A New Suite of Allelic-Exchange Vectors for the Scarless Modification of Proteobacterial Genomes

• Published in: Applied and environmental microbiology Vol. 85; no. 16
• Main Authors: Lazarus, Jacob E, Warr, Alyson R, Kuehl, Carole J, Giorgio, Rachel T, Davis, Brigid M, Waldor, Matthew K
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 01.08.2019
• Subjects: Alleles; Amides; Anti-Bacterial Agents - pharmacology; Antibiotic resistance; Antibiotics; Bacteria; beta-Lactams - pharmacology; Binding sites; Crossovers; Derepression; Disruption; E coli; Enterobacter cloacae; Exchanging; Gene expression; Genetic analysis; Genetic engineering; Genetic Vectors - genetics; Genetic Vectors - metabolism; Genome, Bacterial; Genomes; Gram-negative bacteria; Homologous recombination; Homology; Methods; Microbial Sensitivity Tests; Mutation; Peptidoglycans; Plasmids - genetics; Plasmids - metabolism; Proteobacteria - drug effects; Proteobacteria - genetics; Proteobacteria - metabolism; Rhamnose; Serratia marcescens; Spotlight; Toxins; Transcription; Vectors (Biology); β-Lactam antibiotics; ampC; type VI toxin; allelic exchange; antibiotic resistance; AmilCP gene; Serratia marcescens; toxin-antitoxin; sacB; beta-lactamase; ampD
• ISSN: 0099-2240; 1098-5336
• DOI: 10.1128/AEM.00990-19

Despite the advent of new techniques for genetic engineering of bacteria, allelic exchange through homologous recombination remains an important tool for genetic analysis. Currently, -based vector systems are often used for allelic exchange, but counterselection escape, which prevents isolation of cells with the desired mutation, occasionally limits their utility. To circumvent this, we engineered a series of "pTOX" allelic-exchange vectors. Each plasmid encodes one of a set of inducible toxins, chosen for their potential utility in a wide range of medically important proteobacteria. A codon-optimized transcriptional activator with a strong synthetic ribosome-binding site enables tight toxin induction even in organisms lacking an endogenous rhamnose regulon. Expression of the gene encoding blue AmilCP or magenta TsPurple nonfluorescent chromoprotein facilitates monitoring of successful single- and double-crossover events using these vectors. The versatility of these vectors was demonstrated by deleting genes in , O157:H7, , and Finally, pTOX was used to characterize the impact of disruption of all combinations of the 3 paralogous peptidoglycan amidohydrolases on chromosomal β-lactamase activity and the corresponding β-lactam antibiotic resistance. Mutation of multiple amidohydrolases was necessary for high-level derepression and β-lactam resistance. These data suggest why β-lactam resistance may emerge during treatment less frequently in than in other AmpC-producing pathogens, like Collectively, our findings suggest that the pTOX vectors should be broadly useful for genetic engineering of Gram-negative bacteria. Targeted modification of bacterial genomes is critical for genetic analysis of microorganisms. Allelic exchange is a technique that relies on homologous recombination to replace native loci with engineered sequences. However, current allelic-exchange vectors often enable only weak selection for successful homologous recombination. We developed a suite of new allelic-exchange vectors, pTOX, which were validated in several medically important proteobacteria. They encode visible nonfluorescent chromoproteins that enable easy identification of colonies bearing integrated vectors and permit stringent selection for the second step of homologous recombination. We demonstrate the utility of these vectors by using them to investigate the effect of inactivation of peptidoglycan amidohydrolases on β-lactam antibiotic resistance.