Retraction: Study on Molecular Qualitative Detection Technology of Potato Scab Disease (IOP Conf. Ser.: Earth Environ. Sci. 769 022010)

This article has been retracted by the authors following correspondence with IOP Publishing in which the authors claim the work is unreliable. The author's explanation follows: "The material of the paper is bacteria, it is not be visible to the naked eyes, the material was contaminated by the drugs that out of date and got polluted, and it caused the serious mistake in the figure 2. The result of different strains of DNA by the primer in 3.3 was not match of our material. The figure 2 was the amplification results of different strains of DNA , and the fragment size of different strains were same in the result, but the result should not be same , so the result was wrong. When we continue to the study, we got new result about the figure 2. There was the amplification results of different strains of DNA by primer TXT in repeated experiment , and the result in the published article was wrong, the material was contaminated. We are afraid that other results were also incorrect in this paper." IOP Publishing cannot verify this information as accurate, however in the interest of transparency and reproducibility, IOP Publishing agrees to retract this article. This notice will be updated if more information comes to light. Retraction published: 21 December 2021

The {FeO2}8 Intermediate of the TxtE Nitration Pathway Resists Reduction, Facilitating Its Reaction with Nitric Oxide

<p>TxtE is a cytochome P450 (CYP) homolog that mediates a nitric oxide (NO)-dependent direct nitration of l-tryptophan (l-Trp) to form 4-nitrotryptophan (4-NO₂-l-Trp). This nitrated product is a precursor for thaxtomin A, a virulence factor produced by plant-pathogenic bacteria that causes the disease potato scab. A recent study provided the first characterization of intermediates along the TxtE nitration pathway.¹ The authors’ accumulated evidence supported a mechanism in which O₂ binds to Fe^II TxtE to form an {FeO₂}⁸ intermediate, which subsequently reacted with NO to ultimately form Fe^III TxtE and 4-NO₂-l-Trp. Typical CYP mechanisms reduce and protonate the {FeO₂}⁸ intermediate to form a ferric-hydroperoxo species (Fe^III–OOH) en route to formation of the active oxidant compound I. The previously reported lack of hydroxylated tryptophan resulting from TxtE turnover suggests that the TxtE cycle must stall at the {FeO₂}⁸ intermediate to avoid hydroxylation. Here we present LC-MS experiments showing suggesting that TxtE can hydroxylate l-Trp by the peroxide shunt but not via reduction of the {FeO₂}⁸ intermediate. Comparison of stopped-flow time courses in the presence and absence of excess reducing equivalents and common CYP electron transfer partners shown no spectral or kinetic evidence for reduction of the {FeO₂}⁸ intermediate. Furthermore, the electron coupling efficiency of TB14—a self-sufficient TxtE variant with C-terminal reductase domain—to form 4-NO₂-l-Trp exhibits a 3% electron coupling efficiency when it is loaded with one reducing equivalent. This efficiency <i>increases</i> by 2-fold when TB14 is loaded with two or four reducing equivalents. This observation provides further evidence for our key conclusion that the TxtE {FeO₂}⁸ intermediate resists reduction. The resistance of the {FeO₂}⁸ intermediate to reduction is a key feature of TxtE, enabling reaction with NO and efficient nitration turnover.<b></b></p>

The {FeO2}8 Intermediate of the TxtE Nitration Pathway Resists Reduction, Facilitating Its Reaction with Nitric Oxide

<p>TxtE is a cytochome P450 (CYP) homolog that mediates a nitric oxide (NO)-dependent direct nitration of l-tryptophan (l-Trp) to form 4-nitrotryptophan (4-NO₂-l-Trp). This nitrated product is a precursor for thaxtomin A, a virulence factor produced by plant-pathogenic bacteria that causes the disease potato scab. A recent study provided the first characterization of intermediates along the TxtE nitration pathway.¹ The authors’ accumulated evidence supported a mechanism in which O₂ binds to Fe^II TxtE to form an {FeO₂}⁸ intermediate, which subsequently reacted with NO to ultimately form Fe^III TxtE and 4-NO₂-l-Trp. Typical CYP mechanisms reduce and protonate the {FeO₂}⁸ intermediate to form a ferric-hydroperoxo species (Fe^III–OOH) en route to formation of the active oxidant compound I. The previously reported lack of hydroxylated tryptophan resulting from TxtE turnover suggests that the TxtE cycle must stall at the {FeO₂}⁸ intermediate to avoid hydroxylation. Here we present LC-MS experiments showing suggesting that TxtE can hydroxylate l-Trp by the peroxide shunt but not via reduction of the {FeO₂}⁸ intermediate. Comparison of stopped-flow time courses in the presence and absence of excess reducing equivalents and common CYP electron transfer partners shown no spectral or kinetic evidence for reduction of the {FeO₂}⁸ intermediate. Furthermore, the electron coupling efficiency of TB14—a self-sufficient TxtE variant with C-terminal reductase domain—to form 4-NO₂-l-Trp exhibits a 3% electron coupling efficiency when it is loaded with one reducing equivalent. This efficiency <i>increases</i> by 2-fold when TB14 is loaded with two or four reducing equivalents. This observation provides further evidence for our key conclusion that the TxtE {FeO₂}⁸ intermediate resists reduction. The resistance of the {FeO₂}⁸ intermediate to reduction is a key feature of TxtE, enabling reaction with NO and efficient nitration turnover.<b></b></p>