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Guo Y, Wu W, Yang X. Coordinated microRNA/mRNA Expression Profiles Reveal Unique Skin Color Regulatory Mechanisms in Chinese Giant Salamander (Andrias davidianus). Animals (Basel) 2023; 13:ani13071181. [PMID: 37048437 PMCID: PMC10093658 DOI: 10.3390/ani13071181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/18/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
The Chinese giant salamander (Andrias davidianus) has been increasingly popular in the aquaculture market in China in recent years. In the breeding process of Andrias davidianus, we found that some albino individuals were extremely rare and could not be inherited stably, which severely limits their commercialization in the aquaculture market. In this study, we performed transcriptome and small RNA (sRNA) sequencing analyses in the skin samples of wild-type (WT) and albino (AL) Andrias davidianus. In total, among 5517 differentially expressed genes (DEGs), 2911 DEGs were down-regulated in AL, including almost all the key genes involved in melanin formation. A total of 25 miRNAs were differentially expressed in AL compared to WT, of which 17 were up-regulated. Through the integrated analysis, no intersection was found between the target genes of the differentially expressed miRNAs and the key genes for melanin formation. Gene Ontology (GO) and KEGG pathway analyses on DEGs showed that these genes involved multiple processes relevant to melanin synthesis and the key signal pathway MAPK. Interestingly, the transcription factors SOX10 and PAX3 and the Wnt signaling pathway that play a key role in other species were not included, while the other two transcription factors in the SOX family, SOX21 and SOX7, were included. After analyzing the key genes for melanin formation, it was interesting to note an alternative splicing form of the MITF in WT and a critical mutation of the SLC24A5 gene in AL, which might be the main reason for the skin color change of Andrias davidianus. The results contributed to understanding the molecular mechanism of skin pigmentation in Andrias davidianus and accelerating the acquisition process of individuals with specific body colors by genetic means.
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Guillaubez JV, Pitrat D, Bretonnière Y, Lemoine J, Girod M. Relative quantification of sulfenic acids in plasma proteins using differential labelling and mass spectrometry coupled with 473 nm photo-dissociation analysis: A multiplexed approach applied to an Alzheimer's disease cohort. Talanta 2022; 250:123745. [PMID: 35870285 DOI: 10.1016/j.talanta.2022.123745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/11/2022] [Accepted: 07/15/2022] [Indexed: 10/17/2022]
Abstract
Cysteine (Cys) is subject to a variety of reversible post-translational modifications such as formation of sulfenic acid (Cys-SOH). If this modification is often involved in normal biological activities, it can also be the result of oxidative damage. Indeed, oxidative stress yields abnormal cysteine oxidations that affect protein function and structure and can lead to neurodegenerative diseases. In a context of population ageing, validation of novel biomarkers for detection of neurodegenerative diseases is important. However, Cys-SOH proteins investigation in large human cohorts is challenging due to their low abundance and lability under endogenous conditions. To improve the detection specificity towards the oxidized protein subpopulation, we developed a method that makes use of a mass spectrometer coupled with visible laser induced dissociation (LID) to add a stringent optical specificity to the mass selectivity. Since peptides do not naturally absorb in the visible range, this approach relies on the proper chemical derivatization of Cys-SOH with a chromophore functionalized with a cyclohexanedione. To compensate for the significant variability in total protein expression within the samples and any experimental bias, a normalizing strategy using free thiol (Cys-SH) cysteine peptides derivatized with a maleimide chromophore as internal references was used. Thanks to the differential tagging, oxidative ratios were then obtained for 69 Cys-containing peptides from 19 proteins tracked by parallel reaction monitoring (PRM) LID, in a cohort of 49 human plasma samples from Alzheimer disease (AD) patients. A statistical analysis indicated that, for the proteins monitored, the Cys oxidative ratio does not correlate with the diagnosis of AD. Nevertheless, the PRM-LID method allows the unbiased, sensitive and robust relative quantification of Cys oxidation within cohorts of samples.
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Affiliation(s)
- Jean-Valery Guillaubez
- Institut des Sciences Analytiques, UMR, 5280, Université Lyon 1, CNRS, Villeurbanne, France
| | - Delphine Pitrat
- Laboratoire de Chimie ENS Lyon, UMR, 5582, ENS Lyon CNRS et Université Lyon 1, France
| | - Yann Bretonnière
- Laboratoire de Chimie ENS Lyon, UMR, 5582, ENS Lyon CNRS et Université Lyon 1, France
| | - Jérôme Lemoine
- Institut des Sciences Analytiques, UMR, 5280, Université Lyon 1, CNRS, Villeurbanne, France
| | - Marion Girod
- Institut des Sciences Analytiques, UMR, 5280, Université Lyon 1, CNRS, Villeurbanne, France.
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Dai X, Shen L. Advances and Trends in Omics Technology Development. Front Med (Lausanne) 2022; 9:911861. [PMID: 35860739 PMCID: PMC9289742 DOI: 10.3389/fmed.2022.911861] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/09/2022] [Indexed: 12/11/2022] Open
Abstract
The human history has witnessed the rapid development of technologies such as high-throughput sequencing and mass spectrometry that led to the concept of “omics” and methodological advancement in systematically interrogating a cellular system. Yet, the ever-growing types of molecules and regulatory mechanisms being discovered have been persistently transforming our understandings on the cellular machinery. This renders cell omics seemingly, like the universe, expand with no limit and our goal toward the complete harness of the cellular system merely impossible. Therefore, it is imperative to review what has been done and is being done to predict what can be done toward the translation of omics information to disease control with minimal cell perturbation. With a focus on the “four big omics,” i.e., genomics, transcriptomics, proteomics, metabolomics, we delineate hierarchies of these omics together with their epiomics and interactomics, and review technologies developed for interrogation. We predict, among others, redoxomics as an emerging omics layer that views cell decision toward the physiological or pathological state as a fine-tuned redox balance.
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Iannetta AA, Hicks LM. Maximizing Depth of PTM Coverage: Generating Robust MS Datasets for Computational Prediction Modeling. Methods Mol Biol 2022; 2499:1-41. [PMID: 35696073 DOI: 10.1007/978-1-0716-2317-6_1] [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] [Indexed: 06/15/2023]
Abstract
Post-translational modifications (PTMs) regulate complex biological processes through the modulation of protein activity, stability, and localization. Insights into the specific modification type and localization within a protein sequence can help ascertain functional significance. Computational models are increasingly demonstrated to offer a low-cost, high-throughput method for comprehensive PTM predictions. Algorithms are optimized using existing experimental PTM data, thus accurate prediction performance relies on the creation of robust datasets. Herein, advancements in mass spectrometry-based proteomics technologies to maximize PTM coverage are reviewed. Further, requisite experimental validation approaches for PTM predictions are explored to ensure that follow-up mechanistic studies are focused on accurate modification sites.
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Affiliation(s)
- Anthony A Iannetta
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Lara-Rojas F, Sarmiento-López LG, Pascual-Morales E, Ryken SE, Bezanilla M, Cardenas L. Using DCP-Rho1 as a fluorescent probe to visualize sulfenic acid-containing proteins in living plant cells. Methods Enzymol 2022; 683:291-308. [PMID: 37087193 DOI: 10.1016/bs.mie.2022.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Among the biologically relevant reactive oxygen species (ROS), hydrogen peroxide (H2O2) has special properties. H2O2 can diffuse across membranes, has a low reactivity, and is very stable. Deprotonated cysteine residues in proteins can be oxidized by H2O2 into a highly reactive sulfenic acid derivative (-SOH), which can react with another cysteine to form a disulfide. Under higher oxidative stress the sulfenic acid undergo further oxidation to sulfinic acid (Cys-SO2H), which can subsequently be reduced. The sulfinic acid can be hyperoxidized to sulfonic acid (Cys-SO3H), whose reduction is irreversible. Formation of sulfenic acids can have a role in sensing oxidative stress, signal transduction, modulating localization and activity to regulate protein functions. Therefore, there is an emerging interest in trying to understand the pool of proteins that result in these sorts of modification in response to oxidative stress. This is known as the sulfenome and several approaches have been developed in animal and plant cells to analyze the sulfenome under different stress responses. These approaches can be proteomic, molecular, immunological (i.e., antibodies), or expressing genetically encoded probes that specifically react to sulfenic modifications. In this chapter, we describe an additional approach that allows visualization of sulfenic modification in vivo. This is newly developed fluorescent probe DCP-Rho1 can be implemented in any plant cell to analyze the sulfenic modification.
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Affiliation(s)
- Fernando Lara-Rojas
- Centro de Desarrollo de Productos Bióticos, Instituto Politécnico Nacional, Yautepec, Morelos, México
| | | | - Edgar Pascual-Morales
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Samantha E Ryken
- Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
| | - Magdalena Bezanilla
- Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
| | - Luis Cardenas
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
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Khan ZU, Pi D. DeepSSPred: A Deep Learning Based Sulfenylation Site Predictor Via a Novel nSegmented Optimize Federated Feature Encoder. Protein Pept Lett 2021; 28:708-721. [PMID: 33267753 DOI: 10.2174/0929866527666201202103411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 10/14/2020] [Accepted: 10/18/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND S-sulfenylation (S-sulphenylation, or sulfenic acid) proteins, are special kinds of post-translation modification, which plays an important role in various physiological and pathological processes such as cytokine signaling, transcriptional regulation, and apoptosis. Despite these aforementioned significances, and by complementing existing wet methods, several computational models have been developed for sulfenylation cysteine sites prediction. However, the performance of these models was not satisfactory due to inefficient feature schemes, severe imbalance issues, and lack of an intelligent learning engine. OBJECTIVE In this study, our motivation is to establish a strong and novel computational predictor for discrimination of sulfenylation and non-sulfenylation sites. METHODS In this study, we report an innovative bioinformatics feature encoding tool, named DeepSSPred, in which, resulting encoded features is obtained via nSegmented hybrid feature, and then the resampling technique called synthetic minority oversampling was employed to cope with the severe imbalance issue between SC-sites (minority class) and non-SC sites (majority class). State of the art 2D-Convolutional Neural Network was employed over rigorous 10-fold jackknife cross-validation technique for model validation and authentication. RESULTS Following the proposed framework, with a strong discrete presentation of feature space, machine learning engine, and unbiased presentation of the underline training data yielded into an excellent model that outperforms with all existing established studies. The proposed approach is 6% higher in terms of MCC from the first best. On an independent dataset, the existing first best study failed to provide sufficient details. The model obtained an increase of 7.5% in accuracy, 1.22% in Sn, 12.91% in Sp and 13.12% in MCC on the training data and12.13% of ACC, 27.25% in Sn, 2.25% in Sp, and 30.37% in MCC on an independent dataset in comparison with 2nd best method. These empirical analyses show the superlative performance of the proposed model over both training and Independent dataset in comparison with existing literature studies. CONCLUSION In this research, we have developed a novel sequence-based automated predictor for SC-sites, called DeepSSPred. The empirical simulations outcomes with a training dataset and independent validation dataset have revealed the efficacy of the proposed theoretical model. The good performance of DeepSSPred is due to several reasons, such as novel discriminative feature encoding schemes, SMOTE technique, and careful construction of the prediction model through the tuned 2D-CNN classifier. We believe that our research work will provide a potential insight into a further prediction of S-sulfenylation characteristics and functionalities. Thus, we hope that our developed predictor will significantly helpful for large scale discrimination of unknown SC-sites in particular and designing new pharmaceutical drugs in general.
