[Show abstract][Hide abstract] ABSTRACT: With the wide availability of whole-genome sequencing (WGS), genetic mapping has become the rate-limiting step, inhibiting
unbiased forward genetics in even the most tractable model organisms. We introduce a rapid deconvolution resource and method
for untagged causative mutations after mutagenesis, screens, and WGS in Escherichia coli. We created Deconvoluter—ordered libraries with selectable insertions every 50 kb in the E. coli genome. The Deconvoluter method uses these for replacement of untagged mutations in the genome using a phage-P1-based gene-replacement
strategy. We validate the Deconvoluter resource by deconvolution of 17 of 17 phenotype-altering mutations from a screen of
N-ethyl-N-nitrosourea-induced mutants. The Deconvoluter resource permits rapid unbiased screens and gene/function identification and
will enable exploration of functions of essential genes and undiscovered genes/sites/alleles not represented in existing deletion
collections. This resource for unbiased forward-genetic screens with mapping-by-sequencing (‘forward genomics’) demonstrates
a strategy that could similarly enable rapid screens in many other microbes.
Full-text · Article · Nov 2015 · Nucleic Acids Research
[Show abstract][Hide abstract] ABSTRACT: Salmonella enterica Serovar Typhimurium U288 is an emerging pathogen of pigs. The strain contains three plasmids of diverse origin that encode traits that are of concern for food security and safety, these include antibiotic resistant determinants, an array of functions that can modify cell physiology and permit genetic mobility. At 148,711 bp, pSTU288-1 appears to be a hybrid plasmid containing a conglomerate of genes found in pSLT of S. Typhimurium LT2, coupled with a mosaic of horizontally-acquired elements. Class I integron containing gene cassettes conferring resistance against clinically important antibiotics and compounds are present in pSTU288-1. A curious feature of the plasmid involves the deletion of two genes encoded in the Salmonella plasmid virulence operon (spvR and spvA) following the insertion of a tnpA IS26-like element coupled to a blaTEM gene. The spv operon is considered to be a major plasmid-encoded Salmonella virulence factor that is essential for the intracellular lifecycle. The loss of the positive regulator SpvR may impact on the pathogenesis of S. Typhimurium U288. A second 11,067 bp plasmid designated pSTU288-2 contains further antibiotic resistance determinants, as well as replication and mobilization genes. Finally, a small 4,675 bp plasmid pSTU288-3 was identified containing mobilization genes and a pleD-like G-G-D/E-E-F conserved domain protein that modulate intracellular levels of cyclic di-GMP, and are associated with motile to sessile transitions in growth.
[Show abstract][Hide abstract] ABSTRACT: Campylobacter jejuni strain PT14 is a clinical isolate previously used to propagate bacteriophages in the United Kingdom phage typing scheme.
The strain has proven useful in the isolation of Campylobacter bacteriophages from several sources, and it functions as a model host in phage therapy experiments with poultry and poultry
Full-text · Article · Oct 2013 · Genome Announcements