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Westhauser F, Arango-Ospina M, Hupa L, Renkawitz T, Boccaccini AR, Kunisch E. A comparative analysis of the cytocompatibility, protein adsorption, osteogenic and angiogenic properties of the 45S5- and S53P4-bioactive glass compositions. Biomed Mater 2024; 19:025027. [PMID: 38266275 DOI: 10.1088/1748-605x/ad2210] [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: 09/29/2023] [Accepted: 01/24/2024] [Indexed: 01/26/2024]
Abstract
Despite their long history of application in orthopedics, the osteogenic and angiogenic properties as well as the cytocompatibility and protein adsorption of the 45S5- (in wt%: 45.0 SiO2, 24.5 Na2O, 24.5 CaO, 6.0 P2O5) and S53P4- (in wt%: 53.0 SiO2, 23.0 Na2O, 20.0 CaO, 4.0 P2O5) bioactive glass (BG) compositions have not yet been directly compared in one and the same experimental setting. In this study, the influence of morphologically equal granules of both BGs on proliferation, viability, osteogenic differentiation and angiogenic response of human bone-marrow-derived mesenchymal stromal cells (BMSCs) was assessed. Furthermore, their impact on vascular tube formation and adsorption of relevant proteins was evaluated. Both BGs showed excellent cytocompatibility and stimulated osteogenic differentiation of BMSCs. The 45S5-BG showed enhanced stimulation of bone morphogenic protein 2 (BMP2) gene expression and protein production compared to S53P4-BG. While gene expression and protein production of vascular endothelial growth factor (VEGF) were stimulated, both BGs had only limited influence on tubular network formation. 45S5-BG adsorbed a higher portion of proteins, namely BMP2 and VEGF, on its surface. In conclusion, both BGs show favorable properties with slight advantages for 45S5-BG. Since protein adsorption on BG surfaces is important for their biological performance, the composition of the proteome formed by osteogenic cells cultured on BGs should be analyzed in order to gain a deeper understanding of the mechanisms that are responsible for BG-mediated stimulation of osteogenic differentiation.
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Affiliation(s)
- Fabian Westhauser
- Department of Orthopedics, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Leena Hupa
- Johan Gadolin Process Chemistry Centre, Åbo Akademi University, Turku, Finland
| | - Tobias Renkawitz
- Department of Orthopedics, Heidelberg University Hospital, Heidelberg, Germany
| | - Aldo R Boccaccini
- Institute of Biomaterials, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Elke Kunisch
- Department of Orthopedics, Heidelberg University Hospital, Heidelberg, Germany
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2
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Matarèse BFE, Rusin A, Seymour C, Mothersill C. Quantum Biology and the Potential Role of Entanglement and Tunneling in Non-Targeted Effects of Ionizing Radiation: A Review and Proposed Model. Int J Mol Sci 2023; 24:16464. [PMID: 38003655 PMCID: PMC10671017 DOI: 10.3390/ijms242216464] [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: 09/20/2023] [Revised: 11/01/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
It is well established that cells, tissues, and organisms exposed to low doses of ionizing radiation can induce effects in non-irradiated neighbors (non-targeted effects or NTE), but the mechanisms remain unclear. This is especially true of the initial steps leading to the release of signaling molecules contained in exosomes. Voltage-gated ion channels, photon emissions, and calcium fluxes are all involved but the precise sequence of events is not yet known. We identified what may be a quantum entanglement type of effect and this prompted us to consider whether aspects of quantum biology such as tunneling and entanglement may underlie the initial events leading to NTE. We review the field where it may be relevant to ionizing radiation processes. These include NTE, low-dose hyper-radiosensitivity, hormesis, and the adaptive response. Finally, we present a possible quantum biological-based model for NTE.
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Affiliation(s)
- Bruno F. E. Matarèse
- Department of Haematology, University of Cambridge, Cambridge CB2 1TN, UK;
- Department of Physics, University of Cambridge, Cambridge CB2 1TN, UK
| | - Andrej Rusin
- Department of Biology, McMaster University, Hamilton, ON L8S 4L8, Canada; (A.R.); (C.S.)
| | - Colin Seymour
- Department of Biology, McMaster University, Hamilton, ON L8S 4L8, Canada; (A.R.); (C.S.)
| | - Carmel Mothersill
- Department of Biology, McMaster University, Hamilton, ON L8S 4L8, Canada; (A.R.); (C.S.)
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Daly MJ. The scientific revolution that unraveled the astonishing DNA repair capacity of the Deinococcaceae: 40 years on. Can J Microbiol 2023; 69:369-386. [PMID: 37267626 DOI: 10.1139/cjm-2023-0059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The family Deinococcaceae exhibits exceptional radiation resistance and possesses all the necessary traits for surviving in radiation-exposed environments. Their survival strategy involves the coupling of metabolic and DNA repair functions, resulting in an extraordinarily efficient homologous repair of DNA double-strand breaks (DSBs) caused by radiation or desiccation. The keys to their survival lie in the hyperaccumulation of manganous (Mn2+)-metabolite antioxidants that protect their DNA repair proteins under extreme oxidative stress and the persistent structural linkage by Holliday junctions of their multiple genome copies per cell that facilitates DSB repair. This coupling of metabolic and DNA repair functions has made polyploid Deinococcus bacteria a useful tool in environmental biotechnology, radiobiology, aging, and planetary protection. The review highlights the groundbreaking contributions of the late Robert G.E. Murray to the field of Deinococcus research and the emergent paradigm-shifting discoveries that revolutionized our understanding of radiation survivability and oxidative stress defense, demonstrating that the proteome, rather than the genome, is the primary target responsible for survivability. These discoveries have led to the commercial development of irradiated vaccines using Deinococcus Mn-peptide antioxidants and have significant implications for various fields.
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Affiliation(s)
- Michael J Daly
- Uniformed Services University of the Health Sciences (USUHS), School of Medicine, Department of Pathology, Bethesda, MD 20814-4799, USA
- Committee on Planetary Protection (CoPP), National Academies of Sciences, Washington, DC 20001, USA
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4
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Morresi C, Luccarini A, Marcheggiani F, Ferretti G, Damiani E, Bacchetti T. Modulation of paraoxonase-2 in human dermal fibroblasts by UVA-induced oxidative stress: A new potential marker of skin photodamage. Chem Biol Interact 2023; 384:110702. [PMID: 37717644 DOI: 10.1016/j.cbi.2023.110702] [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: 06/29/2023] [Revised: 09/05/2023] [Accepted: 09/08/2023] [Indexed: 09/19/2023]
Abstract
Paraoxonase-2 (PON2) is an intracellular protein, that exerts a protective role against cell oxidative stress and apoptosis. Genetic and environmental factors (i.e. dietary factors, cigarette smoke, drugs) are able to modulate cellular PON2 levels. The effect of ultraviolet A radiation (UVA), the oxidizing component of sunlight, on PON2 in human dermal fibroblasts (HuDe) has not been previously explored. Excessive UVA radiation is known to cause direct and indirect skin damage by influencing intracellular signalling pathways through oxidative stress mediated by reactive oxygen species (ROS) that modulate the expression of downstream genes involved in different processes, e.g. skin photoaging and cancer. The aim of this study was, therefore, to investigate the modulation of PON2 in terms of protein expression and enzyme activity in HuDe exposed to UVA (270 kJ/m2). Our results show that PON2 is up-regulated immediately after UVA exposure and that its levels and activity decrease in the post-exposure phase, in a time-dependent manner (2-24 h). The trend in PON2 levels mirror the time-course study of UVA-induced ROS. To confirm this, experiments were also performed in the presence of a SPF30 sunscreen used as shielding agent to revert modulation of PON2 at 0 and 2 h post-UVA exposure where other markers of photo-oxidative stress were also examined (NF-KB, γH2AX, advanced glycation end products). Overall, our results show that the upregulation of PON2 might be related to the increase in intracellular ROS and may play an important role in mitigation of UVA-mediated damage and in the prevention of the consequences of UV exposure, thus representing a new marker of early-response to UVA-induced damage in skin fibroblasts.
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Affiliation(s)
- Camilla Morresi
- Department of Life and Environmental Sciences, Marche Polytechnic University, Via Brecce Bianche, Ancona 60131, Italy
| | - Alessia Luccarini
- Department of Life and Environmental Sciences, Marche Polytechnic University, Via Brecce Bianche, Ancona 60131, Italy
| | - Fabio Marcheggiani
- Department of Life and Environmental Sciences, Marche Polytechnic University, Via Brecce Bianche, Ancona 60131, Italy
| | - Gianna Ferretti
- Department of Clinical Science and Odontostomatology, Marche Polytechnic University, Via Brecce Bianche, Ancona 60131, Italy
| | - Elisabetta Damiani
- Department of Life and Environmental Sciences, Marche Polytechnic University, Via Brecce Bianche, Ancona 60131, Italy.
| | - Tiziana Bacchetti
- Department of Life and Environmental Sciences, Marche Polytechnic University, Via Brecce Bianche, Ancona 60131, Italy.
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Benoit I, Burty-Valin E, Radman M. A Proteome-Centric View of Ageing, including that of the Skin and Age-Related Diseases: Considerations of a Common Cause and Common Preventative and Curative Interventions. CLINICAL, COSMETIC AND INVESTIGATIONAL DERMATOLOGY 2023; 16:79-85. [PMID: 36660191 PMCID: PMC9842513 DOI: 10.2147/ccid.s397751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/06/2023] [Indexed: 01/13/2023]
Abstract
The proteome comprises all proteins of a cell or organism. To carry their catalytic and structure-related functions, proteins must be correctly folded into their unique native three-dimensional structures. Common oxidative protein damage affects their functionality by impairing their catalytic and interactive specificities. Oxidative damage occurs preferentially to misfolded proteins and fixes the misfolded state. This review provides an overview of the mechanism and consequences of oxidative proteome damage - specifically irreversible protein carbonylation - in relation to ageing, including that of the skin as well as to age-related degeneration and diseases (ARDD) and their mitigation. A literature review of published manuscripts, available from PubMed, focusing on proteome, proteostasis, proteotoxicity, protein carbonylation, related inflammatory diseases, ARDD and the impact of the damaged proteome on ageing. During ageing, proteome damage, especially protein carbonylation, correlates with biological age. Carbonylated proteins form aggregates which can be considered as markers and accelerators of ageing and are common markers of most ARDD. Protein carbonylation leads to general ageing of the organism and organs including the skin and potentially to diseases including Alzheimer and Parkinson disease, diabetes, psoriasis, and skin cancer. Current research is promising and may open new therapeutic approaches and perspectives by targeting proteome protection as an age and ARDD management strategy.
