Identification, characterisation and molecular modelling of two <scp>AP</scp> endonucleases from base excision repair pathway in sugarcane provide insights on the early evolution of green plants

Maira, N.; Torres, Taffarel Melo; Oliveira, Aline; Medeiros, Sílvia Regina Batistuzzo de; Agnez-Lima, Lucymara Fassarella; Lima, J. A. S.; Scortecci, Kátia Castanho

doi:10.1111/plb.12083

Cited by 5 publications

(7 citation statements)

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“…Notably, the sequences FEN1A and FEN1B are found at different loci and chromosomes of S. bicolor. Duplication in genes related to BER proteins was observed in AP endonucleases (ScARP1 and ScARP3) and MUMT (ScMUTM1 and ScMUTM2), which also reveal structural differences, as observed in FEN1A_CANA and FEN1B_CANA [34][35][36].…”

Section: Ber Components-missing and Differencesmentioning

confidence: 99%

“…Each of these presents their specifics based on enzymatic activity, regulation, and sub-cellular localization. For sugarcane, two sequences were identified, and their threedimensional structures were inferred: ScARP1 and ScARP3 [35]. By examining the sequences of ScARPs (1 and 3), we can observe the conservation of essential sites for the catalysis and binding of metals (enzymatic cofactors) [34].…”

Section: Ap Site Removal-ap Endonuclease Role In Sugarcanementioning

confidence: 99%

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Base Excision Repair in Sugarcane – A New Outlook

Medeiros¹,

Scortecci²

2021

Sugarcane - Biotechnology for Biofuels

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The base excision repair (BER) pathway has been associated with genome integrity maintenance. Owing to its central role, BER is present in all three domains of life. The studies in plants, considering BER, have been conducted using Arabidopsis and rice models. Therefore, future studies regarding BER are required in other organisms, particularly in crops such as sugarcane, to understand its mechanism, which may reflect the uniqueness of DNA repair in monocots. Our previous results have revealed that sugarcane is an interesting plant for studying this pathway considering the polyploidy genome and genome evolution. This chapter aimed to characterize the BER pathway in sugarcane by using different bioinformatics tools, for example, screening for BER homologs in the sugarcane genome to identify its members. Each sequence obtained was subjected to structural analysis, and certain differences were identified when Arabidopsis was compared to other monocots, including sugarcane. Moreover, ROS1, DEM, and DML3 were not identified as a complete sequence in the sugarcane EST database. Furthermore, FEN1 is present as two sequences, namely FEN1A and FEN1B, both featuring different amino acid sequence and motif presence. Furthermore, FEN1 sequence was selected for further characterization considering its evolutionary history, as sequence duplication was observed only in the Poaceae family. Considering the importance of this protein for BER pathway, this sequence was evaluated using protein models (3D), and a possible conservation was observed during protein–protein interaction. Thus, these results help us understand the roles of certain BER components in sugarcane, and may reveal the aspects and functions of this pathway beyond those already established in the literature.

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Section: Ber Components-missing and Differencesmentioning

confidence: 99%

Section: Ap Site Removal-ap Endonuclease Role In Sugarcanementioning

confidence: 99%

Base Excision Repair in Sugarcane – A New Outlook

Medeiros¹,

Scortecci²

2021

Sugarcane - Biotechnology for Biofuels

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“…APE1L (AT3G48425) and ARP (AT2G41460) are similar to the major human AP endonuclease APE1, and AtAPE2 (AT4G36050) is similar to the human APE2 (Murphy et al, 2009). Homologous sequences have been identified also in sugarcane (Maira et al, 2014; Cabral Medeiros et al, 2019) and rice (Joldybayeva et al, 2014).…”

Section: Ap Site Incisionmentioning

confidence: 99%

DNA Base Excision Repair in Plants: An Unfolding Story With Familiar and Novel Characters

