ArticleJournal of industrial microbiology & biotechnology2012
Optical mapping and sequencing of the Escherichia coli KO11 genome reveal extensive chromosomal rearrangements, and multiple tandem copies of the Zymomonas mobilis pdc and adhB genes.
Article in Journal of industrial microbiology & biotechnology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 44 citations in OpenAlex.
- Design of a stable ethanologenic bacterial strain without heterologous plasmids and antibiotic resistance genes for efficient ethanol production from concentrated dairy waste.Biotechnology for biofuels and bioproducts · 2023Article
- Extrapolation of design strategies for lignocellulosic biomass conversion to the challenge of plastic waste.Journal of industrial microbiology & biotechnology · 2022Article
- Microbial adaptive evolution.Journal of industrial microbiology & biotechnology · 2022Review
- Principles and practice of designing microbial biocatalysts for fuel and chemical production.Journal of industrial microbiology & biotechnology · 2022Review
- Whole Genome Sequencing and TnInternational journal of molecular sciences · 2020Article
- Where did you come from, where did you go: Refining metagenomic analysis tools for horizontal gene transfer characterisation.PLoS computational biology · 2019Article
- Fermentation of lactose to ethanol in cheese whey permeate and concentrated permeate by engineered Escherichia coli.BMC biotechnology · 2017Article
- Complete Genome Sequence of ER2796, a DNA Methyltransferase-Deficient Strain of Escherichia coli K-12.PloS one · 2015Article
- Comparative assembly hubs: web-accessible browsers for comparative genomics.Bioinformatics (Oxford, England) · 2014Article
- Polyamine transporters and polyamines increase furfural tolerance during xylose fermentation with ethanologenic Escherichia coli strain LY180.Applied and environmental microbiology · 2014Article
- Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli.mBio · 2014Article
- Metabolic Engineering of Escherichia coli for Production of Mixed-Acid Fermentation End Products.Frontiers in bioengineering and biotechnology · 2014Review
- Enly: Improving Draft Genomes through Reads Recycling.Journal of genomics · 2014Article
- Advances and computational tools towards predictable design in biological engineering.Computational and mathematical methods in medicine · 2014Review
- An alignment-free test for recombination.Bioinformatics (Oxford, England) · 2013Article
- Evolution of a self-inducible cytolethal distending toxin type V-encoding bacteriophage from Escherichia coli O157:H7 to Shigella sonnei.Journal of virology · 2013Article
- Evidence of microevolution of Salmonella Typhimurium during a series of egg-associated outbreaks linked to a single chicken farm.BMC genomics · 2013Article
- Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes.BMC genomics · 2013Article
- A standard vector for the chromosomal integration and characterization of BioBrick™ parts in Escherichia coli.Journal of biological engineering · 2013Article
- Engineering furfural tolerance in Escherichia coli improves the fermentation of lignocellulosic sugars into renewable chemicals.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
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Authors and funding
9 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Escherichia coli KO11 (ATCC 55124) was engineered in 1990 to produce ethanol by chromosomal insertion of the Zymomonas mobilis pdc and adhB genes into E. coli W (ATCC 9637). KO11FL, our current laboratory version of KO11, and its parent E. coli W were sequenced, and contigs assembled into genomic sequences using optical NcoI restriction maps as templates. E. coli W contained plasmids pRK1 (102.5 kb) and pRK2 (5.4 kb), but KO11FL only contained pRK2. KO11FL optical maps made with AflII and with BamHI showed a tandem repeat region, consisting of at least 20 copies of a 10-kb unit. The repeat region was located at the insertion site for the pdc, adhB, and chloramphenicol-resistance genes. Sequence coverage of these genes was about 25-fold higher than average, consistent with amplification of the foreign genes that were inserted as circularized DNA. Selection for higher levels of chloramphenicol resistance originally produced strains with higher pdc and adhB expression, and hence improved fermentation performance, by increasing the gene copy number. Sequence data for an earlier version of KO11, ATCC 55124, indicated that multiple copies of pdc adhB were present. Comparison of the W and KO11FL genomes showed large inversions and deletions in KO11FL, mostly enabled by IS10, which is absent from W but present at 30 sites in KO11FL. The early KO11 strain ATCC 55124 had no rearrangements, contained only one IS10, and lacked most accumulated single nucleotide polymorphisms (SNPs) present in KO11FL. Despite rearrangements and SNPs in KO11FL, fermentation performance was equal to that of ATCC 55124.
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