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Affiliation(s)
- Isabelle Benoit
- Medical Relations, NAOS-ILS, Aix-en-Provence, France,Correspondence: Isabelle Benoit, NAOS-ILS, Aix-en-Provence, 13593, France, Tel +33442163060, Email
| | | | - Miroslav Radman
- Faculté de Médecine, INSERM U1001, Université R.-Descartes Paris-5, Paris, France,Scientific Affairs, Mediterranean Institute for Life Science, Split, Croatia
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Yamaguchi M, Tatara Y, Nugraha ED, Sato Y, Miura T, Hosoda M, Syaifudin M, Tokonami S, Kashiwakura I. Serum Proteomic and Oxidative Modification Profiling in Mice Exposed to Total Body X-Irradiation. Antioxidants (Basel) 2022; 11:antiox11091710. [PMID: 36139779 PMCID: PMC9495380 DOI: 10.3390/antiox11091710] [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: 07/22/2022] [Revised: 08/25/2022] [Accepted: 08/27/2022] [Indexed: 11/25/2022] Open
Abstract
The details of the dose-dependent response of serum proteins exposed to ionizing radiation, especially the oxidative modification response in amino acid sequences of albumin, the most abundant protein, are unknown. Thus, a proteomic analysis of the serum components from mice exposed to total body X-irradiation (TBI) ranging from 0.5 Gy to 3.0 Gy was conducted using LC-MS/MS. The analysis of oxidative modification sequences of albumin (mOMSA) in TBI mouse serum revealed significant moderate or strong correlations between the X-irradiation exposure dose and modification of 11 mOMSAs (especially the 97th, 267th and 499th lysine residues, 159th methionine residue and 287th tyrosine residues). In the case of X-irradiation of serum alone, significant correlations were also found in the 14 mOMSAs. In addition, a dose-dependent variation in six proteins (Angiotensinogen, Odorant-binding protein 1a, Serine protease inhibitor A3K, Serum paraoxonase/arylesterase 1, Prothrombin and Epidermal growth factor receptor) was detected in the serum of mice exposed to TBI. These findings suggest the possibility that the protein variation and serum albumin oxidative modification responses found in exposed individuals are important indicators for considering the effects of radiation on living organisms, along with DNA damage, and suggests their possible application as biomarkers of radiation dose estimation.
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Affiliation(s)
- Masaru Yamaguchi
- Hirosaki University Graduate School of Health Sciences, 66-1 Hon-cho, Hirosaki 036-8564, Aomori, Japan
| | - Yota Tatara
- Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Aomori, Japan
| | - Eka Djatnika Nugraha
- The Research Center for Safety, Metrology, and Nuclear Quality Technology (PRTKMMN), Research Organization for Nuclear Energy, National Research and Innovation Agency of Indonesia (BRIN), JI. Lebak Bulus Raya No. 49, Jakarta Selatan 12440, DKI Jakarta, Indonesia
| | - Yoshiaki Sato
- Hirosaki University Graduate School of Health Sciences, 66-1 Hon-cho, Hirosaki 036-8564, Aomori, Japan
| | - Tomisato Miura
- Institute of Radiation Emergency Medicine, Hirosaki University, 66-1 Hon-cho, Hirosaki, Aomori 036-8564, Japan
| | - Masahiro Hosoda
- Hirosaki University Graduate School of Health Sciences, 66-1 Hon-cho, Hirosaki 036-8564, Aomori, Japan
- Institute of Radiation Emergency Medicine, Hirosaki University, 66-1 Hon-cho, Hirosaki, Aomori 036-8564, Japan
| | - Mukh Syaifudin
- Research Center for Radioisotope, Radiopharmaceutical and Biodosimetry Technology, Research Organization for Nuclear Energy, National Research and Innovation Agency, Kw. Puspiptek, Setu, Tangerang Selatan 15312, Banten, Indonesia
| | - Shinji Tokonami
- Institute of Radiation Emergency Medicine, Hirosaki University, 66-1 Hon-cho, Hirosaki, Aomori 036-8564, Japan
| | - Ikuo Kashiwakura
- Hirosaki University Graduate School of Health Sciences, 66-1 Hon-cho, Hirosaki 036-8564, Aomori, Japan
- Correspondence:
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7
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Lippi A, Krisko A. CORE at the boundary of stress resistance and longevity. Int J Biochem Cell Biol 2022; 151:106277. [PMID: 35995386 DOI: 10.1016/j.biocel.2022.106277] [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: 06/09/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 10/15/2022]
Abstract
As chronological age of an organism increases, a number of errors accumulate at different levels of biological organization. The tendency of errors to accumulate and cause downstream problems in maintenance of cellular homeostasis is met by numerous protection and repair mechanisms. Maintenance of proteins is vital for cell viability and longevity, thus cellular proteostasis is supported by chaperone networks in every cellular compartment, as well as other pathways ensuring timely chaperone expression and activity. In this minireview, we summarize the progress related to the cross-organelle stress response (CORE), in charge of orchestrating a cell-wide response to compartmentalized proteotoxicity. The proposed CORE pathway encompasses activation of protein conformational maintenance machineries, antioxidant enzymes and metabolic changes simultaneously in the cytosol, mitochondria and the ER. We discuss its importance in cell survival and longevity as well as its potential to serve as a pharmaceutical target in age-related diseases.
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Affiliation(s)
- Alice Lippi
- Department of Experimental Neurodegeneration, University Medical Center Goettingen, Waldweg 33, 37075 Goettingen, Germany
| | - Anita Krisko
- Department of Experimental Neurodegeneration, University Medical Center Goettingen, Waldweg 33, 37075 Goettingen, Germany.
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8
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Wang J, Yano S, Xie K, Ohata Y, Hara T. Genome-Wide RNA Sequencing Analysis in Human Dermal Fibroblasts Exposed to Low-Dose Ultraviolet A Radiation. Genes (Basel) 2022; 13:genes13060974. [PMID: 35741736 PMCID: PMC9222854 DOI: 10.3390/genes13060974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/23/2022] [Accepted: 05/26/2022] [Indexed: 02/01/2023] Open
Abstract
Ultraviolet A (UVA) radiation can pass through the epidermis and reach the dermal skin layer, contributing to photoaging, DNA damage, and photocarcinogenesis in dermal fibroblasts. High-dose UVA exposure induces erythema, whereas low-dose, long-term UVA exposure causes skin damage and cell senescence. Biomarkers for evaluating damage caused by low-dose UVA in fibroblasts are lacking, making it difficult to develop therapeutic agents for skin aging and aging-associated diseases. We performed RNA-sequencing to investigate gene and pathway alterations in low-dose UVA-irradiated human skin-derived NB1RGB primary fibroblasts. Differentially expressed genes were identified and subjected to Gene Ontology and reactome pathway analysis, which revealed enrichment in genes in the senescence-associated secretory phenotype, apoptosis, respiratory electron transport, and transcriptional regulation by tumor suppressor p53 pathways. Insulin-like growth factor binding protein 7 (IGFBP7) showed the lowest p-value in RNA-sequencing analysis and was associated with the senescence-associated secretory phenotype. Protein–protein interaction analysis revealed that Fos proto-oncogene had a high-confidence network with IGFBP7 as transcription factor of the IGFBP7 gene among SASP hit genes, which were validated using RT-qPCR. Because of their high sensitivity to low-dose UVA radiation, Fos and IGFBP7 show potential as biomarkers for evaluating the effect of low-dose UVA radiation on dermal fibroblasts.
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Shcherbakov D, Nigri M, Akbergenov R, Brilkova M, Mantovani M, Petit PI, Grimm A, Karol AA, Teo Y, Sanchón AC, Kumar Y, Eckert A, Thiam K, Seebeck P, Wolfer DP, Böttger EC. Premature aging in mice with error-prone protein synthesis. SCIENCE ADVANCES 2022; 8:eabl9051. [PMID: 35235349 PMCID: PMC8890705 DOI: 10.1126/sciadv.abl9051] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The main source of error in gene expression is messenger RNA decoding by the ribosome. Translational accuracy has been suggested on a purely correlative basis to positively coincide with maximum possible life span among different rodent species, but causal evidence that translation errors accelerate aging in vivo and limit life span is lacking. We have now addressed this question experimentally by creating heterozygous knock-in mice that express the ribosomal ambiguity mutation RPS9 D95N, resulting in genome-wide error-prone translation. Here, we show that Rps9 D95N knock-in mice exhibit reduced life span and a premature onset of numerous aging-related phenotypes, such as reduced weight, chest deformation, hunchback posture, poor fur condition, and urinary syndrome, together with lymphopenia, increased levels of reactive oxygen species-inflicted damage, accelerated age-related changes in DNA methylation, and telomere attrition. Our results provide an experimental link between translational accuracy, life span, and aging-related phenotypes in mammals.
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Affiliation(s)
- Dimitri Shcherbakov
- Institut für Medizinische Mikrobiologie, Universität Zürich, CH-8006 Zurich, Switzerland
| | - Martina Nigri
- Anatomisches Institut, Universität Zürich, and Institut für Bewegungswissenschaften und Sport, ETH Zürich, CH-8057 Zurich, Switzerland
| | - Rashid Akbergenov
- Institut für Medizinische Mikrobiologie, Universität Zürich, CH-8006 Zurich, Switzerland
| | - Margarita Brilkova
- Institut für Medizinische Mikrobiologie, Universität Zürich, CH-8006 Zurich, Switzerland
| | - Matilde Mantovani
- Institut für Medizinische Mikrobiologie, Universität Zürich, CH-8006 Zurich, Switzerland
| | | | - Amandine Grimm
- Universitäre Psychiatrische Kliniken Basel, Transfaculty Research Platform Molecular and Cognitive Neurosciences, CH-4055 Basel, Switzerland
| | - Agnieszka A. Karol
- Musculoskeletal Research Unit (MSRU), Vetsuisse Faculty, University of Zurich, CH-8057 Zurich, Switzerland
| | - Youjin Teo
- Institut für Medizinische Mikrobiologie, Universität Zürich, CH-8006 Zurich, Switzerland
| | - Adrián Cortés Sanchón
- Institut für Medizinische Mikrobiologie, Universität Zürich, CH-8006 Zurich, Switzerland
| | - Yadhu Kumar
- Eurofins Genomics Europe Sequencing GmbH, D-78467 Konstanz, Germany
| | - Anne Eckert
- Universitäre Psychiatrische Kliniken Basel, Transfaculty Research Platform Molecular and Cognitive Neurosciences, CH-4055 Basel, Switzerland
| | | | - Petra Seebeck
- Zurich Integrative Rodent Physiology (ZIRP), University of Zurich, CH-8057 Zurich, Switzerland
| | - David P. Wolfer
- Anatomisches Institut, Universität Zürich, and Institut für Bewegungswissenschaften und Sport, ETH Zürich, CH-8057 Zurich, Switzerland
| | - Erik C. Böttger
- Institut für Medizinische Mikrobiologie, Universität Zürich, CH-8006 Zurich, Switzerland
- Corresponding author.