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Affiliation(s)
- Zaheer Ullah Khan
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Dechang Pi
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, China
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Oshimo M, Nakashima F, Kai K, Matsui H, Shibata T, Akagawa M. Sodium sulfite causes gastric mucosal cell death by inducing oxidative stress. Free Radic Res 2021; 55:731-743. [PMID: 34074194 DOI: 10.1080/10715762.2021.1937620] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Sulfites are commonly used as a preservative and antioxidant additives in the food industry. Sulfites are absorbed by the gastrointestinal tract and distributed essentially to all body tissues. Although sulfites have been believed to be safe food additives, some studies have shown that they exhibit adverse effects in various tissues. In this study, we examined the cytotoxic effect of sodium sulfite (Na2SO3) against rat gastric mucosal cells (RGM1) and further investigated its underlying molecular mechanism. We demonstrated that exposure to Na2SO3 exerts significant cytotoxicity in RGM1 cells through induction of oxidative stress. Exposure of RGM1 cells to Na2SO3 caused a significant formation of protein carbonyls and 8-hydroxy-2'-deoxyguanosine, major oxidative stress markers, with a concomitant accumulation of carbonylated protein-related aggregates. Furthermore, we found that incubation of lysozyme with Na2SO3 evokes protein carbonylation and aggregation via the metal ion-catalyzed free radical formation derived from Na2SO3. Our results suggest that Na2SO3 might lead to gastric tissue injury via induction of oxidative stress by the formation of Na2SO3-related free radicals.
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Affiliation(s)
- Moeri Oshimo
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
| | - Fumie Nakashima
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kenji Kai
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
| | - Hirofumi Matsui
- Division of Gastroenterology, Graduate School for Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Takahiro Shibata
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Mitsugu Akagawa
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
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Guillaubez JV, Pitrat D, Bretonnière Y, Lemoine J, Girod M. Unbiased Detection of Cysteine Sulfenic Acid by 473 nm Photodissociation Mass Spectrometry: Toward Facile In Vivo Oxidative Status of Plasma Proteins. Anal Chem 2021; 93:2907-2915. [PMID: 33522244 DOI: 10.1021/acs.analchem.0c04484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cysteine (Cys) is prone to diverse post-translational modifications in proteins, including oxidation into sulfenic acid (Cys-SOH) by reactive oxygen species generated under oxidative stress. Detection of low-concentration and metastable Cys-SOH within complex biological matrices is challenging due to the dynamic concentration range of proteins in the samples. Herein, visible laser-induced dissociation (LID) implemented in a mass spectrometer was used for streamlining the detection of Cys oxidized proteins owing to proper derivatization of Cys-SOH with a chromophore tag functionalized with a cyclohexanedione group. Once grafted, peptides undergo a high fragmentation yield under LID, leading concomitantly to informative backbone ions and to a chromophore reporter ion. Seventy-nine percent of the Cys-containing tryptic peptides derived from human serum albumin and serotransferrin tracked by parallel reaction monitoring (PRM) were detected as targets subjected to oxidation. These candidates as well as Cys-containing peptides predicted by in silico trypsin digestion of five other human plasma proteins were then tracked in real plasma samples to pinpoint the endogenous Cys-SOH subpopulation. Most of the targeted peptides were detected in all plasma samples by LID-PRM, with significant differences in their relative amounts. By eliminating the signal of interfering co-eluted compounds, LID-PRM surpasses conventional HCD (higher-energy collisional dissociation)-PRM in detecting grafted Cys-SOH-containing peptides and allows now to foresee clinical applications in large human cohorts.
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Affiliation(s)
- Jean-Valery Guillaubez
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, Villeurbanne F-69100, France
| | - Delphine Pitrat
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Université Lyon I, Laboratoire de Chimie, F-69342 Lyon, France
| | - Yann Bretonnière
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Université Lyon I, Laboratoire de Chimie, F-69342 Lyon, France
| | - Jérôme Lemoine
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, Villeurbanne F-69100, France
| | - Marion Girod
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, Villeurbanne F-69100, France
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Mukherjee S. Cysteine modifications (oxPTM) and protein sulphenylation-mediated sulfenome expression in plants: evolutionary conserved signaling networks? PLANT SIGNALING & BEHAVIOR 2021; 16:1831792. [PMID: 33300450 PMCID: PMC7781837 DOI: 10.1080/15592324.2020.1831792] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Plant resilience to oxidative stress possibly operates through the restoration of intracellular redox milieu and the activity of various posttranslationally modified proteins. Among various modes of redox regulation operative in plants cys oxPTMs are brought about by the activity of reactive oxygen species (ROS), reactive nitrogen species (RNS), and hydrogen peroxide. Cysteine oxPTMs are capable of transducing ROS-mediated long-distance hormone signaling (ABA, JA, SA) in plants. S-sulphenylation is an intermediary modification en route to other oxidative states of cysteine. In silico analysis have revealed evolutionary conservation of certain S-sulphenylated proteins across human and plants. Further analysis of protein sulphenylation in plants should be extended to the functional follow-up studies followed by site-specific characterization and case-by-case validation of protein activity. The repertoire of physiological methods (fluorescent conjugates (dimedone) and yeast AP-1 (YAP1)-based genetic probes) in the recent past has been successful in the detection of sulphenylated proteins and other cysteine-based modifications in plants. In view of a better understanding of the sulfur-based redoxome it is necessary to update our timely progress on the methodological advancements for the detection of cysteine-based oxPTM. This substantiative information can extend our investigations on plant-environment interaction thus improving crop manipulation strategies. The simulation-based computational approach has emerged as a new method to determine the directive mechanism of cysteine oxidation in plants. Thus, sulfenome analysis in various plant systems might reflect as a pinnacle of plant redox biology in the future.
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Affiliation(s)
- Soumya Mukherjee
- Department of Botany, Jangipur College, University of Kalyani, West, Bengal, India
- CONTACT Soumya Mukherjee Department of Botany, Jangipur College, University of Kalyani, West, Bengal742213, India
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Ossola R, Clerc B, McNeill K. Mechanistic Insights into Dissolved Organic Sulfur Photomineralization through the Study of Cysteine Sulfinic Acid. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:13066-13076. [PMID: 32936630 DOI: 10.1021/acs.est.0c04340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Photochemical reactions convert dissolved organic matter (DOM) into inorganic and low-molecular-weight organic products, contributing to its cycling across environmental compartments. However, knowledge on the formation mechanisms of these products is still scarce. In this work, we investigate the triplet-sensitized photodegradation of cysteine sulfinic acid, a (photo)degradation product of cysteine, to sulfate (SO42-). We use kinetic analysis, targeted experiments, and previous literature from several fields of chemistry to explain the elementary steps that lead to the release of sulfate. Our analysis indicates that triplet sensitizers act as one-electron oxidants on the sulfinate S lone pair. The resulting radical undergoes C-S fragmentation to form SO2, which becomes hydrated to sulfite/bisulfite (S(IV)). S(IV) is further oxidized to SO42- in the presence of triplet sensitizers and oxygen. We point out that the reaction sequence SO2 ⇌ S(IV) → SO42- is valid independently of the chemical structure of the model compound and might represent a sulfate photoproduction mechanism with general validity for DOS. Our mechanistic investigation revealed that amino acids in general might also be photochemical precursors of CO2, ammonia, acetaldehyde, and H2O2 and that reaction byproducts can influence the rate and mechanism of S(IV) (photo)oxidation.
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Affiliation(s)
- Rachele Ossola
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), Department of Environmental Systems Science, ETH Zurich, 8092 Zurich, Switzerland
| | - Baptiste Clerc
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), Department of Environmental Systems Science, ETH Zurich, 8092 Zurich, Switzerland
| | - Kristopher McNeill
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), Department of Environmental Systems Science, ETH Zurich, 8092 Zurich, Switzerland
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Si Z, Guan N, Zhou Y, Mei L, Li Y, Li Y. A Methionine Sulfoxide Reductase B Is Required for the Establishment of Astragalus sinicus-Mesorhizobium Symbiosis. PLANT & CELL PHYSIOLOGY 2020; 61:1631-1645. [PMID: 32618998 DOI: 10.1093/pcp/pcaa085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 06/16/2020] [Indexed: 06/11/2023]
Abstract
Methionine sulfoxide reductase B (MsrB) is involved in oxidative stress or defense responses in plants. However, little is known about its role in legume-rhizobium symbiosis. In this study, an MsrB gene was identified from Astragalus sinicus and its function in symbiosis was characterized. AsMsrB was induced under phosphorus starvation and displayed different expression patterns under symbiotic and nonsymbiotic conditions. Hydrogen peroxide or methyl viologen treatment enhanced the transcript level of AsMsrB in roots and nodules. Subcellular localization showed that AsMsrB was localized in the cytoplasm of onion epidermal cells and co-localized with rhizobia in nodules. Plants with AsMsrB-RNAi hairy roots exhibited significant decreases in nodule number, nodule nitrogenase activity and fresh weight of the aerial part, as well as an abnormal nodule and symbiosome development. Statistical analysis of infection events showed that plants with AsMsrB-RNAi hairy roots had significant decreases in the number of root hair curling events, infection threads and nodule primordia compared with the control. The content of hydrogen peroxide increased in AsMsrB-RNAi roots but decreased in AsMsrB overexpression roots at the early stage of infection. The transcriptome analysis showed synergistic modulations of the expression of genes involved in reactive oxygen species generation and scavenging, defense and pathogenesis and early nodulation. In addition, a candidate protein interacting with AsMsrB was identified and confirmed by bimolecular fluorescence complementation. Taken together, our results indicate that AsMsrB plays an essential role in nodule development and symbiotic nitrogen fixation by affecting the redox homeostasis in roots and nodules.
