Abstract
Oxidation of RNA is associated with the development of numerous disorders including Alzheimer’s and Parkinson’s diseases, amyotrophic lateral sclerosis (ALS), cancer, and diabetes. Additionally, a correlation has been found between increase in RNA oxidation and the process of aging. In plants, elevated level of oxidatively modified transcripts has been detected during alleviation of seeds dormancy and stress response. Increasing interest on the topic of RNA oxidative modifications requires elaboration of new laboratory techniques. So far, the most common method used for the assessment of RNA oxidation is quantification of 8-hydroxyguanine (8-OHG). However, reactive oxygen species (ROS) induce also numerous other changes in nucleic acids, including formation of abasic sites (AP-sites). Recently, the level of AP-sites in RNA has been measured with the use Aldehyde Reactive Probe (ARP). In the present chapter, we describe application of this technique for the evaluation of the level of AP-sites in plant transcripts.
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Abbreviations
- AP-sites:
-
abasic sites
- ARP:
-
Aldehyde Reactive Probe
- ROS:
-
reactive oxygen species
References
Dumanović J, Nepovimova E, Natić M, Kuča K, Jaćević V (2020) The significance of reactive oxygen species and antioxidant defense system in plants: a concise overview. Front Plant Sci 11:552969. https://doi.org/10.3389/fpls.2020.552969
Mittler R, Vanderauwera S, Suzuki N, Miller G, Tognetti VB, Vandepoele K, Gollery M, Shulaev V, Breusegem FV (2011) ROS signaling: the new wave? Trends Plant Sci 16:300–309. https://doi.org/10.1016/j.tplants.2011.03.007
Chmielowska-Bąk J, Izbiańska K, Deckert J (2015) Products of lipid, protein and RNA oxidation as signals and regulators of gene expression in plants. Front Plant Sci 6:405. https://doi.org/10.3389/fpls.2015.00405
Poulsen HE, Specht E, Broedbaek K, Henriksen T, Ellervik C, Mandrup-Poulsen T, Tonnesen M, Nielsen PE, Andersen HU, Weimann A (2012) RNA modifications by oxidation: a novel disease mechanism? Free Radical Biol Med 52:1353–1361. https://doi.org/10.1016/j.freeradbiomed.2012.01.009
Li Z, Chen X, Liu Z, Ye W, Li L, Qian L, Ding H, Li P, Aung LHH (2020) Recent advances: molecular mechanism of RNA oxidation and its role in various disease. Front Mol Biosci 7:184. https://doi.org/10.3389/fmolb.2020.00184
Bazin J, Langlade N, Vincourt P, Arribat S, Balzergue S, El-Maarouf-Bouteau H, Bailly C (2011) Targeted mRNA oxidation regulates sunflower seed dormancy alleviation during dry after-ripening. Plant Cell 23:2196–2208. https://doi.org/10.1105/tpc.111.086694
Gao F, Rampitsch C, Chitnis VR, Humphreys GD, Jordan MC, Ayele BT (2013) Integrated analysis of seed proteome and mRNA oxidation reveals distinct post-transcriptional features regulating dormancy in wheat (Triticum aesativum L.). Plant Biotechnol J 11:921–932. https://doi.org/10.1111/pbi.12083
Chmielowska-Bąk J, Izbiańska K, Ekner-Grzyb A, Bayar M, Deckert J (2018) Cadmium stress leads to rapid increase in RNA oxidative modifications in soybean seedlings. Front Plant Sci 8:2219. https://doi.org/10.3389/fpls.2017.02219
Labudda M, Różańska E, Czarnocka W, Sobczak M, Dzik JM (2018) Systemic changes in photosynthesis and reactive oxygen species homeostasis in shoots of Arabidopsis thaliana infected with the beet cyst nematode Heterodera schachtii. Mol Plant Pathol 19:1690–1704. https://doi.org/10.1111/mpp.12652
Sytykiewicz H, Łukasik I, Goławska S, Chrzanowski G (2019) Aphid-triggered changes in oxidative damage markers of nucleic acids, proteins, and lipids in maize (Zea mays L.) seedlings. Int J Mol Sci 20:3742. https://doi.org/10.3390/ijms20153742
