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Valipour J, Taghizadeh F, Esfahani R, Ramesh M, Rastegar T. Role of nuclear factor erythroid 2-related factor 2 (Nrf2) in female and male fertility. Heliyon 2024; 10:e29752. [PMID: 38720768 PMCID: PMC11076650 DOI: 10.1016/j.heliyon.2024.e29752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
Oxidative stress refers to a condition where there is an imbalance between the production of reactive oxygen species and their removal by antioxidants. While the function of reactive oxygen species as specific second messengers under physiological conditions is necessary, their overproduction can lead to numerous instances of cell and tissue damage. Nuclear factor erythroid 2-related factor 2 (Nrf2) is a master regulator of many cytoprotective genes that respond to redox stresses. Nrf2 is regularly degraded by kelch-like ECH-associated protein 1 through the ubiquitin-proteasome pathway. The kelch-like ECH-associated protein 1 and Nrf2 complex have attracted attention in both basic and clinical infertility research fields. Oxidative stress is implicated in the pathogenesis of female infertility, including primary ovarian insufficiency, polycystic ovarian syndrome, and endometriosis, as well as male infertility, namely varicocele, cryptorchidism, spermatic cord torsion, and orchitis. Most scientists believe that Nrf2 is a potential therapeutic method in female and male infertility disorders due to its antioxidant effect. Here, the potential roles of oxidative stress and Nrf2 in female and male infertility disorders are reviewed. Moreover, the key role of Nrf2 in the inhibition or induction of these diseases is discussed.
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Affiliation(s)
- Jamal Valipour
- Department of Anatomy, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Taghizadeh
- Department of Anatomy, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Roghayeh Esfahani
- Department of Anatomy, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahya Ramesh
- Department of Anatomy, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Tayebeh Rastegar
- Department of Anatomy, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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2
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Liao Z, Xie Z. Construction of a disulfidptosis-related glycolysis gene risk model to predict the prognosis and immune infiltration analysis of gastric adenocarcinoma. Clin Transl Oncol 2024:10.1007/s12094-024-03457-w. [PMID: 38587603 DOI: 10.1007/s12094-024-03457-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/11/2024] [Indexed: 04/09/2024]
Abstract
BACKGROUND The pattern of cell death known as disulfidptosis was recently discovered. Disulfidptosis, which may affect the growth of tumor cells, represents a potential new approach to treating tumors. Glycolysis affects tumor proliferation, invasion, chemotherapy resistance, the tumor microenvironment (TME), and immune evasion. However, the efficacy and therapeutic significance of disulfidptosis-related glycolysis genes (DRGGs) in stomach adenocarcinoma (STAD) remain uncertain. METHODS STAD clinical data and RNA sequencing data were downloaded from the TCGA database. DRGGs were screened using Cox regression and Lasso regression analysis to construct a prognostic risk model. The accuracy of the model was verified using survival studies, receiver operating characteristic (ROC) curves, column plots, and calibration curves. Additionally, our study investigated the relationships between the risk scores and immune cell infiltration, tumor mutational burden (TMB), and anticancer drug sensitivity. RESULTS We have successfully developed a prognosis risk model with 4 DRGGs (NT5E, ALG1, ANKZF1, and VCAN). The model showed excellent performance in predicting the overall survival of STAD patients. The DRGGs prognostic model significantly correlated with the TME, immune infiltrating cells, and treatment sensitivity. CONCLUSIONS The risk model developed in this work has significant clinical value in predicting the impact of immunotherapy in STAD patients and assisting in the choice of chemotherapeutic medicines. It can correctly estimate the prognosis of STAD patients.
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Affiliation(s)
- Zhaohui Liao
- Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Donghu District, Nanchang, 330006, China
| | - Zhengyuan Xie
- Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Donghu District, Nanchang, 330006, China.
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3
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Wang Z, Chen X, Zhang J, Chen X, Peng J, Huang W. Based on disulfidptosis-related glycolytic genes to construct a signature for predicting prognosis and immune infiltration analysis of hepatocellular carcinoma. Front Immunol 2023; 14:1204338. [PMID: 37680641 PMCID: PMC10482091 DOI: 10.3389/fimmu.2023.1204338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 08/04/2023] [Indexed: 09/09/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) comprises several distinct molecular subtypes with varying prognostic implications. However, a comprehensive analysis of a prognostic signature for HCC based on molecular subtypes related to disulfidptosis and glycolysis, as well as associated metabolomics and the immune microenvironment, is yet to be fully explored. Methods Based on the differences in the expression of disulfide-related glycolytic genes (DRGGs), patients with HCC were divided into different subtypes by consensus clustering. Establish and verify a risk prognosis signature. Finally, the expression level of the key gene SLCO1B1 in the signature was evaluated using immunohistochemistry (IHC) and quantitative real-time PCR (qRT-PCR) in HCC. The association between this gene and immune cells was explored using multiplex immunofluorescence. The biological functions of the cell counting kit-8, wound healing, and colony formation assays were studied. Results Different subtypes of patients have specific clinicopathological features, prognosis and immune microenvironment. We identified seven valuable genes and constructed a risk-prognosis signature. Analysis of the risk score revealed that compared to the high-risk group, the low-risk group had a better prognosis, higher immune scores, and more abundant immune-related pathways, consistent with the tumor subtypes. Furthermore, IHC and qRT-PCR analyses showed decreased expression of SLCO1B1 in HCC tissues. Functional experiments revealed that SLCO1B1 overexpression inhibited the proliferation, migration, and invasion of HCC cells. Conclusion We developed a prognostic signature that can assist clinicians in predicting the overall survival of patients with HCC and provides a reference value for targeted therapy.
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Affiliation(s)
- Zhijian Wang
- Department of General Practice, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xuenuo Chen
- Department of Infectious Disease, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jia Zhang
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xuanxin Chen
- Department of Infectious Disease, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jiayi Peng
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Wenxiang Huang
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Chen X, Wang Z, Wu Y, Lan Y, Li Y. Typing and modeling of hepatocellular carcinoma based on disulfidptosis-related amino acid metabolism genes for predicting prognosis and guiding individualized treatment. Front Oncol 2023; 13:1204335. [PMID: 37637055 PMCID: PMC10454915 DOI: 10.3389/fonc.2023.1204335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/06/2023] [Indexed: 08/29/2023] Open
Abstract
Introduction Hepatocellular carcinoma (HCC) is the most common type of cancer worldwide and is a major public health problem in the 21st century. Disulfidopathy, a novel cystine-associated programmed cell death, plays complex roles in various tumors. However, the relationship between disulfidoptosis and prognosis in patients with HCC remains unclear. This study aimed to explore the relationship between disulfideptosis and the prognosis of liver cancer and to develop a prognostic model based on amino acid metabolism and disulfideptosis genes. Methods We downloaded the clinicopathological information and gene expression data of patients with HCC from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases and classified them into different molecular subtypes based on the expression patterns of disulfidoptosis-associated amino acid metabolism genes (DRAGs). Patients were then classified into different gene subtypes using the differential genes between the molecular subtypes, and the predictive value of staging was assessed using survival and clinicopathological analyses. Subsequently, risk prognosis models were constructed based on Cox regression analysis to assess patient prognosis, receiver operating characteristic (ROC) curves, somatic mutations, microsatellite instability, tumor microenvironment, and sensitivity to antitumor therapeutic agents. Results Patients were classified into two subtypes based on differential DRAGs gene expression, with cluster B having a better survival outcome than cluster A. Three gene subtypes were identified based on the differential genes between the two DRAGs molecular subtypes. The patients in cluster B had the best prognosis, whereas those in cluster C had the worst prognosis. The heat map showed better consistency in the patient subtypes obtained using both typing methods. We screened six valuable genes and constructed a prognostic signature. By scoring, we found that patients in the low-risk group had a better prognosis, higher immune scores, and more abundant immune-related pathways compared to the high-risk group, which was consistent with the tumor subtype results. Discussion In conclusion, we developed a prognostic signature of disulfidptosis-related amino acid metabolism genes to assist clinicians in predicting the survival of patients with HCC and provide a reference value for targeted therapy and immunotherapy for HCC.
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Affiliation(s)
- Xuenuo Chen
- Department of Infectious Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhijian Wang
- Department of Gastroenterology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yilin Wu
- Department of Infectious Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yinghua Lan
- Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yongguo Li
- Department of Infectious Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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5
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Chen Y, Xiong H, Ravelombola W, Bhattarai G, Barickman C, Alatawi I, Phiri TM, Chiwina K, Mou B, Tallury S, Shi A. A Genome-Wide Association Study Reveals Region Associated with Seed Protein Content in Cowpea. PLANTS (BASEL, SWITZERLAND) 2023; 12:2705. [PMID: 37514320 PMCID: PMC10383739 DOI: 10.3390/plants12142705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/16/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023]
Abstract
Cowpea (Vigna unguiculata L. Walp., 2n = 2x = 22) is a protein-rich crop that complements staple cereals for humans and serves as fodder for livestock. It is widely grown in Africa and other developing countries as the primary source of protein in the diet; therefore, it is necessary to identify the protein-related loci to improve cowpea breeding. In the current study, we conducted a genome-wide association study (GWAS) on 161 cowpea accessions (151 USDA germplasm plus 10 Arkansas breeding lines) with a wide range of seed protein contents (21.8~28.9%) with 110,155 high-quality whole-genome single-nucleotide polymorphisms (SNPs) to identify markers associated with protein content, then performed genomic prediction (GP) for future breeding. A total of seven significant SNP markers were identified using five GWAS models (single-marker regression (SMR), the general linear model (GLM), Mixed Linear Model (MLM), Fixed and Random Model Circulating Probability Unification (FarmCPU), and Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK), which are located at the same locus on chromosome 8 for seed protein content. This locus was associated with the gene Vigun08g039200, which was annotated as the protein of the thioredoxin superfamily, playing a critical function for protein content increase and nutritional quality improvement. In this study, a genomic prediction (GP) approach was employed to assess the accuracy of predicting seed protein content in cowpea. The GP was conducted using cross-prediction with five models, namely ridge regression best linear unbiased prediction (rrBLUP), Bayesian ridge regression (BRR), Bayesian A (BA), Bayesian B (BB), and Bayesian least absolute shrinkage and selection operator (BL), applied to seven random whole genome marker sets with different densities (10 k, 5 k, 2 k, 1 k, 500, 200, and 7), as well as significant markers identified through GWAS. The accuracies of the GP varied between 42.9% and 52.1% across the seven SNPs considered, depending on the model used. These findings not only have the potential to expedite the breeding cycle through early prediction of individual performance prior to phenotyping, but also offer practical implications for cowpea breeding programs striving to enhance seed protein content and nutritional quality.
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Affiliation(s)
- Yilin Chen
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Haizheng Xiong
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
| | | | - Gehendra Bhattarai
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Casey Barickman
- Department of Plant and Soil Sciences, Mississippi State University, North Mississippi Research and Extension Center, Verona, MS 38879, USA
| | - Ibtisam Alatawi
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
| | | | - Kenani Chiwina
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Beiquan Mou
- USDA-ARS, Crop Improvement and Protection Research Unit, Salinas, CA 93905, USA
| | - Shyam Tallury
- USDA-ARS, Plant Genetic Resources Conservation Unit, 1109 Experiment Street, Griffin, GA 30223, USA
| | - Ainong Shi
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA
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Pirnie R, P Gillespie K, Mesaros C, Blair IA. Reappraisal of oxidized HMGB1 as a mediator and biomarker. Future Sci OA 2022; 8:FSO828. [PMID: 36874369 PMCID: PMC9979160 DOI: 10.2144/fsoa-2022-0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 01/12/2023] [Indexed: 02/12/2023] Open
Abstract
HMGB1 is a dual-function protein that acts as a chromatin-binding protein and as a danger-associated molecular pattern (DAMP) when released from activated immune cells or injured tissue. In much of the HMGB1 literature, immunomodulatory effects of extracellular HMGB1 are proposed to depend on its oxidation state. However, many of the foundational studies for this model have been retracted or flagged with expressions of concern. The literature on HMGB1 oxidation reveals a diversity of redox proteoforms of HMGB1 that are inconsistent with current models of redox modulation regulating HMGB1 secretion. A recent study of acetaminophen toxicity has identified previously unrecognized HMGB1 oxidized proteoforms. HMGB1 undergoes oxidative modifications that could serve as pathology-specific biomarkers and drug targets.