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Affiliation(s)
- Zaiyong Si
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ning Guan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuan Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lingli Mei
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yixing Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Youguo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
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Relative content detection of oligomannose modification of IgM heavy chain induced by TNP-antigen in an early vertebrate through nanoLC-MS/MS. Talanta 2020; 219:121346. [PMID: 32887075 DOI: 10.1016/j.talanta.2020.121346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/20/2020] [Accepted: 06/24/2020] [Indexed: 01/23/2023]
Abstract
N-glycan modification is reported to be important in regulating the structure and function of immunoglobulins in mammals. While, the study on teleost immunoglobulin glycosylation is still limitted. In this study, we constructed a TNP-antigen driven model, and detected the site-specific N-glycans of PBS-immunized and TNP-specific Oreochromis niloticus serum IgM through 18O-labeling and nanoLC-MS/MS. These methods are widely used for peptide enrichment and protein modification identification, but rarely used in detecting the level of N-glycosylation in teleost Igs that driven by specific antigen. The results revealed that there are four N-glycosylation sites in O.niloticus IgM heavy chain, namely, the Asn-315 site in the CH2 domain, the Asn-338 site in the CH3 domain, and the Asn-509 and Asn-551 sites in the CH4 domain, All of the four residues were efficiently N-glycosylated. After immunized with TNP-antigen, the signal strength of oligomannose in the TNP-specific IgM in primary mass spectrometry was significantly higher than that in the PBS-immunized IgM. Notably, the TNP-specific IgM had an Asn-509 site fully occupied with oligomannose, while only a small amount of oligomannose was found in the PBS-immunized IgM of this site. N-glycans in other sites were mainly complex-type with a low content of fucosylation and sialylated. The oligomannose in TNP-specific IgM was further verified to be essential for the binding of IgM and MBL. These results demonstrated that the TNP-antigen induced the site-specific oligomannose modification of O.niloticus IgM heavy chain, and played an important role in the interaction of IgM and MBL, which provided insights into the evolutionary understanding of the IgM oligomannose modification and function.
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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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Wang M, Cui X, Yu B, Chen C, Ma Q, Zhou H. SulSite-GTB: identification of protein S-sulfenylation sites by fusing multiple feature information and gradient tree boosting. Neural Comput Appl 2020. [DOI: 10.1007/s00521-020-04792-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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15
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Regulation of the Proteolytic Activity of Cysteine Cathepsins by Oxidants. Int J Mol Sci 2020; 21:ijms21061944. [PMID: 32178437 PMCID: PMC7139492 DOI: 10.3390/ijms21061944] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/10/2020] [Accepted: 03/10/2020] [Indexed: 12/21/2022] Open
Abstract
Besides their primary involvement in the recycling and degradation of proteins in endo-lysosomal compartments and also in specialized biological functions, cysteine cathepsins are pivotal proteolytic contributors of various deleterious diseases. While the molecular mechanisms of regulation via their natural inhibitors have been exhaustively studied, less is currently known about how their enzymatic activity is modulated during the redox imbalance associated with oxidative stress and their exposure resistance to oxidants. More specifically, there is only patchy information on the regulation of lung cysteine cathepsins, while the respiratory system is directly exposed to countless exogenous oxidants contained in dust, tobacco, combustion fumes, and industrial or domestic particles. Papain-like enzymes (clan CA, family C1, subfamily C1A) encompass a conserved catalytic thiolate-imidazolium pair (Cys25-His159) in their active site. Although the sulfhydryl group (with a low acidic pKa) is a potent nucleophile highly susceptible to chemical modifications, some cysteine cathepsins reveal an unanticipated resistance to oxidative stress. Besides an introductory chapter and peculiar attention to lung cysteine cathepsins, the purpose of this review is to afford a concise update of the current knowledge on molecular mechanisms associated with the regulation of cysteine cathepsins by redox balance and by oxidants (e.g., Michael acceptors, reactive oxygen, and nitrogen species).
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Investigation of Biogenic Passivating Layers on Corroded Iron. MATERIALS 2020; 13:ma13051176. [PMID: 32155722 PMCID: PMC7085031 DOI: 10.3390/ma13051176] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 02/28/2020] [Accepted: 03/03/2020] [Indexed: 11/16/2022]
Abstract
This study evaluates mechanisms of biogenic mineral formation induced by bacterial iron reduction for the stabilization of corroded iron. As an example, the Desulfitobacterium hafniense strain TCE1 was employed to treat corroded coupons presenting urban natural atmospheric corrosion, and spectroscopic investigations were performed on the samples’ cross-sections to evaluate the corrosion stratigraphy. The treated samples presented a protective continuous layer of iron phosphates (vivianite Fe2+3(PO4)2·8H2O and barbosalite Fe2+Fe3+2(PO4)2(OH)2), which covered 92% of the surface and was associated with a decrease in the thickness of the original corrosion layer. The results allow us to better understand the conversion of reactive corrosion products into stable biogenic minerals, as well as to identify important criteria for the design of a green alternative treatment for the stabilization of corroded iron.
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Zhang L, Kang J, Liu S, Zhang X, Sun J, Hu Y, Yang Y, Chen L. A chemical covalent tactic for bio-thiol sensing and protein labeling agent design. Chem Commun (Camb) 2020; 56:11485-11488. [DOI: 10.1039/d0cc04169f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A chemical covalent tactic was developed for bio-thiol sensing and protein labeling agent design by the installation of a sulfoxide scaffold onto the skeleton of various fluorophores.
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Affiliation(s)
- Liangwei Zhang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation
- Yantai Institute of Coastal Zone Research
- Chinese Academy of Sciences
- Yantai 264003
- China
| | - Jie Kang
- State Key Laboratory of Applied Organic Chemistry and College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
- China
| | - Shudi Liu
- College of Chemistry and Chemical Engineering
- Yantai University
- Yantai 264005
- China
| | - Xia Zhang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation
- Yantai Institute of Coastal Zone Research
- Chinese Academy of Sciences
- Yantai 264003
- China
| | - Jinyu Sun
- State Key Laboratory of Applied Organic Chemistry and College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
- China
| | - Yuesong Hu
- State Key Laboratory of Applied Organic Chemistry and College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
- China
| | - Yang Yang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation
- Yantai Institute of Coastal Zone Research
- Chinese Academy of Sciences
- Yantai 264003
- China
| | - Lingxin Chen
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation
- Yantai Institute of Coastal Zone Research
- Chinese Academy of Sciences
- Yantai 264003
- China
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18
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Wang X, Li C, Li F, Sharma VS, Song J, Webb GI. SIMLIN: a bioinformatics tool for prediction of S-sulphenylation in the human proteome based on multi-stage ensemble-learning models. BMC Bioinformatics 2019; 20:602. [PMID: 31752668 PMCID: PMC6868744 DOI: 10.1186/s12859-019-3178-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 10/28/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND S-sulphenylation is a ubiquitous protein post-translational modification (PTM) where an S-hydroxyl (-SOH) bond is formed via the reversible oxidation on the Sulfhydryl group of cysteine (C). Recent experimental studies have revealed that S-sulphenylation plays critical roles in many biological functions, such as protein regulation and cell signaling. State-of-the-art bioinformatic advances have facilitated high-throughput in silico screening of protein S-sulphenylation sites, thereby significantly reducing the time and labour costs traditionally required for the experimental investigation of S-sulphenylation. RESULTS In this study, we have proposed a novel hybrid computational framework, termed SIMLIN, for accurate prediction of protein S-sulphenylation sites using a multi-stage neural-network based ensemble-learning model integrating both protein sequence derived and protein structural features. Benchmarking experiments against the current state-of-the-art predictors for S-sulphenylation demonstrated that SIMLIN delivered competitive prediction performance. The empirical studies on the independent testing dataset demonstrated that SIMLIN achieved 88.0% prediction accuracy and an AUC score of 0.82, which outperforms currently existing methods. CONCLUSIONS In summary, SIMLIN predicts human S-sulphenylation sites with high accuracy thereby facilitating biological hypothesis generation and experimental validation. The web server, datasets, and online instructions are freely available at http://simlin.erc.monash.edu/ for academic purposes.
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Affiliation(s)
- Xiaochuan Wang
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800 Australia
- Division of Cancer Epidemiology, Cancer Council Victoria, Melbourne, VIC 3004 Australia
| | - Chen Li
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800 Australia
| | - Fuyi Li
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800 Australia
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800 Australia
| | - Varun S. Sharma
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Jiangning Song
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800 Australia
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800 Australia
- ARC Centre of Excellence for Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800 Australia
| | - Geoffrey I. Webb
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800 Australia
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Duport C, Alpha-Bazin B, Armengaud J. Advanced Proteomics as a Powerful Tool for Studying Toxins of Human Bacterial Pathogens. Toxins (Basel) 2019; 11:toxins11100576. [PMID: 31590258 PMCID: PMC6832400 DOI: 10.3390/toxins11100576] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 12/15/2022] Open
Abstract
Exotoxins contribute to the infectious processes of many bacterial pathogens, mainly by causing host tissue damages. The production of exotoxins varies according to the bacterial species. Recent advances in proteomics revealed that pathogenic bacteria are capable of simultaneously producing more than a dozen exotoxins. Interestingly, these toxins may be subject to post-transcriptional modifications in response to environmental conditions. In this review, we give an outline of different bacterial exotoxins and their mechanism of action. We also report how proteomics contributed to immense progress in the study of toxinogenic potential of pathogenic bacteria over the last two decades.
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Affiliation(s)
- Catherine Duport
- SQPOV, UMR0408, Avignon Université, INRA, F-84914 Avignon, France
- Correspondence:
| | - Béatrice Alpha-Bazin
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols sur Cèze, France; (B.A.-B.); (J.A.)
| | - Jean Armengaud
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols sur Cèze, France; (B.A.-B.); (J.A.)
