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Mackova V, Raudenska M, Polanska HH, Jakubek M, Masarik M. Navigating the redox landscape: reactive oxygen species in regulation of cell cycle. Redox Rep 2024; 29:2371173. [PMID: 38972297 DOI: 10.1080/13510002.2024.2371173] [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: 07/09/2024] Open
Abstract
Objectives: To advance our knowledge of disease mechanisms and therapeutic options, understanding cell cycle regulation is critical. Recent research has highlighted the importance of reactive oxygen species (ROS) in cell cycle regulation. Although excessive ROS levels can lead to age-related pathologies, ROS also play an essential role in normal cellular functions. Many cell cycle regulatory proteins are affected by their redox status, but the precise mechanisms and conditions under which ROS promote or inhibit cell proliferation are not fully understood.Methods: This review presents data from the scientific literature and publicly available databases on changes in redox state during the cell cycle and their effects on key regulatory proteins.Results: We identified redox-sensitive targets within the cell cycle machinery and analysed different effects of ROS (type, concentration, duration of exposure) on cell cycle phases. For example, moderate levels of ROS can promote cell proliferation by activating signalling pathways involved in cell cycle progression, whereas excessive ROS levels can induce DNA damage and trigger cell cycle arrest or cell death.Discussion: Our findings encourage future research focused on identifying redox-sensitive targets in the cell cycle machinery, potentially leading to new treatments for diseases with dysregulated cell proliferation.
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Affiliation(s)
- Viktoria Mackova
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Martina Raudenska
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Department of Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Hana Holcova Polanska
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Department of Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Milan Jakubek
- BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic
| | - Michal Masarik
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Department of Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic
- Institute of Pathophysiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
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2
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Zou F, Wu MMH, Tan Z, Lu G, Kwok KWH, Leng Z. Ecotoxicological risk of asphalt pavements to aquatic animals associated with pollutant leaching. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 944:173985. [PMID: 38876354 DOI: 10.1016/j.scitotenv.2024.173985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 06/16/2024]
Abstract
Contaminants such as heavy metals and polycyclic aromatic hydrocarbons (PAHs) can be released from asphalt pavement and transported through stormwater runoff to nearby water bodies, leading to water pollution and potential harm to living aquatic animals. This study characterizes the heavy metal and PAH leaching from various asphalt paving materials and their potential ecotoxicological effects on zebrafish Danio rerio. Artificial runoffs were prepared in the laboratory concerning the effects of water, temperature, and traffic. The concentrations of heavy metals and PAHs in the leachates were quantified, while the toxicity assessment encompassed mortality, metal stress, PAH toxicity, inflammation, carcinogenicity, and oxidative damage. Gene expressions of related proteins or transcription factors were assessed, including metallothionines, aryl hydrocarbon receptors, interleukin-1β, interleukin-10, nuclear factor-κB, tumor necrosis factor-α, tumor suppressor p53, heat shock protein 70, and reactive oxygen species (ROS). The findings demonstrate that leachates from asphalt pavements containing waste bottom ash, crumb rubber, or specific chemicals could induce notable stress and inflammation responses in zebrafish. In addition, potential carcinogenic effects and the elevation of ROS were identified within certain treatment groups. This study represents the first attempt to assess the ecotoxicity of pavement leachates employing a live fish model, thereby improving the current understanding of the environmental impact of asphalt pavements.
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Affiliation(s)
- Fuliao Zou
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Margaret M H Wu
- Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Zhifei Tan
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Guoyang Lu
- Department of Architecture and Civil Engineering, City University of Hong Kong, Kowloon Tong, Kowloon, Hong Kong
| | - Kevin W H Kwok
- Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong; Research Institute for Future Food, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.
| | - Zhen Leng
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong; Research Centre for Resources Engineering towards Carbon Neutrality, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.
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3
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Vojtovič D, Petřivalský M. The optimised method of HPLC analysis of glutathione allows to determine the degree of oxidative stress in plant cell culture. Biochem Biophys Res Commun 2024; 734:150465. [PMID: 39088980 DOI: 10.1016/j.bbrc.2024.150465] [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: 04/26/2024] [Revised: 07/15/2024] [Accepted: 07/26/2024] [Indexed: 08/03/2024]
Abstract
Redox regulations and antioxidant defence play a central role in the acclimation of plants to their environment. Glutathione represents an essential component of the cellular antioxidant defence system, which keeps levels of reactive oxygen species (ROS) under control. High-performance liquid chromatography (HPLC) separation with fluorescence detection is a sensitive method that enables analysis of reduced and oxidised glutathione levels in small samples of plant tissues or plant cell culture. We aimed to optimise the method to obtain more accurate information about the total level of glutathione and the proportion of the reduced form (GSH) by choosing the most suitable reduction reagent and the conditions under which the reduction occurs. The applicability of the developed method was verified by analysing tobacco cells treated with hydrogen peroxide, which caused a decrease in the GSH/total glutathione ratio. Significant changes in the level of glutathione as well as in the GSH/total glutathione ratio were also observed during tobacco cell culture development.
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Affiliation(s)
- Daniel Vojtovič
- Department of Biochemistry, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, 77900, Olomouc, Czech Republic
| | - Marek Petřivalský
- Department of Biochemistry, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, 77900, Olomouc, Czech Republic.
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4
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Liu S, Liu Y, Bao E, Tang S. The Protective Role of Heat Shock Proteins against Stresses in Animal Breeding. Int J Mol Sci 2024; 25:8208. [PMID: 39125776 PMCID: PMC11311290 DOI: 10.3390/ijms25158208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/25/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024] Open
Abstract
Heat shock proteins (HSPs) play an important role in all living organisms under stress conditions by acting as molecular chaperones. The expression of different HSPs during stress varies depending on their protective functions and anti-apoptotic activities. The application of HSPs improves the efficiency and decreases the economic cost of animal breeding. By upregulating the expression of HSPs, feed supplements can improve stress tolerance in farm animals. In addition, high expression of HSPs is often a feature of tumor cells, and inhibiting the expression of HSPs is a promising novel method for killing these cells and treating cancers. In the present review, the findings of previous research on the application of HSPs in animal breeding and veterinary medicine are summarized, and the knowledge of the actions of HSPs in animals is briefly discussed.
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Affiliation(s)
| | | | - Endong Bao
- College of Veterinary Medicine, Nanjing Agricultural University, Weigang No. 1 Road, Nanjing 210095, China; (S.L.); (Y.L.)
| | - Shu Tang
- College of Veterinary Medicine, Nanjing Agricultural University, Weigang No. 1 Road, Nanjing 210095, China; (S.L.); (Y.L.)
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5
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Opdensteinen P, Buyel JF. Optimizing interleukin-6 and 8 expression, clarification and purification in plant cell packs and plants for application in advanced therapy medicinal products and cellular agriculture. J Biotechnol 2024; 390:1-12. [PMID: 38740307 DOI: 10.1016/j.jbiotec.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/20/2024] [Accepted: 05/06/2024] [Indexed: 05/16/2024]
Abstract
Healthcare and nutrition are facing a paradigm shift in light of advanced therapy medicinal products (ATMPs) and cellular agriculture options respectively. Both options heavily rely on some sort of animal cell culture, e.g. autologous stem cells. These cultures require various growth factors, such as interleukin-6 and 8 (IL-6/8), in a pure, safe and sustainable form that can be provided in a scalable manner. Plants seem well suited for this task because purification of small proteins can be readily achieved by membrane separation, human/animal pathogens do not replicate in plants and production can be scaled up using in-door farming or agricultural practices. Here, we illustrate this capacity by first optimizing the codon usage of IL-6/8 for translation in Nicotiana spp., as well as testing the effect of untranslated regions and product targeting to different sub-cellular compartments on expression in a high-throughput plant cell pack (PCP) assay. In the chloroplast, IL-6 accumulated up to 6.9±3.8 (SD, n=2) and 14.4±7.4 mg kg-1 (SD, n=5) were observed in case of IL-8. When transferring IL-8 expression into whole plants, accumulation was 12.3±1.5 mg kg-1 (SD, n=3). After extraction and clarification, IL-8 was purified using a two-stage process consisting of an ultrafiltration/diafiltration step with 100 kDa and 10 kDa cut off membranes followed by an IMAC polishing step. The purity, yield and recovery were 97.8%, 6.6 mg kg-1 and 38%, respectively. We evaluated the ability of the proposed purification process to remove endotoxins to ensure the compatibility of plant-made growth factors with cell culture.
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Affiliation(s)
- P Opdensteinen
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, Aachen 52074, Germany; Institute for Molecular Biotechnology, Worringerweg 1, RWTH Aachen University, Aachen 52074, Germany
| | - J F Buyel
- University of Natural Resources and Life Sciences, Vienna (BOKU), Department of Biotechnology (DBT), Institute of Bioprocess Science and Engineering (IBSE), Muthgasse 18, Vienna A-1190, Austria.
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6
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Wang Y, Tsukamoto Y, Hori M, Iha H. Disulfidptosis: A Novel Prognostic Criterion and Potential Treatment Strategy for Diffuse Large B-Cell Lymphoma (DLBCL). Int J Mol Sci 2024; 25:7156. [PMID: 39000261 PMCID: PMC11241771 DOI: 10.3390/ijms25137156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/24/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
Diffuse Large B-cell Lymphoma (DLBCL), with its intrinsic genetic and epigenetic heterogeneity, exhibits significantly variable clinical outcomes among patients treated with the current standard regimen. Disulfidptosis, a novel form of regulatory cell death triggered by disulfide stress, is characterized by the collapse of cytoskeleton proteins and F-actin due to intracellular accumulation of disulfides. We investigated the expression variations of disulfidptosis-related genes (DRGs) in DLBCL using two publicly available gene expression datasets. The initial analysis of DRGs in DLBCL (GSE12453) revealed differences in gene expression patterns between various normal B cells and DLBCL. Subsequent analysis (GSE31312) identified DRGs strongly associated with prognostic outcomes, revealing eight characteristic DRGs (CAPZB, DSTN, GYS1, IQGAP1, MYH9, NDUFA11, NDUFS1, OXSM). Based on these DRGs, DLBCL patients were stratified into three groups, indicating that (1) DRGs can predict prognosis, and (2) DRGs can help identify novel therapeutic candidates. This study underscores the significant role of DRGs in various biological processes within DLBCL. Assessing the risk scores of individual DRGs allows for more precise stratification of prognosis and treatment strategies for DLBCL patients, thereby enhancing the effectiveness of clinical practice.
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Affiliation(s)
- Yu Wang
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu 879-5593, Japan;
| | - Yoshiyuki Tsukamoto
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Yufu 879-5593, Japan;
| | - Mitsuo Hori
- Department of Hematology, Ibaraki Prefectural Central Hospital, Kasama 309-1703, Japan;
| | - Hidekatsu Iha
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu 879-5593, Japan;
- Division of Pathophysiology, The Research Center for GLOBAL and LOCAL Infectious Diseases (RCGLID), Oita University, Yufu 879-5503, Japan
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7
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Malikidogo KP, Charnay T, Ndiaye D, Choi JH, Bridou L, Chartier B, Erbek S, Micouin G, Banyasz A, Maury O, Martel-Frachet V, Grichine A, Sénèque O. Efficient cytosolic delivery of luminescent lanthanide bioprobes in live cells for two-photon microscopy. Chem Sci 2024; 15:9694-9702. [PMID: 38939128 PMCID: PMC11206396 DOI: 10.1039/d4sc00896k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/26/2024] [Indexed: 06/29/2024] Open
Abstract
Lanthanide(iii) (Ln3+) complexes have desirable photophysical properties for optical bioimaging. However, despite their advantages over organic dyes, their use for microscopy imaging is limited by the high-energy UV excitation they require and their poor ability to cross the cell membrane and reach the cytosol. Here we describe a novel family of lanthanide-based luminescent probes, termed dTAT[Ln·L], based on (i) a DOTA-like chelator with a picolinate moiety, (ii) a two-photon absorbing antenna to shift the excitation to the near infrared and (ii) a dimeric TAT cell-penetrating peptide for cytosolic delivery. Several Tb3+ and Eu3+ probes were prepared and characterized. Two-photon microscopy of live cells was attempted using a commercial microscope with the three probes showing the highest quantum yields (>0.15). A diffuse Ln3+ emission was detected in most cells, which is characteristic of cytosolic delivery of the Ln3+ complex. The cytotoxicity of these three probes was evaluated and the IC50 ranged from 7 μM to >50 μM. The addition of a single positive or negative charge to the antenna of the most cytotoxic compound was sufficient to lower significantly or suppress its toxicity under the conditions used for two-photon microscopy. Therefore, the design reported here provides excellent lanthanide-based probes for two-photon microscopy of living cells.
