Escherichia coli O80 hybrid pathotype strains producing Shiga toxin and ESBL: molecular characterization and potential therapeutic options. its ATPase activity, ATP-binding transport protein; multicopy suppressor of htrB, transport; Transport of small molecules: Other, Mol Microbiol 1993 Jan;7(1):69-79, "The essential Escherichia Eichhorn, I. et al. identified from the Neidhardt E. coli books (Neidhardt and Curtiss, 1996). Microbiol. ATP synthase genes are highlighted in red, LB-specific essential genes are highlighted in blue and GMM-specific essential genes are highlighted in green. Appl. Correspondence to Chemother. Inflamm. J. Syst. Infect. Jordan, I. K., Rogozin, I. Immunol. is available here. For each pair of strains, we used Spearmans correlation coefficient as a measure of the similarity in gene expression profile or gene essentiality profile. and JavaScript. PLoS ONE 7, e46547 (2012). Denamur, E., Clermont, O., Bonacorsi, S. et al. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. J. Infect. Natl Acad. Int. Subashchandrabose, S., Smith, S. N., Spurbeck, R. R., Kole, M. M. & Mobley, H. L. T. Genome-wide detection of fitness genes in uropathogenic Escherichia coli during systemic infection. Petty, N. K. et al. 83, 41034117 (2015). Metabolic cooperation between conspecific genotypic groups contributes to bacterial fitness, Characterization of antibiotic resistomes by reprogrammed bacteriophage-enabled functional metagenomics in clinical strains, Bacterial plasmid-associated and chromosomal proteins have fundamentally different properties in protein interaction networks, https://doi.org/10.1038/s41564-021-00893-0, https://doi.org/10.1038/s41564-021-00889-w, https://doi.org/10.1038/s41579-020-0416-x, https://doi.org/10.1016/j.chom.2020.10.001, https://doi.org/10.1101/2020.06.22.160168, https://doi.org/10.1101/2020.06.22.160242, https://doi.org/10.1016/j.cell.2020.09.065, Extended Data Fig. at 37 degrees C. One method of establishing the essentiality of a gene is the Rousset, F., Cabezas-Caballero, J., Piastra-Facon, F. et al. 1, 15014 (2016). Pneumonia-specific Escherichia coli with distinct phylogenetic and virulence profiles, France, 20122014. CAS 53, 951960 (2015). Two regions of high effective recombination. Evolution 11, 398411 (1957). O.C., S.B. PubMed Williams, G. C. Pleiotropy, natural selection, and the evolution of senescence. Attack of the clones: whole genome-based characterization of two closely related enterohemorrhagic Escherichia coli O26 epidemic lineages. 27, 543574 (2014). Wetmore, K. M. et al. Decano, A. G. & Downing, T. An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates. New Microbes New Infect. In Mycoplasma genitalium at least 18 genes are essential that are not essential in M. bovis. Smati, M. et al. The other 60 percent of E. coli cases are caused by non-0157:H7 . Open Access Proc. Deep mutational scanning can provide significant insights into the function of essential genes in bacteria. PLoS Pathog. Functional genomics of the rapidly replicating bacterium Vibrio natriegens by CRISPRi. Front. Genet. PLoS Pathog. Immun. Roberts, R. J., Vincze, T., Posfai, J. Comparing the 2803 well-annotated genes in E. coli to the 1678 genes in the latest genome-scale ME-model (one of the most comprehensive predictive models of E. coli to-date) , it is clear that the models can grow by over a thousand genes before running up against our lack of knowledge (Figure 2B). In organisms with high functional specificity or whose main objective is to produce certain specified metabolites, like, e.g., red blood cells, physical states are taken to be all those consistent with the mass-balance conditions. J. Bacteriol. Dobrindt, U., Hochhut, B., Hentschel, U. USA 95, 89228926 (1998). protein and GTPase, J Bacteriol 1991 Jun;173(11):3500-6, "ftsZ is an essential Microbes Infect. Patrick, W. M., Quandt, E. M., Swartzlander, D. B. 65, 21302134 (2015). Extended Data Fig. Nucleic Acids Res. This paper presents an original study of the global transcriptome of an EPEC strain and its virulence plasmid mutants, showing molecular crosstalk between the plasmid and the chromosome. Nature Reviews Microbiology EnteroBase: https://enterobase.warwick.ac.uk, Harvest: https://www.cbcb.umd.edu/software/harvest. Immunol. own work. Like multilocus enzyme electrophoresis, multilocus sequence typing uses the allele as the unit of comparison, rather than the nucleotide sequence. Evol. Applying