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20
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Ofman G, Tipple TE. Antioxidants & bronchopulmonary dysplasia: Beating the system or beating a dead horse? Free Radic Biol Med 2019; 142:138-145. [PMID: 30769161 DOI: 10.1016/j.freeradbiomed.2019.01.038] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 01/13/2019] [Accepted: 01/28/2019] [Indexed: 12/21/2022]
Abstract
Preterm birth is a primary cause of worldwide childhood mortality. Bronchopulmonary dysplasia, characterized by impaired alveolar and lung vascular development, affects 25-50% of extremely low birth weight (BW; <1 kg) infants. Abnormalities in lung function persist into childhood in affected infants and are second only to asthma in terms of childhood respiratory disease healthcare costs. While advances in the medical care of preterm infants have reduced mortality, the incidence of BPD has not decreased in the past 10 years. Reactive oxygen intermediates play a key role in the development of lung disease but, despite promising preclinical therapies, antioxidants have failed to translate into meaningful clinical interventions to decrease the incidence of lung disease in premature infants. In this review we will summarize the state of the art research developments in regards to antioxidants and premature lung disease and discuss the limitations of antioxidant therapies in order to more fully comprehend the reasons why therapeutic antioxidant administration failed to prevent BPD. Finally we will review promising therapeutic strategies and targets.
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Affiliation(s)
- Gaston Ofman
- Division of Neonatology, Neonatal Redox Biology Laboratory, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Trent E Tipple
- Division of Neonatology, Neonatal Redox Biology Laboratory, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, USA
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21
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Alli-Oluwafuyi AM, Luis PB, Nakashima F, Giménez-Bastida JA, Presley SH, Duvernay MT, Iwalewa EO, Schneider C. Curcumin induces secretion of glucagon-like peptide-1 through an oxidation-dependent mechanism. Biochimie 2019; 165:250-257. [PMID: 31470039 DOI: 10.1016/j.biochi.2019.08.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 08/24/2019] [Indexed: 10/26/2022]
Abstract
Curcumin shows antiglycemic effects in animals. Curcumin is chemically unstable at physiological pH, and its oxidative degradation products were shown to contribute to its anti-inflammatory effects. Since the degradation products may also contribute to other effects, we analyzed their role in the antiglycemic activity of curcumin. We quantified curcumin-induced release of glucagon-like peptide 1 (GLP-1) from mouse STC-1 cells that represent enteroendocrine L-cells as a major source of this anti-diabetic hormone. Curcumin induced secretion of GLP-1 in a dose-dependent manner. Two chemically stable analogues of curcumin that do not readily undergo degradation, were less active while two unstable analogues were active secretagogues. Chromatographically isolated spiroepoxide, an unstable oxidative metabolite of curcumin with anti-inflammatory activity, also induced secretion of GLP-1. Stable compounds like the final oxidative metabolite bicyclopentadione, and the major plasma metabolite, curcumin-glucuronide, were inactive. GLP-1 secretion induced by curcumin and its oxidative degradation products was associated with activation of PKC, ERK, and CaM kinase II. Since activity largely correlated with instability of curcumin and the analogues, we tested the extent of covalent binding to proteins in STC-1 cells and found it occurred with similar affinity as N-ethylmaleimide, indicating covalent binding occurred with nucleophilic cysteine residues. These results suggest that oxidative metabolites of curcumin are involved in the antiglycemic effects of curcumin. Our findings support the hypothesis that curcumin functions as a pro-drug requiring oxidative activation to reveal its bioactive metabolites that act by binding to target proteins thereby causing a change in function.
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Affiliation(s)
- Abdul-Musawwir Alli-Oluwafuyi
- Department of Pharmacology and Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical School, Nashville, TN, 37232, USA; Department of Pharmacology and Therapeutics, Faculty of Basic Medical Sciences, University of Ilorin, Ilorin, Nigeria
| | - Paula B Luis
- Department of Pharmacology and Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical School, Nashville, TN, 37232, USA
| | - Fumie Nakashima
- Department of Pharmacology and Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical School, Nashville, TN, 37232, USA
| | - Juan A Giménez-Bastida
- Department of Pharmacology and Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical School, Nashville, TN, 37232, USA
| | - Sai Han Presley
- Department of Pharmacology and Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical School, Nashville, TN, 37232, USA
| | - Matthew T Duvernay
- Department of Pharmacology and Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical School, Nashville, TN, 37232, USA
| | - Ezekiel O Iwalewa
- Department of Pharmacology and Therapeutics, Faculty of Basic Medical Sciences, University of Ibadan, Ibadan, Nigeria
| | - Claus Schneider
- Department of Pharmacology and Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical School, Nashville, TN, 37232, USA.
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22
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Chakraborty P, Chatterjee S, Kesarwani P, Thyagarajan K, Iamsawat S, Dalheim A, Nguyen H, Selvam SP, Nasarre P, Scurti G, Hardiman G, Maulik N, Ball L, Gangaraju V, Rubinstein MP, Klauber-DeMore N, Hill EG, Ogretmen B, Yu XZ, Nishimura MI, Mehrotra S. Thioredoxin-1 improves the immunometabolic phenotype of antitumor T cells. J Biol Chem 2019; 294:9198-9212. [PMID: 30971427 DOI: 10.1074/jbc.ra118.006753] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 03/25/2019] [Indexed: 12/16/2022] Open
Abstract
Adoptive transfer of tumor epitope-reactive T cells has emerged as a promising strategy to control tumor growth. However, chronically-stimulated T cells expanded for adoptive cell transfer are susceptible to cell death in an oxidative tumor microenvironment. Because oxidation of cell-surface thiols also alters protein functionality, we hypothesized that increasing the levels of thioredoxin (Trx), an antioxidant molecule facilitating reduction of proteins through cysteine thiol-disulfide exchange, in T cells will promote their sustained antitumor function. Using pre-melanosome protein (Pmel)-Trx1 transgenic mouse-derived splenic T cells, flow cytometry, and gene expression analysis, we observed here that higher Trx expression inversely correlated with reactive oxygen species and susceptibility to T-cell receptor restimulation or oxidation-mediated cell death. These Trx1-overexpressing T cells exhibited a cluster of differentiation 62Lhi (CD62Lhi) central memory-like phenotype with reduced glucose uptake (2-NBDGlo) and decreased effector function (interferon γlo). Furthermore, culturing tumor-reactive T cells in the presence of recombinant Trx increased the dependence of T cells on mitochondrial metabolism and improved tumor control. We conclude that strategies for increasing the antioxidant capacity of antitumor T cells modulate their immunometabolic phenotype leading to improved immunotherapeutic control of established tumors.
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Affiliation(s)
| | | | | | | | | | - Annika Dalheim
- the Department of Surgery, Loyola University, Maywood, Illinois 60153, and
| | | | | | | | - Gina Scurti
- the Department of Surgery, Loyola University, Maywood, Illinois 60153, and
| | | | - Nilanjana Maulik
- the Department of Surgery, University of Connecticut Health Center, Farmington, Connecticut 06030
| | | | | | | | | | - Elizabeth G Hill
- Public Health, Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425
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Chatterjee S, Ghosh S, Mishra S, Das Saha K, Banerji B, Chattopadhyay K. Efficient Detection of Early Events of α-Synuclein Aggregation Using a Cysteine Specific Hybrid Scaffold. Biochemistry 2019; 58:1109-1119. [DOI: 10.1021/acs.biochem.8b01161] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Satadru Chatterjee
- Organic & Medicinal Chemistry Division, Indian Institute of Chemical Biology (CSIR-IICB), Kolkata 700032, India
| | - Sumanta Ghosh
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology (CSIR-IICB), 4 Raja S. C. Mullick Road, Kolkata 700032, India
| | - Snehasis Mishra
- Cancer Biology & Inflammatory Disorder Division, Indian Institute of Chemical Biology (CSIR-IICB), 4 Raja S. C. Mullick Road, Kolkata 700032, India
| | - Krishna Das Saha
- Cancer Biology & Inflammatory Disorder Division, Indian Institute of Chemical Biology (CSIR-IICB), 4 Raja S. C. Mullick Road, Kolkata 700032, India
| | - Biswadip Banerji
- Organic & Medicinal Chemistry Division, Indian Institute of Chemical Biology (CSIR-IICB), Kolkata 700032, India
- Academy of Scientific and Innovative Research (AcSIR), 4 Raja S. C. Mullick Road, Kolkata 700032, India
| | - Krishnananda Chattopadhyay
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology (CSIR-IICB), 4 Raja S. C. Mullick Road, Kolkata 700032, India
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24
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Löwe O, Rezende F, Heidler J, Wittig I, Helfinger V, Brandes RP, Schröder K. BIAM switch assay coupled to mass spectrometry identifies novel redox targets of NADPH oxidase 4. Redox Biol 2019; 21:101125. [PMID: 30716538 PMCID: PMC6360804 DOI: 10.1016/j.redox.2019.101125] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/21/2019] [Accepted: 01/25/2019] [Indexed: 01/21/2023] Open
Abstract
Aim NADPH oxidase (Nox) -derived reactive oxygen species have been implicated in redox signaling via cysteine oxidation in target proteins. Although the importance of oxidation of target proteins is well known, the specificity of such events is often debated. Only a limited number of Nox-oxidized proteins have been identified thus far; especially little is known concerning redox-targets of the constitutively active NADPH oxidase Nox4. In this study, HEK293 cells with tetracycline-inducible Nox4 overexpression (HEK-tet-Nox4), as well as podocytes of WT and Nox4-/- mice, were utilized to identify Nox4-dependent redox-modified proteins. Results TGFβ1 induced an elevation in Nox4 expression in podocytes from WT but not Nox4-/- mice. Using BIAM based redox switch assay in combination with mass spectrometry and western blot analysis, 142 proteins were identified as differentially oxidized in podocytes from wild type vs. Nox4-/- mice and 131 proteins were differentially oxidized in HEK-tet-Nox4 cells upon Nox4 overexpression. A predominant overlap was found for peroxiredoxins and thioredoxins, as expected. More interestingly, the GRB2-associated-binding protein 1 (Gab1) was identified as being differentially oxidized in both approaches. Further analysis using mass spectrometry-coupled BIAM switch assay and site directed mutagenesis, revealed Cys374 and Cys405 as the major Nox4 targeted oxidation sites in Gab1. Innovation & conclusion BIAM switch assay coupled to mass spectrometry is a powerful and versatile tool to identify differentially oxidized proteins in a global untargeted way. Nox4, as a source of hydrogen peroxide, changes the redox-state of numerous proteins. Of those, we identified Gab1 as a novel redox target of Nox4. BIAM switch assay coupled to MS is a powerful tool to identify oxidized proteins. Stable Nox4 overexpression oxidized Prx and Trx in presence of Auranofin only. Gab1 was identified as novel redox-target of Nox4. Cys374 and Cys405 were identified as the major oxidized cysteines in Gab1.
