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Sun S, Li C, Hou H, Li J. Protein-metabolite Interactions Based on Chemical Targeting Methods. Chembiochem 2025; 26:e202400852. [PMID: 39715006 DOI: 10.1002/cbic.202400852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Revised: 12/02/2024] [Accepted: 12/18/2024] [Indexed: 12/25/2024]
Abstract
The importance of the protein-metabolite interaction network extends beyond its relevance to life sciences focused on proteins, it also profoundly influences its mechanisms related to disease targets, drug screening, and clinical diagnosis and treatment. Research methods targeting protein-metabolite interaction focus on enhancing the detectable signals of specific interactions by examining the structural characteristics of both proteins and metabolites in conjunction with chemical molecules, playing a crucial role in elucidating the protein-metabolite interaction network. Consequently, this article outlines several chemical targeting strategies developed in recent years and provides examples of their applications in the discovery and interpretation of new protein-metabolite interaction pathways. Finally, a brief summary will be presented regarding technological advances, research prospects, and current challenges of protein-metabolite interaction research.
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Affiliation(s)
- Shuzhe Sun
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Chuntong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Hongwei Hou
- Beijing Life Science Academy, Beijing, 102209, China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
- Beijing Life Science Academy, Beijing, 102209, China
- New Cornerstone Science Laboratory, Shenzhen, 518054, China
- Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei, 230026, China
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Nijjar S, Brotherton D, Butler J, Dospinescu V, Gannon HG, Linthwaite V, Cann M, Cameron A, Dale N. Multiple carbamylation events are required for differential modulation of Cx26 hemichannels and gap junctions by CO 2. J Physiol 2025; 603:1071-1089. [PMID: 39907096 PMCID: PMC11870076 DOI: 10.1113/jp285885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/13/2025] [Indexed: 02/06/2025] Open
Abstract
CO2 directly modifies the gating of connexin26 (Cx26) gap junction channels and hemichannels. This gating depends upon Lys125, and the proposed mechanism involves carbamylation of Lys125 to allow formation of a salt bridge with Arg104 on the neighbouring subunit. We demonstrate via carbamate trapping and tandem mass spectrometry that five Lys residues within the cytoplasmic loop, including Lys125, are indeed carbamylated by CO2. The cytoplasmic loop appears to provide a chemical microenvironment that facilitates carbamylation. Systematic mutation of these Lys residues to Arg shows that only carbamylation of Lys125 is essential for hemichannel opening. By contrast, carbamylation of Lys108 and Lys125 is essential for gap junction closure to CO2. Chicken (Gallus gallus) Cx26 gap junction channels lack Lys108 and do not close to CO2, as shown by both a dye transfer assay and a high-resolution cryogenic electron microscopy structure. The mutation Lys108Arg prevents CO2-dependent gap junction channel closure in human Cx26. Our findings directly demonstrate carbamylation in connexins, provide further insight into the differential action of CO2 on Cx26 hemichannels and gap junction channels, and increase support for the role of the N-terminus in gating the Cx26 channel. KEY POINTS: Direct evidence of carbamylation of multiple lysine residues in the cytoplasmic loop of Cx26. Concentration-dependent carbamylation at lysines 108, 122 and 125. Only carbamylation of lysine 125 is essential for hemichannel opening to CO2. Carbamylation of lysine 108 along with lysine 125 is essential for CO2-dependent gap junction channel closure.