phylogenomics to understand the emergence of Shiga-toxin-producing Escherichia coli O157:H7 strains causing severe human disease in the UK. Genome-wide CRISPRi-based identification of targets for decoupling growth from production. Gao, L. et al. Erick Denamur. The y-ome defines the 35% of Escherichia coli genes that lack Mol. Also Herring and Open Access Jorgensen, S. L. et al. This repeated emergence of stable and cosmopolitan lineages argues for an optimization of strain fitness through epistatic interactions between the virulence determinants and the remaining genome. & Hacker, J. Genomic islands in pathogenic and environmental microorganisms. Sahl, J. W. et al. B. Molecular mechanisms of Escherichia coli pathogenicity. Escobar-Paramo, P. et al. Microbiol. 194, 11411150 (2006). Alonso, C. A. et al. Agents Chemother. Dis. J. Antimicrob. : Experimental Epidemic profile of Shiga-toxin-producing Escherichia coli O104:H4 outbreak in Germany. Dixit, P. D., Pang, T. Y., Studier, F. W. & Maslov, S. Recombinant transfer in the basic genome of Escherichia coli. Microbiol. USA 95, 31403145 (1998). J. Bacteriol. 65, 651660 (2010). InterPro in 2019: improving coverage, classification and access to protein sequence annotations. USA 97, 1056710572 (2000). A., Perdreau-Remington, F. & Riley, L. W. 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This important paper before the genomic era shows that plasmids are distributed within the E. coli species according to the strain phylogeny. Quantitative analysis of commensal Escherichia coli populations reveals host-specific enterotypes at the intra-species level. [PMC]. Biol. PubMedGoogle Scholar. Maurelli, A. T., Fernandez, R. E., Bloch, C. A., Rode, C. K. & Fasano, A. Environ. Med. performed bioinformatic computation of the E. coli pangenome. & Darfeuille-Michaud, A. Invasive ability of an Escherichia coli strain isolated from the ileal mucosa of a patient with Crohns disease. Zoonoses Public Health 65, 911920 (2018). provided numerous reflections and epidemiologic and genomic data for the main text and the figures. Phylogenetic background and habitat drive the genetic diversification of Escherichia coli. Front. 3, ofw129 https://doi.org/10.1093/ofid/ofw129 (2016). Note that in March 2004 I removed some of the genes previously listed (dinD, Karnisova, L. et al. 41, 49304940 (2003). A Correction to this paper has been published: https://doi.org/10.1038/s41564-021-00893-0, A Correction to this paper has been published: https://doi.org/10.1038/s41564-021-00889-w. Rancati, G., Moffat, J., Typas, A. St-Pierre, F. et al. The nucleotide sequences of sgRNAs are shown in Supplementary Table 8. a, Growth curves were performed in triplicates in LB or GMM with TA447 and TA447dut. Dis. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. & Matsumura, I. Multicopy suppression underpins metabolic evolvability. We first ranked genes previously shown to be essential in a variety of E. coli strains by expression level, and chose ten target genes covering the range of observed expression (Figure 5A). for growth of Escherichia coli". USA 112, 90709075 (2015). 1 Altmetric Metrics Abstract Background Chromosome engineering encompasses a collection of homologous recombination-based techniques that are employed to modify the genome of a model organism in a controlled fashion. J.C.-C. provided experimental assistance. We have applied it to assess the importance of ~3,400 nearly ubiquitous genes in three growth conditions in 18 representative E. coli strains spanning most common phylogroups and lifestyles. Nat. Google Scholar. a, Comparison between screening results in LB and M9-glucose medium highlights auxotrophy genes. Google Scholar. PLoS ONE 10, e0144465 (2015). Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Incentives to define lists of genes that are essential for bacterial survival include the identification of potential targets for antibacterial drug development, genes required for rapid growth for exploitation in biotechnology, and discovery of new biochemical pathways. Nat. Cassini, A. et al. Biol. cytoplasmic membrane protein involved in cell division in Escherichia coli", J Bacteriol 1993 Jun;175(12):3790-7, "Cloning and characterization Grey squares indicate if ybaQ is essential in the corresponding strains. Blattner, 2004. Infect. Genet. Commun. c, Spot assays show the phenotype associated with the repression of kdsB, kpsU or both kdsB and kpsU simultaneously in strains carrying kpsU. i, Two examples of polar effects observed in our screen. Article J. Infect. 