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Biofuels Bioprod."],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      Due to its ability to grow fast on CO\n                      <jats:sub>2<\/jats:sub>\n                      , CO and H\n                      <jats:sub>2<\/jats:sub>\n                      at high temperatures and with high energy efficiency, the thermophilic acetogen\n                      <jats:italic>Thermoanaerobacter<\/jats:italic>\n                      <jats:italic>kivui<\/jats:italic>\n                      could become an attractive host for industrial biotechnology. In a circular carbon economy, diversification and upgrading of C1 platform feedstocks into value-added products (e. g., ethanol, acetone and isopropanol) could become crucial. To that end, genetic and bioprocess engineering tools are required to facilitate the development of bioproduction scenarios. Currently, the genome editing tools available for\n                      <jats:italic>T. kivui<\/jats:italic>\n                      present some limitations in speed and efficiency, thus restricting the development of a powerful strain chassis for industrial applications.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      In this study, we developed the versatile genome editing tool Hi-TARGET, based on the endogenous CRISPR Type I-B system of\n                      <jats:italic>T.\u00a0kivui<\/jats:italic>\n                      . Hi-TARGET demonstrated 100% efficiency for gene knock-out (from both purified plasmid and cloning mixture) and knock-in, and 49% efficiency for creating point mutations. Furthermore, we optimized the transformation and plating protocol and increased transformation efficiency by 245-fold to 1.96\u2009\u00d7\u200910\n                      <jats:sup>4<\/jats:sup>\n                      \u2009\u00b1\u20098.7\u2009\u00d7\u200910\n                      <jats:sup>3<\/jats:sup>\n                      \u00a0CFU\u00a0\u03bcg\n                      <jats:sup>\u22121<\/jats:sup>\n                      . Subsequently, Hi-TARGET was used to demonstrate gene knock-outs (\n                      <jats:italic>pyrE<\/jats:italic>\n                      ,\n                      <jats:italic>rexA<\/jats:italic>\n                      ,\n                      <jats:italic>hrcA<\/jats:italic>\n                      ), a knock-in (\n                      <jats:italic>ldh<\/jats:italic>\n                      ::pFAST), a single nucleotide mutation corresponding to PolC\n                      <jats:sup>C629Y<\/jats:sup>\n                      , and knock-down of the fluorescent protein pFAST. Analysis of the \u2206\n                      <jats:italic>rexA<\/jats:italic>\n                      deletion mutant created with Hi-TARGET revealed that the transcriptional repressor\n                      <jats:italic>rexA<\/jats:italic>\n                      is likely involved in the regulation of the expression of lactate dehydrogenase (\n                      <jats:italic>ldh<\/jats:italic>\n                      ). Following genome engineering, an optimized curing procedure for edited strains was devised. In total, the time required from DNA to a clean, edited strain is 12\u00a0days, rendering Hi-TARGET a fast, robust and complete method for engineering\n                      <jats:italic>T.\u00a0kivui<\/jats:italic>\n                      .\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      The CRISPR-based genome editing tool Hi-TARGET developed for\n                      <jats:italic>T. kivui<\/jats:italic>\n                      can be used for scarless deletion, insertion, point mutation and gene knock-down, thus fast-tracking the generation of industrially-relevant strains for the production of carbon-negative chemicals and fuels as well as facilitating studies of acetogen metabolism and physiology.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s13068-025-02647-0","type":"journal-article","created":{"date-parts":[[2025,4,30]],"date-time":"2025-04-30T23:52:34Z","timestamp":1746057154000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Hi-TARGET: a fast, efficient and versatile CRISPR type I-B genome editing tool for the thermophilic acetogen Thermoanaerobacter kivui"],"prefix":"10.1186","volume":"18","author":[{"given":"Angeliki","family":"Sitara","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"R\u00e9mi","family":"Hocq","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander Jiwei","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Pfl\u00fcgl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,4,30]]},"reference":[{"key":"2647_CR1","doi-asserted-by":"publisher","first-page":"131164","DOI":"10.1016\/j.biortech.2024.131164","volume":"408","author":"A Sitara","year":"2024","unstructured":"Sitara A, Hocq R, Horvath J, Pfl\u00fcgl S. 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