Influence of Sequence and Covalent Modifications on Yeast tRNA Dynamics

Alcohol consumption is a risk factor for the development of several cancers, including those of the head and neck and the esophagus. The underlying mechanisms of alcohol-induced carcinogenesis remain unclear; however, at these sites, alcohol-derived acetaldehyde seems to play a major role. By reacting with DNA, acetaldehyde generates covalent modifications (adducts) that can lead to mutations. Previous studies have shown a dose dependence between levels of a major acetaldehyde-derived DNA adduct and alcohol exposure in oral-cell DNA. The goal of this study was to optimize a mass spectrometry (MS)-based DNA adductomic approach to screen for all acetaldehyde-derived DNA adducts to more comprehensively characterize the genotoxic effects of acetaldehyde in humans. A high-resolution/-accurate-mass data-dependent constant-neutral-loss-MS3 methodology was developed to profile acetaldehyde-DNA adducts in purified DNA. This resulted in the identification of 22 DNA adducts. In addition to the expected N2-ethyldeoxyguanosine (after NaBH3CN reduction), two previously unreported adducts showed prominent signals in the mass spectra. MSn fragmentation spectra and accurate mass were used to hypothesize the structure of the two new adducts, which were then identified as N6-ethyldeoxyadenosine and N4-ethyldeoxycytidine by comparison with synthesized standards. These adducts were quantified in DNA isolated from oral cells collected from volunteers exposed to alcohol, revealing a significant increase after the exposure. In addition, 17 of the adducts identified in vitro were detected in these samples confirming our ability to more comprehensively characterize the DNA damage deriving from alcohol exposures.

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Click Chemistry Enabling Covalent and Non-Covalent Modifications of Graphene with (Poly)saccharides

Polymers ◽

10.3390/polym13010142 ◽

2020 ◽

Vol 13 (1) ◽

pp. 142

Author(s):

Hu Li ◽

Raffaello Papadakis

Keyword(s):

Click Chemistry ◽

Life Science ◽

Environmental Applications ◽

Energy Materials ◽

Sensors And Actuators ◽

Polar Solvents ◽

Wide Range ◽

Potential Applications ◽

Covalent Modifications

Graphene is a material with outstanding properties and numerous potential applications in a wide range of research and technology areas, spanning from electronics, energy materials, sensors, and actuators to life-science and many more. However, the insolubility and poor dispersibility of graphene are two major problems hampering its use in certain applications. Tethering mono-, di-, or even poly-saccharides on graphene through click-chemistry is gaining more and more attention as a key modification approach leading to new graphene-based materials (GBM) with improved hydrophilicity and substantial dispersibility in polar solvents, e.g., water. The attachment of (poly)saccharides on graphene further renders the final GBMs biocompatible and could open new routes to novel biomedical and environmental applications. In this review, recent modifications of graphene and other carbon rich materials (CRMs) through click chemistry are reviewed.

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Yeast tRNA-splicing endonuclease cleaves precursor tRNA in a random pathway.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)54204-6 ◽

1993 ◽

Vol 268 (1) ◽

pp. 672-677

Author(s):

F. Miao ◽

J. Abelson

Keyword(s):

Trna Splicing ◽

Yeast Trna

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Structure and function of the yeast tRNA ligase gene.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)69050-7 ◽

1988 ◽

Vol 263 (7) ◽

pp. 3171-3176 ◽

Cited By ~ 1

Author(s):

S K Westaway ◽

E M Phizicky ◽

J Abelson

Keyword(s):

Structure And Function ◽

Yeast Trna ◽

And Function

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Cysteine of sequence motif VI is essential for nucleophilic catalysis by yeast tRNA m5C methyltransferase

RNA ◽

10.1261/rna.515707 ◽

2007 ◽

Vol 13 (7) ◽

pp. 967-973 ◽

Cited By ~ 15

Author(s):

H. Walbott ◽

C. Husson ◽

S. Auxilien ◽

B. Golinelli-Pimpaneau

Keyword(s):

Sequence Motif ◽

Nucleophilic Catalysis ◽

Yeast Trna

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Epigenetic memory effects in forest trees: a victory of “Michurinian biology”?