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Affiliation(s)
- Ross Pirnie
- Center of Excellence in Environmental Toxicology & Department of Systems Pharmacology & Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kevin P Gillespie
- Center of Excellence in Environmental Toxicology & Department of Systems Pharmacology & Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Clementina Mesaros
- Center of Excellence in Environmental Toxicology & Department of Systems Pharmacology & Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ian A Blair
- Center of Excellence in Environmental Toxicology & Department of Systems Pharmacology & Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
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7
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Nrf2 Knockout Affected the Ferroptosis Signaling Pathway against Cisplatin-Induced Hair Cell-Like HEI-OC1 Cell Death. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:2210733. [PMID: 35814275 PMCID: PMC9270153 DOI: 10.1155/2022/2210733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 05/04/2022] [Indexed: 12/14/2022]
Abstract
Cisplatin is a well-known and widely used anticancer drug with high therapeutic efficacy in solid tumors; however, side effects are common with its use. Because cisplatin can be retained in the cochlea, ototoxicity leading to hearing loss limits its clinical applications. Here, we report that Nrf2 knockout (KO) strongly increased cisplatin resistance in HEI-OC1 cells, which are immortalized cells from the murine organ of Corti. The underlying mechanism of this phenomenon was uncovered, and an important novel therapeutic target for combating cisplatin-induced hearing loss was identified. Preliminary investigations determined that Nrf2 KO markedly decreased TfR1 protein levels and increased GPX4 protein levels. Thus, ferroptosis may protect organisms from cisplatin-induced cell death. Furthermore, Nrf2 KO cells were resistant to the classical ferroptosis inducers RSL3 and erastin, providing solid evidence that Nrf2 KO inhibits ferroptosis and that knocking out Nrf2 may be a new clinical strategy to prevent cisplatin-induced hearing loss.
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8
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Coric V, Milosevic I, Djukic T, Bukumiric Z, Savic-Radojevic A, Matic M, Jerotic D, Todorovic N, Asanin M, Ercegovac M, Ranin J, Stevanovic G, Pljesa-Ercegovac M, Simic T. GSTP1 and GSTM3 Variant Alleles Affect Susceptibility and Severity of COVID-19. Front Mol Biosci 2022; 8:747493. [PMID: 34988113 PMCID: PMC8721193 DOI: 10.3389/fmolb.2021.747493] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 11/09/2021] [Indexed: 12/20/2022] Open
Abstract
Based on the premise that oxidative stress plays an important role in severe acute respiratory syndrome coronavirus (SARS-CoV-2) infection, we speculated that variations in the antioxidant activities of different members of the glutathione S-transferase family of enzymes might modulate individual susceptibility towards development of clinical manifestations in COVID-19. The distribution of polymorphisms in cytosolic glutathione S-transferases GSTA1, GSTM1, GSTM3, GSTP1 (rs1695 and rs1138272), and GSTT1 were assessed in 207 COVID-19 patients and 252 matched healthy individuals, emphasizing their individual and cumulative effect in disease development and severity. GST polymorphisms were determined by appropriate PCR methods. Among six GST polymorphisms analyzed in this study, GSTP1 rs1695 and GSTM3 were found to be associated with COVID-19. Indeed, the data obtained showed that individuals carrying variant GSTP1-Val allele exhibit lower odds of COVID-19 development (p = 0.002), contrary to carriers of variant GSTM3-CC genotype which have higher odds for COVID-19 (p = 0.024). Moreover, combined GSTP1 (rs1138272 and rs1695) and GSTM3 genotype exhibited cumulative risk regarding both COVID-19 occurrence and COVID-19 severity (p = 0.001 and p = 0.025, respectively). Further studies are needed to clarify the exact roles of specific glutathione S-transferases once the SARS-CoV-2 infection is initiated in the host cell.
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Affiliation(s)
- Vesna Coric
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia.,Institute of Medical and Clinical Biochemistry, Belgrade, Serbia
| | - Ivana Milosevic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia.,Clinic of Infectious and Tropical Diseases, Clinical Centre of Serbia, Belgrade, Serbia
| | - Tatjana Djukic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia.,Institute of Medical and Clinical Biochemistry, Belgrade, Serbia
| | - Zoran Bukumiric
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia.,Institute of Medical Statistics and Informatics, Belgrade, Serbia
| | - Ana Savic-Radojevic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia.,Institute of Medical and Clinical Biochemistry, Belgrade, Serbia
| | - Marija Matic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia.,Institute of Medical and Clinical Biochemistry, Belgrade, Serbia
| | - Djurdja Jerotic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia.,Institute of Medical and Clinical Biochemistry, Belgrade, Serbia
| | - Nevena Todorovic
- Clinic of Infectious and Tropical Diseases, Clinical Centre of Serbia, Belgrade, Serbia
| | - Milika Asanin
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia.,Clinic of Neurology, Clinical Centre of Serbia, Belgrade, Serbia
| | - Marko Ercegovac
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia.,Clinic of Cardiology, Clinical Centre of Serbia, Belgrade, Serbia
| | - Jovan Ranin
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia.,Clinic of Infectious and Tropical Diseases, Clinical Centre of Serbia, Belgrade, Serbia
| | - Goran Stevanovic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia.,Clinic of Infectious and Tropical Diseases, Clinical Centre of Serbia, Belgrade, Serbia
| | - Marija Pljesa-Ercegovac
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia.,Institute of Medical and Clinical Biochemistry, Belgrade, Serbia
| | - Tatjana Simic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia.,Institute of Medical and Clinical Biochemistry, Belgrade, Serbia.,Serbian Academy of Sciences and Arts, Belgrade, Serbia
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Boroumand M, Manconi B, Serrao S, Iavarone F, Olianas A, Cabras T, Contini C, Pieroni L, Sanna MT, Vento G, Tirone C, Desiderio C, Fiorita A, Faa G, Messana I, Castagnola M. Investigation by top‐down high‐performance liquid chromatography–mass spectrometry of glutathionylation and cysteinylation of salivary S100A9 and cystatin B in preterm newborns. SEPARATION SCIENCE PLUS 2022. [DOI: 10.1002/sscp.202100049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Mozghan Boroumand
- Laboratorio di Proteomica, Centro Europeo di Ricerca sul Cervello IRCCS Fondazione Santa Lucia Via Ardeatina, 306/354 Roma 00179 Italy
| | - Barbara Manconi
- Dipartimento di Scienze della Vita e dell'Ambiente Università di Cagliari Cagliari Italy
| | - Simone Serrao
- Dipartimento di Scienze della Vita e dell'Ambiente Università di Cagliari Cagliari Italy
| | - Federica Iavarone
- Fondazione Policlinico Universitario “A. Gemelli” ‐ IRCCS Roma Italy
- Dipartimento di Scienze Biotecnologiche di Base Cliniche Intensivologiche e Perioperatorie Facoltà di Medicina e Chirurgia Università Cattolica Sacro Cuore Roma Italy
| | - Alessandra Olianas
- Dipartimento di Scienze della Vita e dell'Ambiente Università di Cagliari Cagliari Italy
| | - Tiziana Cabras
- Dipartimento di Scienze della Vita e dell'Ambiente Università di Cagliari Cagliari Italy
| | - Cristina Contini
- Dipartimento di Scienze della Vita e dell'Ambiente Università di Cagliari Cagliari Italy
| | - Luisa Pieroni
- Laboratorio di Proteomica, Centro Europeo di Ricerca sul Cervello IRCCS Fondazione Santa Lucia Via Ardeatina, 306/354 Roma 00179 Italy
| | - Maria Teresa Sanna
- Dipartimento di Scienze della Vita e dell'Ambiente Università di Cagliari Cagliari Italy
| | - Giovanni Vento
- Fondazione Policlinico Universitario “A. Gemelli” ‐ IRCCS Roma Italy
- Divisione di Neonatologia Dipartimento per la Salute della Donna e del Bambino Università Cattolica del Sacro Cuore Roma Italy
| | - Chiara Tirone
- Fondazione Policlinico Universitario “A. Gemelli” ‐ IRCCS Roma Italy
- Divisione di Neonatologia Dipartimento per la Salute della Donna e del Bambino Università Cattolica del Sacro Cuore Roma Italy
| | - Claudia Desiderio
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” Consiglio Nazionale delle Ricerche Roma Italy
| | - Antonella Fiorita
- Fondazione Policlinico Universitario “A. Gemelli” ‐ IRCCS Roma Italy
- Dipartimento di Scienze dell'Invecchiamento Neurologiche Ortopediche e della Testa e del Collo Università Cattolica del Sacro Cuore Roma Italy
| | - Gavino Faa
- Sezione di Anatomia Patologica Dipartimento di Scienze Mediche e Sanità Pubblica Università di Cagliari Cagliari Italy
- Temple University Philadelphia USA
| | - Irene Messana
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” Consiglio Nazionale delle Ricerche Roma Italy
| | - Massimo Castagnola
- Laboratorio di Proteomica, Centro Europeo di Ricerca sul Cervello IRCCS Fondazione Santa Lucia Via Ardeatina, 306/354 Roma 00179 Italy
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10
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Ambastha V, Sopory SK, Tripathy BC, Tiwari BS. Salt induced programmed cell death in rice: evidence from chloroplast proteome signature. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 48:8-27. [PMID: 32702286 DOI: 10.1071/fp19356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 07/01/2020] [Indexed: 06/11/2023]
Abstract
Soil salinity, depending on its intensity, drives a challenged plant either to death, or survival with compromised productivity. On exposure to moderate salinity, plants can often survive by sacrificing some of their cells 'in target' following a route called programmed cell death (PCD). In animals, PCD has been well characterised, and involvement of mitochondria in the execution of PCD events has been unequivocally proven. In plants, mechanistic details of the process are still in grey area. Previously, we have shown that in green tissues of rice, for salt induced PCD to occur, the presence of active chloroplasts and light are equally important. In the present work, we have characterised the chloroplast proteome in rice seedlings at 12 and 24 h after salt exposure and before the time point where the signature of PCD was observed. We identified almost 100 proteins from chloroplasts, which were divided in to 11 categories based on the biological functions in which they were involved. Our results concerning the differential expression of chloroplastic proteins revealed involvement of some novel candidates. Moreover, we observed maximum phosphorylation pattern of chloroplastic proteins at an early time point (12 h) of salt exposure.
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Affiliation(s)
- Vivek Ambastha
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sudhir K Sopory
- Plant Molecular Biology, International Centre of Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Baishnab C Tripathy
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; and Corresponding author. ; ;
| | - Budhi Sagar Tiwari
- Institute of Advanced Research, Gandhinagar, Gujrat 482007, India; and Corresponding author. ; ;
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11
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Wu F, Jiang G, Yan H, Xiao L, Liang H, Zhang D, Jiang Y, Duan X. Redox regulation of glutathione peroxidase by thioredoxin in longan fruit in relation to senescence and quality deterioration. Food Chem 2020; 345:128664. [PMID: 33340895 DOI: 10.1016/j.foodchem.2020.128664] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 10/02/2020] [Accepted: 11/14/2020] [Indexed: 10/22/2022]
Abstract
Thioredoxins (Trxs) are important redox regulators in organisms. However, their involvement in fruit senescence and quality deterioration remains unclear. In this study, one Trx (DlTrx1) and one NADPH-dependent Trx reductase (DlNRT1) cDNAs, were cloned from longan fruit. The DlTrx1 could be effectively reduced by the DlNTR1. Expression of DlTrx1 and DlNTR1 were up-regulated during fruit senescence and quality deterioration. We further identified 33 potential Trx target proteins in longan, including one glutathione peroxidase (DlGpx). DlTrx1 could physically interact with DlGpx. DlTrx1 in combination with DlNTR1 effectively activated DlGpx activity by regulating its redox state. Cys90 in DlGPx could form a disulfide bond with either Cys42 or Cys71, which were the sites of redox modulation. Furthermore, DlGpx exhibited a higher ratio of disulfide bonds to sulfhydryl groups in senescent or deteriorative fruit. We propose that Trx-mediated redox regulation of DlGpx is involved in senescence or quality deterioration of harvested longan fruit.
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Affiliation(s)
- Fuwang Wu
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; Foshan University, Foshan 528225, China
| | - Guoxiang Jiang
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Huiling Yan
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lu Xiao
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Hanzhi Liang
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dandan Zhang
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yueming Jiang
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xuewu Duan
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China.