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Small-Molecule Mn Antioxidants in Caenorhabditis elegans and Deinococcus radiodurans Supplant MnSOD Enzymes during Aging and Irradiation. mBio 2022; 13:e0339421. [PMID: 35012337 PMCID: PMC8749422 DOI: 10.1128/mbio.03394-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Denham Harman's oxidative damage theory identifies superoxide (O2•-) radicals as central agents of aging and radiation injury, with Mn2+-dependent superoxide dismutase (MnSOD) as the principal O2•--scavenger. However, in the radiation-resistant nematode Caenorhabditis elegans, the mitochondrial antioxidant enzyme MnSOD is dispensable for longevity, and in the model bacterium Deinococcus radiodurans, it is dispensable for radiation resistance. Many radiation-resistant organisms accumulate small-molecule Mn2+-antioxidant complexes well-known for their catalytic ability to scavenge O2•-, along with MnSOD, as exemplified by D. radiodurans. Here, we report experiments that relate the MnSOD and Mn-antioxidant content to aging and oxidative stress resistances and which indicate that C. elegans, like D. radiodurans, may rely on Mn-antioxidant complexes as the primary defense against reactive oxygen species (ROS). Wild-type and ΔMnSOD D. radiodurans and C. elegans were monitored for gamma radiation sensitivities over their life spans while gauging Mn2+-antioxidant content by electron paramagnetic resonance (EPR) spectroscopy, a powerful new approach to determining the in vivo Mn-antioxidant content of cells as they age. As with D. radiodurans, MnSOD is dispensable for radiation survivability in C. elegans, which hyperaccumulates Mn-antioxidants exceptionally protective of proteins. Unexpectedly, ΔMnSOD mutants of both the nematodes and bacteria exhibited increased gamma radiation survival compared to the wild-type. In contrast, the loss of MnSOD renders radiation-resistant bacteria sensitive to atmospheric oxygen during desiccation. Our results support the concept that the disparate responses to oxidative stress are explained by the accumulation of Mn-antioxidant complexes which protect, complement, and can even supplant MnSOD. IMPORTANCE The current theory of cellular defense against oxidative damage identifies antioxidant enzymes as primary defenders against ROS, with MnSOD being the preeminent superoxide (O2•-) scavenger. However, MnSOD is shown to be dispensable both for radiation resistance and longevity in model organisms, the bacterium Deinococcus radiodurans and the nematode Caenorhabditis elegans. Measured by electron paramagnetic resonance (EPR) spectroscopy, small-molecule Mn-antioxidant content was shown to decline in unison with age-related decreases in cell proliferation and radioresistance, which again are independent of MnSOD presence. Most notably, the Mn-antioxidant content of C. elegans drops precipitously in the last third of its life span, which links with reports that the steady-state level of oxidized proteins increases exponentially during the last third of the life span in animals. This leads us to propose that global responses to oxidative stress must be understood through an extended theory that includes small-molecule Mn-antioxidants as potent O2•--scavengers that complement, and can even supplant, MnSOD.
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11
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Correlated Transcriptional Responses Provide Insights into the Synergy Mechanisms of the Furazolidone, Vancomycin, and Sodium Deoxycholate Triple Combination in Escherichia coli. mSphere 2021; 6:e0062721. [PMID: 34494879 PMCID: PMC8550143 DOI: 10.1128/msphere.00627-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Effective therapeutic options are urgently needed to tackle antibiotic resistance. Furazolidone (FZ), vancomycin (VAN), and sodium deoxycholate (DOC) show promise as their combination can synergistically inhibit the growth of, and kill, multidrug-resistant Gram-negative bacteria that are classified as critical priority by the World Health Organization. Here, we investigated the mechanisms of action and synergy of this drug combination using a transcriptomics approach in the model bacterium Escherichia coli. We show that FZ and DOC elicit highly similar gene perturbations indicative of iron starvation, decreased respiration and metabolism, and translational stress. In contrast, VAN induced envelope stress responses, in agreement with its known role in peptidoglycan synthesis inhibition. FZ induces the SOS response consistent with its DNA-damaging effects, but we demonstrate that using FZ in combination with the other two compounds enables lower dosages and largely mitigates its mutagenic effects. Based on the gene expression changes identified, we propose a synergy mechanism where the combined effects of FZ, VAN, and DOC amplify damage to Gram-negative bacteria while simultaneously suppressing antibiotic resistance mechanisms. IMPORTANCE Synergistic antibiotic combinations are a promising alternative strategy for developing effective therapies for multidrug-resistant bacterial infections. The synergistic combination of the existing antibiotics nitrofurans and vancomycin with sodium deoxycholate shows promise in inhibiting and killing multidrug-resistant Gram-negative bacteria. We examined the mechanism of action and synergy of these three antibacterials and proposed a mechanistic basis for their synergy. Our results highlight much-needed mechanistic information necessary to advance this combination as a potential therapy.
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Lee YH, Lee MC, Han J, Park JC, Kim MS, Kim DH, Byeon E, Kim S, Yim JH, Lee JS. iTRAQ-based proteomic profiling, pathway analyses, and apoptotic mechanism in the Antarctic copepod Tigriopus kingsejongensis in response to ultraviolet B radiation. Comp Biochem Physiol C Toxicol Pharmacol 2021; 248:109120. [PMID: 34182096 DOI: 10.1016/j.cbpc.2021.109120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 11/29/2022]
Abstract
iTRAQ proteomic profiling was conducted to examine the proteomic responses of the Antarctic copepod Tigriopus kingsejongensis under ultraviolet B (UVB) exposure. Of the 5507 proteins identified, 3479 proteins were annotated and classified into 25 groups using clusters of orthologous genes analysis. After exposing the T. kingsejongensis to 12 kJ/m2 UVB radiation, 77 biological processes were modulated over different time periods (0, 6, 12, 24, and 48 h) compared with the control. A Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that UVB exposure in T. kingsejongensis downregulated ribosome and glyoxylate and dicarboxylate metabolism at all time points. Furthermore, antioxidant and chaperone proteins were highly downregulated in response to UVB exposure, causing protein damage and activating apoptotic processes in the 48 h UVB exposure group. These proteomic changes show the mechanisms that underlie the detrimental effects of UVB on the cellular defense systems of the Antarctic copepod T. kingsejongensis.
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Affiliation(s)
- Young Hwan Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Min-Chul Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jeonghoon Han
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jun Chul Park
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Min-Sub Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Duck-Hyun Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Eunjin Byeon
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Sanghee Kim
- Division of Polar Life Science, Korea Polar Research Institute, Incheon 21990, South Korea
| | - Joung Han Yim
- Division of Polar Life Science, Korea Polar Research Institute, Incheon 21990, South Korea
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
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13
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Lopes AR, Figueiredo C, Sampaio E, Diniz M, Rosa R, Grilo TF. Impaired antioxidant defenses and DNA damage in the European glass eel (Anguilla anguilla) exposed to ocean warming and acidification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 774:145499. [PMID: 33610990 DOI: 10.1016/j.scitotenv.2021.145499] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/05/2021] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
The European eel (Anguilla anguilla) has attracted scientific inquiry for centuries due to its singular biological traits. Within the European Union, glass eel fisheries have declined sharply since 1980, from up to 2000 t (t) to 62.2 t in 2018, placing wild populations under higher risk of extinction. Among the major causes of glass eels collapse, climate change has become a growing worldwide issue, specifically ocean warming and acidification, but, to our knowledge, data on physiological and biochemical responses of glass eels to these stressors is limited. Within this context, we selected some representative biomarkers [e.g. glutathione peroxidase (GPx), catalase (CAT), total antioxidant capacity (TAC), heat shock proteins (HSP70), ubiquitin (Ub) and DNA damage] to study physiological responses of the European glass eel under distinct laboratory-climate change scenarios, such as increased water temperature (+ 4 °C) and pH reduction (- 0.4 units), for 12 weeks. Overall, the antioxidant enzymatic machinery was impaired, both in the muscle and viscera, manifested by significant changes in CAT, GPx and TAC. Heat shock response varied differently between tissues, increasing with temperature in the muscle, but not in the viscera, and decreasing in both tissues under acidification. The inability of HSP to maintain functional protein conformation was responsible for boosting the production of Ub, particularly under warming and acidification, as sole stressors. The overproduction of reactive oxygen species (ROS), either elicited by warming - due to increased metabolic demand - or acidification - through H+ interaction with O2-, generating H2O2 - overwhelmed defense mechanisms, causing oxidative stress and consequently leading to protein and DNA damage. Our results emphasize the vulnerability of eels' early life stages to climate change, with potential cascading consequences to adult stocks.
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Affiliation(s)
- Ana Rita Lopes
- MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; MARE - Marine and Environmental Sciences Centre, ISPA - Instituto Universitário, Rua Jardim Do Tabaco 34, 1149-041 Lisboa, Portugal
| | - Cátia Figueiredo
- MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; Division of Environmental Oceanography and Bioprospection, IPMA - Portuguese Institute for Sea and Atmosphere, Av. Brasília, 1449-006 Lisboa, Portugal; UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829-516 Caparica, Portugal
| | - Eduardo Sampaio
- MARE - Marine and Environmental Sciences Centre, Laboratório Marítimo da Guia, Faculdade de Ciências da Universidade de Lisboa, Avenida Nossa Senhora do Cabo 939, 2750-374 Cascais, Portugal
| | - Mário Diniz
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829-516 Caparica, Portugal
| | - Rui Rosa
- MARE - Marine and Environmental Sciences Centre, Laboratório Marítimo da Guia, Faculdade de Ciências da Universidade de Lisboa, Avenida Nossa Senhora do Cabo 939, 2750-374 Cascais, Portugal
| | - Tiago F Grilo
- MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal.
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14
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A biomimetic natural sciences approach to understanding the mechanisms of ageing in burden of lifestyle diseases. Clin Sci (Lond) 2021; 135:1251-1272. [PMID: 34037207 DOI: 10.1042/cs20201452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/29/2021] [Accepted: 05/04/2021] [Indexed: 12/12/2022]
Abstract
The worldwide landscape of an ageing population and age-related disease brings with it huge socio-economic and public healthcare concerns across nations. Correspondingly, monumental human and financial resources have been invested in biomedical research, with a mission to decode the mechanisms of ageing and how these contribute to age-related disease. Multiple hallmarks of ageing have been identified that are common across taxa, highlighting their fundamental importance. These include dysregulated mitochondrial metabolism and telomeres biology, epigenetic modifications, cell-matrix interactions, proteostasis, dysregulated nutrient sensing, stem cell exhaustion, inflammageing and immuno-senescence. While our understanding of the molecular basis of ageing is improving, it remains a complex and multifactorial process that remains to be fully understood. A key aspect of the shortfall in our understanding of the ageing process lies in translating data from standard animal models to humans. Consequently, we suggest that a 'biomimetic' and comparative approach, integrating knowledge from species in the wild, as opposed to inbred genetically homogenous laboratory animals, can provide powerful insights into human ageing processes. Here we discuss some particularities and comparative patterns among several species from the animal kingdom, endowed with longevity or short lifespans and unique metabolic profiles that could be potentially exploited to the understanding of ageing and age-related diseases. Based upon lessons from nature, we also highlight several avenues for renewed focus in the pathophysiology of ageing and age-related disease (i.e. diet-microbiome-health axis, oxidative protein damage, adaptive homoeostasis and planetary health). We propose that a biomimetic alliance with collaborative research from different disciplines can improve our understanding of ageing and age-related diseases with long-term sustainable utility.
