title: A markerless gene deletion and integration system for Thermoanaerobacter ethanolicus.
abstract: BACKGROUND
  Thermoanaerobacter ethanolicus produces a considerable amount of ethanol from a range of carbohydrates and is an attractive candidate for applications in bioconversion processes. A genetic system with reusable selective markers would be useful for deleting acid production pathways as well as other genetic modifications.
  
  
  RESULTS
  The thymidine kinase (tdk) gene was deleted from T. ethanolicus JW200 to allow it to be used as a selectable marker, resulting in strain X20. Deletion of the tdk gene reduced growth rate by 20 %; however, this could be reversed by reintroducing the tdk gene (strain X20C). The tdk and high-temperature kanamycin (htk) markers were tested by using them to delete lactate dehydrogenase (ldh). During positive selection of ldh knockouts in strain X20 on kanamycin agar plates, six out of seven picked colonies were verified transformants. Deletion of ldh reduced lactic acid production by 90 %. The tdk and 5-fluoro-2'-deoxyuridine (FUDR) combination worked reliably as demonstrated by successful tdk removal in all 21 colonies tested.
  
  
  CONCLUSIONS
  A gene deletion and integration system with reusable markers has been developed for Thermoanaerobacter ethanolicus JW200 with positive selection on kanamycin and negative selection on FUDR. Gene deletion was demonstrated by ldh gene deletion and gene integration was demonstrated by re-integration of the tdk gene. Transformation via a natural competence protocol could use DNA PCR products amplified directly from Gibson Assembly mixture for efficient genetic modification.
authors.affiliation: 14 Engineering Drive, Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA ; DOE BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA.
authors.forename: Xiongjun
authors.initials: X
authors.lastname: Shao
authors.affiliation: 14 Engineering Drive, Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA ; DOE BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA.
authors.forename: Jilai
authors.initials: J
authors.lastname: Zhou
authors.affiliation: 14 Engineering Drive, Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA ; DOE BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA.
authors.forename: Daniel G
authors.initials: DG
authors.lastname: Olson
authors.affiliation: 14 Engineering Drive, Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA ; DOE BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA.
authors.forename: Lee R
authors.initials: LR
authors.lastname: Lynd
keywords: Clean knockout; FUDR; Gene deletion; Gene integration; Marker removal; Natural competence; Thermoanaerobacter ethanolicus; tdk