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Affiliation(s)
- Oliver Löwe
- Institute for Cardiovascular Physiology, Goethe-University, Frankfurt, Germany
| | - Flávia Rezende
- Institute for Cardiovascular Physiology, Goethe-University, Frankfurt, Germany
| | - Juliana Heidler
- Functional Proteomics, SFB 815 Core Unit, Goethe-University, Frankfurt, Germany
| | - Ilka Wittig
- Functional Proteomics, SFB 815 Core Unit, Goethe-University, Frankfurt, Germany
| | - Valeska Helfinger
- Institute for Cardiovascular Physiology, Goethe-University, Frankfurt, Germany
| | - Ralf P Brandes
- Institute for Cardiovascular Physiology, Goethe-University, Frankfurt, Germany
| | - Katrin Schröder
- Institute for Cardiovascular Physiology, Goethe-University, Frankfurt, Germany.
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25
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Measurement of the total angiotensinogen and its reduced and oxidised forms in human plasma using targeted LC-MS/MS. Anal Bioanal Chem 2019; 411:427-437. [PMID: 30465161 PMCID: PMC6336742 DOI: 10.1007/s00216-018-1455-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 10/17/2018] [Accepted: 10/25/2018] [Indexed: 11/28/2022]
Abstract
Angiotensinogen (AGT) is a critical protein in the renin-angiotensin-aldosterone system and may have an important role in the pathogenesis of pre-eclampsia. The disulphide linkage between cysteines 18 and 138 has a key role in the redox switch of AGT which modulates the release of angiotensin I with consequential effects on blood pressure. In this paper, we report a quantitative targeted LC-MS/MS method for the reliable measurement of the total AGT and its reduced and oxidised forms in human plasma. AGT was selectively enriched from human plasma using two-dimensional chromatography employing concanavalin A lectin affinity and reversed phase steps and then deglycosylated using PNGase F. A differential alkylation approach was coupled with targeted LC-MS/MS method to identify the two AGT forms in the plasma chymotryptic digest. An additional AGT proteolytic marker peptide was identified and used to measure total AGT levels. The developed MS workflow enabled the reproducible detection of total AGT and its two distinct forms in human plasma with analytical precision of ≤ 15%. The LC-MS/MS assay for total AGT in plasma showed a linear response (R2 = 0.992) with a limit of quantification in the low nanomolar range. The method gave suitable validation characteristics for biomedical application to the quantification of the oxidation level and the total level of AGT in plasma samples collected from normal and pre-eclamptic patients.
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26
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Scheuermann MJ, Forbes CR, Zondlo NJ. Redox-Responsive Protein Design: Design of a Small Protein Motif Dependent on Glutathionylation. Biochemistry 2018; 57:6956-6963. [PMID: 30511831 DOI: 10.1021/acs.biochem.8b00973] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cysteine S-glutathionylation is a protein post-translational modification that promotes cellular responses to changes in oxidative conditions. The design of protein motifs that directly depend on defined changes to protein side chains provides new methods for probing diverse protein post-translational modifications. A canonical, 12-residue EF-hand motif was redesigned to be responsive to cysteine glutathionylation. The key design principle was the replacement of the metal-binding Glu12 carboxylate of an EF-hand with a motif capable of metal binding via a free carboxylate in the glutathione-conjugated peptide. In the optimized peptide (DKDADGWCG), metal binding and terbium luminescence were dependent on glutathionylation, with weaker metal binding in the presence of reduced cysteine but increased metal affinity and a 3.5-fold increase in terbium luminescence at 544 nm when cysteine was glutathionylated. Nuclear magnetic resonance spectroscopy indicated that the structure at all residues of the glutathionylated peptide changed in the presence of metal, with chemical shift changes consistent with the adoption of an EF-hand-like structure in the metal-bound glutathionylated peptide. This small protein motif consists of canonical amino acids and is thus genetically encodable, for its potential use as a localized tag to probe protein glutathionylation.
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Affiliation(s)
- Michael J Scheuermann
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Christina R Forbes
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Neal J Zondlo
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
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27
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Fu L, Liu K, Ferreira RB, Carroll KS, Yang J. Proteome-Wide Analysis of Cysteine S-Sulfenylation Using a Benzothiazine-Based Probe. ACTA ACUST UNITED AC 2018; 95:e76. [PMID: 30312022 DOI: 10.1002/cpps.76] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Oxidation of a protein cysteinyl thiol (Cys-SH) to S-sulfenic acid (Cys-SOH) by a reactive oxygen species (e.g., hydrogen peroxide), which is termed protein S-sulfenylation, is a reversible post-translational modification that plays a crucial role in redox regulation of protein function in various biological processes. Due to its intrinsically labile nature, protein S-sulfenylation cannot be directly detected or analyzed. Chemoselective probing has been the method of choice for analyzing S-sulfenylated proteins either in vitro or in situ, as it allows stabilization and direct detection of this transient oxidative intermediate. However, it remains challenging to globally pinpoint the specific S-sulfenylated cysteine sites on complex proteomes and to quantify their dynamic changes upon oxidative stress. This unit describes how a benzothiazine-based chemoselective probe called BTD and mass spectrometry based chemoproteomics can be used to globally and site-specifically identify and quantify protein S-sulfenylation. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Ling Fu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Lifeomics, Beijing, China
| | - Keke Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Lifeomics, Beijing, China
| | - Renan B Ferreira
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida
| | - Kate S Carroll
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida
| | - Jing Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Lifeomics, Beijing, China
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28
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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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29
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Genetic Code Expansion: A Powerful Tool for Understanding the Physiological Consequences of Oxidative Stress Protein Modifications. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:7607463. [PMID: 29849913 PMCID: PMC5937447 DOI: 10.1155/2018/7607463] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 03/19/2018] [Indexed: 12/17/2022]
Abstract
Posttranslational modifications resulting from oxidation of proteins (Ox-PTMs) are present intracellularly under conditions of oxidative stress as well as basal conditions. In the past, these modifications were thought to be generic protein damage, but it has become increasingly clear that Ox-PTMs can have specific physiological effects. It is an arduous task to distinguish between the two cases, as multiple Ox-PTMs occur simultaneously on the same protein, convoluting analysis. Genetic code expansion (GCE) has emerged as a powerful tool to overcome this challenge as it allows for the site-specific incorporation of an Ox-PTM into translated protein. The resulting homogeneously modified protein products can then be rigorously characterized for the effects of individual Ox-PTMs. We outline the strengths and weaknesses of GCE as they relate to the field of oxidative stress and Ox-PTMs. An overview of the Ox-PTMs that have been genetically encoded and applications of GCE to the study of Ox-PTMs, including antibody validation and therapeutic development, is described.
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30
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Alcock LJ, Perkins MV, Chalker JM. Chemical methods for mapping cysteine oxidation. Chem Soc Rev 2018; 47:231-268. [DOI: 10.1039/c7cs00607a] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Methods to characterise oxidative modifications of cysteine help clarify their role in protein function in both healthy and diseased cells.
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Affiliation(s)
- Lisa J. Alcock
- College of Science and Engineering
- Flinders University
- South Australia
- Australia
| | - Michael V. Perkins
- College of Science and Engineering
- Flinders University
- South Australia
- Australia
| | - Justin M. Chalker
- College of Science and Engineering
- Flinders University
- South Australia
- Australia
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31
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Deng L, Xu X, Liu H. PredCSO: an ensemble method for the prediction of S-sulfenylation sites in proteins. Mol Omics 2018; 14:257-265. [DOI: 10.1039/c8mo00089a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Predicting S-sulfenylation sites in proteins based on sequence and structural features by building an ensemble model by gradient tree boosting.
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Affiliation(s)
- Lei Deng
- School of Software, Central South University
- Changsha
- China
| | - Xiaojie Xu
- School of Software, Central South University
- Changsha
- China
| | - Hui Liu
- School of Software, Central South University
- Changsha
- China
- Lab of Information Management, Changzhou University
- Jiangsu
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32
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Echeverri-Ruiz N, Haynes T, Landers J, Woods J, Gemma MJ, Hughes M, Del Rio-Tsonis K. A biochemical basis for induction of retina regeneration by antioxidants. Dev Biol 2017; 433:394-403. [PMID: 29291983 PMCID: PMC5753421 DOI: 10.1016/j.ydbio.2017.08.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 08/04/2017] [Accepted: 08/09/2017] [Indexed: 12/19/2022]
Abstract
The use of antioxidants in tissue regeneration has been studied, but their mechanism of action is not well understood. Here, we analyze the role of the antioxidant N-acetylcysteine (NAC) in retina regeneration. Embryonic chicks are able to regenerate their retina after its complete removal from retinal stem/progenitor cells present in the ciliary margin (CM) of the eye only if a source of exogenous factors, such as FGF2, is present. This study shows that NAC modifies the redox status of the CM, initiates self-renewal of the stem/progenitor cells, and induces regeneration in the absence of FGF2. NAC works as an antioxidant by scavenging free radicals either independently or through the synthesis of glutathione (GSH), and/or by reducing oxidized proteins through a thiol disulfide exchange activity. We dissected the mechanism used by NAC to induce regeneration through the use of inhibitors of GSH synthesis and the use of other antioxidants with different biochemical structures and modes of action, and found that NAC induces regeneration through its thiol disulfide exchange activity. Thus, our results provide, for the first time, a biochemical basis for induction of retina regeneration. Furthermore, NAC induction was independent of FGF receptor signaling, but dependent on the MAPK (pErk1/2) pathway.
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Affiliation(s)
- Nancy Echeverri-Ruiz
- Department of Biology and Center for Visual Sciences at Miami University (CVSMU), Oxford, OH 45056, USA
| | - Tracy Haynes
- Department of Biology and Center for Visual Sciences at Miami University (CVSMU), Oxford, OH 45056, USA
| | - Joseph Landers
- Department of Biology and Center for Visual Sciences at Miami University (CVSMU), Oxford, OH 45056, USA
| | - Justin Woods
- Department of Biology and Center for Visual Sciences at Miami University (CVSMU), Oxford, OH 45056, USA
| | - Michael J Gemma
- Department of Biology and Center for Visual Sciences at Miami University (CVSMU), Oxford, OH 45056, USA
| | - Michael Hughes
- Department of Statistics and Statistical Consulting Center, Miami University, Oxford, OH 45056, USA
| | - Katia Del Rio-Tsonis
- Department of Biology and Center for Visual Sciences at Miami University (CVSMU), Oxford, OH 45056, USA.