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15
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Bruckbauer ST, Minkoff BB, Sussman MR, Cox MM. Proteome Damage Inflicted by Ionizing Radiation: Advancing a Theme in the Research of Miroslav Radman. Cells 2021; 10:cells10040954. [PMID: 33924085 PMCID: PMC8074248 DOI: 10.3390/cells10040954] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 02/03/2023] Open
Abstract
Oxidative proteome damage has been implicated as a major contributor to cell death and aging. Protein damage and aging has been a particular theme of the recent research of Miroslav Radman. However, the study of how cellular proteins are damaged by oxidative processes is still in its infancy. Here we examine oxidative changes in the proteomes of four bacterial populations—wild type E. coli, two isolates from E. coli populations evolved for high levels of ionizing radiation (IR) resistance, and D. radiodurans—immediately following exposure to 3000 Gy of ionizing radiation. By a substantial margin, the most prominent intracellular oxidation events involve hydroxylation of methionine residues. Significant but much less frequent are carbonylation events on tyrosine and dioxidation events on tryptophan. A few proteins are exquisitely sensitive to targeted oxidation events, notably the active site of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in E. coli. Extensive experimental evolution of E. coli for IR resistance has decreased overall proteome sensitivity to oxidation but not to the level seen in D. radiodurans. Many observed oxidation events may reflect aspects of protein structure and/or exposure of protein surfaces to water. Proteins such as GAPDH and possibly Ef-Tu may have an evolved sensitivity to oxidation by H2O2.
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Affiliation(s)
- Steven T. Bruckbauer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; (S.T.B.); (M.R.S.)
| | - Benjamin B. Minkoff
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Michael R. Sussman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; (S.T.B.); (M.R.S.)
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; (S.T.B.); (M.R.S.)
- Correspondence:
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16
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Combes GF, Pellay FX, Radman M. [Common cause and mechanism for all pathologies of aging?]. Med Sci (Paris) 2020; 36:1129-1134. [PMID: 33296629 DOI: 10.1051/medsci/2020221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Health is harmony, aging and its diseases (are) functional disharmony at the molecular, cellular and tissue levels. Our observations lead us to think that there seems to be a common cause and a common mechanism for aging and its many and diverse diseases. This common cause is the oxidative damage to particular proteins emerging from a combination of imperfect folding and oxidative stress. This common cause jointly goes with the biological clock common to various age-related diseases, whose the incidence increases exponentially over time and causes 90% of human mortality. Pharmacological interventions on the common cause could avoid and simultaneously attenuate all degenerative and malignant diseases, as it is the natural case of super-centenarians.
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Affiliation(s)
- Guillaume F Combes
- Mediterranean Institute for Life Sciences (MedILS), Meštrovic΄evo šetalište 45, 21000 Split, Croatie - Naos Institute for Life Sciences, 355 rue Pierre-Simon Laplace, 13593 Aix-en-Provence, France - Inserm U1001, Université Paris-Descartes, Faculté de médecine Paris-Descartes, 24 rue du faubourg Saint-Jacques, 75014 Paris, France - Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM-REI), Interdisciplinary Center for Advanced Sciences and Technology (ICAST), Université de Split, Poljička cesta 35, 21000 Split, Croatie
| | - François-Xavier Pellay
- Mediterranean Institute for Life Sciences (MedILS), Meštrovic΄evo šetalište 45, 21000 Split, Croatie - Naos Institute for Life Sciences, 355 rue Pierre-Simon Laplace, 13593 Aix-en-Provence, France
| | - Miroslav Radman
- Mediterranean Institute for Life Sciences (MedILS), Meštrovic΄evo šetalište 45, 21000 Split, Croatie - Naos Institute for Life Sciences, 355 rue Pierre-Simon Laplace, 13593 Aix-en-Provence, France - Inserm U1001, Université Paris-Descartes, Faculté de médecine Paris-Descartes, 24 rue du faubourg Saint-Jacques, 75014 Paris, France - Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM-REI), Interdisciplinary Center for Advanced Sciences and Technology (ICAST), Université de Split, Poljička cesta 35, 21000 Split, Croatie
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17
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Figueiredo C, Raimundo J, Lopes AR, Lopes C, Rosa N, Brito P, Diniz M, Caetano M, Grilo TF. Warming enhances lanthanum accumulation and toxicity promoting cellular damage in glass eels (Anguilla anguilla). ENVIRONMENTAL RESEARCH 2020; 191:110051. [PMID: 32818498 DOI: 10.1016/j.envres.2020.110051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/19/2020] [Accepted: 08/05/2020] [Indexed: 06/11/2023]
Abstract
Cumulative and continuing human emissions of greenhouse gases to the atmosphere are causing ocean warming. Rising temperature is a major threat to aquatic organisms and may affect physiological responses, such as acid-base balance, often compromising species fitness and survival. It is also expected that warming may influence the availability and toxicological effects of pollutants, including Rare Earth Elements. These are contaminants of environmental emerging concern with great economic interest. This group comprises yttrium, scandium and lanthanides, being Lanthanum (La) one of the most common. The European eel (Anguilla anguilla) is critically endangered and constitutes a delicacy in South East Asia and Europe, being subject to an increasing demand on a global scale. Considering the vulnerability of early life stages to contaminants, we exposed glass eels to 1.5 μg L-1 of La for five days, plus five days of depuration, under a present-day temperature and warming scenarios (△T = +4 °C). The aim of this study was to assess the bioaccumulation, elimination and specific biochemical enzymatic endpoints in glass eels (Anguilla anguilla) tissues, under warming and La. Overall, our results showed that the accumulation and toxicity of La were enhanced with increasing temperature. The accumulation was higher in the viscera, followed by the head, and ultimately the body. Elimination was less effective under warming. Exposure to La did not impact acetylcholinesterase activity. Moreover, lipid peroxidation peaked after five days under the combined exposure of La and warming. The expression of heat shock proteins was majorly suppressed in glass eels exposed to La, at both tested temperatures. This result suggests that, when exposed to La, glass eels were unable to efficiently prevent cellular damage, with a particularly dramatic setup in a near-future scenario. Further studies are needed towards a better understanding of the effects of lanthanum in a changing world.
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Affiliation(s)
- Cátia Figueiredo
- MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal; Division of Oceanography and Marine Environment, IPMA - Portuguese Institute for Sea and Atmosphere, Av. Alfredo Magalhães Ramalho, 6, 1495-165, Algés, Portugal; UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.
| | - Joana Raimundo
- MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal; CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, Avenida General Norton de Matos S/N, 4450-208, Matosinhos, Portugal
| | - Ana Rita Lopes
- MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal; MARE - Marine and Environmental Science Centre, ISPA - Instituto Universitário, R. Jardim Do Tabaco 34, 1100-304, Lisboa, Portugal
| | - Clara Lopes
- Division of Oceanography and Marine Environment, IPMA - Portuguese Institute for Sea and Atmosphere, Av. Alfredo Magalhães Ramalho, 6, 1495-165, Algés, Portugal; CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, Avenida General Norton de Matos S/N, 4450-208, Matosinhos, Portugal
| | - Nuno Rosa
- Division of Oceanography and Marine Environment, IPMA - Portuguese Institute for Sea and Atmosphere, Av. Alfredo Magalhães Ramalho, 6, 1495-165, Algés, Portugal
| | - Pedro Brito
- Division of Oceanography and Marine Environment, IPMA - Portuguese Institute for Sea and Atmosphere, Av. Alfredo Magalhães Ramalho, 6, 1495-165, Algés, Portugal
| | - Mário Diniz
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Miguel Caetano
- Division of Oceanography and Marine Environment, IPMA - Portuguese Institute for Sea and Atmosphere, Av. Alfredo Magalhães Ramalho, 6, 1495-165, Algés, Portugal; CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, Avenida General Norton de Matos S/N, 4450-208, Matosinhos, Portugal
| | - Tiago F Grilo
- MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
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18
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The Boggarts of biology: how non-genetic changes influence the genotype. Curr Genet 2020; 67:65-77. [PMID: 33037901 DOI: 10.1007/s00294-020-01108-5] [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: 07/30/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 01/21/2023]
Abstract
The notion that there is a one-one mapping from genotype to phenotype was overturned a long time ago. Along with genotype and environment, 'non-genetic changes' orchestrated by altered RNA and protein molecules also guide the development of phenotype. The idea that there is a route through which changes in phenotype can lead to changes in genotype impinges on several phenomena of molecular, developmental, evolutionary and applied interest. Phenotypic changes that do not alter the underlying DNA sequence have been studied across model systems (eg: DNA and histone modifications, RNA editing, prion formation) and are known to play an important role in short-term adaptation. However, because of their transient nature and unstable inheritance, the role of such changes in long-term evolution has remained controversial. I classify and review three ways in which non-genetic changes can influence genotype and impact cellular fitness across generations, with an emphasis on the enticing idea that they may act as stepping stones for genetic adaptation. I focus on work from microbial systems and attempt to highlight recent experiments and models that bear on this idea. Overall, I review evidence which suggests that non-genetic changes can impact phenotype via their influence on the genotype, and thus play a role in evolutionary change.
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19
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Abstract
How do organisms deal with free iron? On the one hand, iron is an essential metal that plays crucial structural and functional roles in many organisms. On the other hand, free iron is extremely toxic, particularly under aerobic conditions, where iron rapidly undergoes the Fenton reaction and produces highly reactive hydroxyl radicals. Our study now demonstrates that we have discovered one of the first physiologically relevant nonproteinaceous iron chelators and Fenton inhibitors. We found that polyphosphate, a highly conserved and ubiquitous inorganic polyanion, chelates iron and, through its multivalency, prevents the interaction of iron with peroxide and therefore the formation of hydroxyl radicals. We show that polyP provides a crucial iron reservoir for metalloproteins under nonstress conditions and effectively chelates free iron during iron stress. Importantly, polyP is present in all cells and organisms and hence is likely to take on this crucial function in both prokaryotic and eukaryotic cells. Maintaining cellular iron homeostasis is critical for organismal survival. Whereas iron depletion negatively affects the many metabolic pathways that depend on the activity of iron-containing enzymes, any excess of iron can cause the rapid formation of highly toxic reactive oxygen species (ROS) through Fenton chemistry. Although several cellular iron chelators have been identified, little is known about if and how organisms can prevent the Fenton reaction. By studying the effects of cisplatin, a commonly used anticancer drug and effective antimicrobial, we discovered that cisplatin elicits severe iron stress and oxidative DNA damage in bacteria. We found that both of these effects are successfully prevented by polyphosphate (polyP), an abundant polymer consisting solely of covalently linked inorganic phosphates. Subsequent in vitro and in vivo studies revealed that polyP provides a crucial iron reservoir under nonstress conditions and effectively complexes free iron and blocks ROS formation during iron stress. These results demonstrate that polyP, a universally conserved biomolecule, plays a hitherto unrecognized role as an iron chelator and an inhibitor of the Fenton reaction.