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Affiliation(s)
- Kyangwi P Malikidogo
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, LCBM (UMR 5249) F-38000 Grenoble France
- Univ. Grenoble Alpes, CNRS, DCM (UMR 5250) F-38000 Grenoble France
| | - Thibault Charnay
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, LCBM (UMR 5249) F-38000 Grenoble France
- Univ. Grenoble Alpes, CNRS, DCM (UMR 5250) F-38000 Grenoble France
| | - Daouda Ndiaye
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, LCBM (UMR 5249) F-38000 Grenoble France
| | - Ji-Hyung Choi
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, LCBM (UMR 5249) F-38000 Grenoble France
| | - Lucile Bridou
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Laboratoire de Chimie Lyon F-69342 France
| | - Baptiste Chartier
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, LCBM (UMR 5249) F-38000 Grenoble France
| | - Sule Erbek
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences F-38000 Grenoble France
- EPHE, PSL Research University 4-14 rue Ferrus 75014 Paris France
| | - Guillaume Micouin
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Laboratoire de Chimie Lyon F-69342 France
| | - Akos Banyasz
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Laboratoire de Chimie Lyon F-69342 France
| | - Olivier Maury
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Laboratoire de Chimie Lyon F-69342 France
| | - Véronique Martel-Frachet
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences F-38000 Grenoble France
- EPHE, PSL Research University 4-14 rue Ferrus 75014 Paris France
| | - Alexei Grichine
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences F-38000 Grenoble France
| | - Olivier Sénèque
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, LCBM (UMR 5249) F-38000 Grenoble France
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8
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Yang F, Niu X, Zhou M, Li W. Development and validation of a novel disulfidptosis-related lncRNAs signature in patients with HPV-negative oral squamous cell carcinoma. Sci Rep 2024; 14:14436. [PMID: 38910181 PMCID: PMC11194273 DOI: 10.1038/s41598-024-65194-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 06/18/2024] [Indexed: 06/25/2024] Open
Abstract
Disulfidptosis is a recently identified mode of regulated cell death. Regulating disulfidptosis in carcinoma is a promising therapeutic approach. Long non-coding RNAs (lncRNAs) have been reported to be related to the occurrence and development of many cancers. Disulfidptosis-related lncRNAs (DRLs) in HPV-negative oral squamous cell carcinoma (OSCC) have not been studied. Based on The Cancer Genome Atlas (TCGA) database, least absolute shrinkage selection operator (LASSO) analysis and Cox regression analysis were used to identify overall survival related DRLs and construct the signature. Kaplan-Meier, time-dependent receiver operating characteristics (ROC) and principal component analyses (PCA) were explored to demonstrate the prediction potential of the signature. Subgroup analysis stratified by different clinicopathological characteristics were conducted. Nomogram was established by DRLs signature and independent clinicopathological characteristics. The calibration plots were performed to reveal the accuracy of nomogram. Immune cell subset infiltration, immunotherapy response, drug sensitivity analysis, and tumor mutation burden (TMB) were conducted. Underlying functions and pathways were explored by Gene Set Enrichment Analysis (GSEA) analysis. Previous lncRNA signatures of OSCC were retrieved from PubMed for further validation. Gene expression omnibus (GEO) datasets (GSE41613 and GSE85446) were merged as an external validation for DRLs signature. Consensus clustering analysis of DRLs signature and experimental validation of DRLs were also explored. This research sheds light on the robust performance of DRLs signature in survival prediction, immune cell infiltration, immune escape, and immunotherapy of HPV-negative OSCC.
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Affiliation(s)
- Fan Yang
- Department of Geriatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xinyu Niu
- Department of Geriatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Mingzhu Zhou
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Wei Li
- Department of Geriatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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Liu X, Zhuang L, Gan B. Disulfidptosis: disulfide stress-induced cell death. Trends Cell Biol 2024; 34:327-337. [PMID: 37574347 DOI: 10.1016/j.tcb.2023.07.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/15/2023]
Abstract
The cystine transporter solute carrier family 7 member 11 (SLC7A11) (also known as xCT) promotes glutathione synthesis and counters oxidative stress-induced cell death, including ferroptosis, by importing cystine. Also, SLC7A11 plays a crucial role in tumor development. However, recent studies have uncovered an unexpected role of SLC7A11 in promoting disulfidptosis, a novel form of regulated cell death induced by disulfide stress. In this review, we examine the opposing roles of SLC7A11 in regulating redox homeostasis and cell survival/death, summarize current knowledge on disulfidptosis, and explore its potential in disease treatment. A deeper understanding of disulfidptosis will offer new insights into fundamental cellular homeostasis and facilitate the development of innovative therapies for disease treatment.
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Affiliation(s)
- Xiaoguang Liu
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Li Zhuang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Boyi Gan
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; The University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA.
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Heimfarth L, Dos Santos KS, Monteiro BS, de Souza Oliveira AK, Coutinho HDM, Menezes IRA, Dos Santos MRV, de Souza Araújo AA, Picot L, de Oliveira Júnior RG, Grougnet R, de Souza Siqueira Quintans J, Quintans-Júnior LJ. The protective effects of naringenin, a citrus flavonoid, non-complexed or complexed with hydroxypropyl-β-cyclodextrin against multiorgan damage caused by neonatal endotoxemia. Int J Biol Macromol 2024; 264:130500. [PMID: 38428770 DOI: 10.1016/j.ijbiomac.2024.130500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 02/16/2024] [Accepted: 02/17/2024] [Indexed: 03/03/2024]
Abstract
BACKGROUND Endotoxemia is a severe and dangerous clinical syndrome that results in elevated morbidity, especially in intensive care units. Neonates are particularly susceptible to endotoxemia due to their immature immune systems. There are few effective treatments for neonatal endotoxemia. One group of compounds with potential in the treatment of neonatal inflammatory diseases such as endotoxemia is the flavonoids, mainly due to their antioxidant and anti-inflammatory properties. Among these, naringenin (NGN) is a citrus flavonoid which has already been reported to have anti-inflammatory, antioxidant, anti-nociceptive and anti-cancer effects. Unfortunately, its clinical application is limited by its low solubility and bioavailability. However, cyclodextrins (CDs) have been widely used to improve the solubility of nonpolar drugs and enhance the bioavailability of these natural products. OBJECTIVE We, therefore, aimed to investigate the effects of NGN non-complexed and complexed with hydroxypropyl-β-cyclodextrin (HPβCD) on neonatal endotoxemia injuries in a rodent model and describe the probable molecular mechanisms involved in NGN activities. METHOD We used exposure to a bacterial lipopolysaccharide (LPS) to induce neonatal endotoxemia in the mice. RESULTS It was found that NGN (100 mg/kg i.p.) exposure during the neonatal period reduced leukocyte migration and decreased pro-inflammatory cytokine (TNF-α, IL-1β and IL-6) levels in the lungs, heart, kidneys or cerebral cortex. In addition, NGN upregulated IL-10 production in the lungs and kidneys of neonate mice. The administration of NGN also enhanced antioxidant enzyme catalase and SOD activity, reduced lipid peroxidation and protein carbonylation and increased the reduced sulfhydryl groups in an organ-dependent manner, attenuating the oxidative damage caused by LPS exposure. NGN decreased ERK1/2, p38MAPK and COX-2 activation in the lungs of neonate mice. Moreover, NGN complexed with HPβCD was able to increase the animal survival rate. CONCLUSION NGN attenuated inflammatory and oxidative damage in the lungs, heart and kidneys caused by neonatal endotoxemia through the MAPK signaling pathways regulation. Our results show that NGN has beneficial effects against neonatal endotoxemia and could be useful in the treatment of neonatal inflammatory injuries.
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Affiliation(s)
- Luana Heimfarth
- Laboratory of Neuroscience and Pharmacological Assay (LANEF), Department of Physiology, Federal University of Sergipe, São Cristóvão, Sergipe CEP: 49100-000, Brazil
| | - Katielen Silvana Dos Santos
- Laboratory of Neuroscience and Pharmacological Assay (LANEF), Department of Physiology, Federal University of Sergipe, São Cristóvão, Sergipe CEP: 49100-000, Brazil
| | - Brenda Souza Monteiro
- Laboratory of Neuroscience and Pharmacological Assay (LANEF), Department of Physiology, Federal University of Sergipe, São Cristóvão, Sergipe CEP: 49100-000, Brazil
| | - Anne Karoline de Souza Oliveira
- Laboratory of Neuroscience and Pharmacological Assay (LANEF), Department of Physiology, Federal University of Sergipe, São Cristóvão, Sergipe CEP: 49100-000, Brazil
| | | | - Irwin R A Menezes
- Universidade Regional do Cariri - URCA, Departmento de Química Biológica, Crato, CE, Brazil
| | | | | | - Laurent Picot
- UMR CNRS 7266 LIENSs, La Rochelle Université, 17042 La Rochelle, France
| | - Raimundo Gonçalves de Oliveira Júnior
- Laboratoire de Pharmacognosie-UMR CNRS 8638, Faculté de Pharmacie, Université Paris Cité, Paris, France; CiTCoM UMR 8038 CNRS, Faculté Pharmacie, Université Paris Cité, 75006, Paris, France
| | - Raphaël Grougnet
- Laboratoire de Pharmacognosie-UMR CNRS 8638, Faculté de Pharmacie, Université Paris Cité, Paris, France
| | - Jullyana de Souza Siqueira Quintans
- Laboratory of Neuroscience and Pharmacological Assay (LANEF), Department of Physiology, Federal University of Sergipe, São Cristóvão, Sergipe CEP: 49100-000, Brazil; Graduate Program of Health Sciences, Federal University of Sergipe, Aracaju, Sergipe CEP 49060-025, Brazil
| | - Lucindo José Quintans-Júnior
- Laboratory of Neuroscience and Pharmacological Assay (LANEF), Department of Physiology, Federal University of Sergipe, São Cristóvão, Sergipe CEP: 49100-000, Brazil; Graduate Program of Health Sciences, Federal University of Sergipe, Aracaju, Sergipe CEP 49060-025, Brazil
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11
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Maydaniuk DT, Martens B, Iqbal S, Hogan AM, Lorente Cobo N, Motnenko A, Truong D, Liyanage SH, Yan M, Prehna G, Cardona ST. The mechanism of action of auranofin analogs in B. cenocepacia revealed by chemogenomic profiling. Microbiol Spectr 2024; 12:e0320123. [PMID: 38206016 PMCID: PMC10846046 DOI: 10.1128/spectrum.03201-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/06/2023] [Indexed: 01/12/2024] Open
Abstract
Drug repurposing efforts led to the discovery of bactericidal activity in auranofin, a gold-containing drug used to treat rheumatoid arthritis. Auranofin kills Gram-positive bacteria by inhibiting thioredoxin reductase, an enzyme that scavenges reactive oxygen species (ROS). Despite the presence of thioredoxin reductase in Gram-negative bacteria, auranofin is not always active against them. It is not clear whether the lack of activity in several Gram-negative bacteria is due to the cell envelope barrier or the presence of other ROS protective enzymes such as glutathione reductase (GOR). We previously demonstrated that chemical analogs of auranofin (MS-40 and MS-40S), but not auranofin, are bactericidal against the Gram-negative Burkholderia cepacia complex. Here, we explore the targets of auranofin, MS-40, and MS-40S in Burkholderia cenocepacia and elucidate the mechanism of action of the auranofin analogs by a genome-wide, randomly barcoded transposon screen (BarSeq). Auranofin and its analogs inhibited the B. cenocepacia thioredoxin reductase and induced ROS but did not inhibit the bacterial GOR. Genome-wide, BarSeq analysis of cells exposed to MS-40 and MS-40S compared to the ROS inducers arsenic trioxide, diamide, hydrogen peroxide, and paraquat revealed common and unique mediators of drug susceptibility. Furthermore, deletions of gshA and gshB that encode enzymes in the glutathione biosynthetic pathway led to increased susceptibility to MS-40 and MS-40S. Overall, our data suggest that the auranofin analogs kill B. cenocepacia by inducing ROS through inhibition of thioredoxin reductase and that the glutathione system has a role in protecting B. cenocepacia against these ROS-inducing compounds.IMPORTANCEThe Burkholderia cepacia complex is a group of multidrug-resistant bacteria that can cause infections in the lungs of people with the autosomal recessive disease, cystic fibrosis. Specifically, the bacterium Burkholderia cenocepacia can cause severe infections, reducing lung function and leading to a devastating type of sepsis, cepacia syndrome. This bacterium currently does not have an accepted antibiotic treatment plan because of the wide range of antibiotic resistance. Here, we further the research on auranofin analogs as antimicrobials by finding the mechanism of action of these potent bactericidal compounds, using a powerful technique called BarSeq, to find the global response of the cell when exposed to an antimicrobial.