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33
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Wang H, Chen X, Li C, Liu Y, Yang F, Wang C. Sequence-Based Prediction of Cysteine Reactivity Using Machine Learning. Biochemistry 2017; 57:451-460. [DOI: 10.1021/acs.biochem.7b00897] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Haobo Wang
- Synthetic
and Functional Biomolecules Center, Beijing National Laboratory for
Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of Ministry of Education, Peking University, Beijing 100871, China
- Department
of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xuemin Chen
- Synthetic
and Functional Biomolecules Center, Beijing National Laboratory for
Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of Ministry of Education, Peking University, Beijing 100871, China
- Department
of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Can Li
- Department
of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yuan Liu
- Synthetic
and Functional Biomolecules Center, Beijing National Laboratory for
Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of Ministry of Education, Peking University, Beijing 100871, China
- Department
of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, China
| | - Fan Yang
- Synthetic
and Functional Biomolecules Center, Beijing National Laboratory for
Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of Ministry of Education, Peking University, Beijing 100871, China
- Department
of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chu Wang
- Synthetic
and Functional Biomolecules Center, Beijing National Laboratory for
Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of Ministry of Education, Peking University, Beijing 100871, China
- Department
of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, China
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34
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Borotto NB, McClory PJ, Martin BR, Håkansson K. Targeted Annotation of S-Sulfonylated Peptides by Selective Infrared Multiphoton Dissociation Mass Spectrometry. Anal Chem 2017; 89:8304-8310. [PMID: 28708386 DOI: 10.1021/acs.analchem.7b01461] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein S-sulfinylation (R-SO2-) and S-sulfonylation (R-SO3-) are irreversible oxidative post-translational modifications of cysteine residues. Greater than 5% of cysteines are reported to occupy these higher oxidation states, which effectively inactivate the corresponding thiols and alter the electronic and physical properties of modified proteins. Such higher oxidation states are reached after excessive exposure to cellular oxidants, and accumulate across different disease states. Despite widespread and functionally relevant cysteine oxidation across the proteome, there are currently no robust methods to profile higher order cysteine oxidation. Traditional data-dependent liquid chromatography/tandem mass spectrometry (LC/MS/MS) methods generally miss low-occupancy modifications in complex analyses. Here, we present a data-independent acquisition (DIA) LC/MS-based approach, leveraging the high IR absorbance of sulfoxides at 10.6 μm, for selective dissociation and discovery of S-sulfonated peptides. Across peptide standards and protein digests, we demonstrate selective infrared multiphoton dissociation (IRMPD) of S-sulfonated peptides in the background of unmodified peptides. This selective DIA IRMPD LC/MS-based approach allows identification and annotation of S-sulfonated peptides across complex mixtures while providing sufficient sequence information to localize the modification site.
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Affiliation(s)
- Nicholas B Borotto
- Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Phillip J McClory
- Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Brent R Martin
- Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Kristina Håkansson
- Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
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35
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Williams RM, Winkfein RJ, Ginger RS, Green MR, Schnetkamp PP, Wheeler GN. A functional approach to understanding the role of NCKX5 in Xenopus pigmentation. PLoS One 2017; 12:e0180465. [PMID: 28692664 PMCID: PMC5503238 DOI: 10.1371/journal.pone.0180465] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 06/15/2017] [Indexed: 11/19/2022] Open
Abstract
NCKX5 is an ion exchanger expressed mostly in pigment cells; however, the functional role for this protein in melanogenesis is not clear. A variant allele of SLC24A5, the gene encoding NCKX5, has been shown to correlate with lighter skin pigmentation in humans, indicating a key role for SLC24A5 in determining human skin colour. SLC24A5 expression has been found to be elevated in melanoma. Knockdown analyses have shown SLC24A5 to be important for pigmentation, but to date the function of this ion exchanger in melanogenesis has not been fully established. Our data suggest NCKX5 may have an alternative activity that is key to its role in the regulation of pigmentation. Here Xenopus laevis is employed as an in vivo model system to further investigate the function of NCKX5 in pigmentation. SLC24A5 is expressed in the melanophores as they differentiate from the neural crest and develop in the RPE of the eye. Morpholino knockdown and rescue experiments were designed to elucidate key residues and regions of the NCKX5 protein. Unilateral morpholino injection at the 2 cell stage resulted in a reduction of pigmentation in the eye and epidermis of one lateral side of the tadpole. Xenopus and human SLC24A5 can rescue the morpholino effects. Further rescue experiments including the use of ion exchange inactive SLC24A5 constructs raise the possibility that full ion exchanger function of NCKX5 may not be required for rescue of pigmentation.
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Affiliation(s)
- Ruth M. Williams
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Robert J. Winkfein
- Department of Physiology and Pharmacology, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Rebecca S. Ginger
- Unilever Research and Development, Colworth Science Park, Sharnbrook, Bedfordshire, United Kingdom
| | - Martin R. Green
- Unilever Research and Development, Colworth Science Park, Sharnbrook, Bedfordshire, United Kingdom
| | - Paul P. Schnetkamp
- Department of Physiology and Pharmacology, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Grant N. Wheeler
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
- * E-mail:
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36
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Pilo AL, Zhao F, McLuckey SA. Gas-Phase Oxidation via Ion/Ion Reactions: Pathways and Applications. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:991-1004. [PMID: 28050870 PMCID: PMC5438755 DOI: 10.1007/s13361-016-1554-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 10/31/2016] [Accepted: 11/05/2016] [Indexed: 06/06/2023]
Abstract
Here, we provide an overview of pathways available upon the gas-phase oxidation of peptides and DNA via ion/ion reactions and explore potential applications of these chemistries. The oxidation of thioethers (i.e., methionine residues and S-alkyl cysteine residues), disulfide bonds, S-nitrosylated cysteine residues, and DNA to the [M+H+O]+ derivative via ion/ion reactions with periodate and peroxymono-sulfate anions is demonstrated. The oxidation of neutral basic sites to various oxidized structures, including the [M+H+O]+, [M-H]+, and [M-H-NH3]+ species, via ion/ion reactions is illustrated and the oxidation characteristics of two different oxidizing reagents, periodate and persulfate anions, are compared. Lastly, the highly efficient generation of molecular radical cations via ion/ion reactions with sulfate radical anion is summarized. Activation of the newly generated molecular radical peptide cations results in losses of various neutral side chains, several of which generate dehydroalanine residues that can be used to localize the amino acid from which the dehydroalanine was generated. The chemistries presented herein result in a diverse range of structures that can be used for a variety of applications, including the identification and localization of S-alkyl cysteine residues, the oxidative cleavage of disulfide bonds, and the generation of molecular radical cations from even-electron doubly protonated peptides. Graphical Abstract ᅟ.
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Affiliation(s)
- Alice L Pilo
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Feifei Zhao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA.
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37
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Lisse TS, Rieger S. IKKα regulates human keratinocyte migration through surveillance of the redox environment. J Cell Sci 2017; 130:975-988. [PMID: 28122935 PMCID: PMC5358334 DOI: 10.1242/jcs.197343] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 01/16/2017] [Indexed: 02/06/2023] Open
Abstract
Although the functions of H2O2 in epidermal wound repair are conserved throughout evolution, the underlying signaling mechanisms are largely unknown. In this study we used human keratinocytes (HEK001) to investigate H2O2-dependent wound repair mechanisms. Scratch wounding led to H2O2 production in two or three cell layers at the wound margin within ∼30 min and subsequent cysteine modification of proteins via sulfenylation. Intriguingly, exogenous H2O2 treatment resulted in preferential sulfenylation of keratinocytes that adopted a migratory phenotype and detached from neighboring cells, suggesting that one of the primary functions of H2O2 is to stimulate signaling factors involved in cell migration. Based on previous findings that revealed epidermal growth factor receptor (EGFR) involvement in H2O2-dependent cell migration, we analyzed oxidation of a candidate upstream target, the inhibitor of κB kinase α (IKKα; encoded by CHUK), as a mechanism of action. We show that IKKα is sulfenylated at a conserved cysteine residue in the kinase domain, which correlates with de-repression of EGF promoter activity and increased EGF expression. Thus, this indicates that IKKα promotes migration through dynamic interactions with the EGF promoter depending on the redox state within cells. Summary: This study provides a newly identified mechanism by which H2O2-dependent oxidation of the inhibitor of κB kinase α and de-repression of epidermal growth factor promoter activity stimulates keratinocyte migration.
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Affiliation(s)
- Thomas S Lisse
- Davis Center for Regenerative Biology and Medicine, MDI Biological Laboratory, 159 Old Bar Harbor Road, Salisbury Cove, ME 04672, USA .,The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Sandra Rieger
- Davis Center for Regenerative Biology and Medicine, MDI Biological Laboratory, 159 Old Bar Harbor Road, Salisbury Cove, ME 04672, USA
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38
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Zhou B, Hogg PJ, Gräter F. One-Way Allosteric Communication between the Two Disulfide Bonds in Tissue Factor. Biophys J 2017; 112:78-86. [PMID: 28076818 PMCID: PMC5232894 DOI: 10.1016/j.bpj.2016.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 11/19/2016] [Accepted: 12/01/2016] [Indexed: 11/12/2022] Open
Abstract
Tissue factor (TF) is a transmembrane glycoprotein that plays distinct roles in the initiation of extrinsic coagulation cascade and thrombosis. TF contains two disulfide bonds, one each in the N-terminal and C-terminal extracellular domains. The C-domain disulfide, Cys186-Cys209, has a -RHStaple configuration in crystal structures, suggesting that this disulfide carries high pre-stress. The redox state of this disulfide has been proposed to regulate TF encryption/decryption. Ablating the N-domain Cys49-Cys57 disulfide bond was found to increase the redox potential of the Cys186-Cys209 bond, implying an allosteric communication between the domains. Using molecular dynamics simulations, we observed that the Cys186-Cys209 disulfide bond retained the -RHStaple configuration, whereas the Cys49-Cys57 disulfide bond fluctuated widely. The Cys186-Cys209 bond featured the typical -RHStaple disulfide properties, such as a longer S-S bond length, larger C-S-S angles, and higher bonded prestress, in comparison to the Cys49-Cys57 bond. Force distribution analysis was used to sense the subtle structural changes upon ablating the disulfide bonds, and allowed us to identify a one-way allosteric communication mechanism from the N-terminal to the C-terminal domain. We propose a force propagation pathway using a shortest-pathway algorithm, which we suggest is a useful method for searching allosteric signal transduction pathways in proteins. As a possible explanation for the pathway being one-way, we identified a pronounced lower degree of conformational fluctuation, or effectively higher stiffness, in the N-terminal domain. Thus, the changes of the rigid domain (N-terminal domain) can induce mechanical force propagation to the soft domain (C-terminal domain), but not vice versa.
