Mechanisms of RNA-Modifying and -Editing Enzymes

Garcia, George A.; Goodenough-Lashua, DeeAnne M.

doi:10.1128/9781555818296.ch8

Cited by 23 publications

(6 citation statements)

References 186 publications

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“…Conversion of bicarbonate to the urea moiety of t 6 A requires two activation steps with ATP to satisfy the energetic requirements of the acyl-transfer chemistry (29). The first is needed to form an activated bicarbonate, presumably carboxyl phosphate or carboxy-AMP (Fig.…”

Section: Resultsmentioning

confidence: 99%

Biosynthesis of Threonylcarbamoyl Adenosine (t6A), a Universal tRNA Nucleoside

Deutsch

Yacoubi

Crécy‐Lagard

et al. 2012

Journal of Biological Chemistry

117

147

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Section: Resultsmentioning

confidence: 99%

Biosynthesis of Threonylcarbamoyl Adenosine (t6A), a Universal tRNA Nucleoside

Deutsch

Yacoubi

Crécy‐Lagard

et al. 2012

Journal of Biological Chemistry

117

147

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“…It was suggested that t 6 A synthesis, which is a complex modification, required at least two ATP-dependent activation steps (37). In agreement with this proposal, Deutsch et al reported that both AMP and ADP were produced when all four proteins of the bacterial system were mixed (15).…”

Section: Discussionmentioning

confidence: 99%

In vitro biosynthesis of a universal t6A tRNA modification in Archaea and Eukarya

Perrochia

Crozat

Hecker

et al. 2012

Nucleic Acids Research

120

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N6-threonylcarbamoyladenosine (t6A) is a modified nucleotide found in all transfer RNAs (tRNAs) decoding codons starting with adenosine. Its role is to facilitate codon–anticodon pairing and to prevent frameshifting during protein synthesis. Genetic studies demonstrated that two universal proteins, Kae1/YgjD and Sua5/YrdC, are necessary for t6A synthesis in Saccharomyces cerevisiae and Escherichia coli. In Archaea and Eukarya, Kae1 is part of a conserved protein complex named kinase, endopeptidase and other proteins of small size (KEOPS), together with three proteins that have no bacterial homologues. Here, we reconstituted for the first time an in vitro system for t6A modification in Archaea and Eukarya, using purified KEOPS and Sua5. We demonstrated binding of tRNAs to archaeal KEOPS and detected two distinct adenosine triphosphate (ATP)-dependent steps occurring in the course of the synthesis. Our data, together with recent reconstitution of an in vitro bacterial system, indicated that t6A cannot be catalysed by Sua5/YrdC and Kae1/YgjD alone but requires accessory proteins that are not universal. Remarkably, we observed interdomain complementation when bacterial, archaeal and eukaryotic proteins were combined in vitro, suggesting a conserved catalytic mechanism for the biosynthesis of t6A in nature. These findings shed light on the reaction mechanism of t6A synthesis and evolution of molecular systems that promote translation fidelity in present-day cells.

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“…The total number of modified nucleosides in various types of RNA was found to be 93 [ 26 ], of which more than 53 have been identified in urine, and, of those, 14 are adenosine derivatives [ 27 ]. Enzymatic modification processes like methylation, hydroxylation, reduction, isomerization and addition of complex side chains proceed post-transcriptionally at the macromolecular level [ 28 ]. It is known that patients suffering from cancer diseases excrete with their urine increased amounts of modified nucleosides, including 2-dA.…”

Section: Introductionmentioning

confidence: 99%

Molecularly Imprinted Composite Membranes for Selective Detection of 2-Deoxyadenosine in Urine Samples

Scorrano

Mergola

Bello

et al. 2015

IJMS

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An important challenge for scientific research is the production of artificial systems able to mimic the recognition mechanisms occurring at the molecular level in living systems. A valid contribution in this direction resulted from the development of molecular imprinting. In this work, a novel molecularly imprinted polymer composite membrane (MIM) was synthesized and employed for the selective detection in urine samples of 2-deoxyadenosine (2-dA), an important tumoral marker. By thermal polymerization, the 2-dA-MIM was cross-linked on the surface of a polyvinylidene-difluoride (PVDF) membrane. By characterization techniques, the linking of the imprinted polymer on the surface of the membrane was found. Batch-wise guest binding experiments confirmed the absorption capacity of the synthesized membrane towards the template molecule. Subsequently, a time-course of 2-dA retention on membrane was performed and the best minimum time (30 min) to bind the molecule was established. HPLC analysis was also performed to carry out a rapid detection of target molecule in urine sample with a recovery capacity of 85%. The experiments indicated that the MIM was highly selective and can be used for revealing the presence of 2-dA in urine samples.

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Mechanisms of RNA-Modifying and -Editing Enzymes

Cited by 23 publications

References 186 publications

Biosynthesis of Threonylcarbamoyl Adenosine (t6A), a Universal tRNA Nucleoside

Biosynthesis of Threonylcarbamoyl Adenosine (t6A), a Universal tRNA Nucleoside

In vitro biosynthesis of a universal t6A tRNA modification in Archaea and Eukarya

Molecularly Imprinted Composite Membranes for Selective Detection of 2-Deoxyadenosine in Urine Samples

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