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Affiliation(s)
| | - Brielle Martens
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Sarah Iqbal
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Andrew M. Hogan
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Neil Lorente Cobo
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Anna Motnenko
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Dang Truong
- Department of Chemistry, University of Massachusetts, Lowell, Massachusetts, USA
| | - Sajani H. Liyanage
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
- Department of Chemistry, University of Massachusetts, Lowell, Massachusetts, USA
- Department of Medical Microbiology & Infectious Disease, University of Manitoba, Winnipeg, Canada
| | - Mingdi Yan
- Department of Chemistry, University of Massachusetts, Lowell, Massachusetts, USA
| | - Gerd Prehna
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Silvia T. Cardona
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
- Department of Medical Microbiology & Infectious Disease, University of Manitoba, Winnipeg, Canada
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12
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Filice M, Caferro A, Gattuso A, Sperone E, Agnisola C, Faggio C, Cerra MC, Imbrogno S. Effects of environmental hypoxia on the goldfish skeletal muscle: Focus on oxidative status and mitochondrial dynamics. JOURNAL OF CONTAMINANT HYDROLOGY 2024; 261:104299. [PMID: 38237486 DOI: 10.1016/j.jconhyd.2024.104299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 01/02/2024] [Accepted: 01/11/2024] [Indexed: 02/13/2024]
Abstract
The skeletal muscle is a highly plastic tissue. Its ability to respond to external stimuli and challenges allows it to face the functional needs of the organism. In the goldfish Carassius auratus, a model of hypoxia resistance, exposure to reduced oxygen is accompanied by an improvement of the swimming performance, relying on a sustained contractile behavior of the skeletal muscle. At the moment, limited information is available on the mechanisms underlying these responses. We here evaluated the effects of short- (4 days) and long- (20 days) term exposure to moderate water hypoxia on the goldfish white skeletal muscle, focusing on oxidative status and mitochondrial dynamics. No differences in lipid peroxidation, measured as 2-thiobarbituric acid-reacting substances (TBARS), and oxidatively modified proteins (OMP) were detected in animals exposed to hypoxia with respect to their normoxic counterparts. Exposure to short-term hypoxia was characterized by an enhanced SOD activity and expression, paralleled by increased levels of Nrf2, a regulator of the antioxidant cell response, and HSP70, a chaperone also acting as a redox sensor. The expression of markers of mitochondrial biogenesis (TFAM) and abundance (VDAC) and of the mtDNA/nDNA ratio was similar under normoxia and under both short- and long-term hypoxia, thus excluding a rearrangement of the mitochondrial apparatus. Only an increase of PGC1α (a transcription factor involved in mitochondrial dynamics) was detected after 20 days of hypoxia. Our results revealed novel aspects of the molecular mechanisms that in the goldfish skeletal muscle may sustain the response to hypoxia, thus contributing to adequate tissue function to organism requirements.
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Affiliation(s)
- Mariacristina Filice
- Dept. of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Alessia Caferro
- Dept. of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Alfonsina Gattuso
- Dept. of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy.
| | - Emilio Sperone
- Dept. of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Claudio Agnisola
- Dept. of Biological Sciences, University of Naples Federico II, Napoli, Italy
| | - Caterina Faggio
- Dept. of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy; Dept. of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Naples, Italy.
| | - Maria Carmela Cerra
- Dept. of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Sandra Imbrogno
- Dept. of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
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13
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Funk LM, Poschmann G, Rabe von Pappenheim F, Chari A, Stegmann KM, Dickmanns A, Wensien M, Eulig N, Paknia E, Heyne G, Penka E, Pearson AR, Berndt C, Fritz T, Bazzi S, Uranga J, Mata RA, Dobbelstein M, Hilgenfeld R, Curth U, Tittmann K. Multiple redox switches of the SARS-CoV-2 main protease in vitro provide opportunities for drug design. Nat Commun 2024; 15:411. [PMID: 38195625 PMCID: PMC10776599 DOI: 10.1038/s41467-023-44621-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 12/21/2023] [Indexed: 01/11/2024] Open
Abstract
Besides vaccines, the development of antiviral drugs targeting SARS-CoV-2 is critical for preventing future COVID outbreaks. The SARS-CoV-2 main protease (Mpro), a cysteine protease with essential functions in viral replication, has been validated as an effective drug target. Here, we show that Mpro is subject to redox regulation in vitro and reversibly switches between the enzymatically active dimer and the functionally dormant monomer through redox modifications of cysteine residues. These include a disulfide-dithiol switch between the catalytic cysteine C145 and cysteine C117, and generation of an allosteric cysteine-lysine-cysteine SONOS bridge that is required for structural stability under oxidative stress conditions, such as those exerted by the innate immune system. We identify homo- and heterobifunctional reagents that mimic the redox switching and inhibit Mpro activity. The discovered redox switches are conserved in main proteases from other coronaviruses, e.g. MERS-CoV and SARS-CoV, indicating their potential as common druggable sites.
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Affiliation(s)
- Lisa-Marie Funk
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077, Göttingen, Germany
- Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Gereon Poschmann
- Institute of Molecular Medicine, Proteome Research, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Fabian Rabe von Pappenheim
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077, Göttingen, Germany
- Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Ashwin Chari
- Department of Structural Dynamics, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Kim M Stegmann
- Institute of Molecular Oncology, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Antje Dickmanns
- Institute of Molecular Oncology, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Marie Wensien
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077, Göttingen, Germany
- Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Nora Eulig
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077, Göttingen, Germany
- Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Elham Paknia
- Department of Structural Dynamics, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Gabi Heyne
- Department of Structural Dynamics, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Elke Penka
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077, Göttingen, Germany
- Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Arwen R Pearson
- Institute for Nanostructure and Solid-State Physics, Hamburg Centre for Ultrafast Imaging, Hamburg University, HARBOR, Luruper Chaussee 149, Hamburg, 22761, Germany
| | - Carsten Berndt
- Department of Neurology, Medical Faculty, Heinrich-Heine University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Tobias Fritz
- Institute of Physical Chemistry, Georg-August University Göttingen, Tammannstraße 6, D-37077, Göttingen, Germany
| | - Sophia Bazzi
- Institute of Physical Chemistry, Georg-August University Göttingen, Tammannstraße 6, D-37077, Göttingen, Germany
| | - Jon Uranga
- Institute of Physical Chemistry, Georg-August University Göttingen, Tammannstraße 6, D-37077, Göttingen, Germany
| | - Ricardo A Mata
- Institute of Physical Chemistry, Georg-August University Göttingen, Tammannstraße 6, D-37077, Göttingen, Germany
| | - Matthias Dobbelstein
- Institute of Molecular Oncology, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Rolf Hilgenfeld
- Institute for Biochemistry, Lübeck University, Ratzeburger Allee 160, 23562, Lübeck, Germany
- German Center for Infection Research, Hamburg - Lübeck-Borstel-Riems Site, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Ute Curth
- Institute for Biophysical Chemistry, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Kai Tittmann
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077, Göttingen, Germany.
- Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany.
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14
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Walgraeve J, Ferrero-Bordera B, Maaß S, Becher D, Schwerdtfeger R, van Dijl JM, Seefried M. Diamide-based screening method for the isolation of improved oxidative stress tolerance phenotypes in Bacillus mutant libraries. Microbiol Spectr 2023; 11:e0160823. [PMID: 37819171 PMCID: PMC10714788 DOI: 10.1128/spectrum.01608-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 08/30/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE During their life cycle, bacteria are exposed to a range of different stresses that need to be managed appropriately in order to ensure their growth and viability. This applies not only to bacteria in their natural habitats but also to bacteria employed in biotechnological production processes. Oxidative stress is one of these stresses that may originate either from bacterial metabolism or external factors. In biotechnological settings, it is of critical importance that production strains are resistant to oxidative stresses. Accordingly, this also applies to the major industrial cell factory Bacillus subtilis. In the present study, we, therefore, developed a screen for B. subtilis strains with enhanced oxidative stress tolerance. The results show that our approach is feasible and time-, space-, and resource-efficient. We, therefore, anticipate that it will enhance the development of more robust industrial production strains with improved robustness under conditions of oxidative stress.
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Affiliation(s)
| | | | - Sandra Maaß
- Department of Microbial Proteomics, University of Greifswald, Greifswald, Germany
| | - Dörte Becher
- Department of Microbial Proteomics, University of Greifswald, Greifswald, Germany
| | | | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
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15
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Evic V, Soic R, Mocibob M, Kekez M, Houser J, Wimmerová M, Matković-Čalogović D, Gruic-Sovulj I, Kekez I, Rokov-Plavec J. Evolutionarily conserved cysteines in plant cytosolic seryl-tRNA synthetase are important for its resistance to oxidation. FEBS Lett 2023; 597:2975-2992. [PMID: 37804069 DOI: 10.1002/1873-3468.14748] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 09/08/2023] [Accepted: 09/22/2023] [Indexed: 10/08/2023]
Abstract
We have previously identified a unique disulfide bond in the crystal structure of Arabidopsis cytosolic seryl-tRNA synthetase involving cysteines evolutionarily conserved in all green plants. Here, we discovered that both cysteines are important for protein stability, but with opposite effects, and that their microenvironment may promote disulfide bond formation in oxidizing conditions. The crystal structure of the C244S mutant exhibited higher rigidity and an extensive network of noncovalent interactions correlating with its higher thermal stability. The activity of the wild-type showed resistance to oxidation with H2 O2 , while the activities of cysteine-to-serine mutants were impaired, indicating that the disulfide link may enable the protein to function under oxidative stress conditions which can be beneficial for an efficient plant stress response.
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Affiliation(s)
- Valentina Evic
- Division of Biochemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Ruzica Soic
- Division of General and Inorganic Chemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Marko Mocibob
- Division of Biochemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Mario Kekez
- Division of Biochemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Josef Houser
- Central European Institute of Technology (CEITEC), Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Michaela Wimmerová
- Central European Institute of Technology (CEITEC), Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Dubravka Matković-Čalogović
- Division of General and Inorganic Chemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Ita Gruic-Sovulj
- Division of Biochemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Ivana Kekez
- Division of General and Inorganic Chemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Jasmina Rokov-Plavec
- Division of Biochemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
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16
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Smith N, Horswill AR, Wilson MA. X-ray-driven chemistry and conformational heterogeneity in atomic resolution crystal structures of bacterial dihydrofolate reductases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.07.566054. [PMID: 37986818 PMCID: PMC10659368 DOI: 10.1101/2023.11.07.566054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Dihydrofolate reductase (DHFR) catalyzes the NADPH-dependent reduction of dihydrofolate to tetrahydrofolate. Bacterial DHFRs are targets of several important antibiotics as well as model enzymes for the role of protein conformational dynamics in enzyme catalysis. We collected 0.93 Å resolution X-ray diffraction data from both Bacillus subtilis (Bs) and E. coli (Ec) DHFRs bound to folate and NADP+. These oxidized ternary complexes should not be able to perform chemistry, however electron density maps suggest hydride transfer is occurring in both enzymes. Comparison of low- and high-dose EcDHFR datasets show that X-rays drive partial production of tetrahydrofolate. Hydride transfer causes the nicotinamide moiety of NADP+ to move towards the folate as well as correlated shifts in nearby residues. Higher radiation dose also changes the conformational heterogeneity of Met20 in EcDHFR, supporting a solvent gating role during catalysis. BsDHFR has a different pattern of conformational heterogeneity and an unexpected disulfide bond, illustrating important differences between bacterial DHFRs. This work demonstrates that X-rays can drive hydride transfer similar to the native DHFR reaction and that X-ray photoreduction can be used to interrogate catalytically relevant enzyme dynamics in favorable cases.
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Affiliation(s)
- Nathan Smith
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE, 68588
| | - Alexander R. Horswill
- Department of Immunology & Microbiology, University of Colorado Anschutz School of Medicine, Aurora, CO 80045
| | - Mark A. Wilson
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE, 68588
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17
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Tran N, Dasari S, Barwell SAE, McLeod MJ, Kalyaanamoorthy S, Holyoak T, Ganesan A. The H163A mutation unravels an oxidized conformation of the SARS-CoV-2 main protease. Nat Commun 2023; 14:5625. [PMID: 37699927 PMCID: PMC10497556 DOI: 10.1038/s41467-023-40023-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 07/04/2023] [Indexed: 09/14/2023] Open
Abstract
The main protease of SARS-CoV-2 (Mpro) is an important target for developing COVID-19 therapeutics. Recent work has highlighted Mpro's susceptibility to undergo redox-associated conformational changes in response to cellular and immune-system-induced oxidation. Despite structural evidence indicating large-scale rearrangements upon oxidation, the mechanisms of conformational change and its functional consequences are poorly understood. Here, we present the crystal structure of an Mpro point mutant (H163A) that shows an oxidized conformation with the catalytic cysteine in a disulfide bond. We hypothesize that Mpro adopts this conformation under oxidative stress to protect against over-oxidation. Our metadynamics simulations illustrate a potential mechanism by which H163 modulates this transition and suggest that this equilibrium exists in the wild type enzyme. We show that other point mutations also significantly shift the equilibrium towards this state by altering conformational free energies. Unique avenues of SARS-CoV-2 research can be explored by understanding how H163 modulates this equilibrium.
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Affiliation(s)
- Norman Tran
- Department of Biology, Faculty of Science, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Sathish Dasari
- Department of Chemistry, Faculty of Science, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Sarah A E Barwell
- Department of Biology, Faculty of Science, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | | | - Subha Kalyaanamoorthy
- Department of Chemistry, Faculty of Science, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Todd Holyoak
- Department of Biology, Faculty of Science, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
| | - Aravindhan Ganesan
- ArGan's Lab, School of Pharmacy, Faculty of Science, University of Waterloo, 10A Victoria Street South, Kitchener, ON, N2G 1C5, Canada.