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20
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Mih N, Monk JM, Fang X, Catoiu E, Heckmann D, Yang L, Palsson BO. Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes. BMC Bioinformatics 2020; 21:162. [PMID: 32349661 PMCID: PMC7191737 DOI: 10.1186/s12859-020-3505-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 04/17/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The reconstruction of metabolic networks and the three-dimensional coverage of protein structures have reached the genome-scale in the widely studied Escherichia coli K-12 MG1655 strain. The combination of the two leads to the formation of a structural systems biology framework, which we have used to analyze differences between the reactive oxygen species (ROS) sensitivity of the proteomes of sequenced strains of E. coli. As proteins are one of the main targets of oxidative damage, understanding how the genetic changes of different strains of a species relates to its oxidative environment can reveal hypotheses as to why these variations arise and suggest directions of future experimental work. RESULTS Creating a reference structural proteome for E. coli allows us to comprehensively map genetic changes in 1764 different strains to their locations on 4118 3D protein structures. We use metabolic modeling to predict basal ROS production levels (ROStype) for 695 of these strains, finding that strains with both higher and lower basal levels tend to enrich their proteomes with antioxidative properties, and speculate as to why that is. We computationally assess a strain's sensitivity to an oxidative environment, based on known chemical mechanisms of oxidative damage to protein groups, defined by their localization and functionality. Two general groups - metalloproteins and periplasmic proteins - show enrichment of their antioxidative properties between the 695 strains with a predicted ROStype as well as 116 strains with an assigned pathotype. Specifically, proteins that a) utilize a molybdenum ion as a cofactor and b) are involved in the biogenesis of fimbriae show intriguing protective properties to resist oxidative damage. Overall, these findings indicate that a strain's sensitivity to oxidative damage can be elucidated from the structural proteome, though future experimental work is needed to validate our model assumptions and findings. CONCLUSION We thus demonstrate that structural systems biology enables a proteome-wide, computational assessment of changes to atomic-level physicochemical properties and of oxidative damage mechanisms for multiple strains in a species. This integrative approach opens new avenues to study adaptation to a particular environment based on physiological properties predicted from sequence alone.
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Affiliation(s)
- Nathan Mih
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093 USA
| | - Jonathan M. Monk
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
| | - Xin Fang
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
| | - Edward Catoiu
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
| | - David Heckmann
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
| | - Laurence Yang
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
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21
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Abstract
Cellular parabiosis is tissue-based phenotypic suppression of cellular dysfunction by intercellular molecular traffic keeping initiated age-related diseases and conditions in long latency. Interruption of cellular parabiosis (e.g. by chronic inflammation) promotes the onset of initiated pathologies. The stability of initiated latent cancers and other age-related diseases (ARD) hints to phenotypically silent genome alterations. I propose that latency in the onset of ageing and ARD is largely due to phenotypic suppression of cellular dysfunctions via molecular traffic among neighbouring cells. Intercellular trafficking ranges from the transfer of ions and metabolites (via gap junctions) to entire organelles (via tunnelling nanotubes). Any mechanism of cell-to-cell communication resulting in functional cross-complementation among the cells is called cellular parabiosis. Such ‘cellular solidarity’ creates tissue homeostasis by buffering defects and averaging cellular functions within the tissues. Chronic inflammation is known to (i) interrupt cellular parabiosis by the activity of extracellular proteases, (ii) activate dormant pathologies and (iii) shorten disease latency, as in tumour promotion and inflammaging. Variation in cellular parabiosis and protein oxidation can account for interspecies correlations between body mass, ARD latency and longevity. Now, prevention of ARD onset by phenotypic suppression, and healing by phenotypic reversion, become conceivable.
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Affiliation(s)
- Miroslav Radman
- 1 Mediterranean Institute for Life Sciences (MedILS) , 21000 Split , Croatia.,2 Naos Institute for Life Sciences , 13290 Aix-en-Provence , France.,3 Inserm u-1001, University R. Descartes Medical School , Cochin Site, 75014 Paris , France
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22
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Abstract
Ageing is considered as a snowballing phenotype of the accumulation of damaged dysfunctional or toxic proteins and silent mutations (polymorphisms) that sensitize relevant proteins to oxidative damage as inborn predispositions to age-related diseases. Ageing is not a disease, but it causes (or shares common cause with) age-related diseases as suggested by similar slopes of age-related increase in the incidence of diseases and death. Studies of robust and more standard species revealed that dysfunctional oxidatively damaged proteins are the root cause of radiation-induced morbidity and mortality. Oxidized proteins accumulate with age and cause reversible ageing-like phenotypes with some irreversible consequences (e.g. mutations). Here, we observe in yeast that aggregation rate of damaged proteins follows the Gompertz law of mortality and review arguments for a causal relationship between oxidative protein damage, ageing and disease. Aerobes evolved proteomes remarkably resistant to oxidative damage, but imperfectly folded proteins become sensitive to oxidation. We show that α-synuclein mutations that predispose to early-onset Parkinson's disease bestow an increased intrinsic sensitivity of α-synuclein to in vitro oxidation. Considering how initially silent protein polymorphism becomes phenotypic while causing age-related diseases and how protein damage leads to genome alterations inspires a vision of predictive diagnostic, prognostic, prevention and treatment of degenerative diseases.
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Affiliation(s)
- Anita Krisko
- 1 Mediterranean Institute for Life Sciences (MedILS) , 21000 Split , Croatia
| | - Miroslav Radman
- 1 Mediterranean Institute for Life Sciences (MedILS) , 21000 Split , Croatia.,2 Naos Institute for Life Sciences , 13290 Aix-en-Provence , France.,3 Inserm U-1001, Université Paris-Descartes, Faculté de Médecine Paris-Descartes , 74014 Paris , France
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23
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Global mistranslation increases cell survival under stress in Escherichia coli. PLoS Genet 2020; 16:e1008654. [PMID: 32150542 PMCID: PMC7082066 DOI: 10.1371/journal.pgen.1008654] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 03/19/2020] [Accepted: 02/05/2020] [Indexed: 12/23/2022] Open
Abstract
Mistranslation is typically deleterious for cells, although specific mistranslated proteins can confer a short-term benefit in a particular environment. However, given its large overall cost, the prevalence of high global mistranslation rates remains puzzling. Altering basal mistranslation levels of Escherichia coli in several ways, we show that generalized mistranslation enhances early survival under DNA damage, by rapidly activating the SOS response. Mistranslating cells maintain larger populations after exposure to DNA damage, and thus have a higher probability of sampling critical beneficial mutations. Both basal and artificially increased mistranslation increase the number of cells that are phenotypically tolerant and genetically resistant under DNA damage; they also enhance survival at high temperature. In contrast, decreasing the normal basal mistranslation rate reduces cell survival. This wide-ranging stress resistance relies on Lon protease, which is revealed as a key effector that induces the SOS response in addition to alleviating proteotoxic stress. The new links between error-prone protein synthesis, DNA damage, and generalised stress resistance indicate surprising coordination between intracellular stress responses and suggest a novel hypothesis to explain high global mistranslation rates.
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24
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Pinterić M, Podgorski II, Hadžija MP, Tartaro Bujak I, Dekanić A, Bagarić R, Farkaš V, Sobočanec S, Balog T. Role of Sirt3 in Differential Sex-Related Responses to a High-Fat Diet in Mice. Antioxidants (Basel) 2020; 9:antiox9020174. [PMID: 32093284 PMCID: PMC7071037 DOI: 10.3390/antiox9020174] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 12/13/2022] Open
Abstract
Metabolic homeostasis is differently regulated in males and females. Little is known about the mitochondrial Sirtuin 3 (Sirt3) protein in the context of sex-related differences in the development of metabolic dysregulation. To test our hypothesis that the role of Sirt3 in response to a high-fat diet (HFD) is sex-related, we measured metabolic, antioxidative, and mitochondrial parameters in the liver of Sirt3 wild-type (WT) and knockout (KO) mice of both sexes fed with a standard or HFD for ten weeks. We found that the combined effect of Sirt3 and an HFD was evident in more parameters in males (lipid content, glucose uptake, pparγ, cyp2e1, cyp4a14, Nrf2, MnSOD activity) than in females (protein damage and mitochondrial respiration), pointing towards a higher reliance of males on the effect of Sirt3 against HFD-induced metabolic dysregulation. The male-specific effects of an HFD also include reduced Sirt3 expression in WT and alleviated lipid accumulation and reduced glucose uptake in KO mice. In females, with a generally higher expression of genes involved in lipid homeostasis, either the HFD or Sirt3 depletion compromised mitochondrial respiration and increased protein oxidative damage. This work presents new insights into sex-related differences in the various physiological parameters with respect to nutritive excess and Sirt3.
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Affiliation(s)
- Marija Pinterić
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.P.); (I.I.P.); (M.P.H.); (A.D.); (T.B.)
| | - Iva I. Podgorski
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.P.); (I.I.P.); (M.P.H.); (A.D.); (T.B.)
| | - Marijana Popović Hadžija
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.P.); (I.I.P.); (M.P.H.); (A.D.); (T.B.)
| | - Ivana Tartaro Bujak
- Division of Materials Chemistry, Ruđer Bošković Institute,10000 Zagreb, Croatia
| | - Ana Dekanić
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.P.); (I.I.P.); (M.P.H.); (A.D.); (T.B.)
| | - Robert Bagarić
- Division of Experimental Physics, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (R.B.); (V.F.)
| | - Vladimir Farkaš
- Division of Experimental Physics, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (R.B.); (V.F.)
| | - Sandra Sobočanec
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.P.); (I.I.P.); (M.P.H.); (A.D.); (T.B.)
- Correspondence: ; Tel.: +385-1-4561-172
| | - Tihomir Balog
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.P.); (I.I.P.); (M.P.H.); (A.D.); (T.B.)
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Sartorio MG, Repizo GD, Cortez N. Catalases of the polyextremophylic Andean isolate Acinetobacter sp. Ver 3 confer adaptive response to H 2 O 2 and UV radiation. FEBS J 2020; 287:4525-4539. [PMID: 32037677 DOI: 10.1111/febs.15244] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 11/18/2019] [Accepted: 02/07/2020] [Indexed: 12/13/2022]
Abstract
The polyextremophilic strain Acinetobacter sp. Ver3 isolated from high-altitude Andean lakes exhibits elevated tolerance to UV-B radiation and to pro-oxidants, a feature that has been correlated to its unusually high catalase activity. The Ver3 genome sequence analysis revealed the presence of two genes coding for monofunctional catalases: AV3 KatE1 and AV3 KatE2, the latter harboring an N-terminal signal peptide. We show herein that AV3 KatE1 displays one of the highest catalytic activities reported so far and is constitutively expressed at relatively high amounts in the cytosol, acting as the main protecting catalase against H2 O2 and UV-B radiation. The second catalase, AV3 KatE2, is a periplasmic enzyme strongly induced by both peroxide and UV, conferring supplementary protection against pro-oxidants. The N-terminal signal present in AV3 KatE2 was required not only for transport to the periplasm via the twin-arginine translocation pathway, but also for proper folding and subsequent catalytic activity. The analysis of catalase distribution among 114 Acinetobacter complete genomes revealed a great variability in the catalase classes, with A. baumannii clinical isolates exhibiting higher numbers of isoenzymes and the most variable profiles.