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Affiliation(s)
- Beifei Zhou
- CAS-MPG Partner Institute and Key Laboratory for Computational Biology (PICB), Shanghai, China; Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Philip J Hogg
- The Centenary Institute and National Health and Medical Research Council Clinical Trials Centre, University of Sydney, Sydney, Australia
| | - Frauke Gräter
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; University of Heidelberg, Interdisciplinary Center for Scientific Computing, Heidelberg, Germany.
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39
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Zhou Y, Li W, Wang M, Zhang X, Zhang H, Tong X, Xiao Y. Competitive profiling of celastrol targets in human cervical cancer HeLa cells via quantitative chemical proteomics. MOLECULAR BIOSYSTEMS 2017; 13:83-91. [DOI: 10.1039/c6mb00691d] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We reported the proteome-wide profiling of cellular targets of celastrol in HeLa cellsviacompetitive chemoproteomics approach utilizing a cysteine-targeting activity-based probe.
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Affiliation(s)
- Yiqing Zhou
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
| | - Weichao Li
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
| | - Mingli Wang
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
| | - Xixi Zhang
- University of Chinese Academy of Sciences
- Beijing 100039
- China
- Institute for Nutritional Sciences
- Shanghai Institutes for Biological Sciences
| | - Haibing Zhang
- Institute for Nutritional Sciences
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
- Shanghai 200032
- China
| | - Xiaofeng Tong
- Department of Chemistry
- East China University of Science and Technology
- Shanghai 200001
- China
| | - Youli Xiao
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
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40
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Qian Y, Weerapana E. A Quantitative Mass-Spectrometry Platform to Monitor Changes in Cysteine Reactivity. Methods Mol Biol 2017; 1491:11-22. [PMID: 27778278 DOI: 10.1007/978-1-4939-6439-0_2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cysteine residues on proteins serve diverse functional roles in catalysis and regulation and are susceptible to numerous posttranslational modifications. Methods to monitor the reactivity of cysteines within the context of a complex proteome have facilitated the identification and functional characterization of cysteine residues on disparate proteins. Here, we describe the use of a cysteine-reactive iodoacetamide probe coupled to isotopically labeled, cleavable linkers to identify and quantify cysteine-reactivity changes from two biological samples.
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Affiliation(s)
- Yu Qian
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, USA
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, USA.
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Akter S, Carpentier S, Van Breusegem F, Messens J. Identification of dimedone-trapped sulfenylated proteins in plants under stress. Biochem Biophys Rep 2016; 9:106-113. [PMID: 29114583 PMCID: PMC5632707 DOI: 10.1016/j.bbrep.2016.11.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 10/12/2016] [Accepted: 11/21/2016] [Indexed: 12/16/2022] Open
Abstract
In stressed plants, the reactive oxygen species (ROS) levels rise. Key to ROS signaling research are detection and identification of the protein cysteine sulfenylation (-SOH), the ROS-mediated oxidative product of a thiol (-SH). Arabidopsis thaliana seedlings were stressed with hydrogen peroxide (H2O2) and the sulfenylated proteins were tagged with dimedone. Dimedone-tagged sulfenic acid proteins were visualized on a two-dimensional electrophoresis (2DE) immunoblot with an anticysteine sulfenic acid antibody and were subsequently detected by mass spectrometry. We optimized the detection method for protein sulfenylation in Arabidopsis. We conclude that dimedone can penetrate the cell wall, does not stress plants, and can "read" the changes in the protein sulfenylation pattern under oxidative stress. We observed that the number of sulfenylated proteins in plants treated with 10 mM H2O2 was higher than that in untreated plants. A total of 39 sulfenylated protein spots were found on 2DE immunoblots. By means of mass spectrometry, 11 sulfenylated proteins were discovered involved in primary metabolism, redox regulation, translation and signaling pathways. Hence, by combining an immunochemical 2DE strategy with mass spectrometry, we were able to identify sulfenylated proteins in H2O2-stressed Arabidopsis seedlings. The sulfenylated proteins can be considered for further validation as redox regulators in plants.
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Affiliation(s)
- Salma Akter
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,Structural Biology Research Center, VIB, 1050 Brussels, Belgium.,Brussels Center for Redox Biology, 1050 Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Department of Fisheries, Faculty of Biological Sciences, University of Dhaka, 1000 Dhaka, Bangladesh
| | - Sebastien Carpentier
- Division of Crop Biotechnics, KU Leuven University, 3001 Leuven, Belgium.,Facility for Systems Biology based Mass Spectrometry, KU Leuven University, 3000 Leuven, Belgium
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Joris Messens
- Structural Biology Research Center, VIB, 1050 Brussels, Belgium.,Brussels Center for Redox Biology, 1050 Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
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Gu L, Robinson RAS. Proteomic approaches to quantify cysteine reversible modifications in aging and neurodegenerative diseases. Proteomics Clin Appl 2016; 10:1159-1177. [PMID: 27666938 DOI: 10.1002/prca.201600015] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/13/2016] [Accepted: 09/23/2016] [Indexed: 01/11/2023]
Abstract
Cysteine is a highly reactive amino acid and is subject to a variety of reversible post-translational modifications (PTMs), including nitrosylation, glutathionylation, palmitoylation, as well as formation of sulfenic acid and disulfides. These modifications are not only involved in normal biological activities, such as enzymatic catalysis, redox signaling, and cellular homeostasis, but can also be the result of oxidative damage. Especially in aging and neurodegenerative diseases, oxidative stress leads to aberrant cysteine oxidations that affect protein structure and function leading to neurodegeneration as well as other detrimental effects. Methods that can identify cysteine modifications by type, including the site of modification, as well as the relative stoichiometry of the modification can be very helpful for understanding the role of the thiol proteome and redox homeostasis in the context of disease. Cysteine reversible modifications however, are challenging to investigate as they are low abundant, diverse, and labile especially under endogenous conditions. Thanks to the development of redox proteomic approaches, large-scale quantification of cysteine reversible modifications is possible. These approaches cover a range of strategies to enrich, identify, and quantify cysteine reversible modifications from biological samples. This review will focus on nongel-based redox proteomics workflows that give quantitative information about cysteine PTMs and highlight how these strategies have been useful for investigating the redox thiol proteome in aging and neurodegenerative diseases.
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Affiliation(s)
- Liqing Gu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Renã A S Robinson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
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43
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Pilo AL, Peng Z, McLuckey SA. The dehydroalanine effect in the fragmentation of ions derived from polypeptides. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:857-866. [PMID: 27484024 PMCID: PMC5068825 DOI: 10.1002/jms.3831] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 07/27/2016] [Accepted: 07/28/2016] [Indexed: 05/11/2023]
Abstract
The fragmentation of peptides and proteins upon collision-induced dissociation (CID) is highly dependent on sequence and ion type (e.g. protonated, deprotonated, sodiated, odd electron, etc.). Some amino acids, for example aspartic acid and proline, have been found to enhance certain cleavages along the backbone. Here, we show that peptides and proteins containing dehydroalanine, a non-proteinogenic amino acid with an unsaturated side-chain, undergo enhanced cleavage of the N-Cα bond of the dehydroalanine residue to generate c- and z-ions. Because these fragment ion types are not commonly observed upon activation of positively charged even-electron species, they can be used to identify dehydroalanine residues and localize them within the peptide or protein chain. While dehydroalanine can be generated in solution, it can also be generated in the gas phase upon CID of various species. Oxidized S-alkyl cysteine residues generate dehydroalanine upon activation via highly efficient loss of the alkyl sulfenic acid. Asymmetric cleavage of disulfide bonds upon collisional activation of systems with limited proton mobility also generates dehydroalanine. Furthermore, we show that gas-phase ion/ion reactions can be used to facilitate the generation of dehydroalanine residues via, for example, oxidation of S-alkyl cysteine residues and conversion of multiply-protonated peptides to radical cations. In the latter case, loss of radical side-chains to generate dehydroalanine from some amino acids gives rise to the possibility for residue-specific backbone cleavage of polypeptide ions. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Alice L Pilo
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Zhou Peng
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA.
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Pilo AL, McLuckey SA. Selective Gas-Phase Ion/Ion Reactions: Enabling Disulfide Mapping via Oxidation and Cleavage of Disulfide Bonds in Intermolecularly-Linked Polypeptide Ions. Anal Chem 2016; 88:8972-9. [PMID: 27531151 DOI: 10.1021/acs.analchem.6b01043] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The selective gas-phase oxidation of disulfide bonds to their thiosulfinate form using ion/ion reactions and subsequent cleavage is demonstrated here. Oxidizing reagent anions are observed to attach to all polypeptides, regardless of amino acid composition. Direct proton transfer yielding a charge-reduced peptide is also frequently observed. Activation of the ion/ion complex between an oxidizing reagent anion and a disulfide-containing peptide cation results in oxygen transfer from the reagent anion to the peptide cation to form the [M+H+O](+) species. This thiosulfinate derivative can undergo one of several rearrangements that result in cleavage of the disulfide bond. Species containing an intermolecular disulfide bond undergo separation of the two chains upon activation. Further activation can be used to generate more sequence information from each chain. These oxidation ion/ion reactions have been used to illustrate the identification of S-glutathionylated and S-cysteinylated peptides, in which low molecular weight thiols are attached to cysteine residues in peptides via disulfide bonds. The oxidation chemistry effectively labels peptide ions with readily oxidized groups, such as disulfide bonds. This enables a screening approach for the identification of disulfide-linked peptides in a disulfide mapping application involving enzymatic digestion. The mixtures of ions generated by tryptic and peptic digestions of lysozyme and insulin, respectively, without prior separation or isolation were subjected both to oxidation and proton transfer ion/ion chemistry to illustrate the identification of peptides in the mixtures with readily oxidized groups.
