Profiling of the ADP‐Ribosylome in Living Cells

Lehner, Maike; Rieth, Sonja; Höllmüller, Eva; Spliesgar, Daniel; Mertes, Bastian; Stengel, Florian; Marx, Andreas

doi:10.1002/ange.202200977

Cited by 7 publications

(11 citation statements)

References 67 publications

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“…We are interested in nucleotides and their involvement in processes of post-translational modification (PTM) 10 , 11 . AMPylation is a PTM in which an AMP molecule is covalently bound to a side chain or the C-terminus of a protein 12 , 13 , which is often catalysed by an enzyme using ATP as a co-substrate.…”

Section: Introductionmentioning

confidence: 99%

Chemoproteomic discovery of a human RNA ligase

et al. 2023

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RNA ligases are present across all forms of life. While enzymatic RNA ligation between 5′-PO4 and 3′-OH termini is prevalent in viruses, fungi, and plants, such RNA ligases are yet to be identified in vertebrates. Here, using a nucleotide-based chemical probe targeting human AMPylated proteome, we have enriched and identified the hitherto uncharacterised human protein chromosome 12 open reading frame 29 (C12orf29) as a human enzyme promoting RNA ligation between 5′-PO4 and 3′-OH termini. C12orf29 catalyses ATP-dependent RNA ligation via a three-step mechanism, involving tandem auto- and RNA AMPylation. Knock-out of C12ORF29 gene impedes the cellular resilience to oxidative stress featuring concurrent RNA degradation, which suggests a role of C12orf29 in maintaining RNA integrity. These data provide the groundwork for establishing a human RNA repair pathway.

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Section: Introductionmentioning

confidence: 99%

Chemoproteomic discovery of a human RNA ligase

et al. 2023

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“…In vitro studies have shown that the modification of poly ADP ribosylation can contain up to 200 ADP ribosomes, including linear chains and branched chains [32]. ADP ribosylation can cause functional changes in the modified protein or can serve as a scaffold molecule to recruit other proteins to perform their functions after the protein is modified [33,34]. Poly ADP ribosylation can regulate a variety of cellular processes, including cell division, apoptosis, chromatin structure regulation, transcription, and protein degradation [35].…”

Section: Adp Ribosylation and Parp-1mentioning

confidence: 99%

PARP-1 Is a Potential Marker of Retinal Photooxidation and a Key Signal Regulator in Retinal Light Injury

Zhang

Fan

et al. 2022

Oxidative Medicine and Cellular Longevity

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Advancements in technology have resulted in increasing concerns over the safety of eye exposure to light illumination, since prolonged exposure to intensive visible light, especially to short-wavelength light in the visible spectrum, can cause photochemical damage to the retina through a photooxidation-triggered cascade reaction. Poly(ADP-ribose) polymerase-1 (PARP-1) is the ribozyme responsible for repairing DNA damage. When damage to DNA occurs, including nicks and breaks, PARP-1 is rapidly activated, synthesizing a large amount of PAR and recruiting other nuclear factors to repair the damaged DNA. However, retinal photochemical damage may lead to the overactivation of PARP-1, triggering PARP-dependent cell death, including parthanatos, necroptosis, and autophagy. In this review, we retrieved targeted articles with the keywords such as “PARP-1,” “photoreceptor,” “retinal light damage,” and “photooxidation” from databases and summarized the molecular mechanisms involved in retinal photooxidation, PARP activation, and DNA repair to clarify the key regulatory role of PARP-1 in retinal light injury and to determine whether PARP-1 may be a potential marker in response to retinal photooxidation. The highly sensitive detection of PARP-1 activity may facilitate early evaluation of the effects of light on the retina, which will provide an evidentiary basis for the future assessment of the safety of light illumination from optoelectronic products and medical devices.

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“…A major limitation on the use of NAD + analogues in the study of ADP-ribosylation dynamics and identification of relevant protein substrates is their inability to passively cross cell membranes. Studies employing NAD + analogues have therefore been largely confined to experiments involving cell lysates or involve the use of carrier peptides 24 , transfection reagents 26 or transiently permeabilized cells 27 to deliver NAD + analogues intracellularly, each of which is limited by disruption of the cell membrane. Two previous studies employing clickable adenosine precursors for the identification of intracellular ADP-ribosylation targets via their metabolic conversion into the corresponding NAD + analogues have been performed.…”

Section: Introductionmentioning

confidence: 99%

Chemical Tools for Profiling the Intracellular ADP-ribosylated Proteome

Draganov,

Gruet,

Conole

et al. 2023

Preprint

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The post-translational modification (PTM) ADP-ribosylation plays an important role in cell signaling and regulating protein function and has been implicated in the development of multiple diseases, including breast and ovarian cancers. Studying the underlying mechanisms through which this PTM contributes towards disease development, however, has been hampered by the lack of appropriate tools for reliable identification of physiologically relevant ADP ribosylated proteins in a live-cell environment. Herein, we explore the applications of an alkyne-tagged proprobe, 6Yn-ProTide-Ad (6Yn-Pro) as a chemical tool for the identification of intracellular ADP-ribosylated proteins through metabolic labelling. We applied targeted metabolomics and chemical proteomics in HEK293T cells treated with 6Yn-Pro to demonstrate intracellular metabolic conversion of the probe into ADP-ribosylation cofactor 6Yn NAD+, and subsequent labelling and enrichment of PARP1 and multiple known ADP-ribosylated proteins in cells under hydrogen peroxide-induced stress. We anticipate that the approach and methodology described here will be useful for future identification of novel intracellular ADP-ribosylated proteins.

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Profiling of the ADP‐Ribosylome in Living Cells

Cited by 7 publications

References 67 publications

Chemoproteomic discovery of a human RNA ligase

Chemoproteomic discovery of a human RNA ligase

PARP-1 Is a Potential Marker of Retinal Photooxidation and a Key Signal Regulator in Retinal Light Injury

Chemical Tools for Profiling the Intracellular ADP-ribosylated Proteome

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