Sequencing a piece of history: complete genome sequence of the original Escherichia coli strain

Dunne, Karl A.; Chaudhuri, Roy R.; Rossiter, Amanda E.; Beriotto, Irene; Browning, Douglas F.; Squire, Derrick J. P.; Cunningham, Adam F.; Cole, Jeffrey A.; Loman, Nicholas J.; Henderson, Ian R.

doi:10.1099/mgen.0.000106

Cited by 31 publications

(36 citation statements)

References 50 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It could be that in our selection of mainly clinical samples a certain predilection has occurred towards isolates with particular virulence traits. The gspL gene has been described as being part of the accessory genome of E. coli [49]. Our study supports this finding as some strains did not harbor this gene.…”

Section: Discussionsupporting

confidence: 87%

Genome-wide analysis in Escherichia coli unravels an unprecedented level of genetic homoplasy associated with cefotaxime resistance

Coolen¹,

Drijver

Verweij

et al. 2020

Preprint

View full text Add to dashboard Cite

ABSTRACTCefotaxime (CTX) is a commonly used third-generation cephalosporin (3GC) to treat infections caused by Escherichia coli. Two genetic mechanisms have been associated with 3GC resistance in E. coli. The first is the conjugative transfer of a plasmid harboring antibiotic resistance genes. The second is the introduction of mutations in the promoter region of the ampC β-lactamase gene that cause chromosomal-encoded β-lactamase hyperproduction. A wide variety of promoter mutations related to AmpC hyperproduction have been described. However, their link to a specific 3GC such as CTX resistance has not been reported. Here, we measured CTX MICs in 172 cefoxitin resistant E. coli isolates and performed genome-wide analysis of homoplastic mutations associated with CTX resistance by comparing Illumina whole-genome sequencing data of all isolates to a PacBio tailored-made reference chromosome. We mapped the mutations on the reference chromosome and determined their occurrence in the phylogeny, revealing extreme homoplasy at the −42 position of the ampC promoter. The 24 occurrences of a “T” at the −42 position rather than the wild type “C”, resulted from 18 independent C>T mutations in 5 phylogroups. The −42 C>T mutation was only observed in E. coli lacking a plasmid-encoded ampC gene. The association of the −42 C>T mutation with CTX resistance was confirmed to be significant (FDR < 0.05). To conclude, genome-wide analysis of homoplasy in combination with CTX resistance identifies the −42 C>T mutation of the ampC promotor as significantly associated with CTX resistance and underline the role of recurrent mutations in the spread of antibiotics resistance.Impact StatementIn the past decades, the worldwide spread of extended spectrum beta-lactamases (ESBLs) has led to a substantial increase in the prevalence of resistant common pathogens, thereby restricting available treatment options. Although acquired resistance genes, e.g. ESBLs, get most attention, chromosome-encoded resistance mechanisms may play an important role as well. In E. coli chromosome-encoded β-lactam resistance can be caused by alterations in the promoter region of the ampC gene. To improve our understanding of how frequently these alterations occur, a comprehensive interpretation of the evolution of these mutations is essential. This study is the first to apply genome-wide homoplasy analysis to better perceive adaptation of the E. coli genome to antibiotics. Thereby, this study grants insights into how chromosomal-encoded antibiotic resistance evolves and, by combining genome-wide association studies with homoplasy analyses, provides potential strategies for future association studies into the causes of antibiotics resistance.Data summaryAll data is available under BioProject: PRJNA592140. Raw Illumina sequencing data and metadata of all 171 E. coli isolates used in this study is available from the Sequence Read Archive database under accession no. SAMN15052485 to SAMN15052655. Full reference chromosome of ampC_0069 is available via GenBank accession no. CP046396.1 and NCBI Reference Sequence: NZ_CP046396.1.

show abstract

Section: Discussionsupporting

confidence: 87%

Genome-wide analysis in Escherichia coli unravels an unprecedented level of genetic homoplasy associated with cefotaxime resistance

Coolen¹,

Drijver

Verweij

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…H pylori B128 7.13 is an important strain for the study of H pylori physiology, both in vitro and in vivo 14. 26 Consistent with previous reports of H pylori genomes, including the draft genomes of B128 7.13 that were recently published, 14,26,27 the B128 7.13 genome size is relatively small (1.67 Mbp) in comparison to other gastrointestinal pathogens, such as E coli35 and S. Typhimurium,36…”

supporting

confidence: 67%

Complete genome sequence of Helicobacter pylori B128 7.13 and a single‐step method for the generation of unmarked mutations