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Affiliation(s)
- Mariana Gabriela Sartorio
- Instituto de Biología Molecular y Celular de Rosario (UNR & CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Argentina
| | - Guillermo Daniel Repizo
- Instituto de Biología Molecular y Celular de Rosario (UNR & CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Argentina
| | - Néstor Cortez
- Instituto de Biología Molecular y Celular de Rosario (UNR & CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Argentina
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Hymenobacter jejuensis sp. nov., a UV radiation-tolerant bacterium isolated from Jeju Island. Antonie van Leeuwenhoek 2019; 113:553-561. [PMID: 31823137 DOI: 10.1007/s10482-019-01363-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 11/19/2019] [Indexed: 12/16/2022]
Abstract
A novel Gram-stain negative, aerobic, rod-shaped, non-motile and pink-coloured bacterium, designated strain 17J68-5T, was isolated from soil in Jeju Island, Korea. The strain was found to grow at 18-37 °C (optimum 25 °C) in R2A medium at pH (6.0 to 7.5; optimum 6.5) in the presence of 0% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 17J68-5T forms a distinct lineage within the family Hymenobacteraceae and is closely related to Hymenobacter daecheongensis DSM 21074T (94.9% 16S rRNA gene sequence similarity), Hymenobacter rutilus K2-33028T (94.6%) and Hymenobacter tibetensis XTM003T (94.3%). The draft genome sequence of strain 17J68-5Tis 5.1 Mb size. The calculated average nucleotide identity and the digital DNA-DNA hybridization between strain 17J68-5T and closely related type strains were 81.3 to 84.1 % and 25.5 to 28.1%. The major cellular fatty acids (≥ 10%) of the strain 17J68-5T were identified as summed feature 3 (C16:1ω6c/C16:1ω7c; 21.2%), iso-C15:0 (19.1%), summed feature 4 (C17:1 iso I/C17:1 anteiso B; 17.9%) and C16:1ω5c (13.1%). The predominant respiratory quinones were found to be menaquinone 7 and 6 (MK-7 and MK-6). The major polar lipid was found to be phosphatidylethanolamine. The genomic DNA G + C content based on the whole genome sequence is 59.6 mol %. The phenotypic, chemotaxonomic and genotypic properties clearly indicated that isolate 17J68-5T represents a novel species within the genus Hymenobacter, for which the name Hymenobacter jejuensis sp. nov. is proposed. The type strain of Hymenobacter jejuensis is 17J68-5T (= KCTC 62224T = JCM 33182T).
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Abstract
Cells and organisms grow old and die. We develop a biophysical model of the mechanism. Young cells are kept healthy by the positive processes of protein synthesis, degradation, and chaperoning (the activity of keeping proteins properly folded). But, with age, negative processes increase: Oxidative damage accumulates randomly in the cell’s proteins, healthy synthesis and degradation slow down, and—like overfilled garbage cans—chaperone capacity is exceeded. The chaperones are distracted trying to fold irreversibly damaged proteins, leading to accumulating misfolded and aggregated proteins in the cell. The tipping point to death happens when the negative overwhelms the positive. The model makes several quantitative predictions of the life span of the worm Caenorhabditis elegans. What molecular processes drive cell aging and death? Here, we model how proteostasis—i.e., the folding, chaperoning, and maintenance of protein function—collapses with age from slowed translation and cumulative oxidative damage. Irreparably damaged proteins accumulate with age, increasingly distracting the chaperones from folding the healthy proteins the cell needs. The tipping point to death occurs when replenishing good proteins no longer keeps up with depletion from misfolding, aggregation, and damage. The model agrees with experiments in the worm Caenorhabditis elegans that show the following: Life span shortens nonlinearly with increased temperature or added oxidant concentration, and life span increases in mutants having more chaperones or proteasomes. It predicts observed increases in cellular oxidative damage with age and provides a mechanism for the Gompertz-like rise in mortality observed in humans and other organisms. Overall, the model shows how the instability of proteins sets the rate at which damage accumulates with age and upends a cell’s normal proteostasis balance.
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Boczek E, Gaglia G, Olshina M, Sarraf S. The first Autumn School on Proteostasis: from molecular mechanisms to organismal consequences. Cell Stress Chaperones 2019; 24:481-492. [PMID: 31073902 PMCID: PMC6527634 DOI: 10.1007/s12192-019-00998-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2019] [Indexed: 12/12/2022] Open
Abstract
The first Autumn School on Proteostasis was held at the Mediterranean Institute for Life Sciences (MedILS) in Split, Croatia, from November 12th-16th, 2018, bringing together 44 graduate students and postdoctoral fellows and 22 principal investigators from around the world. This meeting was geared towards providing students with an in-depth understanding of the field of proteostasis, with the aim of broadening their perspectives of the field. Session topics covered multiple aspects of cellular and organismal proteostasis, including fundamental principles, responses to heat shock, aging and disease, and protein folding, misfolding, and degradation. The structure of the meeting and the restricted number of participants afforded the students and postdocs the opportunity to interact with principal investigators to discuss not only their latest research, but also their career prospects and progression in a close, supportive environment.
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Affiliation(s)
- Edgar Boczek
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Giorgio Gaglia
- Brigham Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Maya Olshina
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Shireen Sarraf
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD USA
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Lopes AR, Borges FO, Figueiredo C, Sampaio E, Diniz M, Rosa R, Grilo TF. Transgenerational exposure to ocean acidification induces biochemical distress in a keystone amphipod species (Gammarus locusta). ENVIRONMENTAL RESEARCH 2019; 170:168-177. [PMID: 30583126 DOI: 10.1016/j.envres.2018.12.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 12/14/2018] [Accepted: 12/18/2018] [Indexed: 06/09/2023]
Abstract
Atmospheric carbon dioxide (CO2) levels are increasing at the fastest rate ever recorded, causing higher CO2 dissolution in the ocean, leading to a process known as ocean acidification (OA). Unless anthropogenic CO2 emissions are reduced, they are expected to reach ~900 ppm by the century's end, resulting in a 0.13-0.42 drop in the seawater pH levels. Since the transgenerational effects of high CO2 in marine organisms are still poorly understood at lower levels of biological organization (namely at the biochemical level), here we reared a key ecological relevant marine amphipod, Gammarus locusta, under control and high CO2 conditions for two generations. We measured several stress-related biochemical endpoints: i) oxidative damage [lipid peroxidation (LPO) and DNA damage]; ii) protein repair and removal mechanisms [heat shock proteins (HSPs) and ubiquitin (Ub)]; as well as iii) antioxidant responses [superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx) and glutathione s-transferase (GST)] and total antioxidant capacity (TAC). The present results support the premise that exposure to high CO2 is expected to decrease survival rates in this species and cause within- and transgenerational oxidative damage. More specifically, the predicted upsurge of reactive oxygen and nitrogen species seemed to overwhelm the stimulated amphipod antioxidant machinery, which proved insufficient in circumventing protein damage within the parents. Additionally, negative effects of OA are potentially being inherited by the offspring, since the oxidative stress imposed in the parent's proteome appears to be restricting DNA repair mechanisms efficiency within the offspring's. Thus, we argue that a transgenerational exposure of G. locusta could further increase vulnerability to OA and may endanger the fitness and sustainability of natural populations.
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Affiliation(s)
- Ana Rita Lopes
- MARE - Marine and Environmental Sciences Centre, Laboratório Marítimo da Guia, Faculdade de Ciências da Universidade de Lisboa, Avenida Nossa Senhora do Cabo 939, 2750-374 Cascais, Portugal; UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829-516 Caparica, Portugal.
| | - Francisco Oliveira Borges
- MARE - Marine and Environmental Sciences Centre, Laboratório Marítimo da Guia, Faculdade de Ciências da Universidade de Lisboa, Avenida Nossa Senhora do Cabo 939, 2750-374 Cascais, Portugal
| | - Cátia Figueiredo
- MARE - Marine and Environmental Sciences Centre, Laboratório Marítimo da Guia, Faculdade de Ciências da Universidade de Lisboa, Avenida Nossa Senhora do Cabo 939, 2750-374 Cascais, Portugal
| | - Eduardo Sampaio
- MARE - Marine and Environmental Sciences Centre, Laboratório Marítimo da Guia, Faculdade de Ciências da Universidade de Lisboa, Avenida Nossa Senhora do Cabo 939, 2750-374 Cascais, Portugal
| | - Mário Diniz
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829-516 Caparica, Portugal
| | - Rui Rosa
- MARE - Marine and Environmental Sciences Centre, Laboratório Marítimo da Guia, Faculdade de Ciências da Universidade de Lisboa, Avenida Nossa Senhora do Cabo 939, 2750-374 Cascais, Portugal
| | - Tiago Fernandes Grilo
- MARE - Marine and Environmental Sciences Centre, Laboratório Marítimo da Guia, Faculdade de Ciências da Universidade de Lisboa, Avenida Nossa Senhora do Cabo 939, 2750-374 Cascais, Portugal
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Akkaya Ö, Nikel PI, Pérez-Pantoja D, de Lorenzo V. Evolving metabolism of 2,4-dinitrotoluene triggers SOS-independent diversification of host cells. Environ Microbiol 2018; 21:314-326. [DOI: 10.1111/1462-2920.14459] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/12/2018] [Accepted: 10/21/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Özlem Akkaya
- Department of Molecular Biology and Genetics; Gebze Technical University; Kocaeli Turkey
- Centro Nacional de Biotecnología-CSIC; Campus de Cantoblanco; Madrid 28049 Spain
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; 2800 Kgs Lyngby Denmark
| | - Danilo Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación; Universidad Tecnológica Metropolitana; Ignacio Valdivieso 2409, San Joaquín, Santiago Chile
| | - Víctor de Lorenzo
- Centro Nacional de Biotecnología-CSIC; Campus de Cantoblanco; Madrid 28049 Spain
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Emri G, Paragh G, Tósaki Á, Janka E, Kollár S, Hegedűs C, Gellén E, Horkay I, Koncz G, Remenyik É. Ultraviolet radiation-mediated development of cutaneous melanoma: An update. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2018; 185:169-175. [PMID: 29936410 DOI: 10.1016/j.jphotobiol.2018.06.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/07/2018] [Accepted: 06/13/2018] [Indexed: 12/11/2022]
Abstract
Ultraviolet (UV) light is absorbed by nucleic acids, proteins or other endogenous chromophores, such as porphyrins, flavins and melanin, triggering biological processes in skin cells. Both UV-induced mutations in melanocytes and changes in the immune microenvironment are understood to play a role in the development of cutaneous melanoma. The degree of UV-induced stress and the protection against this stress are influenced by both intracellular and intercellular molecular interactions. The present review summarizes the known major molecular biological changes induced by UV light in the skin that play a role in melanoma initiation and promotion. Nevertheless, cutaneous melanoma is not a homogenous disease, and the interaction of variable environmental exposure and different genetic susceptibility and other host factors lead to the formation of melanomas with different biological behavior and clinical characteristics. This review highlights the challenges in the understanding of how UV radiation contributes to the formation of cutaneous melanoma, and reviews the new results of photobiology and their link to tumor genetics and tumor immunology with potential implications on melanoma prevention and therapeutic strategies. The information presented here is expected to add clarity to ongoing research efforts in this field to aid the development of novel strategies to prevent and treat melanoma.
