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<p>In <i>E. coli</i>, the genes of the D-xylonate catabolic pathway are present in two distinct operons, <i>yagEFG</i>&#xa0;and <i>yjhIHG</i>, which are part of two cryptic phages found in the genome of this bacterium. These operons are under the control of two transcription factors: XynR which acts as a repressor of <i>yagEFG</i> and <i>yjhI</i> which is an activator of <i>yjhIHG</i>. Although D-xylonate is known to induce these two operons, the true inducer has not been identified yet. Through the construction of biosensors based on <i>xynR</i> and <i>yjhI</i>, using <i>syfp2</i> as reporter gene in combination with mutants of genes involved in D-xylonate catabolism, it has been demonstrated that the effector of these operons is 2-keto-3-deoxy-D-xylonate, which is formed by the dehydration of D-xylonate catalyzed by the dehydratases encoded by <i>yagF</i> and <i>yjhG</i> genes. Building on the finding that these two operons were also upregulated in <i>E. coli</i> challenged with high concentration of platform molecule 2,4-dihydroxybutyric acid, it is reported that both XynR- and YjhI-based biosensors were also responsive to the intermediate non-natural molecule 2-oxo-4-hydroxybutyric acid, with characteristic performances in terms of response threshold, sensitivity, cooperativity, and dynamic response comparable to those of the natural effector. Given that the bottlenecks in the production of 2,4-dihydroxybutyrate from C2 and C5/C6 carbon are D-threonate dehydratase and L-homoserine transaminase, respectively, which catalyze the formation of 2-oxo-4-hydroxybutyric acid from either D-threonate or homoserine, we showed that XynR and YjhI-based biosensors could be efficient tools for the screening and selection of more active enzymes producing this compound, thereby improving the production of 2,4-dihydroxybutyrate.</p>

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2-Keto-3-deoxy-D-xylonate and 2-oxo-4-hydroxybutyrate as natural and artificial effectors of transcription factors regulating D-xylonate operons in E. coli

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  • 发表日期：

    2026年5月1日

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  • Thibault Malfoy,
  • Ceren Alkim,
  • Julie Fredonnet,
  • Juan Lajarin-Hernandez,
  • Jean Marie Francois

摘要

In E. coli, the genes of the D-xylonate catabolic pathway are present in two distinct operons, yagEFG and yjhIHG, which are part of two cryptic phages found in the genome of this bacterium. These operons are under the control of two transcription factors: XynR which acts as a repressor of yagEFG and yjhI which is an activator of yjhIHG. Although D-xylonate is known to induce these two operons, the true inducer has not been identified yet. Through the construction of biosensors based on xynR and yjhI, using syfp2 as reporter gene in combination with mutants of genes involved in D-xylonate catabolism, it has been demonstrated that the effector of these operons is 2-keto-3-deoxy-D-xylonate, which is formed by the dehydration of D-xylonate catalyzed by the dehydratases encoded by yagF and yjhG genes. Building on the finding that these two operons were also upregulated in E. coli challenged with high concentration of platform molecule 2,4-dihydroxybutyric acid, it is reported that both XynR- and YjhI-based biosensors were also responsive to the intermediate non-natural molecule 2-oxo-4-hydroxybutyric acid, with characteristic performances in terms of response threshold, sensitivity, cooperativity, and dynamic response comparable to those of the natural effector. Given that the bottlenecks in the production of 2,4-dihydroxybutyrate from C2 and C5/C6 carbon are D-threonate dehydratase and L-homoserine transaminase, respectively, which catalyze the formation of 2-oxo-4-hydroxybutyric acid from either D-threonate or homoserine, we showed that XynR and YjhI-based biosensors could be efficient tools for the screening and selection of more active enzymes producing this compound, thereby improving the production of 2,4-dihydroxybutyrate.