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Affiliation(s)
| | | | - Jack Butler
- School of Life SciencesUniversity of WarwickCoventryUK
| | | | | | | | - Martin Cann
- Department of BiosciencesDurham UniversityDurhamUK
| | | | - Nicholas Dale
- School of Life SciencesUniversity of WarwickCoventryUK
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3
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Reddan B, Cummins EP. The regulation of cell metabolism by hypoxia and hypercapnia. J Biol Chem 2025; 301:108252. [PMID: 39914740 PMCID: PMC11923829 DOI: 10.1016/j.jbc.2025.108252] [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: 09/18/2024] [Revised: 01/13/2025] [Accepted: 01/25/2025] [Indexed: 03/06/2025] Open
Abstract
Every cell in the body is exposed to a certain level of CO2 and O2. Hypercapnia and hypoxia elicit stress signals to influence cellular metabolism and function. Both conditions exert profound yet distinct effects on metabolic pathways and mitochondrial dynamics, highlighting the need for cells to adapt to changes in the gaseous microenvironment. The interplay between hypercapnia and hypoxia signaling is the key for dictating cellular homeostasis as microenvironmental CO2 and O2 levels are inextricably linked. Hypercapnia, characterized by elevated pCO2, introduces metabolic adaptations within the aerobic metabolism pathways, affecting tricarboxylic acid cycle flux, lipid, and amino acid metabolism, oxidative phosphorylation and the electron transport chain. Hypoxia, defined by reduced oxygen availability, necessitates a shift from oxidative phosphorylation to anaerobic glycolysis to sustain ATP production, a process orchestrated by the stabilization of hypoxia-inducible factor-1α. Given that hypoxia and hypercapnia are present in both physiological and cancerous microenvironments, how might the coexistence of hypercapnia and hypoxia influence metabolic pathways and cellular function in physiological niches and the tumor microenvironment?
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Affiliation(s)
- Ben Reddan
- School of Medicine, University College Dublin, Dublin, Ireland; Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Eoin P Cummins
- School of Medicine, University College Dublin, Dublin, Ireland; Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.
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Willems P, Sterck L, Dard A, Huang J, De Smet I, Gevaert K, Van Breusegem F. The Plant PTM Viewer 2.0: in-depth exploration of plant protein modification landscapes. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4611-4624. [PMID: 38872385 DOI: 10.1093/jxb/erae270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 06/13/2024] [Indexed: 06/15/2024]
Abstract
Post-translational modifications (PTMs) greatly increase protein diversity and functionality. To help the plant research community interpret the ever-increasing number of reported PTMs, the Plant PTM Viewer (https://www.psb.ugent.be/PlantPTMViewer) provides an intuitive overview of plant protein PTMs and the tools to assess it. This update includes 62 novel PTM profiling studies, adding a total of 112 000 modified peptides reporting plant PTMs, including 14 additional PTM types and three species (moss, tomato, and soybean). Furthermore, an open modification re-analysis of a large-scale Arabidopsis thaliana mass spectrometry tissue atlas identified previously uncharted landscapes of lysine acylations predominant in seed and flower tissues and 3-phosphoglycerylation on glycolytic enzymes in plants. An extra 'Protein list analysis' tool was developed for retrieval and assessing the enrichment of PTMs in a protein list of interest. We conducted a protein list analysis on nuclear proteins, revealing a substantial number of redox modifications in the nucleus, confirming previous assumptions regarding the redox regulation of transcription. We encourage the plant research community to use PTM Viewer 2.0 for hypothesis testing and new target discovery, and also to submit new data to expand the coverage of conditions, plant species, and PTM types, thereby enriching our understanding of plant biology.