2019

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Base excision repair (BER) is a critical genome defense pathway that deals with a broad range of non-voluminous DNA lesions induced by endogenous or exogenous genotoxic agents. BER is a complex process initiated by the excision of the damaged base, proceeds through a sequence of reactions that generate various DNA intermediates, and culminates with restoration of the original DNA structure. BER has been extensively studied in microbial and animal systems, but knowledge in plants has lagged behind until recently. Results obtained so far indicate that plants share many BER factors with other organisms, but also possess some unique features and combinations. Plant BER plays an important role in preserving genome integrity through removal of damaged bases. However, it performs additional important functions, such as the replacement of the naturally modified base 5-methylcytosine with cytosine in a plant-specific pathway for active DNA demethylation.

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“…However, only the AtARP has been shown to have the AP endonuclease activity [80]. In sugarcane, two sequences were identified, one directed to nuclei (ScARP1) and the second one (ScARP3) directed to chloroplast and/or mitochondria [81]. Furthermore, at least nine genes that codified bifunctional DNA glycosylase have been identified, seven of which were characterized by in vivo experiments -AtMMH, AtNTH1, AtOGG1, DME, ROS1, DML2, and DML3 [82][83][84][85][86].…”

Section: Base Excision Repair (Ber)mentioning

confidence: 99%

Recent Advances in Plant DNA Repair

Medeiros¹,

deMedeiros²,

Silva³

et al. 2015

Advances in DNA Repair

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NaCl (abiotic stress). Its expression increased fivefold in the first hour and then an interactome analysis indicated that OsSUV3 plays an important role in other pathways [18]. These are some examples that show the connection among the DNA repair machinery, stress tolerance, and the ROS production ( Figure 2) [11][12][13][14][15]."Omics" are a powerful tool to identify genes/proteins/metabolites that are involved in the plant response to a specific stress and/or to a DNA repair pathway [19]. Besides, transgenic and mutant plants are also helping in the gene characterization function. The data have shown that plant response is more complicated than previously thought. Not only is the presence of transcript (tissue or time presence) important, but also the signals are important for gene regulation, post-translation modifications (ubiquitination or sumolation), protein degradation, and protein targeting. All these may change when plants are exposed to different environmental conditions [19][20][21][22][23]. Furthermore, the next generation sequence data have shown that the signal transduction pathways actually form a network and the different networks are interconnected [24][25]. miRNAs have also been connected as a key factor for plant response to the stress and tolerance mechanism [25-28].Considering the importance of the plants for food production, it is important to identify which genes/proteins/pathways are involved in these different mechanisms. This knowledge is important for plant breeders to produce new cultivars [17,28]. Moreover, considering all that was explained above, plants are an interesting model to study stresses and DNA repair ( Figure 2) due their sessile condition, genome plasticity, and the fact that these organisms do not have a germinative cell lineage. The apical meristem cells (shoot or root) suffer division continually during plant development and then genome integrity is extremely important [2]. Then, this chapter will focus on DNA repair pathways in plants.This figure illustrates different abiotic factors such as drought, heavy metals, light, heat, ozone, lack of nutrients, cold, freezing, etc. Plants are able to perceive these different conditions or signals (on the right side) and then promote different molecular and physiological responses, which involve changes in gene expression, protein translation, post-translation modifications, degradation, epigenetic changes, and miRNAs. All these together produce a plant response that helps plants to tolerate this stress condition. Represented on the left side are the effects of an imbalance of ROS in DNA repair and the different DNA repair and genes that are involved in these different processes. The DNA repair presented in this figure includes mismatch repair (MMR), excision repair (NER and BER), and double strand breaks (HR and NHEJ).

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Identification, characterisation and molecular modelling of two AP endonucleases from base excision repair pathway in sugarcane provide insights on the early evolution of green plants

Cited by 5 publications

References 61 publications

Base Excision Repair in Sugarcane – A New Outlook

Base Excision Repair in Sugarcane – A New Outlook

DNA Base Excision Repair in Plants: An Unfolding Story With Familiar and Novel Characters

Recent Advances in Plant DNA Repair

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