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Affiliation(s)
- Gabriella Emri
- Department of Dermatology, University of Debrecen, Debrecen, Hungary.
| | - György Paragh
- Department of Dermatology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA; Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Ágnes Tósaki
- Department of Dermatology, University of Debrecen, Debrecen, Hungary
| | - Eszter Janka
- Department of Dermatology, University of Debrecen, Debrecen, Hungary
| | - Sándor Kollár
- Department of Pathology, Kenézy Gyula Hospital, Debrecen, Hungary
| | - Csaba Hegedűs
- Department of Dermatology, University of Debrecen, Debrecen, Hungary
| | - Emese Gellén
- Department of Dermatology, University of Debrecen, Debrecen, Hungary
| | - Irén Horkay
- Department of Dermatology, University of Debrecen, Debrecen, Hungary
| | - Gábor Koncz
- Department of Immunology, University of Debrecen, Debrecen, Hungary
| | - Éva Remenyik
- Department of Dermatology, University of Debrecen, Debrecen, Hungary
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32
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How Do Chaperones Protect a Cell's Proteins from Oxidative Damage? Cell Syst 2018; 6:743-751.e3. [DOI: 10.1016/j.cels.2018.05.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/17/2018] [Accepted: 04/30/2018] [Indexed: 11/22/2022]
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33
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Jönsson KI, Levine EB, Wojcik A, Haghdoost S, Harms-Ringdahl M. Environmental Adaptations: Radiation Tolerance. WATER BEARS: THE BIOLOGY OF TARDIGRADES 2018. [DOI: 10.1007/978-3-319-95702-9_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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G9a coordinates with the RPA complex to promote DNA damage repair and cell survival. Proc Natl Acad Sci U S A 2017; 114:E6054-E6063. [PMID: 28698370 DOI: 10.1073/pnas.1700694114] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Histone methyltransferase G9a has critical roles in promoting cancer-cell growth and gene suppression, but whether it is also associated with the DNA damage response is rarely studied. Here, we report that loss of G9a impairs DNA damage repair and enhances the sensitivity of cancer cells to radiation and chemotherapeutics. In response to DNA double-strand breaks (DSBs), G9a is phosphorylated at serine 211 by casein kinase 2 (CK2) and recruited to chromatin. The chromatin-enriched G9a can then directly interact with replication protein A (RPA) and promote loading of the RPA and Rad51 recombinase to DSBs. This mechanism facilitates homologous recombination (HR) and cell survival. We confirmed the interaction between RPA and G9a to be critical for RPA foci formation and HR upon DNA damage. Collectively, our findings demonstrate a regulatory pathway based on CK2-G9a-RPA that permits HR in cancer cells and provide further rationale for the use of G9a inhibitors as a cancer therapeutic.
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35
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Brem R, Guven M, Karran P. Oxidatively-generated damage to DNA and proteins mediated by photosensitized UVA. Free Radic Biol Med 2017; 107:101-109. [PMID: 27989755 PMCID: PMC5462485 DOI: 10.1016/j.freeradbiomed.2016.10.488] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 10/19/2016] [Accepted: 10/21/2016] [Indexed: 11/19/2022]
Abstract
UVA accounts for about 95% of the solar ultraviolet (UV) radiation that reaches Earth and most likely contributes to human skin cancer risk. In contrast to UVB, which comprises the remaining 5% and is absorbed by DNA nucleobases to cause direct photodamage, UVA damages DNA indirectly. It does this largely through its interactions with cellular chromophores that act as photosensitisers to generate reactive oxygen species. Exogenously supplied chemicals, including some widely-prescribed medicines, may also act as photosensitisers and these drugs are associated with an increased risk of sun-related cancer. Because they amplify the effects of UVA on cells, they provide a means to investigate the mechanisms and effects of UVA-induced photodamage. Here, we describe some of the major lesions induced by two groups of UVA photosensitisers, the DNA thionucleotides and the fluoroquinolone antibiotics. In thionucleotides, replacement of the oxygen atoms of canonical nucleobases by sulfur converts them into strong UVA chromophores that can be incorporated into DNA. The fluoroquinolones are also UVA chromophores. They are not incorporated into DNA and induce a different range of DNA damages. We also draw attention to the potentially important contribution of photochemical protein damage to the cellular effects of photosensitised UVA. Proteins targeted for oxidation damage include DNA repair factors and we suggest that UVA-mediated protein damage may contribute to sunlight-induced cancer risk.
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Affiliation(s)
- Reto Brem
- The Francis Crick Institute, 1, Midland Road, London NW1 1AT, UK
| | - Melisa Guven
- The Francis Crick Institute, 1, Midland Road, London NW1 1AT, UK
| | - Peter Karran
- The Francis Crick Institute, 1, Midland Road, London NW1 1AT, UK.
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36
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Kuzmic M, Javot H, Bonzom JM, Lecomte-Pradines C, Radman M, Garnier-Laplace J, Frelon S. In situ visualization of carbonylation and its co-localization with proteins, lipids, DNA and RNA in Caenorhabditis elegans. Free Radic Biol Med 2016; 101:465-474. [PMID: 27840319 DOI: 10.1016/j.freeradbiomed.2016.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/28/2016] [Accepted: 11/03/2016] [Indexed: 11/26/2022]
Abstract
All key biological macromolecules are susceptible to carbonylation - an irreparable oxidative damage with deleterious biological consequences. Carbonyls in proteins, lipids and DNA from cell extracts have been used as a biomarker of oxidative stress and aging, but formation of insoluble aggregates by carbonylated proteins precludes quantification. Since carbonylated proteins correlate with and become a suspected cause of morbidity and mortality in some organisms, there is a need for their accurate quantification and localization. Using appropriate fluorescent probes, we have developed an in situ detection of total proteins, DNA, RNA, lipids and carbonyl groups at the level of the whole organism. In C. elegans, we found that after UV irradiation carbonylation co-localizes mainly with proteins and, to a lesser degree, with DNA, RNA and lipids. The method efficiency was illustrated by carbonylation induction assessment over 5 different UV doses. The procedure enables the monitoring of carbonylation in the nematode C. elegans during stress, aging and disease along its life cycle including the egg stage.
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Affiliation(s)
- Mira Kuzmic
- Institut de radioprotection et de sûreté nucléaire, Cadarache, 13115 Saint Paul lez Durance cedex, France; Mediterranean Institute for Life Sciences, Mestrovicevo Setaliste 45, 21000 Split, Croatia
| | - Hélène Javot
- CEA, BIAM, Lab Biol Develop Plantes, Saint-Paul-lez-DurIncreased carbonylation, protein aance F-13108, France; CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance F-13108, France; Aix Marseille Université, BVME UMR7265, Marseille F-13284, France
| | - Jean-Marc Bonzom
- Institut de radioprotection et de sûreté nucléaire, Cadarache, 13115 Saint Paul lez Durance cedex, France
| | - Catherine Lecomte-Pradines
- Institut de radioprotection et de sûreté nucléaire, Cadarache, 13115 Saint Paul lez Durance cedex, France
| | - Miroslav Radman
- Mediterranean Institute for Life Sciences, Mestrovicevo Setaliste 45, 21000 Split, Croatia
| | - Jacqueline Garnier-Laplace
- Institut de radioprotection et de sûreté nucléaire, Cadarache, 13115 Saint Paul lez Durance cedex, France
| | - Sandrine Frelon
- Institut de radioprotection et de sûreté nucléaire, Cadarache, 13115 Saint Paul lez Durance cedex, France.
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38
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Abstract
Solar UVB is carcinogenic. Nucleotide excision repair (NER) counteracts the carcinogenicity of UVB by excising potentially mutagenic UVB-induced DNA lesions. Despite this capacity for DNA repair, non-melanoma skin cancers and apparently normal sun-exposed skin contain huge numbers of mutations that are mostly attributable to unrepaired UVB-induced DNA lesions. UVA is about 20-times more abundant than UVB in incident sunlight. It does cause some DNA damage but this does not fully account for its biological impact. The effects of solar UVA are mediated by its interactions with cellular photosensitizers that generate reactive oxygen species (ROS) and induce oxidative stress. The proteome is a significant target for damage by UVA-induced ROS. In cultured human cells, UVA-induced oxidation of DNA repair proteins inhibits DNA repair. This article addresses the possible role of oxidative stress and protein oxidation in determining DNA repair efficiency - with particular reference to NER and skin cancer risk.
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Affiliation(s)
- Peter Karran
- Francis Crick Research Institute, Clare Hall Laboratory, South Mimms, Herts. EN6 3LD, UK.
| | - Reto Brem
- Francis Crick Research Institute, Clare Hall Laboratory, South Mimms, Herts. EN6 3LD, UK
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39
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McAdam E, Brem R, Karran P. Oxidative Stress-Induced Protein Damage Inhibits DNA Repair and Determines Mutation Risk and Therapeutic Efficacy. Mol Cancer Res 2016; 14:612-22. [PMID: 27106867 PMCID: PMC4955916 DOI: 10.1158/1541-7786.mcr-16-0053] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 04/18/2016] [Indexed: 01/16/2023]
Abstract
UNLABELLED The relationship between sun exposure and nonmelanoma skin cancer risk is well established. Solar UV (wavelength 280-400 nm) is firmly implicated in skin cancer development. Nucleotide excision repair (NER) protects against cancer by removing potentially mutagenic DNA lesions induced by UVB (280-320 nm). How the 20-fold more abundant UVA (320-400 nm) component of solar UV radiation increases skin cancer risk is not understood. Here it is demonstrated that the contribution of UVA to the effect of UV radiation on cultured human cells is largely independent of its ability to damage DNA. Instead, the effects of UVA reflect the induction of oxidative stress that causes extensive protein oxidation. Because NER proteins are among those damaged, UVA irradiation inhibits NER and increases the susceptibility of the cells to mutation by UVB. NER inhibition is a common consequence of oxidative stress. Exposure to chemical oxidants, treatment with drugs that deplete cellular antioxidants, and interventions that interfere with glucose metabolism to disrupt the supply of cellular reducing power all inhibit NER. Tumor cells are often in a condition of oxidative stress and one effect of the NER inhibition that results from stress-induced protein oxidation is an increased sensitivity to the anticancer drug cisplatin. IMPLICATIONS As NER is both a defense against cancer and a significant determinant of cell survival after treatment with anticancer drugs, its attenuation by protein damage under conditions of oxidative stress has implications for both cancer risk and for the effectiveness of anticancer therapy. Mol Cancer Res; 14(7); 612-22. ©2016 AACR.
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Affiliation(s)
- Elizabeth McAdam
- The Francis Crick Institute, Clare Hall Laboratory, South Mimms, Hertfordshire, United Kingdom
| | - Reto Brem
- The Francis Crick Institute, Clare Hall Laboratory, South Mimms, Hertfordshire, United Kingdom
| | - Peter Karran
- The Francis Crick Institute, Clare Hall Laboratory, South Mimms, Hertfordshire, United Kingdom.