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18
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Yao H, Chen X, Wang T, Kashif M, Qiao X, Tüksammel E, Larsson LG, Okret S, Sayin VI, Qian H, Bergo MO. A MYC-controlled redox switch protects B lymphoma cells from EGR1-dependent apoptosis. Cell Rep 2023; 42:112961. [PMID: 37561633 DOI: 10.1016/j.celrep.2023.112961] [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: 02/06/2023] [Revised: 06/22/2023] [Accepted: 07/24/2023] [Indexed: 08/12/2023] Open
Abstract
Refractory and relapsed B cell lymphomas are often driven by the difficult-to-target oncogene MYC. Here, we report that high MYC expression stimulates proliferation and protects B lymphoma cells from apoptosis under normal oxidative stress levels and that compounds including N-acetylcysteine (NAC) and vitamin C (VitC) induce apoptosis by reducing oxidative stress. NAC and VitC injections effectively reduce tumor growth in lymphoma cells with high MYC expression but not in those with low MYC expression. MYC knockdown confers tumor resistance to NAC and VitC, while MYC activation renders B cells sensitive to these compounds. Mechanistically, NAC and VitC stimulate MYC binding to EGR1 through Cys117 of MYC, shifting its transcriptional output from cell cycle to apoptosis gene expression. These results identify a redox-controlled mechanism for MYC's role in maintaining proliferation and preventing apoptosis, offering a potential therapeutic rationale for evaluating NAC or VitC in patients with MYC-driven B cell lymphoma.
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Affiliation(s)
- Haidong Yao
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden
| | - Xue Chen
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden; Department of Plastic and Cosmetic Surgery, TongJi Hospital, TongJi Medical College, Huazhong University of Science and Technology, Wuhan 430 030, China
| | - Ting Wang
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden
| | - Muhammad Kashif
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska University Hospital, 141 86 Huddinge, Sweden
| | - Xi Qiao
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden
| | - Elin Tüksammel
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden
| | - Lars-Gunnar Larsson
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum, Karolinska Institutet, Solnavägen 9, Stockholm SE-171 65, Sweden
| | - Sam Okret
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden
| | - Volkan I Sayin
- Sahlgrenska Center for Cancer Research, Department of Surgery, Institute of Clinical Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Hong Qian
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska University Hospital, 141 86 Huddinge, Sweden.
| | - Martin O Bergo
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden.
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19
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Pezzotti G, Adachi T, Imamura H, Bristol DR, Adachi K, Yamamoto T, Kanamura N, Marin E, Zhu W, Kawai T, Mazda O, Kariu T, Waku T, Nichols FC, Riello P, Rizzolio F, Limongi T, Okuma K. In Situ Raman Study of Neurodegenerated Human Neuroblastoma Cells Exposed to Outer-Membrane Vesicles Isolated from Porphyromonas gingivalis. Int J Mol Sci 2023; 24:13351. [PMID: 37686157 PMCID: PMC10488263 DOI: 10.3390/ijms241713351] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
The aim of this study was to elucidate the chemistry of cellular degeneration in human neuroblastoma cells upon exposure to outer-membrane vesicles (OMVs) produced by Porphyromonas gingivalis (Pg) oral bacteria by monitoring their metabolomic evolution using in situ Raman spectroscopy. Pg-OMVs are a key factor in Alzheimer's disease (AD) pathogenesis, as they act as efficient vectors for the delivery of toxins promoting neuronal damage. However, the chemical mechanisms underlying the direct impact of Pg-OMVs on cell metabolites at the molecular scale still remain conspicuously unclear. A widely used in vitro model employing neuroblastoma SH-SY5Y cells (a sub-line of the SK-N-SH cell line) was spectroscopically analyzed in situ before and 6 h after Pg-OMV contamination. Concurrently, Raman characterizations were also performed on isolated Pg-OMVs, which included phosphorylated dihydroceramide (PDHC) lipids and lipopolysaccharide (LPS), the latter in turn being contaminated with a highly pathogenic class of cysteine proteases, a key factor in neuronal cell degradation. Raman characterizations located lipopolysaccharide fingerprints in the vesicle structure and unveiled so far unproved aspects of the chemistry behind protein degradation induced by Pg-OMV contamination of SH-SY5Y cells. The observed alterations of cells' Raman profiles were then discussed in view of key factors including the formation of amyloid β (Aβ) plaques and hyperphosphorylated Tau neurofibrillary tangles, and the formation of cholesterol agglomerates that exacerbate AD pathologies.
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Affiliation(s)
- Giuseppe Pezzotti
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.)
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (T.A.); (O.M.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
- Department of Orthopedic Surgery, Tokyo Medical University, 6-7-1 Nishi-Shinjuku, Shinjuku-ku, Tokyo 160-0023, Japan
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca Degli Abruzzi 24, 10129 Torino, Italy;
- Department of Molecular Science and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; (P.R.); (F.R.)
| | - Tetsuya Adachi
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (T.A.); (O.M.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
- Department of Microbiology, School of Medicine, Kansai Medical University, 2-5-1 Shinmachi, Hirakata 573-1010, Japan
| | - Hayata Imamura
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Davide Redolfi Bristol
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.)
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (T.A.); (O.M.)
- Department of Molecular Science and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; (P.R.); (F.R.)
| | - Keiji Adachi
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Toshiro Yamamoto
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Narisato Kanamura
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Elia Marin
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Wenliang Zhu
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.)
| | - Toshihisa Kawai
- Department of Oral Science and Translational Research, College of Dental Medicine, Nova Southeastern University, 3301 College Avenue, Fort Lauderdale, FL 33314, USA;
| | - Osam Mazda
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (T.A.); (O.M.)
| | - Toru Kariu
- Department of Life Science, Shokei University, Chuo-ku, Kuhonji, Kumamoto 862-8678, Japan;
| | - Tomonori Waku
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan;
| | - Frank C. Nichols
- Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, University of Connecticut, 263 Farmington Avenue, Storrs, CT 06030, USA;
| | - Pietro Riello
- Department of Molecular Science and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; (P.R.); (F.R.)
| | - Flavio Rizzolio
- Department of Molecular Science and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; (P.R.); (F.R.)
| | - Tania Limongi
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca Degli Abruzzi 24, 10129 Torino, Italy;
| | - Kazu Okuma
- Department of Microbiology, School of Medicine, Kansai Medical University, 2-5-1 Shinmachi, Hirakata 573-1010, Japan
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20
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Nikolaienko R, Bovo E, Kahn D, Gracia R, Jamrozik T, Zima AV. Cysteines 1078 and 2991 cross-linking plays a critical role in redox regulation of cardiac ryanodine receptor (RyR). Nat Commun 2023; 14:4498. [PMID: 37495581 PMCID: PMC10372021 DOI: 10.1038/s41467-023-40268-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 07/19/2023] [Indexed: 07/28/2023] Open
Abstract
The most common cardiac pathologies, such as myocardial infarction and heart failure, are associated with oxidative stress. Oxidation of the cardiac ryanodine receptor (RyR2) Ca2+ channel causes spontaneous oscillations of intracellular Ca2+, resulting in contractile dysfunction and arrhythmias. RyR2 oxidation promotes the formation of disulfide bonds between two cysteines on neighboring RyR2 subunits, known as intersubunit cross-linking. However, the large number of cysteines in RyR2 has been a major hurdle in identifying the specific cysteines involved in this pathology-linked post-translational modification of the channel. Through mutagenesis of human RyR2 and in-cell Ca2+ imaging, we identify that only two cysteines (out of 89) in each RyR2 subunit are responsible for half of the channel's functional response to oxidative stress. Our results identify cysteines 1078 and 2991 as a redox-sensitive pair that forms an intersubunit disulfide bond between neighboring RyR2 subunits during oxidative stress, resulting in a pathological "leaky" RyR2 Ca2+ channel.
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Affiliation(s)
- Roman Nikolaienko
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Elisa Bovo
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Daniel Kahn
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Ryan Gracia
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Thomas Jamrozik
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Aleksey V Zima
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL, 60153, USA.
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21
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Wang CG, Peiris MN, Meyer AN, Nelson KN, Donoghue DJ. Oncogenic driver FGFR3-TACC3 requires five coiled-coil heptads for activation and disulfide bond formation for stability. Oncotarget 2023; 14:133-145. [PMID: 36780330 PMCID: PMC9924825 DOI: 10.18632/oncotarget.28359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023] Open
Abstract
FGFR3-TACC3 represents an oncogenic fusion protein frequently identified in glioblastoma, lung cancer, bladder cancer, oral cancer, head and neck squamous cell carcinoma, gallbladder cancer, and cervical cancer. Various exon breakpoints of FGFR3-TACC3 have been identified in cancers; these were analyzed to determine the minimum contribution of TACC3 for activation of the FGFR3-TACC3 fusion protein. While TACC3 exons 11 and 12 are dispensable for activity, our results show that FGFR3-TACC3 requires exons 13-16 for biological activity. A detailed analysis of exon 13, which consists of 8 heptads forming a coiled coil, further defined the minimal region for biological activity as consisting of 5 heptads from exon 13, in addition to exons 14-16. These conclusions were supported by transformation assays of biological activity, examination of MAPK pathway activation, analysis of disulfide-bonded FGFR3-TACC3, and by examination of the Endoglycosidase H-resistant portion of FGFR3-TACC3. These results demonstrate that clinically identified FGFR3-TACC3 fusion proteins differ in their biological activity, depending upon the specific breakpoint. This study further suggests the TACC3 dimerization domain of FGFR3-TACC3 as a novel target in treating FGFR translocation driven cancers.
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Affiliation(s)
- Clark G. Wang
- 1Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA,2Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Malalage N. Peiris
- 1Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - April N. Meyer
- 1Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Katelyn N. Nelson
- 1Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Daniel J. Donoghue
- 1Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA,3Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA 92093, USA,Correspondence to:Daniel J. Donoghue, email:
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22
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Wang Z, Rabb JD, Lin Q. Orthogonal Crosslinking: A Strategy to Generate Novel Protein Topology and Function. Chemistry 2023; 29:e202202828. [PMID: 36251567 PMCID: PMC9839582 DOI: 10.1002/chem.202202828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Indexed: 11/27/2022]
Abstract
Compared to the disulfide bond, other naturally occurring intramolecular crosslinks have received little attention, presumably due to their rarity in the vast protein space. Here we presented examples of natural non-disulfide crosslinks, which we refer to as orthogonal crosslinks, emphasizing their effect on protein topology and function. We summarize recent efforts on expanding orthogonal crosslinks by using either the enzymes that catalyze protein circularization or the genetic code expansion strategy to add electrophilic amino acids site-specifically in proteins. The advantages and disadvantages of each method are discussed, along with their applications to generate novel protein topology and function. In particular, we highlight our recent work on spontaneous orthogonal crosslinking, in which a carbamate-based crosslink was generated in situ, and its applications in designing orthogonally crosslinked domain antibodies with their topology-mimicking bacterial adhesins.
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Affiliation(s)
- Zheng Wang
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, USA
| | - Johnathan D Rabb
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, USA
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, USA
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23
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Gary S, Bloom S. Peptide Carbocycles: From -SS- to -CC- via a Late-Stage "Snip-and-Stitch". ACS CENTRAL SCIENCE 2022; 8:1537-1547. [PMID: 36439308 PMCID: PMC9686213 DOI: 10.1021/acscentsci.2c00456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Indexed: 05/28/2023]
Abstract
One way to improve the therapeutic potential of peptides is through cyclization. This is commonly done using a disulfide bond between two cysteine residues in the peptide. However, disulfide bonds are susceptible to reductive cleavage, and this can deactivate the peptide and endanger endogenous proteins through covalent modification. Substituting disulfide bonds with more chemically robust carbon-based linkers has proven to be an effective strategy to better develop cyclic peptides as drugs, but finding the optimal carbon replacement is synthetically laborious. We report a new late-stage platform wherein a single disulfide bond in a cyclic peptide can serve as the progenitor for any number of new carbon-rich groups, derived from organodiiodides, using a Zn:Cu couple and a hydrosilane. We show that this platform can furnish entirely new carbocyclic scaffolds with enhanced permeability and structural integrity and that the stereochemistry of the new cycles can be biased by a judicious choice in silane.
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Affiliation(s)
- Samuel Gary
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas66045, United States
| | - Steven Bloom
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas66045, United States
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24
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Li X, Zhang T, Day NJ, Feng S, Gaffrey MJ, Qian WJ. Defining the S-Glutathionylation Proteome by Biochemical and Mass Spectrometric Approaches. Antioxidants (Basel) 2022; 11:2272. [PMID: 36421458 PMCID: PMC9687251 DOI: 10.3390/antiox11112272] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 11/14/2022] [Indexed: 08/27/2023] Open
Abstract
Protein S-glutathionylation (SSG) is a reversible post-translational modification (PTM) featuring the conjugation of glutathione to a protein cysteine thiol. SSG can alter protein structure, activity, subcellular localization, and interaction with small molecules and other proteins. Thus, it plays a critical role in redox signaling and regulation in various physiological activities and pathological events. In this review, we summarize current biochemical and analytical approaches for characterizing SSG at both the proteome level and at individual protein levels. To illustrate the mechanism underlying SSG-mediated redox regulation, we highlight recent examples of functional and structural consequences of SSG modifications. Finally, we discuss the analytical challenges in characterizing SSG and the thiol PTM landscape, future directions for understanding of the role of SSG in redox signaling and regulation and its interplay with other PTMs, and the potential role of computational approaches to accelerate functional discovery.
