://doi.org/10.1128/ecosalplus.3.4.1 (2005).
John, M. et al. Use of in vivo-induced antigen technology for identification of Escherichia coli O157:H7 proteins expressed during human infection. Infect. Immun. 73, 2665–2679 (2005).
Segura, A. et al. Transcriptomic analysis reveals specific metabolic pathways of enterohemorrhagic Escherichia coli O157:H7 in bovine digestive contents. BMC Genom. 19, 766 (2018).
Rice, A. J., Park, A. & Pinkett, H. W. Diversity in ABC transporters: type I, II and III importers. Crit. Rev. Biochem. Mol. Biol. 49, 426–437 (2014).
Drousiotis, K. et al. Characterization of the l-arabinofuranose-specific GafABCD ABC transporter essential for l-arabinose-dependent growth of the lignocellulose-degrading bacterium Shewanella sp. ANA-3. Microbiology 169, 3 (2023).
Zschiedrich, C. P., Keidel, V. & Szurmant, H. Molecular mechanisms of two-component signal transduction. J. Mol. Biol. 428, 3752–3775 (2016).
Schleif, R. AraC protein, regulation of the l-arabinose operon in Escherichia coli, and the light switch mechanism of AraC action. FEMS Microbiol. Rev. 34, 779–796 (2010).
Mullineaux-Sanders, C. et al. Citrobacter rodentium relies on commensals for colonization of the colonic mucosa. Cell Rep. 21, 3381–3389 (2017).
Carlson-Banning, K. M. & Sperandio, V. Catabolite and oxygen regulation of enterohemorrhagic Escherichia coli virulence. MBio 7, e01852–16 (2016).
Freter, R., Brickner, H., Fekete, J., Vickerman, M. M. & Carey, K. E. Survival and implantation of Escherichia coli in the intestinal tract. Infect. Immun. 39, 686–703 (1983).
Yip, A. Y. G. et al. Antibiotics promote intestinal growth of carbapenem-resistant Enterobacteriaceae by enriching nutrients and depleting microbial metabolites. Nat. Commun. 14, 5094 (2023).
Liu, B. et al. Enterohaemorrhagic E. coli utilizes host- and microbiota-derived L-malate as a signaling molecule for intestinal colonization. Nat. Commun. 14, 7227 (2023).
Schutte, J. B., de Jong, J., van Weerden, E. J. & Tamminga, S. Nutritional implications of l -arabinose in pigs. Br. J. Nutr. 68, 195–207 (1992).
Schwalm, N. D., Townsend, G. E. & Groisman, E. A. Multiple signals govern utilization of a polysaccharide in the gut bacterium bacteroides thetaiotaomicron. MBio https://doi.org/10.1128/mbio.01342-16 (2016).
Pereira, G. V. et al. Degradation of complex arabinoxylans by human colonic Bacteroidetes. Nat. Commun. 12, 459 (2021).
Martens, E. C. et al. Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts. PLoS Biol. 9, e1001221 (2011).
Rogowski, A. et al. Glycan complexity dictates microbial resource allocation in the large intestine. Nat. Commun. 6, 7481 (2015).
Kyle, J. L., Parker, C. T., Goudeau, D. & Brandl, M. T. Transcriptome analysis of escherichia coli O157:H7 exposed to lysates of lettuce leaves. Appl. Environ. Microbiol. 76, 1375–1387 (2010).
Petty, N. K. et al. The Citrobacter rodentium genome sequence reveals convergent evolution with human pathogenic Escherichia coli. J. Bacteriol. 192, 525–538 (2010).
Harper, L. et al. Staphylococcus aureus responds to the central metabolite pyruvate to regulate virulence. MBio https://doi.org/10.1128/mbio.02272-17 (2018).
Jiang, L. et al. Salmonella Typhimurium reprograms macrophage metabolism via T3SS effector SopE2 to promote intracellular replication and virulence. Nat. Commun. 12, 879 (2021).
Wiebe, M. A. et al. Serine deamination is a new acid tolerance mechanism observed in uropathogenic Escherichia coli. MBio 13, e02963-22 (2022).
Ruddle, S. J., Massis, L. M., Cutter, A. C. & Monack, D. M. Salmonella-liberated dietary L-arabinose promotes expansion in superspreaders. Cell Host Microbe 31, 405–417.e5 (2023).
Neumann, M. et al. Deprivation of dietary fiber in specific-pathogen-free mice promotes susceptibility to the intestinal mucosal pathogen Citrobacter rodentium. Gut Microbes 13, 1966263 (2021).
Desai, M. S. et al. A dietary fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility. Cell 167, 1339–1353.e21 (2016).
An, J. et al. Western-style diet impedes colonization and clearance of Citrobacter rodentium. PLoS Pathog. 17, e1009497 (2021).
Jimenez, A. G., Ellermann, M., Abbott, W. & Sperandio, V. Diet-derived galacturonic acid regulates virulence and intestinal colonization in enterohaemorrhagic Escherichia coli and Citrobacter rodentium. Nat. Microbiol. 5, 368–378 (2020).
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).
Livak, K. J. & Schmittgen, T. D. Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT method. Methods 25, 402–408 (2001).
Patro, R., Duggal, G., Love, M. I., Irizarry, R. A. & Kingsford, C. Salmon provides fast and bias-aware quantification of transcript expression. Nat. Methods 14, 417–419 (2017).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
Szklarczyk, D. et al. The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Res. 49, D605–D612 (2021).
Ewels, P., Magnusson, M., Lundin, S. & Käller, M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32, 3047–3048 (2016).
Wood, D. E. & Salzberg, S. L. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 15, R46 (2014).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
Huang, W., Li, L., Myers, J. R. & Marth, G. T. ART: a next-generation sequencing read simulator. Bioinformatics 28, 593–594 (2012).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
McKenna, A. et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).
Depristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491–501 (2011).
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 6, 80–92 (2012).
Sarovich, D. S. & Price, E. P. SPANDx: a genomics pipeline for comparative analysis of large haploid whole genome re-sequencing datasets. BMC Res. Notes 7, 618 (2014).
Song, L., Florea, L. & Langmead, B. Lighter: fast and memory-efficient sequencing error correction without counting. Genome Biol. 15, 509 (2014).
Magoč, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963 (2011).
Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477 (2012).
Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9, e112963 (2014).
Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29, 1072–1075 (2013).
Larsen, M. V. et al. Multilocus sequence typing of total-genome-sequenced bacteria. J. Clin. Microbiol. 50, 1355–1361 (2012).
Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
Evans, R. et al. Protein complex prediction with AlphaFold-Multimer. Preprint at bioRxiv https://doi.org/10.1101/2021.10.04.463034 (2022).
Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).
Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549 (2018).
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