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Affiliation(s)
- Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9052 Ghent, Belgium
- VIB Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium
| | - Lieven Sterck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Avilien Dard
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Jingjing Huang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, 9052 Ghent, Belgium
- VIB Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
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5
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Linares E, Severino D, Truzzi DR, Rios N, Radi R, Augusto O. Production of Peroxymonocarbonate by Steady-State Micromolar H 2O 2 and Activated Macrophages in the Presence of CO 2/HCO 3- Evidenced by Boronate Probes. Chem Res Toxicol 2024; 37:1129-1138. [PMID: 38916595 PMCID: PMC11256887 DOI: 10.1021/acs.chemrestox.4c00059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 06/13/2024] [Accepted: 06/20/2024] [Indexed: 06/26/2024]
Abstract
Peroxymonocarbonate (HCO4-/HOOCO2-) is produced by the reversible reaction of CO2/HCO3- with H2O2 (K = 0.33 M-1, pH 7.0). Although produced in low yields at physiological pHs and H2O2 and CO2/HCO3- concentrations, HCO4- oxidizes most nucleophiles with rate constants 10 to 100 times higher than those of H2O2. Boronate probes are known examples because HCO4- reacts with coumarin-7-boronic acid pinacolate ester (CBE) with a rate constant that is approximately 100 times higher than that of H2O2 and the same holds for fluorescein-boronate (Fl-B) as reported here. Therefore, we tested whether boronate probes could provide evidence for HCO4- formation under biologically relevant conditions. Glucose/glucose oxidase/catalase were adjusted to produce low steady-state H2O2 concentrations (2-18 μM) in Pi buffer at pH 7.4 and 37 °C. Then, CBE (100 μM) was added and fluorescence increase was monitored with time. The results showed that each steady-state H2O2 concentration reacted more rapidly (∼30%) in the presence of CO2/HCO3- (25 mM) than in its absence, and the data permitted the calculation of consistent rate constants. Also, RAW 264.7 macrophages were activated with phorbol 12-myristate 13-acetate (PMA) (1 μg/mL) at pH 7.4 and 37 °C to produce a time-dependent H2O2 concentration (8.0 ± 2.5 μM after 60 min). The media contained 0, 21.6, or 42.2 mM HCO3- equilibrated with 0, 5, or 10% CO2, respectively. In the presence of CBE or Fl-B (30 μM), a time-dependent increase in the fluorescence of the bulk solution was observed, which was higher in the presence of CO2/HCO3- in a concentration-dependent manner. The Fl-B samples were also examined by fluorescence microscopy. Our results demonstrated that mammalian cells produce HCO4- and boronate probes can evidence and distinguish it from H2O2 under biologically relevant concentrations of H2O2 and CO2/HCO3-.
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Affiliation(s)
- Edlaine Linares
- Departamento
de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo 05508-900, Brazil
| | - Divinomar Severino
- Departamento
de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo 05508-900, Brazil
| | - Daniela R. Truzzi
- Departamento
de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo 05508-900, Brazil
| | - Natalia Rios
- Departamento de Bioquímica and Centro de Investigaciones
Biomédicas
(CEINBIO), Facultad de Medicina, Universidad
de la República, Montevideo 11800, Uruguay
| | - Rafael Radi
- Departamento de Bioquímica and Centro de Investigaciones
Biomédicas
(CEINBIO), Facultad de Medicina, Universidad
de la República, Montevideo 11800, Uruguay
| | - Ohara Augusto
- Departamento
de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo 05508-900, Brazil
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Hudson EP. The Calvin Benson cycle in bacteria: New insights from systems biology. Semin Cell Dev Biol 2024; 155:71-83. [PMID: 37002131 DOI: 10.1016/j.semcdb.2023.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/21/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023]
Abstract
The Calvin Benson cycle in phototrophic and chemolithoautotrophic bacteria has ecological and biotechnological importance, which has motivated study of its regulation. I review recent advances in our understanding of how the Calvin Benson cycle is regulated in bacteria and the technologies used to elucidate regulation and modify it, and highlight differences between and photoautotrophic and chemolithoautotrophic models. Systems biology studies have shown that in oxygenic phototrophic bacteria, Calvin Benson cycle enzymes are extensively regulated at post-transcriptional and post-translational levels, with multiple enzyme activities connected to cellular redox status through thioredoxin. In chemolithoautotrophic bacteria, regulation is primarily at the transcriptional level, with effector metabolites transducing cell status, though new methods should now allow facile, proteome-wide exploration of biochemical regulation in these models. A biotechnological objective is to enhance CO2 fixation in the cycle and partition that carbon to a product of interest. Flux control of CO2 fixation is distributed over multiple enzymes, and attempts to modulate gene Calvin cycle gene expression show a robust homeostatic regulation of growth rate, though the synthesis rates of products can be significantly increased. Therefore, de-regulation of cycle enzymes through protein engineering may be necessary to increase fluxes. Non-canonical Calvin Benson cycles, if implemented with synthetic biology, could have reduced energy demand and enzyme loading, thus increasing the attractiveness of these bacteria for industrial applications.
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Affiliation(s)
- Elton P Hudson
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.