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Affiliation(s)
| | | | | | | | | | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
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25
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Environmental complexity is more important than mutation in driving the evolution of latent novel traits in E. coli. Nat Commun 2022; 13:5904. [PMID: 36202805 PMCID: PMC9537139 DOI: 10.1038/s41467-022-33634-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 09/26/2022] [Indexed: 11/23/2022] Open
Abstract
Recent experiments show that adaptive Darwinian evolution in one environment can lead to the emergence of multiple new traits that provide no immediate benefit in this environment. Such latent non-adaptive traits, however, can become adaptive in future environments. We do not know whether mutation or environment-driven selection is more important for the emergence of such traits. To find out, we evolve multiple wild-type and mutator E. coli populations under two mutation rates in simple (single antibiotic) environments and in complex (multi-antibiotic) environments. We then assay the viability of evolved populations in dozens of new environments and show that all populations become viable in multiple new environments different from those they had evolved in. The number of these new environments increases with environmental complexity but not with the mutation rate. Genome sequencing demonstrates the reason: Different environments affect pleiotropic mutations differently. Our experiments show that the selection pressure provided by an environment can be more important for the evolution of novel traits than the mutational supply experienced by a wild-type and a mutator strain of E. coli. Novel traits without immediate fitness benefit evolve frequently but we don’t know whether mutation or environment-driven selection drives this evolution. Here, using experimental evolution of E. coli populations, the authors demonstrate the importance of selection in the evolution of latent novel traits.
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26
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Marisa I, Asnicar D, Matozzo V, Parolini M, Brianese N, Fedorova M, Hoffman R, Sheehan D, Marin MG. Zinc oxide, titanium dioxide and C 60 fullerene nanoparticles, alone and in mixture, differently affect biomarker responses and proteome in the clam Ruditapes philippinarum. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:155873. [PMID: 35595145 DOI: 10.1016/j.scitotenv.2022.155873] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/06/2022] [Accepted: 05/08/2022] [Indexed: 06/15/2023]
Abstract
Continuous release of nanoparticles (NPs) into marine coastal environments results in an increased risk of exposure to complex NP mixtures for marine organisms. However, to date, the information on the effects at molecular and biochemical levels induced by the exposure to NPs, singly and as a mixture, is still scant. The present work aimed at exploring the independent and combined effects and the mechanism(s) of action induced by 7-days exposure to 1 μg/L nZnO, 1 μg/L nTiO2 and 1 μg/L FC60 fullerene in the Manila clam Ruditapes philippinarum, using a battery of immunological and oxidative stress biomarkers in haemolymph, gills and digestive gland. In addition, proteomics analyses were performed in gills and the digestive gland, where NP bioaccumulation was also assessed. Increased bioaccumulation of single NPs and the mixture was linked with increased oxidative stress and higher damage to proteins, lipids and DNA in all tissues analysed. The proteomics approach highlighted protein modulation in terms of abundance and damage (higher redox-thiol and carbonylated groups content). In particular, the modulated proteins (16 in gills and 18 in digestive gland) were mostly related to cytoskeleton and energetic metabolism. The digestive gland was the tissue more affected. For all biomarkers measured, increased detrimental effects were observed in the mixture compared to single NP exposures.
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Affiliation(s)
- Ilaria Marisa
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - Davide Asnicar
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - Valerio Matozzo
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - Marco Parolini
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Nicola Brianese
- Institute for Energetics and Interphases (IENI), CNR, Corso Stati Uniti 4, 35127 Padova, Italy
| | - Maria Fedorova
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany; Center for Biotechnology and Biomedicine, Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany
| | - Ralf Hoffman
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany; Center for Biotechnology and Biomedicine, Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany
| | - David Sheehan
- Proteomics Research Group, School of Biochemistry and Cell Biology and Environmental Research Institute, University College Cork, Western Rd., Cork, Ireland; Department of Chemistry and Biomedical Research Center, Khalifa University of Science and Technology, P.O. Box 127788, Abu Dhabi, United Arab Emirates
| | - Maria Gabriella Marin
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy.
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27
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Toomey CE, Heywood WE, Evans JR, Lachica J, Pressey SN, Foti SC, Al Shahrani M, D’Sa K, Hargreaves IP, Heales S, Orford M, Troakes C, Attems J, Gelpi E, Palkovits M, Lashley T, Gentleman SM, Revesz T, Mills K, Gandhi S. Mitochondrial dysfunction is a key pathological driver of early stage Parkinson's. Acta Neuropathol Commun 2022; 10:134. [PMID: 36076304 PMCID: PMC9461181 DOI: 10.1186/s40478-022-01424-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The molecular drivers of early sporadic Parkinson's disease (PD) remain unclear, and the presence of widespread end stage pathology in late disease masks the distinction between primary or causal disease-specific events and late secondary consequences in stressed or dying cells. However, early and mid-stage Parkinson's brains (Braak stages 3 and 4) exhibit alpha-synuclein inclusions and neuronal loss along a regional gradient of severity, from unaffected-mild-moderate-severe. Here, we exploited this spatial pathological gradient to investigate the molecular drivers of sporadic PD. METHODS We combined high precision tissue sampling with unbiased large-scale profiling of protein expression across 9 brain regions in Braak stage 3 and 4 PD brains, and controls, and verified these results using targeted proteomic and functional analyses. RESULTS We demonstrate that the spatio-temporal pathology gradient in early-mid PD brains is mirrored by a biochemical gradient of a changing proteome. Importantly, we identify two key events that occur early in the disease, prior to the occurrence of alpha-synuclein inclusions and neuronal loss: (i) a metabolic switch in the utilisation of energy substrates and energy production in the brain, and (ii) perturbation of the mitochondrial redox state. These changes may contribute to the regional vulnerability of developing alpha-synuclein pathology. Later in the disease, mitochondrial function is affected more severely, whilst mitochondrial metabolism, fatty acid oxidation, and mitochondrial respiration are affected across all brain regions. CONCLUSIONS Our study provides an in-depth regional profile of the proteome at different stages of PD, and highlights that mitochondrial dysfunction is detectable prior to neuronal loss, and alpha-synuclein fibril deposition, suggesting that mitochondrial dysfunction is one of the key drivers of early disease.
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Affiliation(s)
- Christina E. Toomey
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- The Francis Crick Institute, London, UK
| | - Wendy E. Heywood
- Translational Mass Spectrometry Research Group, Genetic & Genomic Medicine, Institute of Child Health, UCL, London, UK
| | - James R. Evans
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- The Francis Crick Institute, London, UK
| | - Joanne Lachica
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Sarah N. Pressey
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
| | - Sandrine C. Foti
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Mesfer Al Shahrani
- National Hospital for Neurology and Neurosurgery & Neurometabolic Unit, UCL Great Ormond Street Institute of Child Health, London, UK
- College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Karishma D’Sa
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- The Francis Crick Institute, London, UK
| | - Iain P. Hargreaves
- National Hospital for Neurology and Neurosurgery & Neurometabolic Unit, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Simon Heales
- National Hospital for Neurology and Neurosurgery & Neurometabolic Unit, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Michael Orford
- National Hospital for Neurology and Neurosurgery & Neurometabolic Unit, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Claire Troakes
- London Neurodegenerative Diseases Brain Bank, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, UK
| | - Johannes Attems
- Newcastle Brain Tissue Resource, Institute of Neuroscience and Newcastle University Institute for Ageing, Newcastle upon Tyne, UK
| | - Ellen Gelpi
- Neurological Tissue Bank, University of Barcelona, Barcelona, Spain
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Miklos Palkovits
- Human Brain Tissue Bank, Budapest, Semmelweis University, Budapest, Hungary
| | - Tammaryn Lashley
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | | | - Tamas Revesz
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Kevin Mills
- Translational Mass Spectrometry Research Group, Genetic & Genomic Medicine, Institute of Child Health, UCL, London, UK
| | - Sonia Gandhi
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- The Francis Crick Institute, London, UK
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28
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Smardz P, Sieradzan AK, Krupa P. Mechanical Stability of Ribonuclease A Heavily Depends on the Redox Environment. J Phys Chem B 2022; 126:6240-6249. [PMID: 35975925 PMCID: PMC9421896 DOI: 10.1021/acs.jpcb.2c04718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Disulfide bonds are covalent bonds that connect nonlocal fragments of proteins, and they are unique post-translational modifications of proteins. They require the oxidizing environment to be stable, which occurs for example during oxidative stress; however, in a cell the reductive environment is maintained, lowering their stability. Despite many years of research on disulfide bonds, their role in the protein life cycle is not fully understood and seems to strictly depend on a system or process in which they are involved. In this article, coarse-grained UNited RESidue (UNRES), and all-atom Assisted Model Building with Energy Refinement (AMBER) force fields were applied to run a series of steered molecular dynamics (SMD) simulations of one of the most studied, but still not fully understood, proteins─ribonuclease A (RNase A). SMD simulations were performed to study the mechanical stability of RNase A in different oxidative-reductive environments. As disulfide bonds (and any other covalent bonds) cannot break/form in any classical all-atom force field, we applied additional restraints between sulfur atoms of reduced cysteines which were able to mimic the breaking of the disulfide bonds. On the other hand, the coarse-grained UNRES force field enables us to study the breaking/formation of the disulfide bonds and control the reducing/oxidizing environment owing to the presence of the designed distance/orientation-dependent potential. This study reveals that disulfide bonds have a strong influence on the mechanical stability of RNase A only in a highly oxidative environment. However, the local stability of the secondary structure seems to play a major factor in the overall stability of the protein. Both our thermal unfolding and mechanical stretching studies show that the most stable disulfide bond is Cys65-Cys72. The breaking of disulfide bonds Cys26-Cys84 and Cys58-Cys110 is associated with large force peaks. They are structural bridges, which are mostly responsible for stabilizing the RNase A conformation, while the presence of the remaining two bonds (Cys65-Cys72 and Cys40-Cys95) is most likely connected with the enzymatic activity rather than the structural stability of RNase A in the cytoplasm. Our results prove that disulfide bonds are indeed stabilizing fragments of the proteins, but their role is strongly redox environment-dependent.
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Affiliation(s)
- Pamela Smardz
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Adam K Sieradzan
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Paweł Krupa
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
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29
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Differential Genetic Strategies of Burkholderia vietnamiensis and Paraburkholderia kururiensis for Root Colonization of Oryza sativa subsp.
japonica
and O. sativa subsp.
indica
, as Revealed by Transposon Mutagenesis Sequencing. Appl Environ Microbiol 2022; 88:e0064222. [DOI: 10.1128/aem.00642-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Burkholderiaceae
are frequent and abundant colonizers of the rice rhizosphere and interesting candidates to investigate for growth promotion. Species of
Paraburkholderia
have repeatedly been described to stimulate plant growth.
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30
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West JD. Experimental Approaches for Investigating Disulfide-Based Redox Relays in Cells. Chem Res Toxicol 2022; 35:1676-1689. [PMID: 35771680 DOI: 10.1021/acs.chemrestox.2c00123] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Reversible oxidation of cysteine residues within proteins occurs naturally during normal cellular homeostasis and can increase during oxidative stress. Cysteine oxidation often leads to the formation of disulfide bonds, which can impact protein folding, stability, and function. Work in both prokaryotic and eukaryotic models over the past five decades has revealed several multiprotein systems that use thiol-dependent oxidoreductases to mediate disulfide bond reduction, formation, and/or rearrangement. Here, I provide an overview of how these systems operate to carry out disulfide exchange reactions in different cellular compartments, with a focus on their roles in maintaining redox homeostasis, transducing redox signals, and facilitating protein folding. Additionally, I review thiol-independent and thiol-dependent approaches for interrogating what proteins partner together in such disulfide-based redox relays. While the thiol-independent approaches rely either on predictive measures or standard procedures for monitoring protein-protein interactions, the thiol-dependent approaches include direct disulfide trapping methods as well as thiol-dependent chemical cross-linking. These strategies may prove useful in the systematic characterization of known and newly discovered disulfide relay mechanisms and redox switches involved in oxidant defense, protein folding, and cell signaling.
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Affiliation(s)
- James D West
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, Ohio 44691, United States
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31
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Ascari A, Tran ENH, Eijkelkamp BA, Morona R. Detection of a disulphide bond and conformational changes in Shigella flexneri Wzy, and the role of cysteine residues in polymerase activity. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183871. [PMID: 35090897 DOI: 10.1016/j.bbamem.2022.183871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 01/11/2022] [Accepted: 01/19/2022] [Indexed: 10/19/2022]
Abstract
Shigella flexneri utilises the Wzy-dependent pathway for the production of a plethora of complex polysaccharides, including the lipopolysaccharide O-antigen (Oag) component. The inner membrane protein WzySF polymerises Oag repeat units, whilst two co-polymerase proteins, WzzSF and WzzpHS-2, together interact with WzySF to regulate production of short- (S-Oag) and very long- (VL-Oag) Oag modal lengths, respectively. The 2D arrangement of WzySF transmembrane and soluble regions has been previously deciphered, however, attaining information on the 3D structural and conformational arrangement of WzySF, or any homologue, has proven difficult. For the first time, the current study detected insights into the in situ WzySF arrangement. In vitro assays using thiol-reactive PEG-maleimide were used to probe WzySF conformation, which additionally detected novel, unique conformational changes in response to interaction with intrinsic factors, including WzzSF and WzzpHS-2, and extrinsic factors, such as temperature. Site-directed mutagenesis of WzySF cysteine residues revealed the presence of a putative intramolecular disulphide bond, between cysteine moieties 13 and 60. Subsequent analyses highlighted both the structural and functional importance of WzySF cysteines. Substitution of WzySF cysteine residues significantly decreased biosynthesis of the VL-Oag modal length, without disruption to S-Oag production. This phenotype was corroborated in the absence of co-polymerase competition for WzySF interaction. These data suggest WzySF cysteine substitutions directly impair the interaction between Wzy/WzzpHS-2, without altering the Wzy/WzzSF interplay, and in combination with structural data, we propose that the N- and C-termini of WzySF are arranged in close proximity, and together may form the unique WzzpHS-2 interaction site.