68, 334337 (2019). Dis. CAS Here, we have developed a CRISPR interference platform for high-throughput gene repression that is compatible with most E. coli isolates and closely related species. 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Background By definition, essential proteins of a cellular organism are necessary to live and replicate, and are therefore attractive targets for antimicrobial treatments. Evol. Proc. Nat. Clermont, O., Gordon, D. M., Brisse, S., Walk, S. T. & Denamur, E. Characterization of the cryptic Escherichia lineages: rapid identification and prevalence. Lukjancenko, O., Wassenaar, T. M. & Ussery, D. W. Comparison of 61 sequenced Escherichia coli genomes. PubMed Microbiol. 54, 108127 (2017). Pooled CRISPRi screening of the cyanobacterium Synechocystis sp PCC 6803 for enhanced industrial phenotypes. 15, e1007652 (2019). Although recent advances in bacterial genomics have unravelled genes required for fitness in various experimental conditions, most studies have focused on single model strains. nov., isolated from faeces of Marmota himalayana. We also thank J. Rodrguez-Beltrn and S. Brisse for providing a strain of Citrobacter freundii and Klebsiella pneumoniae, respectively. Ingle, D. J. et al. J. Antimicrob. Open Access articles citing this article. & Denamur, E. Sex in Escherichia coli does not disrupt the clonal structure of the population: evidence from random amplified polymorphic DNA and restriction-fragment-length polymorphism. PLoS ONE 4, e5553 (2009). 60, 303311 (2016). The essential genome of Escherichia coli K-12. van Opijnen, T., Dedrick, S. & Bento, J. . Front. You are using a browser version with limited support for CSS. A specific genetic background is required for acquisition and expression of virulence factors in Escherichia coli. Transposon-insertion sequencing screens unveil requirements for EHEC growth and intestinal colonization. S2 (rpsB)", PNAS U S A 1992 May 1;89(9):3995-8, "The gene for a tRNA modifying Pooled CRISPR interference screening enables genome-scale functional genomics study in bacteria with superior performance. & Denamur, E. The population genetics of commensal Escherichia coli. J. Clin. F.R. DeLong, E. R., DeLong, D. M. & Clarke-Pearson, D. L. Comparing the areas under two or more correlated receiver operating characteristic curves: a nonparametric approach. Evol. O.C. We have applied it to assess the importance of ~3,400 nearly ubiquitous genes in three growth conditions in 18 representative E. coli strains spanning most common phylogroups and lifestyles of the species. The sequence of the ybaQ sgRNA is provided in Supplementary Table 8. c, Silencing ybaQ in strain S88 induces the expression of higB-1. 31, 19291936 (2014). Alnajar, S. & Gupta, R. S. Phylogenomics and comparative genomic studies delineate six main clades within the family Enterobacteriaceae and support the reclassification of several polyphyletic members of the family. The dashed black line marks the threshold chosen in further analysis (gene score<-3). Science 328, 469 (2010). Escherichia coli (abbreviated as E. coli) are bacteria found in the environment, foods, and intestines of people and animals.E. Biol. Here, we report a genome-wide CRISPR-dCas9 screen using a starting pool of ~ 92,000 sgRNAs which target random positions in the chromosome of E. coli. contracts here. Each gene is identified by a Bnum, Magnum, gene product type and gene product (Function April 2001). Decrulle, A., Fernandez Rodriguez, J., Duportet, X. Animal and human pathogenic Escherichia coli strains share common genetic backgrounds. Synthetic Biology, Department of Microbiology, Institut Pasteur, Paris, France, Franois Rousset,Jose Cabezas-Caballero,Florence Piastra-Facon&David Bikard, Sorbonne Universit, Collge Doctoral, Paris, France, Universit de Paris, IAME, INSERM UMR1137, Paris, France, AP-HP, Laboratoire de Gntique Molculaire, Hpital Bichat, Paris, France, Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, France, You can also search for this author in USA 95, 39433948 (1998). Sci. transcriptional organization, and insertional mutagenesis of the envA gene Bowel Dis. Synopsis The study presents a CRISPR/Cas9-mediated genomic error-prone editing (CREPE) technology for generating a library of mutants within a targeted Escherichia coli gene in its native genomic context.