Steady-State Kinetics and Spectroscopic Characterization of Enzyme–tRNA Interactions for the Non-Heme Diiron tRNA-Monooxygenase, MiaE

Subedi, Bishnu P.; Corder, Andra L.; Zhang, Siai; Foss, Frank W.; Pierce, Brad S.

doi:10.1021/bi5012207

Cited by 12 publications

(6 citation statements)

References 63 publications

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“…It is generally accepted that tRNA 2MeSiPR monooxygenase (MiaE), the only enzyme known to hydroxylate tRNA-bound iP, synthesizes 2MeScZRMP and cZRMP [ 10 , 51 , 61 ]. Yet, trans -selective hydroxylation of tRNA-bound iPR or 2MeSiPR by the same enzyme was reported by others [ 62 , 63 ]. The origin of zeatins in the tRNA of some organisms is entirely unclear, as the presence of the miaE gene is reportedly limited to a few bacterial genera [ 64 ]; however, up-to-date results of BLASTp searches (not shown) using MiaE from Pseudomonas putida [ 65 ] as a query suggests the far wider distribution of MiaE among bacteria than previously anticipated.…”

Section: Formation Of Trans -Zeatin: Unclarified Pathwayssupporting

confidence: 69%

Biochemical and Structural Aspects of Cytokinin Biosynthesis and Degradation in Bacteria

Frébortová

Frébort

2021

Microorganisms

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It has been known for quite some time that cytokinins, hormones typical of plants, are also produced and metabolized in bacteria. Most bacteria can only form the tRNA-bound cytokinins, but there are examples of plant-associated bacteria, both pathogenic and beneficial, that actively synthesize cytokinins to interact with their host. Similar to plants, bacteria produce diverse cytokinin metabolites, employing corresponding metabolic pathways. The identification of genes encoding the enzymes involved in cytokinin biosynthesis and metabolism facilitated their detailed characterization based on both classical enzyme assays and structural approaches. This review summarizes the present knowledge on key enzymes involved in cytokinin biosynthesis, modifications, and degradation in bacteria, and discusses their catalytic properties in relation to the presence of specific amino acid residues and protein structure.

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Section: Formation Of Trans -Zeatin: Unclarified Pathwayssupporting

confidence: 69%

Biochemical and Structural Aspects of Cytokinin Biosynthesis and Degradation in Bacteria

Frébortová

Frébort

2021

Microorganisms

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“…It is worth noting that the present spectroscopic characterization of Pp-MiaE is in agreement with previous characterization of S. typhimurium , which also revealed a mixed-valent state \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${\rm{[Fe}}_{{\rm{S = 2}}}^{{\rm{II}}}{\rm{ - Fe}}_{{\rm{S = 5/2}}}^{{\rm{III}}}{\rm{]}}$\end{document} in the as-isolated enzyme ( 27 ). However, these results are in contrast with those published by Pierce's group indicating that no mixed-valent species could be detected by either EPR or Mössbauer spectroscopy ( 29 ).…”

Section: Resultscontrasting

confidence: 99%

Structural, biochemical and functional analyses of tRNA-monooxygenase enzyme MiaE from Pseudomonas putida provide insights into tRNA/MiaE interaction

Carpentier

Leprêtre

Basset

et al. 2020

Nucleic Acids Research

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MiaE (2-methylthio-N6-isopentenyl-adenosine37-tRNA monooxygenase) is a unique non-heme diiron enzyme that catalyzes the O2-dependent post-transcriptional allylic hydroxylation of a hypermodified nucleotide 2-methylthio-N6-isopentenyl-adenosine (ms2i6A37) at position 37 of selected tRNA molecules to produce 2-methylthio-N6–4-hydroxyisopentenyl-adenosine (ms2io6A37). Here, we report the in vivo activity, biochemical, spectroscopic characterization and X-ray crystal structure of MiaE from Pseudomonas putida. The investigation demonstrates that the putative pp-2188 gene encodes a MiaE enzyme. The structure shows that Pp-MiaE consists of a catalytic diiron(III) domain with a four alpha-helix bundle fold. A docking model of Pp-MiaE in complex with tRNA, combined with site directed mutagenesis and in vivo activity shed light on the importance of an additional linker region for substrate tRNA recognition. Finally, krypton-pressurized Pp-MiaE experiments, revealed the presence of defined O2 site along a conserved hydrophobic tunnel leading to the diiron active center.

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“…In each case, in vitro evidence argues for the lack of effect of the primary targeted modifications on the nearby modifications. In vitro evidence shows that the modification enzymes encoded by tgt ( 53 ) and miaA ( 71 ) function even on unmodified tRNA transcripts. For all these reasons we believe that it is unlikely that the phenotypes associated with the lack of the modification enzymes result from disruption of other nearby modifications.…”

Section: Discussionmentioning

confidence: 99%

Effects of tRNA modification on translational accuracy depend on intrinsic codon–anticodon strength

et al. 2015

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Cellular health and growth requires protein synthesis to be both efficient to ensure sufficient production, and accurate to avoid producing defective or unstable proteins. The background of misreading error frequency by individual tRNAs is as low as 2 × 10−6 per codon but is codon-specific with some error frequencies above 10−3 per codon. Here we test the effect on error frequency of blocking post-transcriptional modifications of the anticodon loops of four tRNAs in Escherichia coli. We find two types of responses to removing modification. Blocking modification of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${\rm tRNA}_{{\rm UUC}}^{{\rm Glu}}$\end{document} and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${\rm tRNA}^{\rm Asp}_{\rm QUC}$\end{document} increases errors, suggesting that the modifications act at least in part to maintain accuracy. Blocking even identical modifications of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${\rm tRNA}^{\rm Lys}_{\rm UUU}$\end{document} and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${\rm tRNA}^{\rm Tyr}_{\rm QUA}$\end{document} has the opposite effect of decreasing errors. One explanation could be that the modifications play opposite roles in modulating misreading by the two classes of tRNAs. Given available evidence that modifications help preorder the anticodon to allow it to recognize the codons, however, the simpler explanation is that unmodified ‘weak’ tRNAs decode too inefficiently to compete against cognate tRNAs that normally decode target codons, which would reduce the frequency of misreading.

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Steady-State Kinetics and Spectroscopic Characterization of Enzyme–tRNA Interactions for the Non-Heme Diiron tRNA-Monooxygenase, MiaE

Cited by 12 publications

References 63 publications

Biochemical and Structural Aspects of Cytokinin Biosynthesis and Degradation in Bacteria

Biochemical and Structural Aspects of Cytokinin Biosynthesis and Degradation in Bacteria

Structural, biochemical and functional analyses of tRNA-monooxygenase enzyme MiaE from Pseudomonas putida provide insights into tRNA/MiaE interaction

Effects of tRNA modification on translational accuracy depend on intrinsic codon–anticodon strength

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