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Perić M, Bou Dib P, Dennerlein S, Musa M, Rudan M, Lovrić A, Nikolić A, Šarić A, Sobočanec S, Mačak Ž, Raimundo N, Kriško A. Crosstalk between cellular compartments protects against proteotoxicity and extends lifespan. Sci Rep 2016; 6:28751. [PMID: 27346163 PMCID: PMC4921836 DOI: 10.1038/srep28751] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 06/08/2016] [Indexed: 11/09/2022] Open
Abstract
In cells living under optimal conditions, protein folding defects are usually prevented by the action of chaperones. Here, we investigate the cell-wide consequences of loss of chaperone function in cytosol, mitochondria or the endoplasmic reticulum (ER) in budding yeast. We find that the decline in chaperone activity in each compartment results in loss of respiration, demonstrating the dependence of mitochondrial activity on cell-wide proteostasis. Furthermore, each chaperone deficiency triggers a response, presumably via the communication among the folding environments of distinct cellular compartments, termed here the cross-organelle stress response (CORE). The proposed CORE pathway encompasses activation of protein conformational maintenance machineries, antioxidant enzymes, and metabolic changes simultaneously in the cytosol, mitochondria, and the ER. CORE induction extends replicative and chronological lifespan in budding yeast, highlighting its protective role against moderate proteotoxicity and its consequences such as the decline in respiration. Our findings accentuate that organelles do not function in isolation, but are integrated in a functional crosstalk, while also highlighting the importance of organelle communication in aging and age-related diseases.
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Affiliation(s)
- Matea Perić
- Mediterranean Institute for Life Sciences - MedILS, Meštrovićevo šetalište 45, 21000 Split, Croatia
| | - Peter Bou Dib
- Universitätsmedizin Göttingen, Institut für Zellbiochemie, Humboldtallee 23, D-37073 Göttingen, Germany
| | - Sven Dennerlein
- Universitätsmedizin Göttingen, Institut für Zellbiochemie, Humboldtallee 23, D-37073 Göttingen, Germany
| | - Marina Musa
- Mediterranean Institute for Life Sciences - MedILS, Meštrovićevo šetalište 45, 21000 Split, Croatia
| | - Marina Rudan
- Mediterranean Institute for Life Sciences - MedILS, Meštrovićevo šetalište 45, 21000 Split, Croatia
| | - Anita Lovrić
- Mediterranean Institute for Life Sciences - MedILS, Meštrovićevo šetalište 45, 21000 Split, Croatia
| | - Andrea Nikolić
- Mediterranean Institute for Life Sciences - MedILS, Meštrovićevo šetalište 45, 21000 Split, Croatia
| | - Ana Šarić
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Sandra Sobočanec
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Željka Mačak
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Nuno Raimundo
- Universitätsmedizin Göttingen, Institut für Zellbiochemie, Humboldtallee 23, D-37073 Göttingen, Germany
| | - Anita Kriško
- Mediterranean Institute for Life Sciences - MedILS, Meštrovićevo šetalište 45, 21000 Split, Croatia
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41
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Musa M, Radman M, Krisko A. Decreasing translation error rate in Escherichia coli increases protein function. BMC Biotechnol 2016; 16:28. [PMID: 26969280 PMCID: PMC4788870 DOI: 10.1186/s12896-016-0259-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 03/07/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Over-expressed native or recombinant proteins are commonly used for industrial and pharmaceutical purposes, as well as for research. Proteins of interest need to be purified in sufficient quantity, quality and specific activity to justify their commercial price and eventual medical use. Proteome quality was previously positively correlated with ribosomal fidelity, but not on a single protein level. Here, we show that decreasing translational error rate increases the activity of single proteins. In order to decrease the amount of enzyme needed for catalysis, we propose an expression system bearing rpsL141 mutation, which confers high ribosomal fidelity. Using alpha-glucosidase (exo-alpha-1,4-glucosidase) and beta-glucanase (beta-D-glucanase) as examples, we show that proteins purified from Escherichia coli bearing rpsL141 mutation have superior activity compared to those purified from wild type E. coli, as well as some commercially available industrial enzymes. RESULTS Our results indicate that both alpha-glucosidase and beta-glucanase isolated from E. coli bearing rpsL141 mutation have increased activity compared to those isolated from wild type E. coli. Alpha-glucosidase from rpsL141 background has a higher activity than the purchased enzymes, while beta-glucanase from the same background has a higher activity compared to the beta-glucanase purchased from Sigma, but not compared to the one purchased from Megazyme. CONCLUSION Reduction of the error rate in protein biosynthesis via ribosomal rpsL141 mutation results in superior functionality of single proteins. We conclude that this is a viable system for expressing proteins with higher activity and that it can be easily scaled up and combined with other expression systems to meet the industrial needs.
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Affiliation(s)
- Marina Musa
- Mediterranean Institute for Life Sciences (MedILS), Mestrovicevo setaliste 45, 21000, Split, Croatia
| | - Miroslav Radman
- Mediterranean Institute for Life Sciences (MedILS), Mestrovicevo setaliste 45, 21000, Split, Croatia
| | - Anita Krisko
- Mediterranean Institute for Life Sciences (MedILS), Mestrovicevo setaliste 45, 21000, Split, Croatia.
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Branduardi P. Synthetic Biology for Cellular Remodelling to Elicit Industrially Relevant Microbial Phenotypes. Synth Biol (Oxf) 2016. [DOI: 10.1007/978-3-319-22708-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Girod M, Enjalbert Q, Brunet C, Antoine R, Lemoine J, Lukac I, Radman M, Krisko A, Dugourd P. Structural basis of protein oxidation resistance: a lysozyme study. PLoS One 2014; 9:e101642. [PMID: 24999730 PMCID: PMC4085010 DOI: 10.1371/journal.pone.0101642] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 06/09/2014] [Indexed: 11/19/2022] Open
Abstract
Accumulation of oxidative damage in proteins correlates with aging since it can cause irreversible and progressive degeneration of almost all cellular functions. Apparently, native protein structures have evolved intrinsic resistance to oxidation since perfectly folded proteins are, by large most robust. Here we explore the structural basis of protein resistance to radiation-induced oxidation using chicken egg white lysozyme in the native and misfolded form. We study the differential resistance to oxidative damage of six different parts of native and misfolded lysozyme by a targeted tandem/mass spectrometry approach of its tryptic fragments. The decay of the amount of each lysozyme fragment with increasing radiation dose is found to be a two steps process, characterized by a double exponential evolution of their amounts: the first one can be largely attributed to oxidation of specific amino acids, while the second one corresponds to further degradation of the protein. By correlating these results to the structural parameters computed from molecular dynamics (MD) simulations, we find the protein parts with increased root-mean-square deviation (RMSD) to be more susceptible to modifications. In addition, involvement of amino acid side-chains in hydrogen bonds has a protective effect against oxidation Increased exposure to solvent of individual amino acid side chains correlates with high susceptibility to oxidative and other modifications like side chain fragmentation. Generally, while none of the structural parameters alone can account for the fate of peptides during radiation, together they provide an insight into the relationship between protein structure and susceptibility to oxidation.
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Affiliation(s)
- Marion Girod
- Université de Lyon, 69622, Lyon, France
- Institut des Sciences Analytiques, UMR 5280, CNRS, Université Claude Bernard Lyon 1, Lyon, France
| | - Quentin Enjalbert
- Université de Lyon, 69622, Lyon, France
- Institut Lumière Matière, UMR 5306, CNRS, Université Claude Bernard Lyon 1, Lyon, France
| | - Claire Brunet
- Université de Lyon, 69622, Lyon, France
- Institut Lumière Matière, UMR 5306, CNRS, Université Claude Bernard Lyon 1, Lyon, France
| | - Rodolphe Antoine
- Université de Lyon, 69622, Lyon, France
- Institut Lumière Matière, UMR 5306, CNRS, Université Claude Bernard Lyon 1, Lyon, France
| | - Jérôme Lemoine
- Université de Lyon, 69622, Lyon, France
- Institut des Sciences Analytiques, UMR 5280, CNRS, Université Claude Bernard Lyon 1, Lyon, France
| | - Iva Lukac
- Mediterranean Institute for Life Sciences, Split, Croatia
- Liverpool John Moores University, School of Pharmacy and Biomolecular Sciences, Liverpool, Merseyside, England
| | - Miroslav Radman
- Mediterranean Institute for Life Sciences, Split, Croatia
- INSERM U1001, Faculte de Medecine, Universite R. Descartes Paris-5, Paris, France
| | - Anita Krisko
- Mediterranean Institute for Life Sciences, Split, Croatia
- * E-mail: (PD) (AK); (AK) (PD)
| | - Philippe Dugourd
- Université de Lyon, 69622, Lyon, France
- Institut Lumière Matière, UMR 5306, CNRS, Université Claude Bernard Lyon 1, Lyon, France
- * E-mail: (PD) (AK); (AK) (PD)
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Vidovic A, Supek F, Nikolic A, Krisko A. Signatures of conformational stability and oxidation resistance in proteomes of pathogenic bacteria. Cell Rep 2014; 7:1393-1400. [PMID: 24882003 DOI: 10.1016/j.celrep.2014.04.057] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 03/26/2014] [Accepted: 04/30/2014] [Indexed: 10/25/2022] Open
Abstract
Protein oxidation is known to compromise vital cellular functions. Therefore, invading pathogenic bacteria must resist damage inflicted by host defenses via reactive oxygen species. Using comparative genomics and experimental approaches, we provide multiple lines of evidence that proteins from pathogenic bacteria have acquired resistance to oxidative stress by an increased conformational stability. Representative pathogens exhibited higher survival upon HSP90 inhibition and a less-oxidation-prone proteome. A proteome signature of the 46 pathogenic bacteria encompasses 14 physicochemical features related to increasing protein conformational stability. By purifying ten representative proteins, we demonstrate in vitro that proteins with a pathogen-like signature are more resistant to oxidative stress as a consequence of their increased conformational stability. A compositional signature of the pathogens' proteomes allowed the design of protein fragments more resilient to both unfolding and carbonylation, validating the relationship between conformational stability and oxidability with implications for synthetic biology and antimicrobial strategies.
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Affiliation(s)
- Anita Vidovic
- Mediterranean Institute for Life Sciences, Mestrovicevo setaliste 45, 21000 Split, Croatia
| | - Fran Supek
- Division of Electronics, Rudjer Boskovic Institute, Bijenicka cesta 54, 10000 Zagreb, Croatia; EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Andrea Nikolic
- Mediterranean Institute for Life Sciences, Mestrovicevo setaliste 45, 21000 Split, Croatia
| | - Anita Krisko
- Mediterranean Institute for Life Sciences, Mestrovicevo setaliste 45, 21000 Split, Croatia.
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45
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de Lorenzo V. From theselfish genetoselfish metabolism: Revisiting the central dogma. Bioessays 2014; 36:226-35. [DOI: 10.1002/bies.201300153] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Víctor de Lorenzo
- Systems & Synthetic Biology Program; Centro Nacional de Biotecnología CSIC Cantoblanco; Madrid Spain
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