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Affiliation(s)
- Alice Ascari
- School of Biological Sciences, Department of Molecular and Biomedical Science, Research Centre for Infectious Diseases, University of Adelaide, Adelaide 5005, Australia.
| | - Elizabeth Ngoc Hoa Tran
- School of Biological Sciences, Department of Molecular and Biomedical Science, Research Centre for Infectious Diseases, University of Adelaide, Adelaide 5005, Australia.
| | - Bart A Eijkelkamp
- Molecular Sciences and Technology, College of Science and Engineering, Flinders University, Adelaide 5042, South Australia, Australia.
| | - Renato Morona
- School of Biological Sciences, Department of Molecular and Biomedical Science, Research Centre for Infectious Diseases, University of Adelaide, Adelaide 5005, Australia.
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32
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Peñaflor-Téllez Y, Chávez-Munguía B, Lagunes-Guillén A, Salazar-Villatoro L, Gutiérrez-Escolano AL. The Feline Calicivirus Leader of the Capsid Protein Has the Functional Characteristics of a Viroporin. Viruses 2022; 14:v14030635. [PMID: 35337042 PMCID: PMC8955107 DOI: 10.3390/v14030635] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 12/27/2022] Open
Abstract
The leader of the capsid (LC) protein is exclusive to the Vesivirus genus, and it is needed for successful feline calicivirus (FCV) replication, as well as an efficient apoptosis induction through the mitochondrial pathway. In this work, we aimed to determine if the LC protein from the FCV is a viroporin. Although lacking in a transmembrane domain or an amphipathic helix, the LC protein from the FCV is toxic when expressed in bacteria and it oligomerizes through disulfide bonds, which are both key characteristics of viroporins. An electron microscopy analysis of LC-expressing E. coli cells suggest that the protein induces osmotic stress. Moreover, we found that the previously studied C40A LC mutant, that fails to induce apoptosis and that hinders the replication cycle, also oligomerizes but it has a reduced toxicity and fails to induce osmotic stress in bacteria. We propose that the LC protein is a viroporin that acts as a disulfide bond-dependent antimicrobial peptide, similar to the Ebola virus delta peptide.
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33
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Gao H, Niu J, Zhao W, Zhang D, Li S, Xu Y, Liu Y. The Effect and Regulation Mechanism of Powdery Mildew on Wheat Grain Carbon Metabolism. STARCH-STARKE 2022. [DOI: 10.1002/star.202100239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hongyun Gao
- School of Life Sciences Zhengzhou Normal University Zhengzhou 450044 China
| | - Jishan Niu
- National Centre of Engineering and Technological Research for Wheat Henan Agricultural University Zhengzhou 450046 China
| | - Wanyong Zhao
- College of Food and Bioengineering Zhengzhou University of Light Industry Zhengzhou 450000 China
| | - Dale Zhang
- School of Life Sciences Henan University Kaifeng 475004 China
| | - Suoping Li
- School of Life Sciences Henan University Kaifeng 475004 China
| | - Yanhua Xu
- School of Life Sciences Zhengzhou Normal University Zhengzhou 450044 China
| | - Yumiao Liu
- School of Life Sciences Zhengzhou Normal University Zhengzhou 450044 China
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Fossum CJ, Laatsch BF, Lowater HR, Narkiewicz-Jodko AW, Lonzarich L, Hati S, Bhattacharyya S. Pre-Existing Oxidative Stress Creates a Docking-Ready Conformation of the SARS-CoV-2 Receptor-Binding Domain. ACS BIO & MED CHEM AU 2022; 2:84-93. [PMID: 37155555 PMCID: PMC8631169 DOI: 10.1021/acsbiomedchemau.1c00040] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
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The redox-dependent changes on the binding between the receptor-binding domain of the
severe acute respiratory syndrome-coronavirus-2 spike protein and the peptidase domain
of the human cell surface receptor angiotensin-converting enzyme II were investigated by
performing molecular dynamics simulations. The reduced states of the protein partners
were generated in silico by converting the disulfides to thiols. The role of redox
transformation on the protein–protein binding affinity was assessed from the
time-evolved structures after 200 ns simulations using electrostatic field calculations
and implicit solvation. The present simulations revealed that the bending motion at the
protein–protein interface is significantly altered when the disulfides are
reduced to thiols. In the native complex, the presence of disulfide bonds preserves the
structural complementarity of the protein partners and maintains the intrinsic
conformational dynamics. Also, the study demonstrates that when already bound, the
disulfide-to-thiol conversion of the receptor-binding domain has a limited impact on the
binding of the spike protein to the receptor. However, if the reduction occurs before
binding to the receptor, a spectacular conformational change of the receptor-binding
domain occurs that fully impairs the binding. In other words, the formation of disulfide
bonds, prevalent during oxidative stress, creates a conformation ready to bind to the
receptor. Taken together, the present study demonstrates the role of pre-existing
oxidative stress in elevating the binding affinity of the spike protein for the human
receptor, offering future clues for alternate therapeutic possibilities.
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Affiliation(s)
- Carl J. Fossum
- Department of Chemistry and Biochemistry, University of Wisconsin101 Roosevelt Avenue Eau Claire, Wisconsin 54701, United States
| | - Bethany F. Laatsch
- Department of Chemistry and Biochemistry, University of Wisconsin101 Roosevelt Avenue Eau Claire, Wisconsin 54701, United States
| | - Harrison R. Lowater
- Department of Chemistry and Biochemistry, University of Wisconsin101 Roosevelt Avenue Eau Claire, Wisconsin 54701, United States
| | - Alex W. Narkiewicz-Jodko
- Department of Chemistry and Biochemistry, University of Wisconsin101 Roosevelt Avenue Eau Claire, Wisconsin 54701, United States
| | - Leo Lonzarich
- Department of Chemistry and Biochemistry, University of Wisconsin101 Roosevelt Avenue Eau Claire, Wisconsin 54701, United States
| | - Sanchita Hati
- Department of Chemistry and Biochemistry, University of Wisconsin101 Roosevelt Avenue Eau Claire, Wisconsin 54701, United States
| | - Sudeep Bhattacharyya
- Department of Chemistry and Biochemistry, University of Wisconsin101 Roosevelt Avenue Eau Claire, Wisconsin 54701, United States
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35
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Karve S, Wagner A. Multiple novel traits without immediate benefits originate in bacteria evolving on single antibiotics. Mol Biol Evol 2021; 39:6448767. [PMID: 34865131 PMCID: PMC8789282 DOI: 10.1093/molbev/msab341] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
How new traits originate in evolution is a fundamental question of evolutionary biology. When such traits arise, they can either be immediately beneficial in their environment of origin, or they may become beneficial only in a future environment. Compared to immediately beneficial novel traits, novel traits without immediate benefits remain poorly studied. Here we use experimental evolution to study novel traits that are not immediately beneficial but that allow bacteria to survive in new environments. Specifically, we evolved multiple E. coli populations in five antibiotics with different mechanisms of action, and then determined their ability to grow in more than 200 environments that are different from the environment in which they evolved. Our populations evolved viability in multiple environments that contain not just clinically relevant antibiotics, but a broad range of antimicrobial molecules, such as surfactants, organic and inorganic salts, nucleotide analogues and pyridine derivatives. Genome sequencing of multiple evolved clones shows that pleiotropic mutations are important for the origin of these novel traits. Our experiments, which lasted fewer than 250 generations, demonstrate that evolution can readily create an enormous reservoir of latent traits in microbial populations. These traits can facilitate adaptive evolution in a changing world.
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Affiliation(s)
- Shraddha Karve
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich Switzerland
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, Switzerland.,The Santa Fe Institute, Santa Fe, New Mexico, USA.,Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, 7600, South Africa
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36
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Liu X, Zhang Y, Zhuang L, Olszewski K, Gan B. NADPH debt drives redox bankruptcy: SLC7A11/xCT-mediated cystine uptake as a double-edged sword in cellular redox regulation. Genes Dis 2021; 8:731-745. [PMID: 34522704 PMCID: PMC8427322 DOI: 10.1016/j.gendis.2020.11.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/03/2020] [Accepted: 11/18/2020] [Indexed: 01/18/2023] Open
Abstract
Cystine/glutamate antiporter solute carrier family 7 member 11 (SLC7A11; also known as xCT) plays a key role in antioxidant defense by mediating cystine uptake, promoting glutathione synthesis, and maintaining cell survival under oxidative stress conditions. Recent studies showed that, to prevent toxic buildup of highly insoluble cystine inside cells, cancer cells with high expression of SLC7A11 (SLC7A11high) are forced to quickly reduce cystine to more soluble cysteine, which requires substantial NADPH supply from the glucose-pentose phosphate pathway (PPP) route, thereby inducing glucose- and PPP-dependency in SLC7A11high cancer cells. Limiting glucose supply to SLC7A11high cancer cells results in significant NADPH “debt”, redox “bankruptcy”, and subsequent cell death. This review summarizes our current understanding of NADPH-generating and -consuming pathways, discusses the opposing role of SLC7A11 in protecting cells from oxidative stress–induced cell death such as ferroptosis but promoting glucose starvation–induced cell death, and proposes the concept that SLC7A11-mediated cystine uptake acts as a double-edged sword in cellular redox regulation. A detailed understanding of SLC7A11 in redox biology may identify metabolic vulnerabilities in SLC7A11high cancer for therapeutic targeting.
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Affiliation(s)
- Xiaoguang Liu
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yilei Zhang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Li Zhuang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Boyi Gan
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,The University of Texas, MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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37
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Iglesias V, Santos J, Santos-Suárez J, Pintado-Grima C, Ventura S. SGnn: A Web Server for the Prediction of Prion-Like Domains Recruitment to Stress Granules Upon Heat Stress. Front Mol Biosci 2021; 8:718301. [PMID: 34490351 PMCID: PMC8416484 DOI: 10.3389/fmolb.2021.718301] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/09/2021] [Indexed: 11/15/2022] Open
Abstract
Proteins bearing prion-like domains (PrLDs) are essential players in stress granules (SG) assembly. Analysis of data on heat stress-induced recruitment of yeast PrLDs to SG suggests that this propensity might be connected with three defined protein biophysical features: aggregation propensity, net charge, and the presence of free cysteines. These three properties can be read directly in the PrLDs sequences, and their combination allows to predict protein recruitment to SG under heat stress. On this basis, we implemented SGnn, an online predictor of SG recruitment that exploits a feed-forward neural network for high accuracy classification of the assembly behavior of PrLDs. The simplicity and precision of our strategy should allow its implementation to identify heat stress-induced SG-forming proteins in complete proteomes.
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Affiliation(s)
- Valentín Iglesias
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Jaime Santos
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Juan Santos-Suárez
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Carlos Pintado-Grima
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
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38
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Huleani S, Roberts MR, Beales L, Papaioannou EH. Escherichia coli as an antibody expression host for the production of diagnostic proteins: significance and expression. Crit Rev Biotechnol 2021; 42:756-773. [PMID: 34470557 DOI: 10.1080/07388551.2021.1967871] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
This review article concerns the production of recombinant antibody fragments for applications mainly in the diagnostic sector. The so-called "point of care diagnostics" is very important for timely diagnosis and treatment, thus being able to save lives and resources. There is intense pressure for more accurate and less expensive rapid diagnostic tests, with a value preferably <$1. Thus, the large-scale cost-effective production of recombinant antibodies is vital. The importance of Escherichia coli toward the production of inexpensive rapid tests will be explained in this review paper. Details about the different strains of E. coli, the strategies used for the insertion and the expression of recombinant proteins, and the challenges that still exist are provided. Afterward, the importance of the expression scale and culture parameters in the final yield of the antibodies are examined. From this analysis, it appears that for good yields of recombinant antibodies, aside from appropriate gene transfer and expression, the culturing parameters are of paramount importance. Larger scale production is more favorable, mainly due to the higher cell densities that can be achieved. Yields of functional Fab fragments in the range of 10-20 mg/L are considered good in shake flasks, whereas in bioreactors can be up to 1-2 g/L. An amount of 10-500 mg of such antibody per million rapid tests is required. Despite the substantial importance of the production of the antibodies and their fragments, their downstream processing should be appropriately considered from the beginning for achieving the target value of the final rapid diagnostic tests.
