Thionucleosides in transfer ribonucleic acid: diversity, structure, biosynthesis, and function.

Ajitkumar, P; Cherayil, J D

doi:10.1128/mmbr.52.1.103-113.1988

Cited by 35 publications

(49 citation statements)

References 73 publications

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“…Specifically, in the biosynthesis of 2-methylthio-N6isopentenyladenosine, modification takes place in a sequential manner, thiolation followed by methylation. The source of the sulfur atom is cysteine and the methyl group comes from S-adenosylmethionine (reviewed in Ajitkumar & Cherayil, 1988). Although the structuraVfunctiona1 role of this novel posttranslational modification is unknown, its importance can be inferred from several lines of evidence.…”

Section: Discussionmentioning

confidence: 99%

β‐Methylthio‐aspartic acid: Identification of a novel posttranslational modification in ribosomal protein S12 from escherichia coli

Kowalak

Walsh

1996

Protein Science

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Utilizing microscale chemical derivatization reactions and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, we have identified a novel posttranslational modification of aspartic acid, j3-methylthio-aspartic acid. The modified residue is located at position 88 in ribosomal protein S12 from Escherichia coli, a phylogenetically conserved protein that has been implicated in maintaining translational accuracy of the ribosome.Keywords: j3-methylthio-aspartic acid; MALDI-TOF; postsource decay; posttranslational modification As a research tool, mass spectrometry has become an integral component in modern biochemistry, where it has been useful in elucidation of the primary structures of all classes of biopolymers, and especially in the characterization of posttranscriptional and posttranslational modifications. Mass spectrometry techniques are inherently advantageous because the intrinsic property of molecular mass provides objective chemical information as an element of the characterization of modified residues (for example, see Biemann, 1988Biemann, , 1990, and references therein). Matrix-assisted laser desorption/ionization time-offlight mass spectrometry (Hillenkamp et al., 1991) offers the additional advantage of adhering to criteria of exceptionally low detection limits (femtomoles to picomoles), low sample consumption (typically I pL) and compatibility with a wide range of buffer components, while generating high quality molecular weight information. Furthermore, valuable sequence informa- During the course of examining Escherichia coli ribosomal proteins isolated from 30s subunits by MALDI-TOF MS, it was observed that the molecular mass of protein S12 was 46 Da heavier that that predicted from the gene sequence (Post & Nomura, 1980). Inspection of the literature revealed that the amino acid at residue 88 in S12 had not been identified (Funatsu Utilizing microscale chemical derivatization techniques (Knapp, 1979(Knapp, , 1990) and relying heavily on MALDI-TOF MS for molecular weight information and PSD for peptide sequencing, we now describe the identification of a novel posttranslationally modified amino acid, 0-methylthio-aspartic acid, at position 88 in ribosomal protein S12 from E. coli. ResultsE. coli ribosomal proteins were isolated from purified 30s subunits and fractionated by reversed-phase HPLC. The molecular mass of ribosomal protein Si2 was measured to be 13,652.0Da by MALDI-TOF MS (Fig. 1). Using electrospray ionization mass spectrometry, two species were observed: a minor one (approximately lo%), M , , 13,605.2; and a major one, M2r 13,652.1 Da (data not shown). From the corresponding gene sequence (Post & Nomura, 1980), the expected mass was of S12 calculated to be 13,605.9 Da. These data suggest posttranscriptional modification of S12 as indicated by a mass increment of 46 Da. It is not clear whether the unmodified form of S12 is a 1625

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Section: Discussionmentioning

confidence: 99%

β‐Methylthio‐aspartic acid: Identification of a novel posttranslational modification in ribosomal protein S12 from escherichia coli

Kowalak

Walsh

1996

Protein Science

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“…Thiated nucleobases (thiobases), where one or more oxygen atoms of a canonical nucleobase are exchanged for sulfur, are a very good example of the above-described behavior. Thiobases are found in several types of RNA 12 but also have been employed as drugs. For example, 6-thioguanine (6TG) is a very important cancer and anti-inflammatory drug, listed as an essential medicine by the WHO.…”

Section: Introductionmentioning

confidence: 99%

A Static Picture of the Relaxation and Intersystem Crossing Mechanisms of Photoexcited 2-Thiouracil

2015

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Accurate excited-state quantum chemical calculations on 2-thiouracil, employing large active spaces and up to quadruple-ζ quality basis sets in multistate complete active space perturbation theory calculations, are reported. The results suggest that the main relaxation path for 2-thiouracil after photoexcitation should be S2 → S1 → T2 → T1, and that this relaxation occurs on a subpicosecond time scale. There are two deactivation pathways from the initially excited bright S2 state to S1, one of which is nearly barrierless and should promote ultrafast internal conversion. After relaxation to the S1 minimum, small singlet–triplet energy gaps and spin–orbit couplings of about 130 cm–1 are expected to facilitate intersystem crossing to T2, from where very fast internal conversion to T1 occurs. An important finding is that 2-thiouracil shows strong pyramidalization at the carbon atom of the thiocarbonyl group in several excited states.

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“…In fact, 2-thiouracil (2t-Ura), 4-thiouridine (4t-Urd), 2-thiocytidine (2t-Cyd) and 2-selenouracil were found in transfer ribonucleic acids (tRNAS) of some bacteria such as Escherichia coli or Bacillus subtiles , yeasts and other higher organisms, and have been related to the improvement of the accuracy and efficiency of the translation process, fostered by the electronic properties and the size of S and Se elements [ 9 , 10 ]. Recent studies on non-enzymatic replication [ 7 , 8 ] have discovered that the exchange of Uracil (U) by 2t-Ura mends important problems along the replication process, such as the slow rate when copying RNA templates or the occurrence of G:T and A:C mispairs [ 7 ].…”

Section: Introductionmentioning

confidence: 99%

Photophysics and Photochemistry of Canonical Nucleobases’ Thioanalogs: From Quantum Mechanical Studies to Time Resolved Experiments

2017

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Interest in understanding the photophysics and photochemistry of thiated nucleobases has been awakened because of their possible involvement in primordial RNA or their potential use as photosensitizers in medicinal chemistry. The interpretation of the photodynamics of these systems, conditioned by their intricate potential energy surfaces, requires the powerful interplay between experimental measurements and state of the art molecular simulations. In this review, we provide an overview on the photophysics of natural nucleobases’ thioanalogs, which covers the last 30 years and both experimental and computational contributions. For all the canonical nucleobase’s thioanalogs, we have compiled the main steady state absorption and emission features and their interpretation in terms of theoretical calculations. Then, we revise the main topographical features, including stationary points and interstate crossings, of their potential energy surfaces based on quantum mechanical calculations and we conclude, by combining the outcome of different spectroscopic techniques and molecular dynamics simulations, with the mechanism by which these nucleobase analogs populate their triplet excited states, which are at the origin of their photosensitizing properties.

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Thionucleosides in transfer ribonucleic acid: diversity, structure, biosynthesis, and function.

Cited by 35 publications

References 73 publications

β‐Methylthio‐aspartic acid: Identification of a novel posttranslational modification in ribosomal protein S12 from escherichia coli

β‐Methylthio‐aspartic acid: Identification of a novel posttranslational modification in ribosomal protein S12 from escherichia coli

A Static Picture of the Relaxation and Intersystem Crossing Mechanisms of Photoexcited 2-Thiouracil

Photophysics and Photochemistry of Canonical Nucleobases’ Thioanalogs: From Quantum Mechanical Studies to Time Resolved Experiments

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