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Malvestio C, Onor M, Bramanti E, Pagliano E, Campanella B. Determination of methionine and selenomethionine in food matrices by gas chromatography mass spectrometry after aqueous derivatization with triethyloxonium salts. Food Chem 2024; 433:137341. [PMID: 37660603 DOI: 10.1016/j.foodchem.2023.137341] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/07/2023] [Accepted: 08/28/2023] [Indexed: 09/05/2023]
Abstract
A novel analytical method for the simultaneous gas chromatography-mass spectrometry (GC-MS) determination of methionine and selenomethionine in food samples is described. Samples were digested with methanesulfonic acid in a closed vessel without the need for reflux. A single step derivatization using triethyloxonium tetrafluoroborate was optimized for the conversion of the analytes into their ethyl derivatives, followed by their extraction with hexane and GC-MS analysis.. This derivatization approach was simpler and/or safer with respect to current methods based on alkyl chloroformate or silylating reagents and it yielded very clean chromatography. A design of experiment approach, based on an open source chemometric software, was used to optimize the experimental conditions. When analysis of a 1 mL volume of aqueous standard was performed, detection limits of 1 ng/g methionine and 10 ng/g for selenomethionine were obtained. The method was validated by analysis of a selenized yeast Certified Reference Material NRC SELM-1.
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Affiliation(s)
- Cosimo Malvestio
- Department of Chemistry and Industrial Chemistry, University of Pisa, via Giuseppe Moruzzi 13, 56124 Pisa, Italy
| | - Massimo Onor
- Institute of Chemistry of Organometallic Compounds, National Research Council, via Giuseppe Moruzzi 1, 56124 Pisa, Italy
| | - Emilia Bramanti
- Institute of Chemistry of Organometallic Compounds, National Research Council, via Giuseppe Moruzzi 1, 56124 Pisa, Italy
| | - Enea Pagliano
- National Research Council Canada, 1200 Montreal Road, K1A0R6 Ottawa, Ontario, Canada
| | - Beatrice Campanella
- Institute of Chemistry of Organometallic Compounds, National Research Council, via Giuseppe Moruzzi 1, 56124 Pisa, Italy.
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8
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Casalino-Matsuda SM, Chen F, Gonzalez-Gonzalez FJ, Matsuda H, Nair A, Abdala-Valencia H, Budinger GS, Dong JT, Beitel GJ, Sporn PH. Myeloid Zfhx3 deficiency protects against hypercapnia-induced suppression of host defense against influenza A virus. JCI Insight 2024; 9:e170316. [PMID: 38227369 PMCID: PMC11143927 DOI: 10.1172/jci.insight.170316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 01/10/2024] [Indexed: 01/17/2024] Open
Abstract
Hypercapnia, elevation of the partial pressure of CO2 in blood and tissues, is a risk factor for mortality in patients with severe acute and chronic lung diseases. We previously showed that hypercapnia inhibits multiple macrophage and neutrophil antimicrobial functions and that elevated CO2 increases the mortality of bacterial and viral pneumonia in mice. Here, we show that normoxic hypercapnia downregulates innate immune and antiviral gene programs in alveolar macrophages (AMØs). We also show that zinc finger homeobox 3 (Zfhx3) - a mammalian ortholog of zfh2, which mediates hypercapnic immune suppression in Drosophila - is expressed in mouse and human macrophages. Deletion of Zfhx3 in the myeloid lineage blocked the suppressive effect of hypercapnia on immune gene expression in AMØs and decreased viral replication, inflammatory lung injury, and mortality in hypercapnic mice infected with influenza A virus. To our knowledge, our results establish Zfhx3 as the first known mammalian mediator of CO2 effects on immune gene expression and lay the basis for future studies to identify therapeutic targets to interrupt hypercapnic immunosuppression in patients with advanced lung disease.