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Affiliation(s)
- Alice L Pilo
- Department of Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Scott A McLuckey
- Department of Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
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Kim S, Ahn SH, Yang HY, Lee JS, Choi HG, Park YK, Lee TH. Modification of cysteine 457 in plakoglobin modulates the proliferation and migration of colorectal cancer cells by altering binding to E-cadherin/catenins. Redox Rep 2016; 22:272-281. [PMID: 27571934 DOI: 10.1080/13510002.2016.1215120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
OBJECTIVES In tissue samples from patients with colorectal cancer (CRC), oxidation of C420 and C457 of plakoglobin (Pg) within tumor tissue was identified by proteomic analysis. The aim of this study was to identify the roles of Pg C420 and C457. METHODS Human CRC tissues, CRC and breast cancer cells, and normal mouse colon were prepared to validate Pg oxidation. MC38 cells were co-transfected with E-cadherin plus wild type (WT) or mutant (C420S or C457S) Pg to evaluate protein interactions and cellular localization, proliferation, and migration. RESULTS Pg was more oxidized in stage III CRC tumor tissue than in non-tumor tissue. Similar oxidation of Pg was elicited by H2O2 treatment in normal colon and cancer cells. C457S Pg exhibited diminished binding to E-cadherin and α-catenin, and reduced the assembly of E-cadherin-α-/β-catenin complexes. Correspondingly, immunofluorescent analysis of Pg cellular localization suggested impaired binding of C457S Pg to membranes. Cell migration and proliferation were also suppressed in C457S-expressing cells. DISCUSSION Pg appears to be redox-sensitive in cancer, and the C457 modification may impair cell migration and proliferation by affecting its interaction with the E-cadherin/catenin axis. Our findings suggest that redox-sensitive cysteines of Pg may be the targets for CRC therapy.
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Affiliation(s)
- Suhee Kim
- a Department of Oral Biochemistry , Dental Science Research Institute, Medical Research Center for Biomineralization Disorders, School of Dentistry, Chonnam National University , Gwangju , Republic of Korea.,b Department of Molecular Medicine (BK21plus) , Chonnam National University Graduate School , Gwangju , Republic of Korea
| | - Sun Hee Ahn
- a Department of Oral Biochemistry , Dental Science Research Institute, Medical Research Center for Biomineralization Disorders, School of Dentistry, Chonnam National University , Gwangju , Republic of Korea
| | - Hee-Young Yang
- a Department of Oral Biochemistry , Dental Science Research Institute, Medical Research Center for Biomineralization Disorders, School of Dentistry, Chonnam National University , Gwangju , Republic of Korea
| | - Jin-Sil Lee
- a Department of Oral Biochemistry , Dental Science Research Institute, Medical Research Center for Biomineralization Disorders, School of Dentistry, Chonnam National University , Gwangju , Republic of Korea
| | - Hyang-Gi Choi
- a Department of Oral Biochemistry , Dental Science Research Institute, Medical Research Center for Biomineralization Disorders, School of Dentistry, Chonnam National University , Gwangju , Republic of Korea.,b Department of Molecular Medicine (BK21plus) , Chonnam National University Graduate School , Gwangju , Republic of Korea
| | - Young-Kyu Park
- c Department of Surgery , Chonnam National University Hwasun Hospital , Hwasun , Republic of Korea
| | - Tae-Hoon Lee
- a Department of Oral Biochemistry , Dental Science Research Institute, Medical Research Center for Biomineralization Disorders, School of Dentistry, Chonnam National University , Gwangju , Republic of Korea.,b Department of Molecular Medicine (BK21plus) , Chonnam National University Graduate School , Gwangju , Republic of Korea
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Chen C, Wang J, Cai R, Yuan Y, Guo Z, Grewer C, Zhang Z. Identification of a Disulfide Bridge in Sodium-Coupled Neutral Amino Acid Transporter 2(SNAT2) by Chemical Modification. PLoS One 2016; 11:e0158319. [PMID: 27355203 PMCID: PMC4927162 DOI: 10.1371/journal.pone.0158319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 06/14/2016] [Indexed: 12/02/2022] Open
Abstract
Sodium-coupled neutral amino acid transporter 2 (SNAT2) belongs to solute carrier 38 (SLC38) family of transporters, which is ubiquitously expressed in mammalian tissues and mediates transport of small, neutral amino acids, exemplified by alanine(Ala, A). Yet structural data on SNAT2, including the relevance of intrinsic cysteine residues on structure and function, is scarce, in spite of its essential roles in many tissues. To better define the potential of intrinsic cysteines to form disulfide bonds in SNAT2, mutagenesis experiments and thiol-specific chemical modifications by N-ethylmaleimide (NEM) and methoxy-polyethylene glycol maleimide (mPEG-Mal, MW 5000) were performed, with or without the reducing regent dithiothreitol (DTT) treatment. Seven single mutant transporters with various cysteine (Cys, C) to alanine (Ala, A) substitutions, and a C245,279A double mutant were introduced to SNAT2 with a hemagglutinin (HA) tag at the C-terminus. The results showed that the cells expressing C245A or C279A were labeled by one equivalent of mPEG-Mal in the presence of DTT, while wild-type or all the other single Cys to Ala mutants were modified by two equivalents of mPEG-Mal. Furthermore, the molecular weight of C245,279A was not changed in the presence or absence of DTT treatment. The results suggest a disulfide bond between Cys245 and Cys279 in SNAT2 which has no effect on cell surface trafficking, as well as transporter function. The proposed disulfide bond may be important to delineate proximity in the extracellular domain of SNAT2 and related proteins.
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Affiliation(s)
- Chen Chen
- College of Life Science and Biopharmacy, Shenyang Pharmaceutical University, Shenyang 110015, People’s Republic of China
| | - Jiahong Wang
- College of Life Science and Biopharmacy, Shenyang Pharmaceutical University, Shenyang 110015, People’s Republic of China
| | - Ruiping Cai
- College of Life Science and Biopharmacy, Shenyang Pharmaceutical University, Shenyang 110015, People’s Republic of China
| | - Yanmeng Yuan
- College of Life Science and Biopharmacy, Shenyang Pharmaceutical University, Shenyang 110015, People’s Republic of China
| | - Zhanyun Guo
- Institute of Protein Research, College of Life Sciences and Technology, Tongji University, Shanghai 200092, People’s Republic of China
| | - Christof Grewer
- Departments of Chemistry and Biological Sciences, Binghamton University, Binghamton, New York, 13902, United States of America
| | - Zhou Zhang
- College of Life Science and Biopharmacy, Shenyang Pharmaceutical University, Shenyang 110015, People’s Republic of China
- * E-mail:
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47
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Pan J, Carroll KS. Chemical biology approaches to study protein cysteine sulfenylation. Biopolymers 2016; 101:165-72. [PMID: 23576224 DOI: 10.1002/bip.22255] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 04/01/2013] [Indexed: 01/08/2023]
Abstract
The oxidation of cysteine thiol side chains by hydrogen peroxide to afford protein sulfenyl modifications is an important mechanism in signal transduction. In addition, aberrant protein sulfenylation contributes to a range of human pathologies, including cancer. Efforts to elucidate the roles of protein sulfenylation in physiology and disease have been hampered by the lack of techniques to probe these modifications in native environments with molecular specificity. In this review, we trace the history of chemical and biological methods that have been developed to detect protein sulfenylation and illustrate how a recent cell-permeable chemical reporter, DYn-2, has been used to detect and identify intracellular targets of endogenous H2 O2 during growth factor signaling, including the epidermal growth factor receptor. The array of new tools and methods discussed herein enables the discovery of new biological roles for cysteine sulfenylation in human health and disease.
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Affiliation(s)
- Jia Pan
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33456
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48
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Gupta V, Paritala H, Carroll KS. Reactivity, Selectivity, and Stability in Sulfenic Acid Detection: A Comparative Study of Nucleophilic and Electrophilic Probes. Bioconjug Chem 2016; 27:1411-8. [PMID: 27123991 DOI: 10.1021/acs.bioconjchem.6b00181] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The comparative reaction efficiencies of currently used nucleophilic and electrophilic probes toward cysteine sulfenic acid have been thoroughly evaluated in two different settings-(i) a small molecule dipeptide based model and (ii) a recombinant protein model. We further evaluated the stability of corresponding thioether and sulfoxide adducts under reducing conditions which are commonly encountered during proteomic protocols and in cell analysis. Powered by the development of new cyclic and linear C-nucleophiles, the unsurpassed efficiency in the capture of sulfenic acid under competitive conditions is achieved and thus holds great promise as highly potent tools for activity-based sulfenome profiling.
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Affiliation(s)
- Vinayak Gupta
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Hanumantharao Paritala
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Kate S Carroll
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
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49
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Zhou P, Yao J, Hu G, Fang J. Naphthalimide Scaffold Provides Versatile Platform for Selective Thiol Sensing and Protein Labeling. ACS Chem Biol 2016; 11:1098-105. [PMID: 26813105 DOI: 10.1021/acschembio.5b00856] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Reversible thiol modifications are fundamental of cellular redox regulation. Specific thiol detection, including thiol sensing and protein thiols labeling, is critical to study such modifications. We reported the discovery of 4-methylsulfonyl-N-n-butyl-1,8-naphthalimide (MSBN), a highly selective fluorogenic probe for thiols based on the 1,8-naphthalimide scaffold. Thiols react with MSBN nearly quantitatively via nucleophilic aromatic substitution to replace the methylsulfonyl group and restore the quenched fluorescence (>100-fold increase). MSBN was employed to selectively image thiols in live cells and specifically label protein thiols with a turn-on signal to determine diverse reversible protein thiol modifications. In addition, we introduced a bulky group into the MSBN as a mass tag to create a probe MSBN-TPP, which readily discriminates the reduced thioredoxin from the oxidized one. The specific reaction of MSBN with thiols and the easy manipulation of the naphthalimide unit enable MSBN a versatile scaffold in developing novel probes for thiol-based protein bioconjugation and studying various thiol modifications.
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Affiliation(s)
- Pengcheng Zhou
- State Key Laboratory of Applied
Organic Chemistry and College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Juan Yao
- State Key Laboratory of Applied
Organic Chemistry and College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Guodong Hu
- State Key Laboratory of Applied
Organic Chemistry and College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Jianguo Fang
- State Key Laboratory of Applied
Organic Chemistry and College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
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Margaritelis NV, Cobley JN, Paschalis V, Veskoukis AS, Theodorou AA, Kyparos A, Nikolaidis MG. Principles for integrating reactive species into in vivo biological processes: Examples from exercise physiology. Cell Signal 2016; 28:256-71. [DOI: 10.1016/j.cellsig.2015.12.011] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 12/07/2015] [Accepted: 12/20/2015] [Indexed: 12/14/2022]
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