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12
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Yu J, Li Y, Qin Z, Guo S, Li Y, Miao Y, Song C, Chen S, Dai S. Plant Chloroplast Stress Response: Insights from Thiol Redox Proteomics. Antioxid Redox Signal 2020; 33:35-57. [PMID: 31989831 DOI: 10.1089/ars.2019.7823] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Significance: Plant chloroplasts generate reactive oxygen species (ROS) during photosynthesis, especially under stresses. The sulfhydryl groups of protein cysteine residues are susceptible to redox modifications, which regulate protein structure and function, and thus different signaling and metabolic processes. The ROS-governed protein thiol redox switches play important roles in chloroplasts. Recent Advances: Various high-throughput thiol redox proteomic approaches have been developed, and they have enabled the improved understanding of redox regulatory mechanisms in chloroplasts. For example, the thioredoxin-modulated antioxidant enzymes help to maintain cellular ROS homeostasis. The light- and dark-dependent redox regulation of photosynthetic electron transport, the Calvin/Benson cycle, and starch biosynthesis ensures metabolic coordination and efficient energy utilization. In addition, redox cascades link the light with the dynamic changes of metabolites in nitrate and sulfur assimilation, shikimate pathway, and biosynthesis of fatty acid hormone as well as purine, pyrimidine, and thiamine. Importantly, redox regulation of tetrapyrrole and chlorophyll biosynthesis is critical to balance the photodynamic tetrapyrrole intermediates and prevent oxidative damage. Moreover, redox regulation of diverse elongation factors, chaperones, and kinases plays an important role in the modulation of gene expression, protein conformation, and posttranslational modification that contribute to photosystem II (PSII) repair, state transition, and signaling in chloroplasts. Critical Issues: This review focuses on recent advances in plant thiol redox proteomics and redox protein networks toward understanding plant chloroplast signaling, metabolism, and stress responses. Future Directions: Using redox proteomics integrated with biochemical and molecular genetic approaches, detailed studies of cysteine residues, their redox states, cross talk with other modifications, and the functional implications will yield a holistic understanding of chloroplast stress responses.
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Affiliation(s)
- Juanjuan Yu
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China.,Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China.,College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Ying Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
| | - Zhi Qin
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Siyi Guo
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, China
| | - Yongfang Li
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Yuchen Miao
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, China
| | - Chunpeng Song
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, China
| | - Sixue Chen
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
| | - Shaojun Dai
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China.,Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
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Abstract
The catalase-negative streptococci produce as well as tolerate high levels of H2O2. This work reports the molecular mechanisms of low-H2O2-concentration-induced adaptation to higher H2O2 stress in a Streptococcus species, in which the peroxide-responsive repressor PerR and its redox regulons play the major role. Distinct from the Bacillus subtilis PerR, which is inactivated by H2O2 through histidine oxidation by the Fe2+-triggered Fenton reaction, the streptococcal PerR is inactivated by H2O2 oxidation of the structural Zn2+ binding cysteine residues and thus derepresses the expression of genes defending against oxidative stress. The reversible cysteine oxidation could provide flexibility for PerR regulation in streptococci, and the mechanism might be widely used by lactic acid bacteria, including pathogenic streptococci, containing high levels of cellular manganese, in coping with oxidative stress. The adaptation mechanism could also be applied in oral hygiene by facilitating the fitness and adaptability of the oral commensal streptococci to suppress the pathogens. Preexposure to a low concentration of H2O2 significantly increases the survivability of catalase-negative streptococci in the presence of a higher concentration of H2O2. However, the mechanisms of this adaptation remain unknown. Here, using a redox proteomics assay, we identified 57 and 35 cysteine-oxidized proteins in Streptococcus oligofermentans bacteria that were anaerobically cultured and then pulsed with 40 μM H2O2 and that were statically grown in a 40-ml culture, respectively. The oxidized proteins included the peroxide-responsive repressor PerR, the manganese uptake repressor MntR, thioredoxin system proteins Trx and Tpx, and most glycolytic proteins. Cysteine oxidations of these proteins were verified through redox Western blotting, immunoprecipitation, and liquid chromatography-tandem mass spectrometry assays. In particular, Zn2+-coordinated Cys139 and Cys142 mutations eliminated the H2O2 oxidation of PerR, and inductively coupled plasma mass spectrometry detected significantly decreased amounts of Zn2+ in H2O2-treated PerR, demonstrating that cysteine oxidation results in Zn2+ loss. An electrophoretic mobility shift assay (EMSA) determined that the DNA binding of Mn2+-bound PerR protein (PerR:Zn,Mn) was abolished by H2O2 treatment but was restored by dithiothreitol reduction, verifying that H2O2 inactivates streptococcal PerR:Zn,Mn through cysteine oxidation, analogous to the findings for MntR. Quantitative PCR and EMSA demonstrated that tpx, mntA, mntR, and dpr belonged to the PerR regulons but that only dpr was directly regulated by PerR; mntA was also controlled by MntR. Deletion of mntR significantly reduced the low-H2O2-concentration-induced adaptation of S. oligofermentans to a higher H2O2 concentration, while the absence of PerR completely abolished the self-protection. Therefore, a low H2O2 concentration resulted in the cysteine-reversible oxidations of PerR and MntR to derepress their regulons, which function in cellular metal and redox homeostasis and which endow streptococci with the antioxidative capability. This work reveals a novel Cys redox-based H2O2 defense strategy employed by catalase-negative streptococci in Mn2+-rich cellular environments. IMPORTANCE The catalase-negative streptococci produce as well as tolerate high levels of H2O2. This work reports the molecular mechanisms of low-H2O2-concentration-induced adaptation to higher H2O2 stress in a Streptococcus species, in which the peroxide-responsive repressor PerR and its redox regulons play the major role. Distinct from the Bacillus subtilis PerR, which is inactivated by H2O2 through histidine oxidation by the Fe2+-triggered Fenton reaction, the streptococcal PerR is inactivated by H2O2 oxidation of the structural Zn2+ binding cysteine residues and thus derepresses the expression of genes defending against oxidative stress. The reversible cysteine oxidation could provide flexibility for PerR regulation in streptococci, and the mechanism might be widely used by lactic acid bacteria, including pathogenic streptococci, containing high levels of cellular manganese, in coping with oxidative stress. The adaptation mechanism could also be applied in oral hygiene by facilitating the fitness and adaptability of the oral commensal streptococci to suppress the pathogens.
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14
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Pljesa-Ercegovac M, Savic-Radojevic A, Coric V, Radic T, Simic T. Glutathione transferase genotypes may serve as determinants of risk and prognosis in renal cell carcinoma. Biofactors 2020; 46:229-238. [PMID: 31483924 DOI: 10.1002/biof.1560] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 08/18/2019] [Indexed: 12/25/2022]
Abstract
Renal cell carcinoma (RCC) represents a group of histologically similar neoplasms with significant intratumor and intertumor genetic heterogeneity. Recognized risk factors for RCC development include smoking, hypertension, obesity, as well as von Hippel-Lindau (VHL) disease. Inactivation of VHL, deregulated nuclear factor (erythroid-derived 2)-like 2 (Nrf2) pathway, and altered redox homeostasis, together with changes in glutathione transferase (GST) profile, are considered as important contributing factors in RCC development and progression. Although the available results of both gene-gene and gene-environment analysis are quite heterogeneous, they clearly indicate that certain GST genotypes may play a role as risk modifiers, either individually or in combination with other Phase I or Phase II gene polymorphisms, as well as in subjects exposed to relevant substrates. Seemingly, GST genotyping could identify individuals with impaired detoxification in renal parenchyma that are at higher risk of developing RCC. In addition to well established roles of GSTs in conjugation and biotransformation of xenobiotics, GSTs have emerged as significant regulators of pathways determining cell proliferation and survival. Indeed, there are evidence in favor of GST significance, not only in terms of risk for RCC development, but also with respect to progression and prognosis. So far, GSTM1-active genotype was confirmed to be an independent predictor of higher risk of overall mortality. Therefore, it is reasonable to assume that certain GST variants may assist in individual RCC risk assessment, as well as postoperative prognosis. Even more, GST profiling might contribute to development of personalized targeted therapy in RCC patients.
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Affiliation(s)
- Marija Pljesa-Ercegovac
- Institute of Medical and Clinical Biochemistry, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Ana Savic-Radojevic
- Institute of Medical and Clinical Biochemistry, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Vesna Coric
- Institute of Medical and Clinical Biochemistry, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Tanja Radic
- Institute of Medical and Clinical Biochemistry, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Tatjana Simic
- Institute of Medical and Clinical Biochemistry, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
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15
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Bonzon-Kulichenko E, Camafeita E, López JA, Gómez-Serrano M, Jorge I, Calvo E, Núñez E, Trevisan-Herraz M, Bagwan N, Bárcena JA, Peral B, Vázquez J. Improved integrative analysis of the thiol redox proteome using filter-aided sample preparation. J Proteomics 2019; 214:103624. [PMID: 31874222 DOI: 10.1016/j.jprot.2019.103624] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 12/20/2019] [Accepted: 12/20/2019] [Indexed: 02/08/2023]
Abstract
Changes in the oxidation state of protein Cys residues are involved in cell signalling and play a key role in a variety of pathophysiological states. We had previously developed GELSILOX, an in-gel method that enables the large-scale, parallel analysis of dynamic alterations to the redox state of Cys sites and protein abundance changes. Here we present FASILOX, a further development of the GELSILOX approach featuring: i) significantly increased peptide recovery, ii) enhanced sensitivity for the detection of Cys oxidative alterations, and iii) streamlined workflow that results in shortened assay duration. In mitochondria isolated from the adipose tissue of obese, diabetic patients, FASILOX revealed a sexually dimorphic trait of Cys oxidation involving mainly mitochondrial oxidative phosphorylation complexes. These results provide the first evidence for a decreased efficiency in the antioxidant response of men as compared to women.
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Affiliation(s)
- Elena Bonzon-Kulichenko
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Emilio Camafeita
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain.
| | - Juan Antonio López
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - María Gómez-Serrano
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain; Instituto de Investigaciones Biomédicas, Alberto Sols, (IIBM), Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
| | - Inmaculada Jorge
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Enrique Calvo
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Estefanía Núñez
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Marco Trevisan-Herraz
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Navratan Bagwan
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - José Antonio Bárcena
- Dept. Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain; Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
| | - Belén Peral
- Instituto de Investigaciones Biomédicas, Alberto Sols, (IIBM), Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
| | - Jesús Vázquez
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
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16
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Blond F, Léveillard T. Functional Genomics of the Retina to Elucidate its Construction and Deconstruction. Int J Mol Sci 2019; 20:E4922. [PMID: 31590277 PMCID: PMC6801968 DOI: 10.3390/ijms20194922] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 10/01/2019] [Indexed: 12/20/2022] Open
Abstract
The retina is the light sensitive part of the eye and nervous tissue that have been used extensively to characterize the function of the central nervous system. The retina has a central position both in fundamental biology and in the physiopathology of neurodegenerative diseases. We address the contribution of functional genomics to the understanding of retinal biology by reviewing key events in their historical perspective as an introduction to major findings that were obtained through the study of the retina using genomics, transcriptomics and proteomics. We illustrate our purpose by showing that most of the genes of interest for retinal development and those involved in inherited retinal degenerations have a restricted expression to the retina and most particularly to photoreceptors cells. We show that the exponential growth of data generated by functional genomics is a future challenge not only in terms of storage but also in terms of accessibility to the scientific community of retinal biologists in the future. Finally, we emphasize on novel perspectives that emerge from the development of redox-proteomics, the new frontier in retinal biology.
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Affiliation(s)
- Frédéric Blond
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France.
| | - Thierry Léveillard
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France.
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17
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Zaffagnini M, Fermani S, Marchand CH, Costa A, Sparla F, Rouhier N, Geigenberger P, Lemaire SD, Trost P. Redox Homeostasis in Photosynthetic Organisms: Novel and Established Thiol-Based Molecular Mechanisms. Antioxid Redox Signal 2019; 31:155-210. [PMID: 30499304 DOI: 10.1089/ars.2018.7617] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Significance: Redox homeostasis consists of an intricate network of reactions in which reactive molecular species, redox modifications, and redox proteins act in concert to allow both physiological responses and adaptation to stress conditions. Recent Advances: This review highlights established and novel thiol-based regulatory pathways underlying the functional facets and significance of redox biology in photosynthetic organisms. In the last decades, the field of redox regulation has largely expanded and this work is aimed at giving the right credit to the importance of thiol-based regulatory and signaling mechanisms in plants. Critical Issues: This cannot be all-encompassing, but is intended to provide a comprehensive overview on the structural/molecular mechanisms governing the most relevant thiol switching modifications with emphasis on the large genetic and functional diversity of redox controllers (i.e., redoxins). We also summarize the different proteomic-based approaches aimed at investigating the dynamics of redox modifications and the recent evidence that extends the possibility to monitor the cellular redox state in vivo. The physiological relevance of redox transitions is discussed based on reverse genetic studies confirming the importance of redox homeostasis in plant growth, development, and stress responses. Future Directions: In conclusion, we can firmly assume that redox biology has acquired an established significance that virtually infiltrates all aspects of plant physiology.
