Biological Mechanisms Induced by Soybean Agglutinin Using an Intestinal Cell Model of Monogastric Animals

Soybean agglutinin (SBA) has a toxic effect on most animals. The anti-nutritional mechanisms of SBA are not fully understood, in terms of cell survival activity and metabolism of intestinal cells. This study aims to investigate the effects of SBA on the cell cycle, apoptosis, and to verify the mechanism of SBA anti-nutritional characters based on proteomic-based analysis. The IPEC-J2 cell line was cultured with medium containing 0.0, 0.5, or 2.0 mg/mL SBA. With increasing SBA levels, the percentage of the cells at G0/G1 phase, cell apoptosis rates, expressions of Bax and p21, and the activities of Casp-3 and Casp-9 were increased, while cyclin D1 and Bcl-2 expressions were declined (p < 0.05). The proteomic analysis showed that the numbers of differentially expressed proteins, induced by SBA, were mainly enriched in different pathways including DNA replication, base excision repair, nucleus excision repair, mismatch repair, amide and peptide biosynthesis, ubiquitin-mediated proteolysis, as well as structures and functions of mitochondria and ribosome. In conclusion, the anti-nutritional mechanism of SBA is a complex cellular process. Such process including DNA related activities; protein synthesis and metabolism; signal-conducting relation; as well as subcellular structure and function. This study provides comprehensive information to understand the toxic mechanism of SBA in monogastrics.

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Cooperation of the NEIL3 and Fanconi anemia/BRCA pathways in interstrand crosslink repair

Nucleic Acids Research ◽

10.1093/nar/gkaa038 ◽

2020 ◽

Vol 48 (6) ◽

pp. 3014-3028 ◽

Cited By ~ 10

Author(s):

Niu Li ◽

Jian Wang ◽

Susan S Wallace ◽

Jing Chen ◽

Jia Zhou ◽

...

Keyword(s):

Fanconi Anemia ◽

Excision Repair ◽

Human Cells ◽

Dependent Manner ◽

Major Pathway ◽

Interstrand Crosslinks ◽

Interstrand Crosslink ◽

Pathway Activation ◽

Base Excision ◽

And Function

Abstract The NEIL3 DNA glycosylase is a base excision repair enzyme that excises bulky base lesions from DNA. Although NEIL3 has been shown to unhook interstrand crosslinks (ICL) in Xenopus extracts, how NEIL3 participants in ICL repair in human cells and its corporation with the canonical Fanconi anemia (FA)/BRCA pathway remain unclear. Here we show that the NEIL3 and the FA/BRCA pathways are non-epistatic in psoralen-ICL repair. The NEIL3 pathway is the major pathway for repairing psoralen-ICL, and the FA/BRCA pathway is only activated when NEIL3 is not present. Mechanistically, NEIL3 is recruited to psoralen-ICL in a rapid, PARP-dependent manner. Importantly, the NEIL3 pathway repairs psoralen-ICLs without generating double-strand breaks (DSBs), unlike the FA/BRCA pathway. In addition, we found that the RUVBL1/2 complex physically interact with NEIL3 and function within the NEIL3 pathway in psoralen-ICL repair. Moreover, TRAIP is important for the recruitment of NEIL3 but not FANCD2, and knockdown of TRAIP promotes FA/BRCA pathway activation. Interestingly, TRAIP is non-epistatic with both NEIL3 and FA pathways in psoralen-ICL repair, suggesting that TRAIP may function upstream of the two pathways. Taken together, the NEIL3 pathway is the major pathway to repair psoralen-ICL through a unique DSB-free mechanism in human cells.

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The Response to Oxidative DNA Damage in Neurons: Mechanisms and Disease

Neural Plasticity ◽

10.1155/2016/3619274 ◽

2016 ◽

Vol 2016 ◽

pp. 1-14 ◽

Cited By ~ 28

Author(s):

Laura Narciso ◽

Eleonora Parlanti ◽

Mauro Racaniello ◽

Valeria Simonelli ◽

Alessio Cardinale ◽

...

Keyword(s):

Dna Damage ◽

Genome Stability ◽

Oxidative Dna Damage ◽

Excision Repair ◽

Strand Breaks ◽

Single Strand Breaks ◽

Age Related ◽

Neurological Alterations ◽

Base Excision ◽

And Function

There is a growing body of evidence indicating that the mechanisms that control genome stability are of key importance in the development and function of the nervous system. The major threat for neurons is oxidative DNA damage, which is repaired by the base excision repair (BER) pathway. Functional mutations of enzymes that are involved in the processing of single-strand breaks (SSB) that are generated during BER have been causally associated with syndromes that present important neurological alterations and cognitive decline. In this review, the plasticity of BER during neurogenesis and the importance of an efficient BER for correct brain function will be specifically addressed paying particular attention to the brain region and neuron-selectivity in SSB repair-associated neurological syndromes and age-related neurodegenerative diseases.

