Identification of the magnesium, europium and lead binding sites in <i>E. coli</i> and lupine tRNA<sup>Phe</sup> by specific metal ion‐induced cleavages

Marciniec, Tadeusz; Ciesiołka, Jerzy; Wrzesiński, Jan; Krzyżosiak, Włodzimierz J.

doi:10.1016/0014-5793(89)80148-6

Cited by 42 publications

(30 citation statements)

References 14 publications

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“…At the highest concentration of europium ions (100 yM) a random hydrolysis of yeast tRNAE"' also takes place to some extent. This property has been also found recently in E. coli tRNAPh" [12].…”

Section: Europium-induced Cleavagessupporting

confidence: 76%

“…It is now well established that tightly bound metal ions induce specific cleavages of some phosphodiester bonds in the single-stranded regions of yeast tRNAPh' [5][6][7][8][9][10]. Highly nucleophilic metal-ion-bound hydroxyl groups, present at or near the physiological pH, can abstract a proton from the ribose 2'OH groups located in their vicinity, at an appriopriate distance, facilitating polynucleotide chain scission.…”

Section: Discussionmentioning

confidence: 99%

“…This approach has been recently proposed in our detailed study of the hydrolysis of yeast tRNAPhe in solution induced by lead [5], europium [6] and magnesium [7]. It is based on the results of X-ray studies on lead-induced cleavage of yeast tRNAPhe in crystal form [8 -101.…”

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confidence: 99%

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Analysis of magnesium, europium and lead binding sites in methionine initiator and elongator tRNAs by specific metal‐ion‐induced cleavages

Ciesiołka

Wrzesiński

Górnicki

et al. 1989

European Journal of Biochemistry

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The specificity of cleavages in yeast and lupin initiator and elongator methionine tRNAs induced by magnesium, europium and lead has been analysed and compared with known patterns of yeast tRNAPhe hydrolysis. The strong D-loop cleavages occu.+n methionine elongator tRNAs at similar positions and with comparable efficiency to those found in tRNAPh", while the sites of weak anticodon loop cuts, identical in methionine elongator tRNAs, differ from those found in tRNAPhe. Methioz.ine initiator tRNAs differ from their elongator counterparts : (a) they are cleaved in the D-loop with much lower efficiency; (b) they are cleaved in the variable loop which is completely resistant to hydrolysis in elongator tRNAs; (c) cleavages in the anticodon loop are stronger in initiator tRNAs and they are located mostly at the 5' side of the loop whereas in elongator tRNAs they occur mostly at the opposite, 3' side of the loop. The distinct pattern of the anticodon loop cleavages is considered to be related to different conformations of the anticodon loop in the two types of methionine tRNAs.Two distinct methionine tRNAs are required for protein biosynthesis: the initiator tRNA (tRNAye') that binds to the ribosome in the presence of initiation factors and mRNA and initiates polypeptide synthesis; and the elongator tRNA (tRNA2") that interacts with elongation factor, binds to the ribosome A-site and inserts methionine at internal positions of a growing polypeptide. This functional diversity has been correlated with several structural features distinct for initiator and elongator tRNAs [I]. In eukaryots, however, a run of three consecutive G . C base pairs in the anticodon stem is the only motif found in all initiator tRNAs which is absent in elongator species. It was proposed a decade ago that the role of this structure is to impose a unique conformation on the anticodon loop in order to facilitate direct binding of initiator tRNA to the ribosomal P-site [2]. This hypothesis was based on a distinct nuclease S1 cleavage pattern found in the anticodon loop of initiator and elongator tRNAs, both prokaryotic and eukaryotic [2]. The hypothesis has been recently supported, in both its structural and functional aspects. A progressive loss of the initiator-tRNA-specific conformation, coupled with a gradual decrease of its activity in initiation of protein biosynthesis, has been observed for Escherichia coli tRNAp' mutants lacking one, two or all three of these G . C base pairs [3].Despite many attempts, kinetics of tRNA digestion by S1 nuclease is the only successful approach demonstrating different conformations of initiator and elongator tRNAs in solution. Understanding the exact nature of the difference in the anticodon loop conformation requires, however, further efforts. The X-ray structure of yeast tRNAY ' [4] shows overall high similarity to yeast tRNAPhe but, unfortunately, the data at low 0.4-nm resolution do not allow one to detect the details of the structure that distinguish initiator and elongator tRNAs.Our method, designed to ga...