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Affiliation(s)
- Mirko Zaffagnini
- 1 Department of Pharmacy and Biotechnology and University of Bologna, Bologna, Italy
| | - Simona Fermani
- 2 Department of Chemistry Giacomo Ciamician, University of Bologna, Bologna, Italy
| | - Christophe H Marchand
- 3 Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, UMR8226, Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Sorbonne Université, Paris, France
| | - Alex Costa
- 4 Department of Biosciences, University of Milan, Milan, Italy
| | - Francesca Sparla
- 1 Department of Pharmacy and Biotechnology and University of Bologna, Bologna, Italy
| | | | - Peter Geigenberger
- 6 Department Biologie I, Ludwig-Maximilians-Universität München, LMU Biozentrum, Martinsried, Germany
| | - Stéphane D Lemaire
- 3 Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, UMR8226, Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Sorbonne Université, Paris, France
| | - Paolo Trost
- 1 Department of Pharmacy and Biotechnology and University of Bologna, Bologna, Italy
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18
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The role of low molecular weight thiols in Mycobacterium tuberculosis. Tuberculosis (Edinb) 2019; 116:44-55. [PMID: 31153518 DOI: 10.1016/j.tube.2019.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 04/16/2019] [Accepted: 04/22/2019] [Indexed: 02/06/2023]
Abstract
Low molecular weight (LMW) thiols are molecules with a functional sulfhydryl group that enable them to detoxify reactive oxygen species, reactive nitrogen species and other free radicals. Their roles range from their ability to modulate the immune system to their ability to prevent damage of biological molecules such as DNA and proteins by protecting against oxidative, nitrosative and acidic stress. LMW thiols are synthesized and found in both eukaryotes and prokaryotes. Due to their beneficial role to both eukaryotes and prokaryotes, their specific functions need to be elucidated, most especially in pathogenic prokaryotes such as Mycobacterium tuberculosis (M.tb), in order to provide a rationale for targeting their biosynthesis for drug development. Ergothioneine (ERG), mycothiol (MSH) and gamma-glutamylcysteine (GGC) are LMW thiols that have been shown to interplay to protect M.tb against cellular stress. Though ERG, MSH and GGC seem to have overlapping functions, studies are gradually revealing their unique physiological roles. Understanding their unique physiological role during the course of tuberculosis (TB) infection, would pave the way for the development of drugs that target their biosynthetic pathway. This review identifies the knowledge gap in the unique physiological roles of LMW thiols and proposes their mechanistic roles based on previous studies. In addition, it gives an update on identified inhibitors of their biosynthetic enzymes.
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19
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Structural and Biochemical Insights into the Reactivity of Thioredoxin h1 from Chlamydomonas reinhardtii. Antioxidants (Basel) 2019; 8:antiox8010010. [PMID: 30609656 PMCID: PMC6356897 DOI: 10.3390/antiox8010010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 12/14/2018] [Accepted: 12/18/2018] [Indexed: 02/07/2023] Open
Abstract
Thioredoxins (TRXs) are major protein disulfide reductases of the cell. Their redox activity relies on a conserved Trp-Cys-(Gly/Pro)-Pro-Cys active site bearing two cysteine (Cys) residues that can be found either as free thiols (reduced TRXs) or linked together by a disulfide bond (oxidized TRXs) during the catalytic cycle. Their reactivity is crucial for TRX activity, and depends on the active site microenvironment. Here, we solved and compared the 3D structure of reduced and oxidized TRX h1 from Chlamydomonas reinhardtii (CrTRXh1). The three-dimensional structure was also determined for mutants of each active site Cys. Structural alignments of CrTRXh1 with other structurally solved plant TRXs showed a common spatial fold, despite the low sequence identity. Structural analyses of CrTRXh1 revealed that the protein adopts an identical conformation independently from its redox state. Treatment with iodoacetamide (IAM), a Cys alkylating agent, resulted in a rapid and pH-dependent inactivation of CrTRXh1. Starting from fully reduced CrTRXh1, we determined the acid dissociation constant (pKa) of each active site Cys by Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry analyses coupled to differential IAM-based alkylation. Based on the diversity of catalytic Cys deprotonation states, the mechanisms and structural features underlying disulfide redox activity are discussed.
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20
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Reducing Complexity? Cysteine Reduction and S-Alkylation in Proteomic Workflows: Practical Considerations. Methods Mol Biol 2019; 1977:83-97. [PMID: 30980324 DOI: 10.1007/978-1-4939-9232-4_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Reduction and alkylation are common processing steps in sample preparation for qualitative and quantitative proteomic analyses. In principle, these steps mitigate the limitations resulting from the presence of disulfide bridges. There has been recurring debate in the proteomics community around their use, with concern over negative impacts that result from overalkylation (off-target, non-thiol sites) or incomplete reduction and/or S-alkylation of cysteine. This chapter integrates findings from a number of studies on different reduction and alkylation strategies, to guide users in experimental design for their optimal use in proteomic workflows.
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21
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López-Grueso MJ, González-Ojeda R, Requejo-Aguilar R, McDonagh B, Fuentes-Almagro CA, Muntané J, Bárcena JA, Padilla CA. Thioredoxin and glutaredoxin regulate metabolism through different multiplex thiol switches. Redox Biol 2018; 21:101049. [PMID: 30639960 PMCID: PMC6327914 DOI: 10.1016/j.redox.2018.11.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/08/2018] [Accepted: 11/11/2018] [Indexed: 12/19/2022] Open
Abstract
The aim of the present study was to define the role of Trx and Grx on metabolic thiol redox regulation and identify their protein and metabolite targets. The hepatocarcinoma-derived HepG2 cell line under both normal and oxidative/nitrosative conditions by overexpression of NO synthase (NOS3) was used as experimental model. Grx1 or Trx1 silencing caused conspicuous changes in the redox proteome reflected by significant changes in the reduced/oxidized ratios of specific Cys's including several glycolytic enzymes. Cys91 of peroxiredoxin-6 (PRDX6) and Cys153 of phosphoglycerate mutase-1 (PGAM1), that are known to be involved in progression of tumor growth, are reported here for the first time as specific targets of Grx1. A group of proteins increased their CysRED/CysOX ratio upon Trx1 and/or Grx1 silencing, including caspase-3 Cys163, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) Cys247 and triose-phosphate isomerase (TPI) Cys255 likely by enhancement of NOS3 auto-oxidation. The activities of several glycolytic enzymes were also significantly affected. Glycolysis metabolic flux increased upon Trx1 silencing, whereas silencing of Grx1 had the opposite effect. Diversion of metabolic fluxes toward synthesis of fatty acids and phospholipids was observed in siRNA-Grx1 treated cells, while siRNA-Trx1 treated cells showed elevated levels of various sphingomyelins and ceramides and signs of increased protein degradation. Glutathione synthesis was stimulated by both treatments. These data indicate that Trx and Grx have both, common and specific protein Cys redox targets and that down regulation of either redoxin has markedly different metabolic outcomes. They reflect the delicate sensitivity of redox equilibrium to changes in any of the elements involved and the difficulty of forecasting metabolic responses to redox environmental changes. Trx1 and Grx1 Cys redox targets are abundant among Glycolytic enzymes. PRDX6-Cys91 and PGAM-Cys153 are specific targets of Grx1. Down regulation of thioredoxin and glutaredoxin have different metabolic outcomes. Glutathione synthesis and membrane lipid composition are sensitive to Trx1 and Grx1 down regulation. Redoxins down regulation also induce target Cys reductive changes under NOS3 overexpression.
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Affiliation(s)
- M J López-Grueso
- Dept. Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain; Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
| | - R González-Ojeda
- Institute of Biomedicine of Seville (IBIS), IBiS/"Virgen del Rocío" University Hospital/CSIC/University of Seville, Seville, Spain
| | - R Requejo-Aguilar
- Dept. Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain; Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
| | - B McDonagh
- Dept. of Physiology, School of Medicine, NUI Galway, Ireland
| | | | - J Muntané
- Dept. of Physiology, School of Medicine, NUI Galway, Ireland
| | - J A Bárcena
- Dept. Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain; Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain.
| | - C A Padilla
- Dept. Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain; Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
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22
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Mitoproteomics: Tackling Mitochondrial Dysfunction in Human Disease. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:1435934. [PMID: 30533169 PMCID: PMC6250043 DOI: 10.1155/2018/1435934] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/29/2018] [Indexed: 12/11/2022]
Abstract
Mitochondria are highly dynamic and regulated organelles that historically have been defined based on their crucial role in cell metabolism. However, they are implicated in a variety of other important functions, making mitochondrial dysfunction an important axis in several pathological contexts. Despite that conventional biochemical and molecular biology approaches have provided significant insight into mitochondrial functionality, innovative techniques that provide a global view of the mitochondrion are still necessary. Proteomics fulfils this need by enabling accurate, systems-wide quantitative analysis of protein abundance. More importantly, redox proteomics approaches offer unique opportunities to tackle oxidative stress, a phenomenon that is intimately linked to aging, cardiovascular disease, and cancer. In addition, cutting-edge proteomics approaches reveal how proteins exert their functions in complex interaction networks where even subtle alterations stemming from early pathological states can be monitored. Here, we describe the proteomics approaches that will help to deepen the role of mitochondria in health and disease by assessing not only changes to mitochondrial protein composition but also alterations to their redox state and how protein interaction networks regulate mitochondrial function and dynamics. This review is aimed at showing the reader how the application of proteomics approaches during the last 20 years has revealed crucial mitochondrial roles in the context of aging, neurodegenerative disorders, metabolic disease, and cancer.
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SVM-SulfoSite: A support vector machine based predictor for sulfenylation sites. Sci Rep 2018; 8:11288. [PMID: 30050050 PMCID: PMC6062547 DOI: 10.1038/s41598-018-29126-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 07/02/2018] [Indexed: 12/15/2022] Open
Abstract
Protein S-sulfenylation, which results from oxidation of free thiols on cysteine residues, has recently emerged as an important post-translational modification that regulates the structure and function of proteins involved in a variety of physiological and pathological processes. By altering the size and physiochemical properties of modified cysteine residues, sulfenylation can impact the cellular function of proteins in several different ways. Thus, the ability to rapidly and accurately identify putative sulfenylation sites in proteins will provide important insights into redox-dependent regulation of protein function in a variety of cellular contexts. Though bottom-up proteomic approaches, such as tandem mass spectrometry (MS/MS), provide a wealth of information about global changes in the sulfenylation state of proteins, MS/MS-based experiments are often labor-intensive, costly and technically challenging. Therefore, to complement existing proteomic approaches, researchers have developed a series of computational tools to identify putative sulfenylation sites on proteins. However, existing methods often suffer from low accuracy, specificity, and/or sensitivity. In this study, we developed SVM-SulfoSite, a novel sulfenylation prediction tool that uses support vector machines (SVM) to identify key determinants of sulfenylation among five feature classes: binary code, physiochemical properties, k-space amino acid pairs, amino acid composition and high-quality physiochemical indices. Using 10-fold cross-validation, SVM-SulfoSite achieved 95% sensitivity and 83% specificity, with an overall accuracy of 89% and Matthew’s correlation coefficient (MCC) of 0.79. Likewise, using an independent test set of experimentally identified sulfenylation sites, our method achieved scores of 74%, 62%, 80% and 0.42 for accuracy, sensitivity, specificity and MCC, with an area under the receiver operator characteristic (ROC) curve of 0.81. Moreover, in side-by-side comparisons, SVM-SulfoSite performed as well as or better than existing sulfenylation prediction tools. Together, these results suggest that our method represents a robust and complementary technique for advanced exploration of protein S-sulfenylation.
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Serrato AJ, Romero-Puertas MC, Lázaro-Payo A, Sahrawy M. Regulation by S-nitrosylation of the Calvin-Benson cycle fructose-1,6-bisphosphatase in Pisum sativum. Redox Biol 2018; 14:409-416. [PMID: 29059554 PMCID: PMC5651545 DOI: 10.1016/j.redox.2017.10.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 10/03/2017] [Accepted: 10/11/2017] [Indexed: 11/21/2022] Open
Abstract
Redox regulation is of great importance in chloroplasts. Many chloroplast enzymes, such as those belonging to the Calvin-Benson cycle (CBC), have conserved regulatory cysteines which form inhibitory disulphide bridges when physiological conditions become unfavourable. Amongst these enzymes, cFBP1, the CBC fructose-1,6-bisphosphatase (FBPase) isoform, is well known to be redox activated by thioredoxin f through the reduction of a disulphide bridge involving Cys153 and Cys173. Moreover, data obtained during recent years point to S-nitrosylation as another redox post-translational modification putatively regulating an increasing number of plant enzymes, including cFBP1. In this study we have shown that the Pisum sativum cFBP1 can be efficiently S-nitrosylated by GSNO and SNAP, triggering the formation of the regulatory disulphide. Using in vivo experiments with P. sativum we have established that cFBP1 S-nitrosylation only occurs during the light period and we have elucidated by activity assays with Cys-to-Ser mutants that this enzyme may be inactivated through the S-nitrosylation of Cys153. Finally, in the light of the new data, we have proposed an extended redox-regulation model by integrating the S-nitrosylation and the TRX f-mediated regulation of cFBP1.