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Affiliation(s)
- Sergiu Huleani
- Engineering Building, Lancaster University, Lancaster, UK
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39
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Haddad M, Hervé V, Ben Khedher MR, Rabanel JM, Ramassamy C. Glutathione: An Old and Small Molecule with Great Functions and New Applications in the Brain and in Alzheimer's Disease. Antioxid Redox Signal 2021; 35:270-292. [PMID: 33637005 DOI: 10.1089/ars.2020.8129] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Significance: Glutathione (GSH) represents the most abundant and the main antioxidant in the body with important functions in the brain related to Alzheimer's disease (AD). Recent Advances: Oxidative stress is one of the central mechanisms in AD. We and others have demonstrated the alteration of GSH levels in the AD brain, its important role in the detoxification of advanced glycation end-products and of acrolein, a by-product of lipid peroxidation. Recent in vivo studies found a decrease of GSH in several areas of the brain from control, mild cognitive impairment, and AD subjects, which are correlated with cognitive decline. Critical Issues: Several strategies were developed to restore its intracellular level with the l-cysteine prodrugs or the oral administration of γ-glutamylcysteine to prevent alterations observed in AD. To date, no benefit on GSH level or on oxidative biomarkers has been reported in clinical trials. Thus, it remains uncertain if GSH could be considered a potential preventive or therapeutic approach or a biomarker for AD. Future Directions: We address how GSH-coupled nanocarriers represent a promising approach for the functionalization of nanocarriers to overcome the blood/brain barrier (BBB) for the brain delivery of GSH while avoiding cellular toxicity. It is also important to address the presence of GSH in exosomes for its potential intercellular transfer or its shuttle across the BBB under certain conditions. Antioxid. Redox Signal. 35, 270-292.
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Affiliation(s)
- Mohamed Haddad
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Canada.,Institute on Nutrition and Functional Foods, Université Laval, Québec, Canada
| | - Vincent Hervé
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Canada.,Institute on Nutrition and Functional Foods, Université Laval, Québec, Canada
| | - Mohamed Raâfet Ben Khedher
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Canada.,Institute on Nutrition and Functional Foods, Université Laval, Québec, Canada
| | | | - Charles Ramassamy
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Canada.,Institute on Nutrition and Functional Foods, Université Laval, Québec, Canada
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40
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Tye BW, Churchman LS. Hsf1 activation by proteotoxic stress requires concurrent protein synthesis. Mol Biol Cell 2021; 32:1800-1806. [PMID: 34191586 PMCID: PMC8684711 DOI: 10.1091/mbc.e21-01-0014] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Heat shock factor 1 (Hsf1) activation is responsible for increasing the abundance of protein-folding chaperones and degradation machinery in response to proteotoxic conditions that give rise to misfolded or aggregated proteins. Here we systematically explored the link between concurrent protein synthesis and proteotoxic stress in the budding yeast, Saccharomyces cerevisiae. Consistent with prior work, inhibiting protein synthesis before inducing proteotoxic stress prevents Hsf1 activation, which we demonstrated across a broad array of stresses and validate using orthogonal means of blocking protein synthesis. However, other stress-dependent transcription pathways remained activatable under conditions of translation inhibition. Titrating the protein denaturant ethanol to a higher concentration results in Hsf1 activation in the absence of translation, suggesting extreme protein-folding stress can induce proteotoxicity independent of protein synthesis. Furthermore, we demonstrate this connection under physiological conditions where protein synthesis occurs naturally at reduced rates. We find that disrupting the assembly or subcellular localization of newly synthesized proteins is sufficient to activate Hsf1. Thus, new proteins appear to be especially sensitive to proteotoxic conditions, and we propose that their aggregation may represent the bulk of the signal that activates Hsf1 in the wake of these insults.
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Affiliation(s)
- Blake W Tye
- Department of Genetics, Harvard Medical School, Boston, MA 02115.,Program in Chemical Biology, Harvard University, Cambridge, MA 02138
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41
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Mills A, Gago F. On the Need to Tell Apart Fraternal Twins eEF1A1 and eEF1A2, and Their Respective Outfits. Int J Mol Sci 2021; 22:6973. [PMID: 34203525 PMCID: PMC8268798 DOI: 10.3390/ijms22136973] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/25/2021] [Accepted: 06/25/2021] [Indexed: 01/03/2023] Open
Abstract
eEF1A1 and eEF1A2 are paralogous proteins whose presence in most normal eukaryotic cells is mutually exclusive and developmentally regulated. Often described in the scientific literature under the collective name eEF1A, which stands for eukaryotic elongation factor 1A, their best known activity (in a monomeric, GTP-bound conformation) is to bind aminoacyl-tRNAs and deliver them to the A-site of the 80S ribosome. However, both eEF1A1 and eEF1A2 are endowed with multitasking abilities (sometimes performed by homo- and heterodimers) and can be located in different subcellular compartments, from the plasma membrane to the nucleus. Given the high sequence identity of these two sister proteins and the large number of post-translational modifications they can undergo, we are often confronted with the dilemma of discerning which is the particular proteoform that is actually responsible for the ascribed biochemical or cellular effects. We argue in this review that acquiring this knowledge is essential to help clarify, in molecular and structural terms, the mechanistic involvement of these two ancestral and abundant G proteins in a variety of fundamental cellular processes other than translation elongation. Of particular importance for this special issue is the fact that several de novo heterozygous missense mutations in the human EEF1A2 gene are associated with a subset of rare but severe neurological syndromes and cardiomyopathies.
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Affiliation(s)
| | - Federico Gago
- Department of Biomedical Sciences & “Unidad Asociada IQM-CSIC”, School of Medicine and Health Sciences, University of Alcalá, E-28805 Alcalá de Henares, Spain;
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42
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Saito T, Chiku T, Oka M, Wada-Kakuda S, Nobuhara M, Oba T, Shinno K, Abe S, Asada A, Sumioka A, Takashima A, Miyasaka T, Ando K. Disulfide bond formation in microtubule-associated tau protein promotes tau accumulation and toxicity in vivo. Hum Mol Genet 2021; 30:1955-1967. [PMID: 34137825 PMCID: PMC8522637 DOI: 10.1093/hmg/ddab162] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/11/2021] [Accepted: 06/11/2021] [Indexed: 11/12/2022] Open
Abstract
Accumulation of microtubule-associated tau protein is thought to cause neuron loss in a group of neurodegenerative diseases called tauopathies. In diseased brains, tau molecules adopt pathological structures that propagate into insoluble forms with disease-specific patterns. Several types of posttranslational modifications in tau are known to modulate its aggregation propensity in vitro, but their influence on tau accumulation and toxicity at the whole-organism level has not been fully elucidated. Herein, we utilized a series of transgenic Drosophila models to compare systematically the toxicity induced by five tau constructs with mutations or deletions associated with aggregation, including substitutions at seven disease-associated phosphorylation sites (S7A and S7E), deletions of PHF6 and PHF6* sequences (ΔPHF6 and ΔPHF6*), and substitutions of cysteine residues in the microtubule binding repeats (C291/322A). We found that substitutions and deletions resulted in different patterns of neurodegeneration and accumulation, with C291/322A having a dramatic effect on both tau accumulation and neurodegeneration. These cysteines formed disulfide bonds in mouse primary cultured neurons and in the fly retina, and stabilized tau proteins. Additionally, they contributed to tau accumulation under oxidative stress. We also found that each of these cysteine residues contributes to the microtubule polymerization rate and microtubule levels at equilibrium, but none of them affected tau binding to polymerized microtubules. Since tau proteins expressed in the Drosophila retina are mostly present in the early stages of tau filaments self-assembly, our results suggest that disulfide bond formation by these cysteine residues could be attractive therapeutic targets.
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Affiliation(s)
- Taro Saito
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan.,Department of Biological Sciences, Faculty of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Tomoki Chiku
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Mikiko Oka
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Satoko Wada-Kakuda
- Department of Neuropathology, Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Mika Nobuhara
- Department of Neuropathology, Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Toshiya Oba
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Kanako Shinno
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Saori Abe
- Department of Biological Sciences, Faculty of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Akiko Asada
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan.,Department of Biological Sciences, Faculty of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Akio Sumioka
- Faculty of Science, Department of Life Science, Gakushuin University, Tokyo, Japan
| | - Akihiko Takashima
- Faculty of Science, Department of Life Science, Gakushuin University, Tokyo, Japan
| | - Tomohiro Miyasaka
- Department of Neuropathology, Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Kanae Ando
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan.,Department of Biological Sciences, Faculty of Science, Tokyo Metropolitan University, Tokyo, Japan
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43
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Lai HL, Fan XX, Li RZ, Wang YW, Zhang J, Liu L, Neher E, Yao XJ, Leung ELH. Roles of Ion Fluxes, Metabolism, and Redox Balance in Cancer Therapy. Antioxid Redox Signal 2021; 34:1108-1127. [PMID: 33115253 DOI: 10.1089/ars.2020.8125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Recent Advances: The 2019 Nobel Prize awarded to the mechanisms for oxygen sensing and adaptation according to oxygen availability, highlighting the fundamental importance of gaseous molecules. Gaseous molecules, including reactive oxygen species (ROS), can interact with different cations generated during metabolic and redox dysregulation in cancer cells. Cross talk between calcium signaling and metabolic/redox pathways leads to network-based dyregulation in cancer. Significance: Recent discovery on using small molecules targeting the ion channels, redox signaling, and protein modification on metabolic enzymes can effectively inhibit cancer growth. Several FDA-approved drugs and clinical trials are ongoing to target the calcium channels, such as TRPV6 and TRPM8. Multiple small molecules from natural products target metablic and redox enzymes to exert an anticancer effect. Critical Issues: Small molecules targeting key ion channels, metabolic enzymes that control key aspects of metabolism, and redox proteins are promising, but their action mechanisms of the target are needed to be elucidated with advanced-omic technologies, which can give network-based and highly dimensioal data. In addition, small molecules that can directly modify the protein residues have emerged as a novel anticancer strategy. Future Directions: Advanced technology accelerates the detection of ions and metabolic and redox changes in clinical samples for diagnosis and informs the decision of cancer treatment. The improvement of ROS detection, ROS target identification, and computational-aid drug discovery also improves clincal outcome.Overall, network-based or holistic regulations of cancer via ion therapy and metabolic and redox intervention are promising as new anticancer strategies. Antioxid. Redox Signal. 34, 1108-1127.
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Affiliation(s)
- Huan-Ling Lai
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute For Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), China
| | - Xing-Xing Fan
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute For Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), China
| | - Run-Ze Li
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute For Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), China
| | - Yu-Wei Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute For Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), China
| | - Junmin Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute For Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), China.,School of Pharmacy & State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou, China
| | - Liang Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute For Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), China
| | - Erwin Neher
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute For Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), China.,Membrane Biophysics Emeritus Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Xiao-Jun Yao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute For Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), China
| | - Elaine Lai-Han Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute For Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), China
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Tran HT, Bonilla CY. SigB-regulated antioxidant functions in gram‐positive bacteria. World J Microbiol Biotechnol 2021; 37:38. [DOI: 10.1007/s11274-021-03004-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 01/12/2021] [Indexed: 12/26/2022]
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45
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Carriles AA, Mills A, Muñoz-Alonso MJ, Gutiérrez D, Domínguez JM, Hermoso JA, Gago F. Structural Cues for Understanding eEF1A2 Moonlighting. Chembiochem 2020; 22:374-391. [PMID: 32875694 DOI: 10.1002/cbic.202000516] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/01/2020] [Indexed: 12/16/2022]
Abstract
Spontaneous mutations in the EEF1A2 gene cause epilepsy and severe neurological disabilities in children. The crystal structure of eEF1A2 protein purified from rabbit skeletal muscle reveals a post-translationally modified dimer that provides information about the sites of interaction with numerous binding partners, including itself, and maps these mutations onto the dimer and tetramer interfaces. The spatial locations of the side chain carboxylates of Glu301 and Glu374, to which phosphatidylethanolamine is uniquely attached via an amide bond, define the anchoring points of eEF1A2 to cellular membranes and interorganellar membrane contact sites. Additional bioinformatic and molecular modeling results provide novel structural insight into the demonstrated binding of eEF1A2 to SH3 domains, the common MAPK docking groove, filamentous actin, and phosphatidylinositol-4 kinase IIIβ. In this new light, the role of eEF1A2 as an ancient, multifaceted, and articulated G protein at the crossroads of autophagy, oncogenesis and viral replication appears very distant from the "canonical" one of delivering aminoacyl-tRNAs to the ribosome that has dominated the scene and much of the thinking for many decades.