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The archaeal RecJ-like proteins: nucleases and ex-nucleases with diverse roles in replication and repair

Emerging Topics in Life Sciences ◽

10.1042/etls20180017 ◽

2018 ◽

Vol 2 (4) ◽

pp. 493-501

Author(s):

Stuart A. MacNeill

Keyword(s):

Excision Repair ◽

Current Knowledge ◽

Nuclease Activity ◽

Dna Helicase ◽

Archaeal Species ◽

Genes Encoding ◽

Domains Of Life ◽

Base Excision ◽

Almost All ◽

And Function

RecJ proteins belong to the DHH superfamily of phosphoesterases that has members in all three domains of life. In bacteria, the archetypal RecJ is a 5′ → 3′ ssDNA exonuclease that functions in homologous recombination, base excision repair and mismatch repair, while in eukaryotes, the RecJ-like protein Cdc45 (which has lost its nuclease activity) is a key component of the CMG (Cdc45–MCM–GINS) complex, the replicative DNA helicase that unwinds double-stranded DNA at the replication fork. In archaea, database searching identifies genes encoding one or more RecJ family proteins in almost all sequenced genomes. Biochemical analysis has confirmed that some but not all of these proteins are components of archaeal CMG complexes and has revealed a surprising diversity in mode of action and substrate preference. In addition to this, some archaea encode catalytically inactive RecJ-like proteins, and others a mix of active and inactive proteins, with the inactive proteins being confined to structural roles only. Here, I summarise current knowledge of the structure and function of the archaeal RecJ-like proteins, focusing on similarities and differences between proteins from different archaeal species, between proteins within species and between the archaeal proteins and their bacterial and eukaryotic relatives. Models for RecJ-like function are described and key areas for further study highlighted.

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The Whole Cell Proteome-based Study on The Mechanism of Apoptosis Induced by Soybean Agglutinin on IPEC-J2

10.21203/rs.3.rs-62411/v1 ◽

2020 ◽

Author(s):

Li Pan ◽

Yan Liu ◽

Mohammed Hamdy Farouk ◽

Nan Bao ◽

Yuan Zhao ◽

...

Keyword(s):

Cell Cycle ◽

Dna Replication ◽

Cyclin D1 ◽

Cell Apoptosis ◽

Excision Repair ◽

Phase Cell ◽

G1 Phase ◽

Intestinal Cells ◽

Soybean Agglutinin ◽

Whole Cell

Abstract Background: Soybean agglutinin (SBA), a major anti-nutritional factor in soybean, may induce abnormal health and metabolism of intestinal cells, resulting in the reduction of the production performance of animals. The anti-nutritional mechanisms of SBA are not fully understood, in terms of the cell life activities and metabolism of intestinal cells. This research aims to find the effects of SBA on the cell cycle, apoptosis and proteomic, and furtherly to get more findings for verifying the mechanism of SBA anti-nutritional characters.Methods: The IPEC-J2 cell line was cultured with the medium containing 0.0, 0.5 or 2.0 mg/mL SBA, respectively, for 24 h. The percentage of the cells at different cell cycle phases (G0/G1 phase, S phase and G2 phase) and cell apoptosis rates were measured with flow cytometry. The expressions of Cyclin D1, active p21, Bcl-2, and Bax were determined by western blotting. The activity of caspase-3 (Casp-3) and caspase-9 (Casp-9) were tested with ELISA. The whole-cell quantitative proteome were detected by TMT/iTRAQ Labeling, HPLC fractionation and LC-MS/MS Analysis. The functions and characteristics of the differential expressed proteins in the proteome results were analyzed from the aspects of GO annotation and KEGG pathway. The relationship between the results of proteomics and apoptosis or cell cycle were analyzed and discussed.Results: The percentage of the cells at G0/G1 phase, cell apoptosis rates, expressions of Bax and p21, and the activities of Casp-3 and Casp-9 were increased, cyclin D1 and Bcl-2 expression were declined with the increased of the SBA treatment levels (p<0.05). The proteomic measurements showed that a numbers of differentially expressed proteins, caused by SBA treatment, were mainly enriched in the DNA replication, base excision repair, nucleus excision repair, mismatch repair, ubiquitin-mediated proteolysis pathway, cell structural-proteins, and structures and functions of mitochondria. Moreover, the differential expressed proteins enriched in AMP-activated protein kinase (AMPK) pathway and the process of synthesis and metabolism of proteins were only found in 2.0 mg/mL SBA treatment.Conclusion: The results of this experiment demonstrated that cell cycle arrest and apoptosis induced by SBA may be resulted from the downregulating the expression of the proteins related to DNA replication and repair, protein translation, signal-conducting relation, cell structure, and subcellular structure and function.