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Affiliation(s)
- Antonio Jesús Serrato
- Departamento de Bioquímica, Biología Molecular y Celular de Plantas, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, 18008 Granada, Spain.
| | - María C Romero-Puertas
- Departamento de Bioquímica, Biología Molecular y Celular de Plantas, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, 18008 Granada, Spain.
| | - Alfonso Lázaro-Payo
- Departamento de Bioquímica, Biología Molecular y Celular de Plantas, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, 18008 Granada, Spain.
| | - Mariam Sahrawy
- Departamento de Bioquímica, Biología Molecular y Celular de Plantas, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, 18008 Granada, Spain.
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Pérez-Pérez ME, Mauriès A, Maes A, Tourasse NJ, Hamon M, Lemaire SD, Marchand CH. The Deep Thioredoxome in Chlamydomonas reinhardtii: New Insights into Redox Regulation. MOLECULAR PLANT 2017; 10:1107-1125. [PMID: 28739495 DOI: 10.1016/j.molp.2017.07.009] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/04/2017] [Accepted: 07/11/2017] [Indexed: 05/20/2023]
Abstract
Thiol-based redox post-translational modifications have emerged as important mechanisms of signaling and regulation in all organisms, and thioredoxin plays a key role by controlling the thiol-disulfide status of target proteins. Recent redox proteomic studies revealed hundreds of proteins regulated by glutathionylation and nitrosylation in the unicellular green alga Chlamydomonas reinhardtii, while much less is known about the thioredoxin interactome in this organism. By combining qualitative and quantitative proteomic analyses, we have comprehensively investigated the Chlamydomonas thioredoxome and 1188 targets have been identified. They participate in a wide range of metabolic pathways and cellular processes. This study broadens not only the redox regulation to new enzymes involved in well-known thioredoxin-regulated metabolic pathways but also sheds light on cellular processes for which data supporting redox regulation are scarce (aromatic amino acid biosynthesis, nuclear transport, etc). Moreover, we characterized 1052 thioredoxin-dependent regulatory sites and showed that these data constitute a valuable resource for future functional studies in Chlamydomonas. By comparing this thioredoxome with proteomic data for glutathionylation and nitrosylation at the protein and cysteine levels, this work confirms the existence of a complex redox regulation network in Chlamydomonas and provides evidence of a tremendous selectivity of redox post-translational modifications for specific cysteine residues.
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Affiliation(s)
- María Esther Pérez-Pérez
- Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Universités, UPMC Univ Paris 06, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Adeline Mauriès
- Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Universités, UPMC Univ Paris 06, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Alexandre Maes
- Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Universités, UPMC Univ Paris 06, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Nicolas J Tourasse
- Institut de Biologie Physico-Chimique, Plateforme de Protéomique, FRC550, CNRS, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Marion Hamon
- Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Universités, UPMC Univ Paris 06, 13 rue Pierre et Marie Curie, 75005 Paris, France; Institut de Biologie Physico-Chimique, Plateforme de Protéomique, FRC550, CNRS, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Stéphane D Lemaire
- Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Universités, UPMC Univ Paris 06, 13 rue Pierre et Marie Curie, 75005 Paris, France.
| | - Christophe H Marchand
- Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Universités, UPMC Univ Paris 06, 13 rue Pierre et Marie Curie, 75005 Paris, France; Institut de Biologie Physico-Chimique, Plateforme de Protéomique, FRC550, CNRS, 13 rue Pierre et Marie Curie, 75005 Paris, France.
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26
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Sun MA, Wang Y, Zhang Q, Xia Y, Ge W, Guo D. Prediction of reversible disulfide based on features from local structural signatures. BMC Genomics 2017; 18:279. [PMID: 28376774 PMCID: PMC5379614 DOI: 10.1186/s12864-017-3668-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 03/28/2017] [Indexed: 11/12/2022] Open
Abstract
Background Disulfide bonds are traditionally considered to play only structural roles. In recent years, increasing evidence suggests that the disulfide proteome is made up of structural disulfides and reversible disulfides. Unlike structural disulfides, reversible disulfides are usually of important functional roles and may serve as redox switches. Interestingly, only specific disulfide bonds are reversible while others are not. However, whether reversible disulfides can be predicted based on structural information remains largely unknown. Methods In this study, two datasets with both types of disulfides were compiled using independent approaches. By comparison of various features extracted from the local structural signatures, we identified several features that differ significantly between reversible and structural disulfides, including disulfide bond length, along with the number, amino acid composition, secondary structure and physical-chemical properties of surrounding amino acids. A SVM-based classifier was developed for predicting reversible disulfides. Results By 10-fold cross-validation, the model achieved accuracy of 0.750, sensitivity of 0.352, specificity of 0.953, MCC of 0.405 and AUC of 0.751 using the RevSS_PDB dataset. The robustness was further validated by using RevSS_RedoxDB as independent testing dataset. This model was applied to proteins with known structures in the PDB database. The results show that one third of the predicted reversible disulfide containing proteins are well-known redox enzymes, while the remaining are non-enzyme proteins. Given that reversible disulfides are frequently reported from functionally important non-enzyme proteins such as transcription factors, the predictions may provide valuable candidates of novel reversible disulfides for further experimental investigation. Conclusions This study provides the first comparative analysis between the reversible and the structural disulfides. Distinct features remarkably different between these two groups of disulfides were identified, and a SVM-based classifier for predicting reversible disulfides was developed accordingly. A web server named RevssPred can be accessed freely from: http://biocomputer.bio.cuhk.edu.hk/RevssPred. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3668-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ming-An Sun
- School of Life Sciences and the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, SAR, China
| | - Yejun Wang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Shenzhen University Health Science Center, Nanhai Ave 3688, Shenzhen, 518060, China
| | - Qing Zhang
- School of Life Sciences and the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, SAR, China
| | - Yiji Xia
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong, SAR, China
| | - Wei Ge
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Dianjing Guo
- School of Life Sciences and the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, SAR, China.
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27
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Mori MP, Costa RAP, Soltys DT, Freire TDS, Rossato FA, Amigo I, Kowaltowski AJ, Vercesi AE, de Souza-Pinto NC. Lack of XPC leads to a shift between respiratory complexes I and II but sensitizes cells to mitochondrial stress. Sci Rep 2017; 7:155. [PMID: 28273955 PMCID: PMC5427820 DOI: 10.1038/s41598-017-00130-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 02/08/2017] [Indexed: 12/13/2022] Open
Abstract
Genomic instability drives tumorigenesis and DNA repair defects are associated with elevated cancer. Metabolic alterations are also observed during tumorigenesis, although a causal relationship between these has not been clearly established. Xeroderma pigmentosum (XP) is a DNA repair disease characterized by early cancer. Cells with reduced expression of the XPC protein display a metabolic shift from OXPHOS to glycolysis, which was linked to accumulation of nuclear DNA damage and oxidants generation via NOX-1. Using XP-C cells, we show that mitochondrial respiratory complex I (CI) is impaired in the absence of XPC, while complex II (CII) is upregulated in XP-C cells. The CI/CII metabolic shift was dependent on XPC, as XPC complementation reverted the phenotype. We demonstrate that mitochondria are the primary source of H2O2 and glutathione peroxidase activity is compromised. Moreover, mtDNA is irreversibly damaged and accumulates deletions. XP-C cells were more sensitive to the mitochondrial inhibitor antimycin A, an effect also prevented in XPC-corrected cells. Our results show that XPC deficiency leads to alterations in mitochondrial redox balance with a CI/CII shift as a possible adaptation to lower CI activity, but at the cost of sensitizing XP-C cells to mitochondrial oxidative stress.
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Affiliation(s)
- Mateus P Mori
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo (USP), São Paulo, SP, Brazil
| | - Rute A P Costa
- Department of Clinical Pathology, School of Medical Sciences, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Daniela T Soltys
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo (USP), São Paulo, SP, Brazil
| | - Thiago de S Freire
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo (USP), São Paulo, SP, Brazil
| | - Franco A Rossato
- Department of Clinical Pathology, School of Medical Sciences, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Ignácio Amigo
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo (USP), São Paulo, SP, Brazil
| | - Alicia J Kowaltowski
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo (USP), São Paulo, SP, Brazil
| | - Aníbal E Vercesi
- Department of Clinical Pathology, School of Medical Sciences, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Nadja C de Souza-Pinto
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo (USP), São Paulo, SP, Brazil.
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28
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Abstract
Thiol groups in protein cysteine residues can be subjected to different oxidative modifications by reactive oxygen/nitrogen species. Reversible cysteine oxidation, including S-nitrosylation, S-sulfenylation, S-glutathionylation, and disulfide formation, modulate multiple biological functions, such as enzyme catalysis, antioxidant, and other signaling pathways. However, the biological relevance of reversible cysteine oxidation is typically underestimated, in part due to the low abundance and high reactivity of some of these modifications, and the lack of methods to enrich and quantify them. To facilitate future research efforts, this chapter describes detailed procedures to target the different modifications using mass spectrometry-based biotin switch assays. By switching the modification of interest to a biotin moiety, these assays leverage the high affinity between biotin and avidin to enrich the modification. The use of stable isotope labeling and a range of selective reducing agents facilitate the quantitation of individual as well as total reversible cysteine oxidation. The biotin switch assay has been widely applied to the quantitative analysis of S-nitrosylation in different disease models and is now also emerging as a valuable research tool for other oxidative cysteine modifications, highlighting its relevance as a versatile, robust strategy for carrying out in-depth studies in redox proteomics.
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Affiliation(s)
- R Li
- The Biomedical Research Centre, University of British Columbia, Vancouver, BC, Canada; University of British Columbia, Vancouver, BC, Canada
| | - J Kast
- The Biomedical Research Centre, University of British Columbia, Vancouver, BC, Canada; University of British Columbia, Vancouver, BC, Canada; Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada.
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29
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Ullevig SL, Kim HS, Short JD, Tavakoli S, Weintraub ST, Downs K, Asmis R. Protein S-Glutathionylation Mediates Macrophage Responses to Metabolic Cues from the Extracellular Environment. Antioxid Redox Signal 2016; 25:836-851. [PMID: 26984580 PMCID: PMC5107721 DOI: 10.1089/ars.2015.6531] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
AIMS Protein S-glutathionylation, the formation of a mixed disulfide between glutathione and protein thiols, is an oxidative modification that has emerged as a new signaling paradigm, potentially linking oxidative stress to chronic inflammation associated with heart disease, diabetes, cancer, lung disease, and aging. Using a novel, highly sensitive, and selective proteomic approach to identify S-glutathionylated proteins, we tested the hypothesis that monocytes and macrophages sense changes in their microenvironment and respond to metabolic stress by altering their protein thiol S-glutathionylation status. RESULTS We identified over 130 S-glutathionylated proteins, which were associated with a variety of cellular functions, including metabolism, transcription and translation, protein folding, free radical scavenging, cell motility, and cell death. Over 90% of S-glutathionylated proteins identified in metabolically stressed THP-1 monocytes were also found in hydrogen peroxide (H2O2)-treated cells, suggesting that H2O2 mediates metabolic stress-induced protein S-glutathionylation in monocytes and macrophages. We validated our findings in mouse peritoneal macrophages isolated from both healthy and dyslipidemic atherosclerotic mice and found that 52% of the S-glutathionylated proteins found in THP-1 monocytes were also identified in vivo. Changes in macrophage protein S-glutathionylation induced by dyslipidemia were sexually dimorphic. INNOVATION We provide a novel mechanistic link between metabolic (and thiol oxidative) stress, macrophage dysfunction, and chronic inflammatory diseases associated with metabolic disorders. CONCLUSION Our data support the concept that changes in the extracellular metabolic microenvironment induce S-glutathionylation of proteins central to macrophage metabolism and a wide array of cellular signaling pathways and functions, which in turn initiate and promote functional and phenotypic changes in macrophages. Antioxid. Redox Signal. 25, 836-851.