Central European Forestry Journal ◽

10.1515/forj-2017-0024 ◽

2017 ◽

Vol 63 (4) ◽

pp. 173-179 ◽

Cited By ~ 5

Author(s):

Dušan Gömöry ◽

Matúš Hrivnák ◽

Diana Krajmerová ◽

Roman Longauer

Keyword(s):

Molecular Mechanisms ◽

Cytosine Methylation ◽

Epigenetic Inheritance ◽

Memory Effects ◽

Forest Trees ◽

Small Interfering Rnas ◽

Adaptation To Climate Change ◽

Growth Environment ◽

Micro Rnas ◽

Covalent Modifications

AbstractThe study reviews trait inheritance, which is in contradiction with the rules of Mendelian genetics, and which was object of controversies among biologists (sometimes with grave political consequences) in the USSR and Sovietcontrolled countries in the 1930s-1960s. “Carryover” or “memory” effects of the climate, to which maternal trees are exposed during seed development, on phenological behavior and other adaptively relevant traits of their offspring in conifers are mentioned; similar effects are associated with the germination and early growth environment. Molecular mechanisms underlying these effects include covalent modifications of DNA or DNA-associated proteins (cytosine methylation, various types of histone modifications), micro-RNAs and small interfering RNAs. Tools for the identification of these modifications are reviewed with a focus on cytosine methylation, along with an overview of the hitherto knowledge on the occurrence of DNA modifications in forest trees. The practical implications of epigenetic inheritance in forest trees are discussed with the focus on the adaptation to climate change and legislation on forest reproductive materials.

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Stabilization of Polar Localization of a Chemoreceptor via Its Covalent Modifications and Its Communication with a Different Chemoreceptor

Journal of Bacteriology ◽

10.1128/jb.187.22.7647-7654.2005 ◽

2005 ◽

Vol 187 (22) ◽

pp. 7647-7654 ◽

Cited By ~ 29

Author(s):

Daisuke Shiomi ◽

Satomi Banno ◽

Michio Homma ◽

Ikuro Kawagishi

Keyword(s):

Histidine Kinase ◽

Fluorescent Protein ◽

Adaptor Protein ◽

Molecular Assembly ◽

Covalent Modification ◽

Polar Localization ◽

Receptor Localization ◽

A Cell ◽

Covalent Modifications ◽

Green Fluorescent

ABSTRACT In the chemotaxis of Escherichia coli, polar clustering of the chemoreceptors, the histidine kinase CheA, and the adaptor protein CheW is thought to be involved in signal amplification and adaptation. However, the mechanism that leads to the polar localization of the receptor is still largely unknown. In this study, we examined the effect of receptor covalent modification on the polar localization of the aspartate chemoreceptor Tar fused to green fluorescent protein (GFP). Amidation (and presumably methylation) of Tar-GFP enhanced its own polar localization, although the effect was small. The slight but significant effect of amidation on receptor localization was reinforced by the fact that localization of a noncatalytic mutant version of GFP-CheR that targets to the C-terminal pentapeptide sequence of Tar was similarly facilitated by receptor amidation. Polar localization of the demethylated version of Tar-GFP was also enhanced by increasing levels of the serine chemoreceptor Tsr. The effect of covalent modification on receptor localization by itself may be too small to account for chemotactic adaptation, but receptor modification is suggested to contribute to the molecular assembly of the chemoreceptor/histidine kinase array at a cell pole, presumably by stabilizing the receptor dimer-to-dimer interaction.

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Computational Resources for Understanding Biomacromolecular Covalent Modifications

10.3389/978-2-88971-319-6 ◽

2021 ◽

Keyword(s):

Covalent Modifications ◽

Computational Resources

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The Distinctive Regulation of Cyanobacterial Glutamine Synthetase

Life ◽

10.3390/life8040052 ◽

2018 ◽

Vol 8 (4) ◽

pp. 52 ◽

Cited By ~ 10

Author(s):

Paul Bolay ◽

M. Muro-Pastor ◽

Francisco Florencio ◽

Stephan Klähn

Keyword(s):

Glutamine Synthetase ◽

Gene Expression Regulation ◽

Feedback Inhibition ◽

Current Knowledge ◽

Transcriptional Level ◽

Distinctive Features ◽

Small Proteins ◽

Regulatory Systems ◽

Covalent Modifications ◽

Post Transcriptional Regulation

Glutamine synthetase (GS) features prominently in bacterial nitrogen assimilation as it catalyzes the entry of bioavailable nitrogen in form of ammonium into cellular metabolism. The classic example, the comprehensively characterized GS of enterobacteria, is subject to exquisite regulation at multiple levels, among them gene expression regulation to control GS abundance, as well as feedback inhibition and covalent modifications to control enzyme activity. Intriguingly, the GS of the ecologically important clade of cyanobacteria features fundamentally different regulatory systems to those of most prokaryotes. These include the interaction with small proteins, the so-called inactivating factors (IFs) that inhibit GS linearly with their abundance. In addition to this protein interaction-based regulation of GS activity, cyanobacteria use alternative elements to control the synthesis of GS and IFs at the transcriptional level. Moreover, cyanobacteria evolved unique RNA-based regulatory mechanisms such as glutamine riboswitches to tightly tune IF abundance. In this review, we aim to outline the current knowledge on the distinctive features of the cyanobacterial GS encompassing the overall control of its activity, sensing the nitrogen status, transcriptional and post-transcriptional regulation, as well as strain-specific differences.

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