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Affiliation(s)
- S. Marina Casalino-Matsuda
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Fei Chen
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Francisco J. Gonzalez-Gonzalez
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Hiroaki Matsuda
- Department of Physical Sciences and Engineering, Wilbur Wright College, Chicago, Illinois, USA
| | - Aisha Nair
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Hiam Abdala-Valencia
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - G.R. Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, USA
| | - Jin-Tang Dong
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Greg J. Beitel
- Department of Molecular Biosciences, Weinberg College of Arts and Sciences, Northwestern University, Evanston, Illinois, USA
| | - Peter H.S. Sporn
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, USA
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9
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Gannon HG, Riaz-Bradley A, Cann MJ. A Non-Functional Carbon Dioxide-Mediated Post-Translational Modification on Nucleoside Diphosphate Kinase of Arabidopsis thaliana. Int J Mol Sci 2024; 25:898. [PMID: 38255974 PMCID: PMC10815852 DOI: 10.3390/ijms25020898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
The carbamate post-translational modification (PTM), formed by the nucleophilic attack of carbon dioxide by a dissociated lysine epsilon-amino group, is proposed as a widespread mechanism for sensing this biologically important bioactive gas. Here, we demonstrate the discovery and in vitro characterization of a carbamate PTM on K9 of Arabidopsis nucleoside diphosphate kinase (AtNDK1). We demonstrate that altered side chain reactivity at K9 is deleterious for AtNDK1 structure and catalytic function, but that CO2 does not impact catalysis. We show that nucleotide substrate removes CO2 from AtNDK1, and the carbamate PTM is functionless within the detection limits of our experiments. The AtNDK1 K9 PTM is the first demonstration of a functionless carbamate. In light of this finding, we speculate that non-functionality is a possible feature of the many newly identified carbamate PTMs.
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Affiliation(s)
- Harry G. Gannon
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK; (H.G.G.)
| | - Amber Riaz-Bradley
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK; (H.G.G.)
| | - Martin J. Cann
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK; (H.G.G.)
- Biophysical Sciences Institute, Durham University, South Road, Durham DH1 3LE, UK
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10
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Ohde D, Thomas B, Bubenheim P, Liese A. Enzymatic Carboxylation of Resorcinol in Aqueous Triethanolamine at Elevated CO 2 Pressure. Molecules 2023; 29:25. [PMID: 38202608 PMCID: PMC10779730 DOI: 10.3390/molecules29010025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/10/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024] Open
Abstract
The fixation of CO2 by enzymatic carboxylation for production of valuable carboxylic acids is one way to recycle carbon. Unfortunately, this type of reaction is limited by an unfavourable thermodynamic equilibrium. An excess of the C1 substrate is required to increase conversions. Solvents with a high CO2 solubility, such as amines, can provide the C1 substrate in excess. Here, we report on the effect of CO2 pressures up to 1100 kPa on the enzymatic carboxylation of resorcinol in aqueous triethanolamine. Equilibrium yields correlate to the bicarbonate concentration. However, inhibition is observed at elevated pressure, severely reducing the enzyme activity. The reaction yields were reduced at higher pressures, whereas at ambient pressure, higher yields were achieved. Overall, CO2 pressures above 100 kPa have been demonstrated to be counterproductive for improving the biotransformation, as productivity decreases rapidly for only a modest improvement in conversion. It is expected that CO2 carbamylation intensifies at elevated CO2 pressures, causing the inhibition of the enzyme. To further increase the reaction yield, the in situ product precipitation is tested by the addition of the quaternary ammonium salt tetrabutylammonium bromide.
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Affiliation(s)
- Daniel Ohde
- Institute of Technical Biocatalysis, Hamburg University of Technology, 21073 Hamburg, Germany; (B.T.); (P.B.)
| | | | | | - Andreas Liese
- Institute of Technical Biocatalysis, Hamburg University of Technology, 21073 Hamburg, Germany; (B.T.); (P.B.)