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Affiliation(s)
- Sarah L Ullevig
- 1 Department of Kinesiology, Health, and Nutrition, University of Texas at San Antonio , San Antonio, Texas
| | - Hong Seok Kim
- 2 Department of Molecular Medicine, College of Medicine, Inha University , Incheon, Korea
| | - John D Short
- 3 Department of Pharmacology, University of Texas Health Science Center at San Antonio , San Antonio, Texas
| | - Sina Tavakoli
- 4 Department of Radiology, University of Texas Health Science Center at San Antonio , San Antonio, Texas
| | - Susan T Weintraub
- 5 Institutional Mass Spectrometry Core Laboratory, University of Texas Health Science Center at San Antonio , San Antonio, Texas.,6 Department of Biochemistry, University of Texas Health Science Center at San Antonio , San Antonio, Texas
| | - Kevin Downs
- 7 Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio , San Antonio, Texas
| | - Reto Asmis
- 4 Department of Radiology, University of Texas Health Science Center at San Antonio , San Antonio, Texas.,6 Department of Biochemistry, University of Texas Health Science Center at San Antonio , San Antonio, Texas.,8 Department of Clinical Laboratory Sciences, University of Texas Health Science Center at San Antonio , San Antonio, Texas
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30
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Sánchez-Riego AM, Mata-Cabana A, Galmozzi CV, Florencio FJ. NADPH-Thioredoxin Reductase C Mediates the Response to Oxidative Stress and Thermotolerance in the Cyanobacterium Anabaena sp. PCC7120. Front Microbiol 2016; 7:1283. [PMID: 27588019 PMCID: PMC4988983 DOI: 10.3389/fmicb.2016.01283] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 08/04/2016] [Indexed: 12/30/2022] Open
Abstract
NADPH-thioredoxin reductase C (NTRC) is a bimodular enzyme composed of an NADPH-thioredoxin reductase and a thiioredoxin domain extension in the same protein. In plants, NTRC has been described to be involved in the protection of the chloroplast against oxidative stress damage through reduction of the 2-Cys peroxiredoxin (2-Cys Prx) as well as through other functions related to redox enzyme regulation. In cyanobacteria, the Anabaena NTRC has been characterized in vitro, however, nothing was known about its in vivo function. In order to study that, we have generated the first knockout mutant strain (ΔntrC), apart from the previously described in Arabidopsis. Detailed characterization of this strain reveals a differential sensitivity to oxidative stress treatments with respect to the wild-type Anabaena strain, including a higher level of ROS (reactive oxygen species) in normal growth conditions. In the mutant strain, different oxidative stress treatments such as hydrogen peroxide, methyl-viologen or high light irradiance provoke an increase in the expression of genes related to ROS detoxification, including AnNTRC and peroxiredoxin genes, with a concomitant increase in the amount of AnNTRC and 2-Cys Prx. Moreover, the role of AnNTRC in the antioxidant response is confirmed by the observation of a pronounced overoxidation of the 2-Cys Prx and a time-delay recovery of the reduced form of this protein upon oxidative stress treatments. Our results suggest the participation of this enzyme in the peroxide detoxification in Anabaena. In addition, we describe the role of Anabaena NTRC in thermotolerance, by the appearance of high molecular mass AnNTRC complexes, showing that the mutant strain is more sensitive to high temperature treatments.
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Affiliation(s)
- Ana M Sánchez-Riego
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-Consejo Superior de Investigaciones Científicas Seville, Spain
| | - Alejandro Mata-Cabana
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-Consejo Superior de Investigaciones Científicas Seville, Spain
| | - Carla V Galmozzi
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-Consejo Superior de Investigaciones Científicas Seville, Spain
| | - Francisco J Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-Consejo Superior de Investigaciones Científicas Seville, Spain
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31
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Pillay CS, Eagling BD, Driscoll SRE, Rohwer JM. Quantitative measures for redox signaling. Free Radic Biol Med 2016; 96:290-303. [PMID: 27151506 DOI: 10.1016/j.freeradbiomed.2016.04.199] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 04/25/2016] [Accepted: 04/29/2016] [Indexed: 12/17/2022]
Abstract
Redox signaling is now recognized as an important regulatory mechanism for a number of cellular processes including the antioxidant response, phosphokinase signal transduction and redox metabolism. While there has been considerable progress in identifying the cellular machinery involved in redox signaling, quantitative measures of redox signals have been lacking, limiting efforts aimed at understanding and comparing redox signaling under normoxic and pathogenic conditions. Here we have outlined some of the accepted principles for redox signaling, including the description of hydrogen peroxide as a signaling molecule and the role of kinetics in conferring specificity to these signaling events. Based on these principles, we then develop a working definition for redox signaling and review a number of quantitative methods that have been employed to describe signaling in other systems. Using computational modeling and published data, we show how time- and concentration- dependent analyses, in particular, could be used to quantitatively describe redox signaling and therefore provide important insights into the functional organization of redox networks. Finally, we consider some of the key challenges with implementing these methods.
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Affiliation(s)
- Ché S Pillay
- School of Life Sciences, University of KwaZulu-Natal, Carbis Road, Pietermaritzburg 3201, South Africa.
| | - Beatrice D Eagling
- School of Life Sciences, University of KwaZulu-Natal, Carbis Road, Pietermaritzburg 3201, South Africa
| | - Scott R E Driscoll
- School of Life Sciences, University of KwaZulu-Natal, Carbis Road, Pietermaritzburg 3201, South Africa
| | - Johann M Rohwer
- Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland, 7602 Stellenbosch, South Africa
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Launay H, Barré P, Puppo C, Manneville S, Gontero B, Receveur-Bréchot V. Absence of residual structure in the intrinsically disordered regulatory protein CP12 in its reduced state. Biochem Biophys Res Commun 2016; 477:20-26. [PMID: 27268235 DOI: 10.1016/j.bbrc.2016.06.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 06/02/2016] [Indexed: 10/21/2022]
Abstract
The redox switch protein CP12 is a key player of the regulation of the Benson-Calvin cycle. Its oxidation state is controlled by the formation/dissociation of two intramolecular disulphide bridges during the day/night cycle. CP12 was known to be globally intrinsically disordered on a large scale in its reduced state, while being partly ordered in the oxidised state. By combining Nuclear Magnetic Resonance and Small Angle X-ray Scattering experiments, we showed that, contrary to secondary structure or disorder predictions, reduced CP12 is fully disordered, with no transient or local residual structure likely to be precursor of the structures identified in the oxidised active state and/or in the bound state with GAPDH or PRK. These results highlight the diversity of the mechanisms of regulation of conditionally disordered redox switches, and question the stability of oxidised CP12 scaffold.
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Affiliation(s)
- Hélène Launay
- Laboratory of integrative Structural and Chemical Biology (iSCB), Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS UMR 7258, INSERM U 1068, Institut Paoli-Calmettes, Aix-Marseille Universités, Marseille 13009, France
| | - Patrick Barré
- Laboratory of integrative Structural and Chemical Biology (iSCB), Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS UMR 7258, INSERM U 1068, Institut Paoli-Calmettes, Aix-Marseille Universités, Marseille 13009, France
| | - Carine Puppo
- Aix-Marseille Université, Centre National de la Recherche Scientifique, UMR 7281, Laboratoire de Bioénergétique et Ingénierie des Protéines, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France
| | - Stéphanie Manneville
- Laboratory of integrative Structural and Chemical Biology (iSCB), Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS UMR 7258, INSERM U 1068, Institut Paoli-Calmettes, Aix-Marseille Universités, Marseille 13009, France
| | - Brigitte Gontero
- Aix-Marseille Université, Centre National de la Recherche Scientifique, UMR 7281, Laboratoire de Bioénergétique et Ingénierie des Protéines, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France
| | - Véronique Receveur-Bréchot
- Laboratory of integrative Structural and Chemical Biology (iSCB), Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS UMR 7258, INSERM U 1068, Institut Paoli-Calmettes, Aix-Marseille Universités, Marseille 13009, France.
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Naranjo B, Mignée C, Krieger-Liszkay A, Hornero-Méndez D, Gallardo-Guerrero L, Cejudo FJ, Lindahl M. The chloroplast NADPH thioredoxin reductase C, NTRC, controls non-photochemical quenching of light energy and photosynthetic electron transport in Arabidopsis. PLANT, CELL & ENVIRONMENT 2016; 39:804-22. [PMID: 26476233 DOI: 10.1111/pce.12652] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/23/2015] [Accepted: 09/24/2015] [Indexed: 05/19/2023]
Abstract
High irradiances may lead to photooxidative stress in plants, and non-photochemical quenching (NPQ) contributes to protection against excess excitation. One of the NPQ mechanisms, qE, involves thermal dissipation of the light energy captured. Importantly, plants need to tune down qE under light-limiting conditions for efficient utilization of the available quanta. Considering the possible redox control of responses to excess light implying enzymes, such as thioredoxins, we have studied the role of the NADPH thioredoxin reductase C (NTRC). Whereas Arabidopsis thaliana plants lacking NTRC tolerate high light intensities, these plants display drastically elevated qE, have larger trans-thylakoid ΔpH and have 10-fold higher zeaxanthin levels under low and medium light intensities, leading to extremely low linear electron transport rates. To test the impact of the high qE on plant growth, we generated an ntrc-psbs double-knockout mutant, which is devoid of qE. This double mutant grows faster than the ntrc mutant and has a higher chlorophyll content. The photosystem II activity is partially restored in the ntrc-psbs mutant, and linear electron transport rates under low and medium light intensities are twice as high as compared with plants lacking ntrc alone. These data uncover a new role for NTRC in the control of photosynthetic yield.
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Affiliation(s)
- Belén Naranjo
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas (CSIC) - Universidad de Sevilla, 410 92, Seville, Spain
| | - Clara Mignée
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA) Saclay, Institut de Biologie et de Technologie de Saclay, Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, 91191, Gif-sur-Yvette Cedex, France
| | - Anja Krieger-Liszkay
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA) Saclay, Institut de Biologie et de Technologie de Saclay, Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, 91191, Gif-sur-Yvette Cedex, France
| | - Dámaso Hornero-Méndez
- Departamento de Fitoquímica de los Alimentos, Instituto de la Grasa, CSIC, 41013, Seville, Spain
| | | | - Francisco Javier Cejudo
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas (CSIC) - Universidad de Sevilla, 410 92, Seville, Spain
| | - Marika Lindahl
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas (CSIC) - Universidad de Sevilla, 410 92, Seville, Spain
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Wessels HJCT, de Almeida NM, Kartal B, Keltjens JT. Bacterial Electron Transfer Chains Primed by Proteomics. Adv Microb Physiol 2016; 68:219-352. [PMID: 27134025 DOI: 10.1016/bs.ampbs.2016.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Electron transport phosphorylation is the central mechanism for most prokaryotic species to harvest energy released in the respiration of their substrates as ATP. Microorganisms have evolved incredible variations on this principle, most of these we perhaps do not know, considering that only a fraction of the microbial richness is known. Besides these variations, microbial species may show substantial versatility in using respiratory systems. In connection herewith, regulatory mechanisms control the expression of these respiratory enzyme systems and their assembly at the translational and posttranslational levels, to optimally accommodate changes in the supply of their energy substrates. Here, we present an overview of methods and techniques from the field of proteomics to explore bacterial electron transfer chains and their regulation at levels ranging from the whole organism down to the Ångstrom scales of protein structures. From the survey of the literature on this subject, it is concluded that proteomics, indeed, has substantially contributed to our comprehending of bacterial respiratory mechanisms, often in elegant combinations with genetic and biochemical approaches. However, we also note that advanced proteomics offers a wealth of opportunities, which have not been exploited at all, or at best underexploited in hypothesis-driving and hypothesis-driven research on bacterial bioenergetics. Examples obtained from the related area of mitochondrial oxidative phosphorylation research, where the application of advanced proteomics is more common, may illustrate these opportunities.
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Affiliation(s)
- H J C T Wessels
- Nijmegen Center for Mitochondrial Disorders, Radboud Proteomics Centre, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - N M de Almeida
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - B Kartal
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands; Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | - J T Keltjens
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands.
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Structure, function and disease relevance of Omega-class glutathione transferases. Arch Toxicol 2016; 90:1049-67. [PMID: 26993125 DOI: 10.1007/s00204-016-1691-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/10/2016] [Indexed: 12/13/2022]
Abstract
The Omega-class cytosolic glutathione transferases (GSTs) have distinct structural and functional attributes that allow them to perform novel roles unrelated to the functions of other GSTs. Mammalian GSTO1-1 has been found to play a previously unappreciated role in the glutathionylation cycle that is emerging as significant mechanism regulating protein function. GSTO1-1-catalyzed glutathionylation or deglutathionylation of a key signaling protein may explain the requirement for catalytically active GSTO1-1 in LPS-stimulated pro-inflammatory signaling through the TLR4 receptor. The observation that ML175 a specific GSTO1-1 inhibitor can block LPS-stimulated inflammatory signaling has opened a new avenue for the development of novel anti-inflammatory drugs that could be useful in the treatment of toxic shock and other inflammatory disorders. The role of GSTO2-2 remains unclear. As a dehydroascorbate reductase, it could contribute to the maintenance of cellular redox balance and it is interesting to note that the GSTO2 N142D polymorphism has been associated with multiple diseases including Alzheimer's disease, Parkinson's disease, familial amyotrophic lateral sclerosis, chronic obstructive pulmonary disease, age-related cataract and breast cancer.
