First Advisor

Dirk Iwata-Reuyl

Term of Graduation

2021

Date of Publication

1-1-2011

Document Type

Dissertation

Degree Name

Doctor of Philosophy (Ph.D.) in Chemistry

Department

Chemistry

Language

English

Subjects

Biosynthesis, Transfer RNA, Chemical kinetics

DOI

10.15760/etd.140

Physical Description

1 online resource (x, 151 p.) : ill. (some col)

Abstract

The 7-deazaguanosine nucleosides queuosine (Q) and archaeosine (G⁺) are two of the most structurally complex modified nucleosides found in tRNA. Q is found exclusively in the wobble position of tRNAGUN coding for the amino acids asparagine, aspartate, histidine and tyrosine in eukarya and bacteria, while (G⁺) occurs in nearly all archaeal tRNA at position 15. In archaea preQ₀ is inserted into tRNA by the enzyme tRNA-guanine transglycosylase (TGT), which catalyzes the exchange of guanine with preQ₀ to produce preQ₀-tRNA. The first objective of this study was to identify and characterize the enzyme(s) catalyzing the conversion of preQ₀-tRNA to G+-tRNA. Comparative genomics identified a protein family possibly involved in the final steps of archaeosine biosynthesis, which was annotated as TgtA2. Structure based alignments comparing TGT and TgtA2 revealed that TgtA2 lacked key TGT catalytic residues and contained an additional module. The gene corresponding to "tgtA2" from "Methanocaldococcus jannaschii (mj1022)" was cloned, expressed and the purified recombinant enzyme characterized. Recombinant MjTgtA2 was shown to convert preQ₀-tRNA to G⁺-tRNA using glutamine, asparagine or NH₄⁺ as nitrogen donors in an ATP-independent reaction. This is the only example of the conversion of a nitrile to a formamidine known in biology. QueF catalyzes the reduction of preQ₀ to 7-aminomethyl-7-deazaguanine preQ₀ in the queuosine biosynthetic pathway. The second aim of this study was the transient state kinetic analysis of substrate binding and catalysis by the enzyme QueF, as well as investigation of the effects of ligands on its quaternary structure. Gel filtration and sedimentation equilibrium analyses indicated that QueF exists as a hybrid population in a rapid equilibrium between decamer and pentamer states. Addition of preQ₀ to QueF resulted in shifting the equilibrium towards the decamer state, as did the addition of divalent metals. Potassium chloride at high concentrations was found to disrupt the quaternary structure of QueF. Intrinsic tryptophan and NADPH fluorescence was used to determine the substrate binding to QueF by stopped-flow kinetic studies. Studies on the binding of preQ₀ to QueF in conjuction with binding NADPH to the QueF mutant E78A-thioimide intermediate suggested a two-step mechanism consisting of a fast bimolecular process and a subsequent slower unimolecular process, while the binding of preQ₀ to the C55A mutant was monophasic, consisting of only the fast bimolecular process. Thioimide formation was monitored by UV-Vis; under single turnover conditions the data fit well to single exponential rise. However, at high preQ₀ concentrations two phases could be observed. The reduction of the thioimide was determined under single turnover conditions by both UV-Vis and fluorescence, and comparable rates were obtained from both techniques. These results indicate that the binding of preQ₀ and NADPH to QueF, as well as thioimide formation, are very rapid; and that reduction of the thioimide is most likely the rate limiting step. Analysis of component rates suggests structural changes occur between these steps, further limiting the overall rate.

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Comments

Portland State University. Dept. of Chemistry

Persistent Identifier

http://archives.pdx.edu/ds/psu/6944

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