Functions of Conserved Domains of Human Polynucleotide Phosphorylase on RNA Oxidation

Malla, Sulochan; Li, Zhongwei

doi:10.36959/584/448

Cited by 3 publications

(2 citation statements)

References 27 publications

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“…Locating the oxidation sites with or without protein presence could also help answer this query. Increased fragmentation of oxidized RNA in the cellular conditions might be due to the higher affinity of oxidized RNA to enzymes such as polynucleotide phosphorylase leading to RNA degradation ( Hayakawa et al, 2001 ; Malla and Li, 2019 ).…”

Section: Discussionmentioning

confidence: 99%

Oxidative Damage to RNA is Altered by the Presence of Interacting Proteins or Modified Nucleosides

Estevez

Valesyan

Jora

et al. 2021

Front. Mol. Biosci.

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Oxidative stress triggered by the Fenton reaction (chemical) or UVR exposure (photo) can damage cellular biomolecules including RNA through oxidation of nucleotides. Besides such xenobiotic chemical modifications, RNA also contains several post-transcriptional nucleoside modifications that are installed by enzymes to modulate structure, RNA-protein interactions, and biochemical functions. We examined the extent of oxidative damage to naturally modified RNA which is required for cellular protein synthesis under two different contexts. The extent of oxidative damage is higher when RNA is not associated with proteins, but the degree of damage is lower when the RNA is presented in the form of a ribonucleoprotein complex, such as an intact ribosome. Our studies also indicate that absence of methylations in ribosomal RNA at specific positions could make it more susceptible to photooxidative stress. However, the extent of guanosine oxidation varied with the position at which the modification is deficient, indicating position-dependent structural effects. Further, an E. coli strain deficient in 5-methylaminomethyl-2-thiouridine (mnm5s2U) (found in lysine and glutamate tRNA anticodon) is more vulnerable to oxidative RNA damage compared to its wildtype strain suggesting an auxiliary function for the mnm5s2U modification. These studies indicate that oxidative damage to RNA is altered by the presence of enzymatic modified nucleosides or protein association inside the cell.

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Section: Discussionmentioning

confidence: 99%

Oxidative Damage to RNA is Altered by the Presence of Interacting Proteins or Modified Nucleosides

Estevez

Valesyan

Jora

et al. 2021

Front. Mol. Biosci.

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“…Loss of these modifications would be expected to adversely affect those functions during cellular translation, thereby making such tRNA targets for degradation. Indeed, the growth delay effect observed soon after UVR exposure could be related to the clearing of damaged tRNA [65] following recognition and binding by proteins such as polynucleotide phosphorylase in E. coli [77,78] and potentially YB-1 protein in humans [79] for subsequent turnover by RNA degradation machinery in E. coli [80,81] and the eukaryotic exosome [82]. However, further studies are required to understand the fate of cellular tRNA that has undergone partial degradation of PTMs and their relationship to the oxidation of canonical bases such as guanosine.…”

Section: Potential Consequences On Trna Due To Photooxidative Degradation Of Ptmsmentioning

confidence: 99%

Characterization of UVA-Induced Alterations to Transfer RNA Sequences

2020

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Ultraviolet radiation (UVR) adversely affects the integrity of DNA, RNA, and their nucleoside modifications. By employing liquid chromatography–tandem mass spectrometry (LC–MS/MS)-based RNA modification mapping approaches, we identified the transfer RNA (tRNA) regions most vulnerable to photooxidation. Photooxidative damage to the anticodon and variable loop regions was consistently observed in both modified and unmodified sequences of tRNA upon UVA (λ 370 nm) exposure. The extent of oxidative damage measured in terms of oxidized guanosine, however, was higher in unmodified RNA compared to its modified version, suggesting an auxiliary role for nucleoside modifications. The type of oxidation product formed in the anticodon stem–loop region varied with the modification type, status, and whether the tRNA was inside or outside the cell during exposure. Oligonucleotide-based characterization of tRNA following UVA exposure also revealed the presence of novel photoproducts and stable intermediates not observed by nucleoside analysis alone. This approach provides sequence-specific information revealing potential hotspots for UVA-induced damage in tRNAs.

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How RNases Shape Mitochondrial Transcriptomes

Cartalas

Coudray

Gobert

2022

IJMS

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Mitochondria are the power houses of eukaryote cells. These endosymbiotic organelles of prokaryote origin are considered as semi-autonomous since they have retained a genome and fully functional gene expression mechanisms. These pathways are particularly interesting because they combine features inherited from the bacterial ancestor of mitochondria with characteristics that appeared during eukaryote evolution. RNA biology is thus particularly diverse in mitochondria. It involves an unexpectedly vast array of factors, some of which being universal to all mitochondria and others being specific from specific eukaryote clades. Among them, ribonucleases are particularly prominent. They play pivotal functions such as the maturation of transcript ends, RNA degradation and surveillance functions that are required to attain the pool of mature RNAs required to synthesize essential mitochondrial proteins such as respiratory chain proteins. Beyond these functions, mitochondrial ribonucleases are also involved in the maintenance and replication of mitochondrial DNA, and even possibly in the biogenesis of mitochondrial ribosomes. The diversity of mitochondrial RNases is reviewed here, showing for instance how in some cases a bacterial-type enzyme was kept in some eukaryotes, while in other clades, eukaryote specific enzymes were recruited for the same function.

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Functions of Conserved Domains of Human Polynucleotide Phosphorylase on RNA Oxidation

Cited by 3 publications

References 27 publications

Oxidative Damage to RNA is Altered by the Presence of Interacting Proteins or Modified Nucleosides

Oxidative Damage to RNA is Altered by the Presence of Interacting Proteins or Modified Nucleosides

Characterization of UVA-Induced Alterations to Transfer RNA Sequences

How RNases Shape Mitochondrial Transcriptomes

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