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Liu Y, Yang X, Yin Y, Lin J, Chen C, Pan J, Si M, Shen X. Mycothiol protects Corynebacterium glutamicum against acid stress via maintaining intracellular pH homeostasis, scavenging ROS, and S-mycothiolating MetE. J GEN APPL MICROBIOL 2016; 62:144-53. [DOI: 10.2323/jgam.2016.02.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Yingbao Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University
- College of Life Science, Yangtze University
| | - Xiaobing Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University
| | - Yajie Yin
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences
| | - Jinshui Lin
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University
| | - Can Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University
| | - Junfeng Pan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University
| | - Meiru Si
- College of Life Sciences, Qufu Normal University
| | - Xihui Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University
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Role of two sequence motifs of mesencephalic astrocyte-derived neurotrophic factor in its survival-promoting activity. Cell Death Dis 2015; 6:e2032. [PMID: 26720341 PMCID: PMC4720903 DOI: 10.1038/cddis.2015.371] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 11/17/2015] [Accepted: 11/19/2015] [Indexed: 12/21/2022]
Abstract
Mesencephalic astrocyte-derived neurotrophic factor (MANF) is a prosurvival protein that protects the cells when applied intracellularly in vitro or extracellularly in vivo. Its protective mechanisms are poorly known. Here we studied the role of two short sequence motifs within the carboxy-(C) terminal domain of MANF in its neuroprotective activity: the CKGC sequence (a CXXC motif) that could be involved in redox reactions, and the C-terminal RTDL sequence, an endoplasmic reticulum (ER) retention signal. We mutated these motifs and analyzed the antiapoptotic effect and intracellular localization of these mutants of MANF when overexpressed in cultured sympathetic or sensory neurons. As an in vivo model for studying the effect of these mutants after their extracellular application, we used the rat model of cerebral ischemia. Even though we found no evidence for oxidoreductase activity of MANF, the mutation of CXXC motif completely abolished its protective effect, showing that this motif is crucial for both MANF's intracellular and extracellular activity. The RTDL motif was not needed for the neuroprotective activity of MANF after its extracellular application in the stroke model in vivo. However, in vitro the deletion of RTDL motif inactivated MANF in the sympathetic neurons where the mutant protein localized to Golgi, but not in the sensory neurons where the mutant localized to the ER, showing that intracellular MANF protects these peripheral neurons in vitro only when localized to the ER.
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Kalinina EV, Chernov NN, Novichkova MD. Role of glutathione, glutathione transferase, and glutaredoxin in regulation of redox-dependent processes. BIOCHEMISTRY (MOSCOW) 2015; 79:1562-83. [PMID: 25749165 DOI: 10.1134/s0006297914130082] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Over the last decade fundamentally new features have been revealed for the participation of glutathione and glutathione-dependent enzymes (glutathione transferase and glutaredoxin) in cell proliferation, apoptosis, protein folding, and cell signaling. Reduced glutathione (GSH) plays an important role in maintaining cellular redox status by participating in thiol-disulfide exchange, which regulates a number of cell functions including gene expression and the activity of individual enzymes and enzyme systems. Maintaining optimum GSH/GSSG ratio is essential to cell viability. Decrease in the ratio can serve as an indicator of damage to the cell redox status and of changes in redox-dependent gene regulation. Disturbance of intracellular GSH balance is observed in a number of pathologies including cancer. Consequences of inappropriate GSH/GSSG ratio include significant changes in the mechanism of cellular redox-dependent signaling controlled both nonenzymatically and enzymatically with the participation of isoforms of glutathione transferase and glutaredoxin. This review summarizes recent data on the role of glutathione, glutathione transferase, and glutaredoxin in the regulation of cellular redox-dependent processes.
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Affiliation(s)
- E V Kalinina
- Peoples' Friendship University of Russia, Moscow, 117198, Russia.
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Cabras T, Sanna M, Manconi B, Fanni D, Demelia L, Sorbello O, Iavarone F, Castagnola M, Faa G, Messana I. Proteomic investigation of whole saliva in Wilson's disease. J Proteomics 2015; 128:154-63. [PMID: 26254010 DOI: 10.1016/j.jprot.2015.07.033] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 07/20/2015] [Accepted: 07/28/2015] [Indexed: 01/20/2023]
Abstract
Wilson's disease is a rare inherited disorder of copper metabolism, manifesting hepatic, neurological and psychiatric symptoms. Early diagnosis is often unfeasible and a unique diagnostic test is currently inapplicable. We performed the qualitative/quantitative characterization of the salivary proteome/peptidome of 32 Wilson's disease patients by an integrated top-down/bottom-up approach. Patients exhibited significant higher levels of S100A9 and S100A8 proteoforms, and their oxidized forms with respect to controls. Oxidation occurred on methionine and tryptophan residues, and on the unique cysteine residue, in position 42 in S100A8, and 3 in S100A9, that generated glutathionylated, cysteinylated, sulfinic, sulfonic, and disulfide dimeric forms. Wilson's disease patient saliva showed high levels of two new fragments of the polymeric immunoglobulin receptor, and of α-defensins 2 and 4. Overall, the salivary proteome of Wilson's disease patients reflected oxidative stress and inflammatory conditions characteristic of the pathology, highlighting differences that could be useful clues of disease exacerbation.
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Affiliation(s)
- Tiziana Cabras
- Department of Life and Environmental Sciences, Biomedical section, University of Cagliari, Monserrato Campus 09042, Monserrato, CA, Italy.
| | - Monica Sanna
- Department of Life and Environmental Sciences, Biomedical section, University of Cagliari, Monserrato Campus 09042, Monserrato, CA, Italy
| | - Barbara Manconi
- Department of Life and Environmental Sciences, Biomedical section, University of Cagliari, Monserrato Campus 09042, Monserrato, CA, Italy
| | - Daniela Fanni
- Department of Surgery Sciences, University of Cagliari, Monserrato Campus 09042, Monserrato, CA, Italy
| | - Luigi Demelia
- Department of Medical Sciences "M. Aresu", AOU, University of Cagliari, Monserrato Campus 09042, Monserrato, CA, Italy
| | - Orazio Sorbello
- Department of Medical Sciences "M. Aresu", AOU, University of Cagliari, Monserrato Campus 09042, Monserrato, CA, Italy
| | - Federica Iavarone
- Biochemistry and Clinical Biochemistry Institute, Medicine Faculty, Catholic University of Rome, L.go F. Vito 1, 00168 Rome, Italy
| | - Massimo Castagnola
- Biochemistry and Clinical Biochemistry Institute, Medicine Faculty, Catholic University of Rome, L.go F. Vito 1, 00168 Rome, Italy; Institute of Chemistry of the Molecular Recognition CNR, L.go F. Vito 1, 00168 Rome, Italy
| | - Gavino Faa
- Department of Surgery Sciences, University of Cagliari, Monserrato Campus 09042, Monserrato, CA, Italy
| | - Irene Messana
- Department of Life and Environmental Sciences, Biomedical section, University of Cagliari, Monserrato Campus 09042, Monserrato, CA, Italy
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Capillary electrophoresis with mass spectrometric detection for separation of S-nitrosoglutathione and its decomposition products: a deeper insight into the decomposition pathways. Anal Bioanal Chem 2015; 407:6221-6. [DOI: 10.1007/s00216-015-8786-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Revised: 05/14/2015] [Accepted: 05/18/2015] [Indexed: 10/23/2022]
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Santelia D, Trost P, Sparla F. New insights into redox control of starch degradation. CURRENT OPINION IN PLANT BIOLOGY 2015; 25:1-9. [PMID: 25899330 DOI: 10.1016/j.pbi.2015.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/31/2015] [Accepted: 04/03/2015] [Indexed: 05/04/2023]
Abstract
Starch is one of the major sinks of fixed carbon in photosynthetic tissues of higher plants. Carbon fixation and the synthesis of primary starch occur during the day in the chloroplast stroma, whereas starch degradation typically occurs during the following night to fuel the whole plant with energy and carbon in the absence of photosynthesis. Redox-based regulatory systems play a central role in the modulation of several chloroplastic pathways. Reversible oxidations of cysteine residues are post-translational modifications that orchestrate the precise functioning of chloroplast pathways together with changes in pH, Mg(2+) and concentrations of metabolic intermediates. Leaf starch metabolism has been intensively studied. The enzymes involved in starch synthesis and degradation have been identified and characterized. However, the redox control of the enzymes responsible for starch degradation at night remains elusive, and their response to redox transitions conflicts with the timing of the physiological events. Most of the enzymes of starch degradation are activated by reducing conditions, characteristic of daytime. Thus, redox control may have only a minor role during starch degradation at night, but could become relevant for daily stomatal opening in guard cells or in the re-allocation of fixed carbon in mesophyll cells in response to stress conditions.
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Affiliation(s)
- Diana Santelia
- Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, CH-8008 Zurich, Switzerland
| | - Paolo Trost
- Department of Pharmacy and Biotechnology FaBiT, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy
| | - Francesca Sparla
- Department of Pharmacy and Biotechnology FaBiT, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy.
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Structural and Mechanistic Insights into the Pseudomonas fluorescens 2-Nitrobenzoate 2-Nitroreductase NbaA. Appl Environ Microbiol 2015; 81:5266-77. [PMID: 26025888 DOI: 10.1128/aem.01289-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 05/20/2015] [Indexed: 01/23/2023] Open
Abstract
The bacterial 2-nitroreductase NbaA is the primary enzyme initiating the degradation of 2-nitrobenzoate (2-NBA), and its activity is controlled by posttranslational modifications. To date, the structure of NbaA remains to be elucidated. In this study, the crystal structure of a Cys194Ala NbaA mutant was determined to a 1.7-Å resolution. The substrate analog 2-NBA methyl ester was used to decipher the substrate binding site by inhibition of the wild-type NbaA protein. Tandem mass spectrometry showed that 2-NBA methyl ester produced a 2-NBA ester bond at the Tyr193 residue in the wild-type NbaA but not residues in the Tyr193Phe mutant. Moreover, covalent binding of the 2-NBA methyl ester to Tyr193 reduced the reactivity of the Cys194 residue on the peptide link. The Tyr193 hydroxyl group was shown to be essential for enzyme catalysis, as a Tyr193Phe mutant resulted in fast dissociation of flavin mononucleotide (FMN) from the protein with the reduced reactivity of Cys194. FMN binding to NbaA varied with solution NaCl concentration, which was related to the catalytic activity but not to cysteine reactivity. These observations suggest that the Cys194 reactivity is negatively affected by a posttranslational modification of the adjacent Tyr193 residue, which interacts with FMN and the substrate in the NbaA catalytic site.
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Sevilla F, Camejo D, Ortiz-Espín A, Calderón A, Lázaro JJ, Jiménez A. The thioredoxin/peroxiredoxin/sulfiredoxin system: current overview on its redox function in plants and regulation by reactive oxygen and nitrogen species. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2945-55. [PMID: 25873657 DOI: 10.1093/jxb/erv146] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In plants, the presence of thioredoxin (Trx), peroxiredoxin (Prx), and sulfiredoxin (Srx) has been reported as a component of a redox system involved in the control of dithiol-disulfide exchanges of target proteins, which modulate redox signalling during development and stress adaptation. Plant thiols, and specifically redox state and regulation of thiol groups of cysteinyl residues in proteins and transcription factors, are emerging as key components in the plant response to almost all stress conditions. They function in both redox sensing and signal transduction pathways. Scarce information exists on the transcriptional regulation of genes encoding Trx/Prx and on the transcriptional and post-transcriptional control exercised by these proteins on their putative targets. As another point of control, post-translational regulation of the proteins, such as S-nitrosylation and S-oxidation, is of increasing interest for its effect on protein structure and function. Special attention is given to the involvement of the Trx/Prx/Srx system and its redox state in plant signalling under stress, more specifically under abiotic stress conditions, as an important cue that influences plant yield and growth. This review focuses on the regulation of Trx and Prx through cysteine S-oxidation and/or S-nitrosylation, which affects their functionality. Some examples of redox regulation of transcription factors and Trx- and Prx-related genes are also presented.