et al. 2019

View full text Add to dashboard Cite

Background Helicobacter pylori represents an interesting model of bacterial pathogenesis given that most infections are asymptomatic, while a minority of infections cause severe gastric disease. H pylori strain B128 7.13 is used extensively to understand H pylori pathophysiology. Due to extensive restriction‐modification systems, the fact that only some H pylori strains are naturally transformable, the inability of common plasmid and transposon vectors to replicate in this bacterium, as well as the limited number of antibiotic cassettes that are functional in H pylori , there are relatively few genetic tools for the mutagenesis of this bacterium. Materials and Methods Here, we use PacBio and Illumina sequencing to reveal the complete genome sequence of H pylori B128 7.13. Furthermore, we describe a system to generate markerless and scarless mutations on the H pylori chromosome using the counter‐selection marker, galactokinase from Escherichia coli . Results We show that this mutagenesis strategy can be used to generate in‐frame insertions, gene deletions, and multiple independent mutations in B128 7.13. Using the closed genome as a reference, we also report the absence of second site chromosomal mutations and/or rearrangements in our mutagenized strains. We compare the genome sequence of H pylori B128 7.13 with a closely related strain, H pylori B8, and reveal one notable region of difference, which is a 1430 bp insertion encoding a H pylori‐ specific DUF874 family protein of unknown function. Conclusions This article reports the closed genome of the important H pylori B128 7.13 strain and a mutagenesis method that can be adopted by researchers as an alternative strategy to generate isogenic mutants of H pylori in order to further our understanding of this bacterium.

show abstract

“…For instance, all 300 TFs are not always present in E. coli 25 ; some TFs are not always functional because of a lack of effector ligands; and TFs compete with each other and with other DNA-binding proteins in binding to targets on the genome 1,5,7 . Although genome regulation models have been constructed based upon experimental data obtained using varieties of E. coli strains 8 , but the number of TF genes common to all E. coli strains represents only a small fraction of the entire E. coli gene pool 26,27 . www.nature.com/scientificreports www.nature.com/scientificreports/ To avoid the problems associated with in vivo approaches, we developed two-lines of in vitro approach: gSE-LEX (Genomic SELEX) 8,9 and PS(promoter-specific)-TF screening systems 28,29 .…”

Section: Discussion Gselex Search For Complete Set Of the Regulatory mentioning

confidence: 99%

Regulatory Role of PlaR (YiaJ) for Plant Utilization in Escherichia coli K-12

Shimada

Yokoyama

Anzai

et al. 2019

Sci Rep

View full text Add to dashboard Cite

Outside a warm-blooded animal host, the enterobacterium Escherichia coli K-12 is also able to grow and survive in stressful nature. The major organic substance in nature is plant, but the genetic system of E. coli how to utilize plant-derived materials as nutrients is poorly understood. Here we describe the set of regulatory targets for uncharacterized IclR-family transcription factor YiaJ on the E. coli genome, using gSELEX screening system. Among a total of 18 high-affinity binding targets of YiaJ, the major regulatory target was identified to be the yiaLMNOPQRS operon for utilization of ascorbate from fruits and galacturonate from plant pectin. The targets of YiaJ also include the genes involved in the utilization for other plant-derived materials as nutrients such as fructose, sorbitol, glycerol and fructoselysine. Detailed in vitro and in vivo analyses suggest that L-ascorbate and α-D-galacturonate are the effector ligands for regulation of YiaJ function. These findings altogether indicate that YiaJ plays a major regulatory role in expression of a set of the genes for the utilization of plant-derived materials as nutrients for survival. PlaR was also suggested to play protecting roles of E. coli under stressful environments in nature, including the formation of biofilm. We then propose renaming YiaJ to PlaR (regulator of plant utilization). Bacteria constantly monitor environmental conditions, and respond for adaptation and survival by modulating the expression pattern of their genomes. Transcription, the major regulation step in gene expression, is carried out by a single species of RNA polymerase (RNAP). The intracellular concentration of RNAP core enzyme in growing Escherichia coli K-12 W3110 strain is about 2,000 molecules per genome, which is less than the total of about 4,500 genes on its genome 1,2. The expression pattern of a total of about 4,500 genes in its genome, however, can be modulated through alteration of the promoter selectivity of RNAP after interaction with two groups of the regulatory proteins, i.e., seven species of the promoter recognition subunit sigma 1,3,4 and about 300 species of the DNA-binding transcription factors (TFs) 5,6. Based on the protein structure of DNA-binding motifs, these TFs were classified into 54 families (5; TEC database [www.shigen.nig.ac.jp/ecoli/tec/]). Up to the present time, more than 80% of the estimated 300 TFs in E. coli K-12 have been linked to at least one regulatory target gene or operon in its genome. The search for regulatory targets of these TFs has been carried out in vivo using both the ordinary molecular genetic approaches and the modern methodologies such as transcriptome using DNA microarrays and chromatin immunoprecipitation (ChIP) approaches. Using only in vivo analyses, however, it is difficult to get the complete set of regulatory targets because the binding in vivo of test TFs to their DNA targets is interfered with by both approximately 300 species of co-existing TFs and a number of nucleoid-associated DNA-binding proteins 5. The regulato...

show abstract

Sequencing a piece of history: complete genome sequence of the original Escherichia coli strain

Cited by 31 publications

References 50 publications

Genome-wide analysis in Escherichia coli unravels an unprecedented level of genetic homoplasy associated with cefotaxime resistance

Genome-wide analysis in Escherichia coli unravels an unprecedented level of genetic homoplasy associated with cefotaxime resistance

Complete genome sequence of Helicobacter pylori B128 7.13 and a single‐step method for the generation of unmarked mutations

Regulatory Role of PlaR (YiaJ) for Plant Utilization in Escherichia coli K-12

Contact Info

Product

Resources

About