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Section: Europium-induced Cleavagessupporting

confidence: 76%

Section: Discussionmentioning

confidence: 99%

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Analysis of magnesium, europium and lead binding sites in methionine initiator and elongator tRNAs by specific metal‐ion‐induced cleavages

Ciesiołka

Wrzesiński

Górnicki

et al. 1989

European Journal of Biochemistry

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“…11,12 Lanthanides have also been used as chemical and optical probes for DNA, 13,14 and can cleave RNA. 15 It is however still difficult to rationally design DNA sequences that can selectively bind lanthanides; many other metals also have high affinity for DNA.…”

Section: Introductionmentioning

confidence: 99%

In Vitro Selection of a New Lanthanide-Dependent DNAzyme for Ratiometric Sensing Lanthanides

2014

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“…[19][20][21][22][23] They are quite effective in hydrolyzing RNA, 24 and early examples can be traced back to the cleavage of tRNA. 25 Ln 3+ inhibit the hammerhead ribozyme and the 8-17 DNAzyme, 22,26 but accelerate the leadzyme and a Mg 2+ -dependent ligase. 33,34 Ln 3+ were also used to select DNAcleaving DNAzymes together with Zn 2+ .…”

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confidence: 99%

Biochemical Characterization of a Lanthanide-Dependent DNAzyme with Normal and Phosphorothioate-Modified Substrates

et al. 2015

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A trivalent lanthanide (Ln 3+ )-dependent RNAcleaving DNAzyme, Ce13d, was recently isolated via in vitro selection. Ce13d is active in the presence of all Ln 3+ ions. Via introduction of a single phosphorothioate (PS) modification at the cleavage site, its activity with Ln 3+ decreases while all thiophilic metals can activate this DNAzyme. This property is unique to Ce13d and is not found in many other tested DNAzymes. This suggests the presence of a well-defined but general metal binding site. Herein, a systematic study of Ce13d with the PO substrate (using Ce 3+ ) and the PS substrate (using Cd 2+ ) is performed. In both the PO and PS systems, the highest activity was with ∼10 μM metal ions. Higher concentrations of Ce 3+ completely inhibit the activity, while Cd 2+ only slows the activity. A comparison of different metal ions suggests that the role of metal is to neutralize the phosphate negative charge. Both systems follow a similar pH−rate profile with a single deprotonation step, indicating similar reaction mechanisms. The activity difference between the R p and S p form of the PS substrate is <10-fold, which is much smaller than most known RNA-cleaving enzymes. Mutation studies identified eight highly conserved purines, among which the two adenines play mainly structural roles, while the guanines are likely to be involved in metal binding. Ce13d can serve as a model system for further understanding of DNAzyme biochemistry and bioinorganic chemistry.

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Identification of the magnesium, europium and lead binding sites in E. coli and lupine tRNA^Phe by specific metal ion‐induced cleavages

Cited by 42 publications

References 14 publications

Analysis of magnesium, europium and lead binding sites in methionine initiator and elongator tRNAs by specific metal‐ion‐induced cleavages

Analysis of magnesium, europium and lead binding sites in methionine initiator and elongator tRNAs by specific metal‐ion‐induced cleavages

In Vitro Selection of a New Lanthanide-Dependent DNAzyme for Ratiometric Sensing Lanthanides

Biochemical Characterization of a Lanthanide-Dependent DNAzyme with Normal and Phosphorothioate-Modified Substrates

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Identification of the magnesium, europium and lead binding sites in E. coli and lupine tRNAPhe by specific metal ion‐induced cleavages

Cited by 42 publications

References 14 publications

Analysis of magnesium, europium and lead binding sites in methionine initiator and elongator tRNAs by specific metal‐ion‐induced cleavages

Analysis of magnesium, europium and lead binding sites in methionine initiator and elongator tRNAs by specific metal‐ion‐induced cleavages

In Vitro Selection of a New Lanthanide-Dependent DNAzyme for Ratiometric Sensing Lanthanides

Biochemical Characterization of a Lanthanide-Dependent DNAzyme with Normal and Phosphorothioate-Modified Substrates

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Identification of the magnesium, europium and lead binding sites in E. coli and lupine tRNA^Phe by specific metal ion‐induced cleavages