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Affiliation(s)
- F Sevilla
- Department of Stress Biology and Plant Pathology, CEBAS-CSIC, Campus Universitario de Espinardo, 30100 Murcia, Spain
| | - D Camejo
- Department of Stress Biology and Plant Pathology, CEBAS-CSIC, Campus Universitario de Espinardo, 30100 Murcia, Spain
| | - A Ortiz-Espín
- Department of Stress Biology and Plant Pathology, CEBAS-CSIC, Campus Universitario de Espinardo, 30100 Murcia, Spain
| | - A Calderón
- Department of Stress Biology and Plant Pathology, CEBAS-CSIC, Campus Universitario de Espinardo, 30100 Murcia, Spain
| | - J J Lázaro
- Department of Biochemistry, Cellular and Molecular Biology of Plants, EEZ, CSIC, 18007 Granada, Spain
| | - A Jiménez
- Department of Stress Biology and Plant Pathology, CEBAS-CSIC, Campus Universitario de Espinardo, 30100 Murcia, Spain
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Groh KJ, Suter MJF. Stressor-induced proteome alterations in zebrafish: a meta-analysis of response patterns. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2015; 159:1-12. [PMID: 25498419 DOI: 10.1016/j.aquatox.2014.11.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Revised: 11/05/2014] [Accepted: 11/18/2014] [Indexed: 06/04/2023]
Abstract
Proteomics approaches are being increasingly applied in ecotoxicology on the premise that the identification of specific protein expression changes in response to a particular chemical would allow elucidation of the underlying molecular pathways leading to an adverse effect. This in turn is expected to promote the development of focused testing strategies for specific groups of toxicants. Although both gel-based and gel-free global characterization techniques provide limited proteome coverage, the conclusions regarding the cellular processes affected are still being drawn based on the few changes detected. To investigate how specific the detected responses are, we analyzed a set of studies that characterized proteome alterations induced by various physiological, chemical and biological stressors in zebrafish, a popular model organism. Our analysis highlights several proteins and protein groups, including heat shock and oxidative stress defense proteins, energy metabolism enzymes and cytoskeletal proteins, to be most frequently identified as responding to diverse stressors. In contrast, other potentially more specifically responding protein groups are detected much less frequently. Thus, zebrafish proteome responses to stress reported by different studies appear to depend mostly on the level of stress rather than on the specific stressor itself. This suggests that the most broadly used current proteomics technologies do not provide sufficient proteome coverage to allow in-depth investigation of specific mechanisms of toxicant action. We suggest that the results of any differential proteomics experiment performed with zebrafish should be interpreted keeping in mind the list of the most frequent responders that we have identified. Similar reservations should apply to any other species where proteome responses are analyzed by global proteomics methods. Careful consideration of the reliability and significance of observed changes is necessary in order not to over-interpret the experimental results and to prevent the proliferation of false positive linkages between the chemical and the cellular functions it perturbs. We further discuss the implications of the identified "top lists" of frequently responding proteins and protein families, and suggest further directions for proteomics research in ecotoxicology. Apart from improving the proteome coverage, further research should focus on defining the significance of the observed stress response patterns for organism phenotypes and on searching for common upstream regulators that can be targeted by specific assays.
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Affiliation(s)
- Ksenia J Groh
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland; ETH Zürich, Swiss Federal Institute of Technology, Department of Chemistry and Applied Biosciences, 8093 Zürich, Switzerland.
| | - Marc J-F Suter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland; ETH Zürich, Swiss Federal Institute of Technology, Department of Environmental Systems Science, 8092 Zürich, Switzerland
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van der Wijst MGP, Venkiteswaran M, Chen H, Xu GL, Plösch T, Rots MG. Local chromatin microenvironment determines DNMT activity: from DNA methyltransferase to DNA demethylase or DNA dehydroxymethylase. Epigenetics 2015; 10:671-6. [PMID: 26098813 PMCID: PMC4622917 DOI: 10.1080/15592294.2015.1062204] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 06/03/2015] [Accepted: 06/09/2015] [Indexed: 12/22/2022] Open
Abstract
Insights on active DNA demethylation disproved the original assumption that DNA methylation is a stable epigenetic modification. Interestingly, mammalian DNA methyltransferases 3A and 3B (DNMT-3A and -3B) have also been reported to induce active DNA demethylation, in addition to their well-known function in catalyzing methylation. In situations of extremely low levels of S-adenosyl methionine (SAM), DNMT-3A and -3B might demethylate C-5 methyl cytosine (5mC) via deamination to thymine, which is subsequently replaced by an unmodified cytosine through the base excision repair (BER) pathway. Alternatively, 5mC when converted to 5- hydroxymethylcytosine (5hmC) by TET enzymes, might be further modified to an unmodified cytosine by DNMT-3A and -3B under oxidized redox conditions, although exact pathways are yet to be elucidated. Interestingly, even direct conversion of 5mC to cytosine might be catalyzed by DNMTs. Here, we summarize the evidence on the DNA dehydroxymethylase and demethylase activity of DNMT-3A and -3B. Although physiological relevance needs to be demonstrated, the current indications on the 5mC- and 5hmC-modifying activities of de novo DNA C-5 methyltransferases shed a new light on these enzymes. Despite the extreme circumstances required for such unexpected reactions to occur, we here put forward that the chromatin microenvironment can be locally exposed to extreme conditions, and hypothesize that such waves of extremes allow enzymes to act in differential ways.
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Key Words
- 5caC, 5-carboxylcytosine
- 5fC, 5-formylcytosine
- 5hmC, 5 hydroxymethylcytosine
- 5mC, 5-methylcytosine
- AID, activation-induced cytidine deaminase
- APOBEC, apolipoprotein B mRNA editing enzyme catalytic polypeptide-like
- BER, base excision and repair
- C, cytosine
- CGI, CpG islands
- DNA dehydroxymethylation
- DNA demethylation
- DNMT, DNA methyltransferase
- DNMTs
- GADD45, growth arrest and DNA-damage-inducible protein 45
- RARE, retinoic acid response element
- S-adenosyl methionine (SAM)
- SAM, S-adenosyl methionine
- TDG, thymine DNA glycosylase
- TET, ten-eleven translocation.
- chromatin microenvironment
- oxidizing redox state
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Affiliation(s)
- Monique G P van der Wijst
- Epigenetic Editing; Department of Pathology and Medical Biology; University Medical Center Groningen; University of Groningen; Groningen, The Netherlands
| | - Muralidhar Venkiteswaran
- Epigenetic Editing; Department of Pathology and Medical Biology; University Medical Center Groningen; University of Groningen; Groningen, The Netherlands
| | - Hui Chen
- Epigenetic Editing; Department of Pathology and Medical Biology; University Medical Center Groningen; University of Groningen; Groningen, The Netherlands
- Group of DNA Metabolism; The State Key Laboratory of Molecular Biology; Institute of Biochemistry and Cell Biology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai, China
| | - Guo-Liang Xu
- Group of DNA Metabolism; The State Key Laboratory of Molecular Biology; Institute of Biochemistry and Cell Biology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai, China
| | - Torsten Plösch
- Department of Obstetrics and Gynecology; University Medical Center Groningen; University of Groningen; Groningen, The Netherlands
| | - Marianne G Rots
- Epigenetic Editing; Department of Pathology and Medical Biology; University Medical Center Groningen; University of Groningen; Groningen, The Netherlands
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Bak DW, Weerapana E. Cysteine-mediated redox signalling in the mitochondria. MOLECULAR BIOSYSTEMS 2015; 11:678-97. [DOI: 10.1039/c4mb00571f] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review represents a novel look at the many sources, cysteine targets, and signaling processes of ROS in the mitochondria.
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Affiliation(s)
- D. W. Bak
- Department of Chemistry
- Merkert Chemistry Center
- Boston College
- Massachusetts 02467
- USA
| | - E. Weerapana
- Department of Chemistry
- Merkert Chemistry Center
- Boston College
- Massachusetts 02467
- USA
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Lukesh JC, Andersen KA, Wallin KK, Raines RT. Organocatalysts of oxidative protein folding inspired by protein disulfide isomerase. Org Biomol Chem 2014; 12:8598-602. [PMID: 25266373 PMCID: PMC4237591 DOI: 10.1039/c4ob01738b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Organocatalysts derived from diethylenetriamine effect the rapid isomerization of non-native protein disulfide bonds to native ones. These catalysts contain a pendant hydrophobic moiety to encourage interaction with the non-native state, and two thiol groups with low pKa values that form a disulfide bond with a high E°' value.
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Affiliation(s)
- John C Lukesh
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
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Balsera M, Uberegui E, Schürmann P, Buchanan BB. Evolutionary development of redox regulation in chloroplasts. Antioxid Redox Signal 2014; 21:1327-55. [PMID: 24483204 DOI: 10.1089/ars.2013.5817] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
SIGNIFICANCE The post-translational modification of thiol groups stands out as a key strategy that cells employ for metabolic regulation and adaptation to changing environmental conditions. Nowhere is this more evident than in chloroplasts-the O2-evolving photosynthetic organelles of plant cells that are fitted with multiple redox systems, including the thioredoxin (Trx) family of oxidoreductases functional in the reversible modification of regulatory thiols of proteins in all types of cells. The best understood member of this family in chloroplasts is the ferredoxin-linked thioredoxin system (FTS) by which proteins are modified via light-dependent disulfide/dithiol (S-S/2SH) transitions. RECENT ADVANCES Discovered in the reductive activation of enzymes of the Calvin-Benson cycle in illuminated chloroplast preparations, recent studies have extended the role of the FTS far beyond its original boundaries to include a spectrum of cellular processes. Together with the NADP-linked thioredoxin reductase C-type (NTRC) and glutathione/glutaredoxin systems, the FTS also plays a central role in the response of chloroplasts to different types of stress. CRITICAL ISSUES The comparisons of redox regulatory networks functional in chloroplasts of land plants with those of cyanobacteria-prokaryotes considered to be the ancestors of chloroplasts-and different types of algae summarized in this review have provided new insight into the evolutionary development of redox regulation, starting with the simplest O2-evolving organisms. FUTURE DIRECTIONS The evolutionary appearance, mode of action, and specificity of the redox regulatory systems functional in chloroplasts, as well as the types of redox modification operating under diverse environmental conditions stand out as areas for future study.
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Affiliation(s)
- Monica Balsera
- 1 Instituto de Recursos Naturales y Agrobiología de Salamanca , Consejo Superior de Investigaciones Científicas, Salamanca, Spain
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Dietz KJ. Redox regulation of transcription factors in plant stress acclimation and development. Antioxid Redox Signal 2014; 21:1356-72. [PMID: 24182193 DOI: 10.1089/ars.2013.5672] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
SIGNIFICANCE The redox regulatory signaling network of the plant cell controls and co-regulates transcriptional activities, thereby enabling adjustment of metabolism and development in response to environmental cues, including abiotic stress. RECENT ADVANCES Our rapidly expanding knowledge on redox regulation of plant transcription is driven by methodological advancements such as sensitive redox proteomics and in silico predictions in combination with classical targeted genetic and molecular approaches, often in Arabidopsis thaliana. Thus, transcription factors (TFs) are both direct and indirect targets of redox-dependent activity modulation. Redox control of TF activity involves conformational switching, nucleo-cytosolic partitioning, assembly with coregulators, metal-S-cluster regulation, redox control of upstream signaling elements, and proteolysis. CRITICAL ISSUES While the significance of redox regulation of transcription is well established for prokaryotes and non-plant eukaryotes, the momentousness of redox-dependent control of transcription in plants still receives insufficient awareness and, therefore, is discussed in detail in this review. FUTURE DIRECTIONS Improved proteome sensitivity will enable characterization of low abundant proteins and to simultaneously address the various post-translational modifications such as nitrosylation, hydroxylation, and glutathionylation. Combining such approaches by gradually increasing biotic and abiotic stress strength is expected to result in a systematic understanding of redox regulation. In the end, only the combination of in vivo, ex vivo, and in vitro results will provide conclusive pictures on the rather complex mechanism of redox regulation of transcription.
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Affiliation(s)
- Karl-Josef Dietz
- Biochemistry and Physiology of Plants, Faculty of Biology, Bielefeld University , Bielefeld, Germany
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Morisse S, Zaffagnini M, Gao XH, Lemaire SD, Marchand CH. Insight into protein S-nitrosylation in Chlamydomonas reinhardtii. Antioxid Redox Signal 2014; 21:1271-84. [PMID: 24328795 PMCID: PMC4158989 DOI: 10.1089/ars.2013.5632] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
AIMS Protein S-nitrosylation, a post-translational modification (PTM) consisting of the covalent binding of nitric oxide (NO) to a cysteine thiol moiety, plays a major role in cell signaling and is recognized to be involved in numerous physiological processes and diseases in mammals. The importance of nitrosylation in photosynthetic eukaryotes has been less studied. The aim of this study was to expand our knowledge on protein nitrosylation by performing a large-scale proteomic analysis of proteins undergoing nitrosylation in vivo in Chlamydomonas reinhardtii cells under nitrosative stress. RESULTS Using two complementary proteomic approaches, 492 nitrosylated proteins were identified. They participate in a wide range of biological processes and pathways, including photosynthesis, carbohydrate metabolism, amino acid metabolism, translation, protein folding or degradation, cell motility, and stress. Several proteins were confirmed in vitro by western blot, site-directed mutagenesis and activity measurements. Moreover, 392 sites of nitrosylation were also identified. These results strongly suggest that S-nitrosylation could constitute a major mechanism of regulation in C. reinhardtii under nitrosative stress conditions. INNOVATION This study constitutes the largest proteomic analysis of protein nitrosylation reported to date. CONCLUSION The identification of 381 previously unrecognized targets of nitrosylation further extends our knowledge on the importance of this PTM in photosynthetic eukaryotes. The data have been deposited to the ProteomeXchange repository with identifier PXD000569.
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Affiliation(s)
- Samuel Morisse
- 1 Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, FRE3354 Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Université Pierre et Marie Curie , Paris, France
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