Shan X, Tashiro H, Lin CG (2003) The identification and characterization of oxidized RNAs in Alzheimer’s disease. J Neurosci 23:4913–4921. https://doi.org/10.1523/JNEUROSCI.23-12-04913.2003
Chang Y, Kong Q, Shan X, Tian G, Llieva H, Cleveland DW, Rothstein JD, Borchelt DR, Wong P, Lin CG (2008) Messenger RNA oxidation occurs early in disease pathogenesis and promotes motor neuron degeneration in ALS. PLoS One 3:e2849. https://doi.org/10.1371/journal.pone.0002849
Pappas-Gogos G, Tellis CC, Tepelenis K, Vlachos K, Chrysos E, Tselepis AD, Glantzounis GK (2021) Urine 8-hydroxyguanine (8-OHG) in patients undergoing surgery for colorectal cancer. J Investig Surg 3(8):e2849. https://doi.org/10.1080/08941939.2021.1904466
Berquist BR, Wilson DM III (2012) Pathways of repairing and tolerating the spectrum of oxidative DNA lesions. Cancer Lett 327:61–72. https://doi.org/10.1016/j.canlet.2012.02.001
Mikowska M, Świergosz-Kowalewska R (2018) DNA damage in liver tissues of metal exposed Clethrionomys glareolus. Chemosphere 199:625–629. https://doi.org/10.1016/j.chemosphere.2018.02.053
Chen H, Cui Z, Hejazi L, Yao L, Walmsley SJ, Rizzo CJ, Turesky RJ (2020) Kinetics of DNA adducts and abasic site formation in tissue of mice treated with nitrogen mustard. Chem Res Toxicol 33:988–998. https://doi.org/10.1021/acs.chemrestox.0c00012
Nakamura T, Keep RF, Hua Y, Nagao S, Hoff JT, Xi G (2006) Iron-induced oxidative brain injury after experimental intracerebral hemorrhage. Acta Neurochir 96:194–198. https://doi.org/10.1007/3-211-30714-1_42
Kubo K, Ide H, Wallace SS, Kow YW (1992) A novel, sensitive, and specific assay for abasic sites, the most commonly produced DNA lesion. Biochemistry 31:3703–3708. https://doi.org/10.1021/bi00129a020
Asaeda A, Ide H, Tano K, Takamori Y, Kubo K (2006) Repair kinetics of abasic sites in mammalian cells monitored by the aldehyde reactive probe (ARP). Nucleos Nucleot Nucl 17:503–513. https://doi.org/10.1080/07328319808005194
Atamna H, Cheung I, Ames BN (2000) A method for detecting abasic sites in living cells: age-dependent changes in base excision repair. Proc Natl Acad Sci 97:686–691. https://doi.org/10.1073/pnas.97.2.686
Lin P-H, Nakamura J, Yamaguchi S, Asakura S, Swenberg JA (2003) Aldehydic DNA lesions induced by catechol estrogens in calf thymus DNA. Carcinogenesis 24:1133–1141. https://doi.org/10.1093/carcin/bgg049
McDorman KC, Pachkowski BF, Nakamura J, Wolf DC, Swenberg JA (2005) Oxidative DNA damage from potassium bromate exposure in Long-Evans rats is not enhanced by a mixture of drinking water disinfection by-products. Chemico-Biol Interact 152:107–117. https://doi.org/10.1016/j.cbi.2005.02.003
Viswesh V, Gates K, Sun D (2010) Characterization of DNA damage induced by natural product antitumor antibiotic leinamycin in human cancer cells. Chem Res Toxicol 23:99–107. https://doi.org/10.1021/tx900301r
Tanaka M, Song H, Küpfer PA, Leuman CJ, Sonntag WE (2011) An assay for RNA oxidation induced abasic sites using the Aldehyde Reactive Probe. Free Radic Res 45:237–247. https://doi.org/10.3109/10715762.2010.535529
Chomczyński P, Sacchi N (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162:156–159. https://doi.org/10.1006/abio.1987.9999
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The method has been applied in research project number 2014/13/D/NZ9/04812 financed by the National Science Center, Poland.
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Chmielowska-Bąk, J., Izbiańska-Jankowska, K., Deckert, J. (2022). Estimation of the Level of Abasic Sites in Plant mRNA Using Aldehyde Reactive Probe. In: Mhamdi, A. (eds) Reactive Oxygen Species in Plants. Methods in Molecular Biology, vol 2526. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2469-2_9
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