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The role of cysteines in the structure and function of OGG1

Journal of Biological Chemistry ◽

10.1074/jbc.ra120.016126 ◽

2020 ◽

pp. jbc.RA120.016126

Author(s):

Katarina Wang ◽

Marah Maayah ◽

Joann B. Sweasy ◽

Khadijeh S. Alnajjar

Keyword(s):

Oxidative Stress ◽

Excision Repair ◽

Cysteine Residue ◽

Structure And Function ◽

Cysteine Residues ◽

Lyase Activity ◽

Integral Role ◽

Base Excision ◽

And Function

8-oxoguanine glycosylase (OGG1) is a base excision repair enzyme responsible for the recognition and removal of 8-oxoguanine, a commonly occurring oxidized DNA modification. OGG1 prevents the accumulation of mutations and regulates the transcription of various oxidative stress-response genes. In addition to targeting DNA, oxidative stress can affect proteins like OGG1 itself, specifically at cysteine residues. Previous work has shown that the function of OGG1 is sensitive to oxidants, with the cysteine residues of OGG1 being the most likely site of oxidation. Due to the integral role of OGG1 in maintaining cellular homeostasis under oxidative stress, it is important to understand the effect of oxidants on OGG1 and the role of cysteines in its structure and function. In this study, we investigate the role of the cysteine residues in the function of OGG1 by mutating and characterizing each cysteine residue. Our results indicate that the cysteines in OGG1 fall into four functional categories: those that are necessary for (1) glycosylase activity (C146 and C255), (2) lyase activity (C140S, C163, C241 and C253), (3) structural stability (C253), and (4) those with no known function (C28 and C75). These results suggest that under conditions of oxidative stress, cysteine can be targeted for modifications, thus altering the response of OGG1 and affecting its downstream cellular functions.

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Architecture of The Human Ape1 Interactome Defines Novel Cancers Signatures

Scientific Reports ◽

10.1038/s41598-019-56981-z ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 1

Author(s):

Dilara Ayyildiz ◽

Giulia Antoniali ◽

Chiara D’Ambrosio ◽

Giovanna Mangiapane ◽

Emiliano Dalla ◽

...

Keyword(s):

Tumor Progression ◽

Cancer Cells ◽

Protein Interactions ◽

Excision Repair ◽

Cell Model ◽

Protein Complexes ◽

Dna Lesions ◽

General Interest ◽

Ppi Network ◽

Base Excision

AbstractAPE1 is essential in cancer cells due to its central role in the Base Excision Repair pathway of DNA lesions and in the transcriptional regulation of genes involved in tumor progression/chemoresistance. Indeed, APE1 overexpression correlates with chemoresistance in more aggressive cancers, and APE1 protein-protein interactions (PPIs) specifically modulate different protein functions in cancer cells. Although important, a detailed investigation on the nature and function of protein interactors regulating APE1 role in tumor progression and chemoresistance is still lacking. The present work was aimed at analyzing the APE1-PPI network with the goal of defining bad prognosis signatures through systematic bioinformatics analysis. By using a well-characterized HeLa cell model stably expressing a flagged APE1 form, which was subjected to extensive proteomics analyses for immunocaptured complexes from different subcellular compartments, we here demonstrate that APE1 is a central hub connecting different subnetworks largely composed of proteins belonging to cancer-associated communities and/or involved in RNA- and DNA-metabolism. When we performed survival analysis in real cancer datasets, we observed that more than 80% of these APE1-PPI network elements is associated with bad prognosis. Our findings, which are hypothesis generating, strongly support the possibility to infer APE1-interactomic signatures associated with bad prognosis of different cancers; they will be of general interest for the future definition of novel predictive disease biomarkers. Future studies will be needed to assess the function of APE1 in the protein complexes we discovered. Data are available via ProteomeXchange with identifier PXD013368.

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