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Affiliation(s)
- Alejandra A Carriles
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry "Rocasolano" CSIC, 28006, Madrid, Spain.,Biocrystallography Unit, Division of Immunology, Transplantation, and Infectious Diseases, IRCCS Scientific Institute San Raffaele, 20132, Milan, Italy
| | - Alberto Mills
- Department of Biomedical Sciences and "Unidad Asociada IQM-CSIC", School of Medicine and Health Sciences, University of Alcalá, 28805, Alcalá de Henares, Madrid, Spain
| | - María-José Muñoz-Alonso
- Department of Cell Biology and Pharmacogenomics, PharmaMar S.A.U., 28770, Colmenar Viejo, Madrid, Spain
| | - Dolores Gutiérrez
- Proteomics Unit, Faculty of Pharmacy, Complutense University, 28040, Madrid, Spain
| | - Juan M Domínguez
- Department of Cell Biology and Pharmacogenomics, PharmaMar S.A.U., 28770, Colmenar Viejo, Madrid, Spain
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry "Rocasolano" CSIC, 28006, Madrid, Spain
| | - Federico Gago
- Department of Biomedical Sciences and "Unidad Asociada IQM-CSIC", School of Medicine and Health Sciences, University of Alcalá, 28805, Alcalá de Henares, Madrid, Spain
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46
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Effects of foetal and breastfeeding exposure to methylmercury (MeHg) and retinol palmitate (Vitamin A) in rats: Redox parameters and susceptibility to DNA damage in liver. Mutat Res 2020; 858-860:503239. [PMID: 33198929 DOI: 10.1016/j.mrgentox.2020.503239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 08/01/2020] [Accepted: 08/14/2020] [Indexed: 01/01/2023]
Abstract
Methylmercury (MeHg) is known to be a chemical that poses a risk to public health. Exposure to MeHg and vitamin A (VitA) occurs through the ingestion of fish, present in the diet of most pregnant women. The absorption of these elements generates oxidative stress and can generate adaptations for future stressful events. Here, we assessed how exposure to VitA and/or MeHg during the fetal and breastfeeding period modulates the toxicity of MeHg reexposure in adulthood. We focus on redox systems and repairing DNA damage. Male rats (n = 50), were divided into 5 groups. Control received mineral oil; The VitA group received VitA during pregnancy, during breastfeeding and was exposed to MeHg in adulthood; VitA + MeHg received VitA and MeHg during pregnancy and breastfeeding and was exposed to MeHg in adulthood. The single exposure group (SE) was exposed to MeHg only in adulthood; and the MeHg group was pre-exposed to MeHg during pregnancy and breastfeeding and re-exposed to MeHg in adulthood. After treating the animals, we evaluated the redox status and the level of DNA damage in all rats. The results revealed that MeHg significantly decreased the activity of glutathione peroxidase (GPx) and sulfhydryl levels and increased the activity of superoxide dismutase (SOD), glutathione transferase, glutathione and carbonyl in all exposed groups. These results suggest that the second exposure to MeHg directly altered the effects of oxidation and that there were no specific effects associated with exposure during the fetal and breastfeeding periods. In addition, our findings indicate that MDA levels increased in MeHg and SE levels and no differences in MDA levels were observed between the VitA and MeHg + VitA groups. We also observed that animals pretreated exclusively with VitA showed residual damage similar to the control's DNA, while the other groups showed statistically higher levels of damage. In conclusion, low doses of MeHg and VitA during fetal and breastfeeding periods were unable to condition an adaptive response to subsequent exposure to MeHg in adulthood in relation to the observed levels of oxidative damage assessed after exposure.
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Flores-Solis D, Mendoza A, Rentería-González I, Casados-Vazquez LE, Trasviña-Arenas CH, Jiménez-Sandoval P, Benítez-Cardoza CG, Del Río-Portilla F, Brieba LG. Solution structure of the inhibitor of cysteine proteases 1 from Entamoeba histolytica reveals a possible auto regulatory mechanism. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140512. [PMID: 32731033 DOI: 10.1016/j.bbapap.2020.140512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 07/07/2020] [Accepted: 07/24/2020] [Indexed: 10/23/2022]
Abstract
The genome of Entamoeba histolytica encodes approximately 50 Cysteine Proteases (CPs) whose activity is regulated by two Inhibitors of Cysteine Proteases (ICPs), EhICP1 and EhICP2. The main difference between both EhICPs is the acquisition of a 17 N-terminal targeting signal in EhICP2 and three exposed cysteine residues in EhICP1. The three exposed cysteines in EhICP1 potentiate the formation of cross-linking species that drive heterogeneity. Here we solved the NMR structure of EhICP1 using a mutant protein without accessible cysteines. Our structural data shows that EhICP1 adopts an immunoglobulin fold composed of seven β-strands, and three solvent exposed loops that resemble the structures of EhICP2 and chagasin. EhICP1 and EhICP2 are able to inhibit the archetypical cysteine protease papain by intercalating their BC loops into the protease active site independently of the character of the residue (serine or threonine) responsible to interact with the active site of papain. EhICP1 and EhICP2 present signals of functional divergence as they clustered in different clades. Two of the three exposed cysteines in EhICP1 are located at the DE loop that intercalates into the CP substrate-binding cleft. We propose that the solvent exposed cysteines of EhICP1 play a role in regulating its inhibitory activity and that in oxidative conditions, the cysteines of EhICP1 react to form intra and intermolecular disulfide bonds that render an inactive inhibitor. EhICP2 is not subject to redox regulation, as this inhibitor does not contain a single cysteine residue. This proposed redox regulation may be related to the differential cellular localization between EhICP1 and EhICP2.
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Affiliation(s)
- David Flores-Solis
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito exterior s/n, Coyoacán, Ciudad de Mexico 04510, Mexico
| | - Angeles Mendoza
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito exterior s/n, Coyoacán, Ciudad de Mexico 04510, Mexico
| | - Itzel Rentería-González
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, km. 9.6 Libramiento Norte Carretera Irapuato-León, CP 36821 Irapuato, Guanajuato, Mexico
| | - Luz E Casados-Vazquez
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, km. 9.6 Libramiento Norte Carretera Irapuato-León, CP 36821 Irapuato, Guanajuato, Mexico
| | - Carlos H Trasviña-Arenas
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, km. 9.6 Libramiento Norte Carretera Irapuato-León, CP 36821 Irapuato, Guanajuato, Mexico
| | - Pedro Jiménez-Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, km. 9.6 Libramiento Norte Carretera Irapuato-León, CP 36821 Irapuato, Guanajuato, Mexico
| | - Claudia G Benítez-Cardoza
- Laboratorio de Investigación Bioquímica, Programa Institucional en Biomedicina Molecular ENMyH-Instituto Politécnico Nacional, Guillermo Massieu Helguera No. 239, La Escalera Ticoman, 07320, D.F, Mexico
| | - Federico Del Río-Portilla
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito exterior s/n, Coyoacán, Ciudad de Mexico 04510, Mexico.
| | - Luis G Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, km. 9.6 Libramiento Norte Carretera Irapuato-León, CP 36821 Irapuato, Guanajuato, Mexico.
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48
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Tang TMS, Cardella D, Lander AJ, Li X, Escudero JS, Tsai YH, Luk LYP. Use of an asparaginyl endopeptidase for chemo-enzymatic peptide and protein labeling. Chem Sci 2020; 11:5881-5888. [PMID: 32874509 PMCID: PMC7441500 DOI: 10.1039/d0sc02023k] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 05/11/2020] [Indexed: 12/19/2022] Open
Abstract
Asparaginyl endopeptidases (AEPs) are ideal for peptide and protein labeling. However, because of the reaction reversibility, a large excess of labels or backbone modified substrates are needed. In turn, simple and cheap reagents can be used to label N-terminal cysteine, but its availability inherently limits the potential applications. Aiming to address these issues, we have created a chemo-enzymatic labeling system that exploits the substrate promiscuity of AEP with the facile chemical reaction between N-terminal cysteine and 2-formyl phenylboronic acid (FPBA). In this approach, AEP is used to ligate polypeptides with a Asn-Cys-Leu recognition sequence with counterparts possessing an N-terminal Gly-Leu. Instead of being a labeling reagent, the commercially available FPBA serves as a scavenger converting the byproduct Cys-Leu into an inert thiazolidine derivative. This consequently drives the AEP labeling reaction forward to product formation with a lower ratio of label to protein substrate. By carefully screening the reaction conditions for optimal compatibility and minimal hydrolysis, conversion to the ligated product in the model reaction resulted in excellent yields. The versatility of this AEP-ligation/FPBA-coupling system was further demonstrated by site-specifically labeling the N- or C-termini of various proteins.
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Affiliation(s)
- T M Simon Tang
- School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff , CF10 3AT , UK .
| | - Davide Cardella
- School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff , CF10 3AT , UK .
| | - Alexander J Lander
- School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff , CF10 3AT , UK .
| | - Xuefei Li
- School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff , CF10 3AT , UK .
| | - Jorge S Escudero
- School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff , CF10 3AT , UK .
| | - Yu-Hsuan Tsai
- School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff , CF10 3AT , UK .
| | - Louis Y P Luk
- School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff , CF10 3AT , UK .
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Rosa-Silva HTD, Panzenhagen AC, Schmidtt V, Alves Teixeira A, Espitia-Pérez P, de Oliveira Franco Á, Mingori M, Torres-Ávila JF, Schnorr CE, Hermann PRS, Moraes DP, Almeida RF, Moreira JCF. Hepatic and neurobiological effects of foetal and breastfeeding and adulthood exposure to methylmercury in Wistar rats. CHEMOSPHERE 2020; 244:125400. [PMID: 31809933 DOI: 10.1016/j.chemosphere.2019.125400] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/20/2019] [Accepted: 11/17/2019] [Indexed: 06/10/2023]
Abstract
Methylmercury (MeHg) is an organic bioaccumulated mercury derivative that strongly affects the environment and represents a public health problem primarily to riparian communities in South America. Our objective was to investigate the hepatic and neurological effects of MeHg exposure during the phases foetal and breast-feeding and adult in Wistar rats. Wistar rats (n = 10) were divided into 3 groups. Control group received mineral oil; The simple exposure (SE) group was exposed only in adulthood (0.5 mg/kg/day); and double exposure (DE) was pre-exposed to MeHg 0.5 mg/kg/day during pregnancy and breastfeeding (±40 days) and re-exposed to MeHg for 45 days from day 100. After, we evaluated possible abnormalities. Behavioral and biochemical parameters in liver and occipital cortex (CO), markers of liver injury, redox and AKT/GSK3β/mTOR signaling pathway. Our results showed that both groups treated with MeHg presented significant alterations, such as decreased locomotion and exploration and impaired visuospatial perception. The rats exposed to MeHg showed severe liver damage and increased hepatic glycogen concentration. The MeHg groups showed significant impairment in redox balance and oxidative damage to liver macromolecules and CO. MeHg upregulated the AKT/GSK3β/mTOR pathway and the phosphorylated form of the Tau protein. In addition, we found a reduction in NeuN and GFAP immunocontent. These results represent the first approach to the hepatotoxic and neural effects of foetal and adult MeHg exposure.
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Affiliation(s)
- Helen Tais da Rosa-Silva
- Centro de Estudos em Estresse Oxidativo, Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.
| | - Alana Castro Panzenhagen
- Centro de Estudos em Estresse Oxidativo, Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Victória Schmidtt
- Centro de Estudos em Estresse Oxidativo, Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Alexsander Alves Teixeira
- Centro de Estudos em Estresse Oxidativo, Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Pedro Espitia-Pérez
- Facultad de Ciencias de la Salud, Laboratorio de Investigación Biomédica y Biología Molecular, Universidad del Sinú, Córdoba, Colombia
| | - Álvaro de Oliveira Franco
- Centro de Estudos em Estresse Oxidativo, Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Moara Mingori
- Centro de Estudos em Estresse Oxidativo, Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - José F Torres-Ávila
- Unit for Development and Innovation in Genetics and Molecular Biology, Universidad Simón Bolívar, Barranquilla, Atlántico, Colombia
| | - Carlos Eduardo Schnorr
- Departamento de Civil y Ambiental, Programa de Ingeniería Ambiental, Universidad de la Costa, Barranquilla, Atlántico, Colombia
| | - Paolla Rissi Silva Hermann
- Instituto de Química, Sala 103, Campus do Vale, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Diogo Pompéu Moraes
- Instituto de Química, Sala 103, Campus do Vale, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Roberto Farina Almeida
- Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - José Cláudio Fonseca Moreira
- Centro de Estudos em Estresse Oxidativo, Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
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50
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Lee HC, Zhao YJ. Resolving the topological enigma in Ca 2+ signaling by cyclic ADP-ribose and NAADP. J Biol Chem 2019; 294:19831-19843. [PMID: 31672920 PMCID: PMC6937575 DOI: 10.1074/jbc.rev119.009635] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cyclic ADP-ribose (cADPR) and nicotinic acid adenine dinucleotide phosphate (NAADP) are two structurally distinct messengers that mobilize the endoplasmic and endolysosomal Ca2+ stores, respectively. Both are synthesized by the CD38 molecule (CD38), which has long been thought to be a type II membrane protein whose catalytic domain, intriguingly, faces to the outside of the cell. Accordingly, for more than 20 years, it has remained unresolved how CD38 can use cytosolic substrates such as NAD and NADP to produce messengers that target intracellular Ca2+ stores. The discovery of type III CD38, whose catalytic domain faces the cytosol, has now begun to clarify this topological conundrum. This article reviews the ideas and clues leading to the discovery of the type III CD38; highlights an innovative approach for uncovering its natural existence; and discusses the regulators of its activity, folding, and degradation. We also review the compartmentalization of cADPR and NAADP biogenesis. We further discuss the possible mechanisms that promote type III CD38 expression and appraise a proposal of a Ca2+-signaling mechanism based on substrate limitation and product translocation. The surprising finding of another enzyme that produces cADPR and NAADP, sterile α and TIR motif-containing 1 (SARM1), is described. SARM1 regulates axonal degeneration and has no sequence similarity with CD38 but can catalyze the same set of multireactions and has the same cytosolic orientation as the type III CD38. The intriguing finding that SARM1 is activated by nicotinamide mononucleotide to produce cADPR and NAADP suggests that it may function as a regulated Ca2+-signaling enzyme like CD38.
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Affiliation(s)
- Hon Cheung Lee
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China, 518055
| | - Yong Juan Zhao
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China, 518055
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