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11
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Abstract
Background Identifying CO2-binding proteins is vital for our knowledge of CO2-regulated molecular processes. The carbamate post-translational modification is a reversible CO2-mediated adduct that can form on neutral N-terminal α-amino or lysine ε-amino groups. Methods We have developed triethyloxonium ion (TEO) as a chemical proteomics tool to trap the carbamate post-translational modification on protein covalently. We use 13C-NMR and TEO and identify ubiquitin as a plant CO2-binding protein. Results We observe the carbamate post-translational modification on the Arabidopsis thaliana ubiquitin ε-amino groups of lysines 6, 33, and 48. We show that biologically relevant near atmospheric PCO2 levels increase ubiquitin conjugation dependent on lysine 6. We further demonstrate that CO2 increases the ubiquitin E2 ligase (AtUBC5) charging step via the transthioesterification reaction in which Ub is transferred from the E1 ligase active site to the E2 active site. Conclusions and general significance Therefore, plant ubiquitin is a CO2-binding protein, and the carbamate post-translational modification represents a potential mechanism through which plant cells can respond to fluctuating PCO2.
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Affiliation(s)
- Harry G Gannon
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
| | - Martin J Cann
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
- Biophysical Sciences Institute, Durham University, South Road, Durham DH1 3LE, UK
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12
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Águila Ruiz-Sola M, Flori S, Yuan Y, Villain G, Sanz-Luque E, Redekop P, Tokutsu R, Küken A, Tsichla A, Kepesidis G, Allorent G, Arend M, Iacono F, Finazzi G, Hippler M, Nikoloski Z, Minagawa J, Grossman AR, Petroutsos D. Light-independent regulation of algal photoprotection by CO 2 availability. Nat Commun 2023; 14:1977. [PMID: 37031262 PMCID: PMC10082802 DOI: 10.1038/s41467-023-37800-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 03/30/2023] [Indexed: 04/10/2023] Open
Abstract
Photosynthetic algae have evolved mechanisms to cope with suboptimal light and CO2 conditions. When light energy exceeds CO2 fixation capacity, Chlamydomonas reinhardtii activates photoprotection, mediated by LHCSR1/3 and PSBS, and the CO2 Concentrating Mechanism (CCM). How light and CO2 signals converge to regulate these processes remains unclear. Here, we show that excess light activates photoprotection- and CCM-related genes by altering intracellular CO2 concentrations and that depletion of CO2 drives these responses, even in total darkness. High CO2 levels, derived from respiration or impaired photosynthetic fixation, repress LHCSR3/CCM genes while stabilizing the LHCSR1 protein. Finally, we show that the CCM regulator CIA5 also regulates photoprotection, controlling LHCSR3 and PSBS transcript accumulation while inhibiting LHCSR1 protein accumulation. This work has allowed us to dissect the effect of CO2 and light on CCM and photoprotection, demonstrating that light often indirectly affects these processes by impacting intracellular CO2 levels.
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Affiliation(s)
- M Águila Ruiz-Sola
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000, Grenoble, France
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla, Sevilla, Spain
| | - Serena Flori
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000, Grenoble, France
| | - Yizhong Yuan
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000, Grenoble, France
| | - Gaelle Villain
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000, Grenoble, France
| | - Emanuel Sanz-Luque
- The Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA
- University of Cordoba, Department of Biochemistry and Molecular Biology, Cordoba, Spain
| | - Petra Redekop
- The Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA
| | - Ryutaro Tokutsu
- Division of Environmental photobiology, National Institute for Basic Biology (NIBB), Nishigonaka 38, Myodaiji, Okazaki, 444-8585, Japan
| | - Anika Küken
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam, Golm, Germany
| | - Angeliki Tsichla
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000, Grenoble, France
| | - Georgios Kepesidis
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000, Grenoble, France
| | - Guillaume Allorent
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000, Grenoble, France
| | - Marius Arend
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam, Golm, Germany
| | - Fabrizio Iacono
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000, Grenoble, France
| | - Giovanni Finazzi
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000, Grenoble, France
| | - Michael Hippler
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms Universität, 48143, Münster, Germany
| | - Zoran Nikoloski
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam, Golm, Germany
| | - Jun Minagawa
- Division of Environmental photobiology, National Institute for Basic Biology (NIBB), Nishigonaka 38, Myodaiji, Okazaki, 444-8585, Japan
| | - Arthur R Grossman
- The Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA
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13
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Casalino-Matsuda SM, Chen F, Gonzalez-Gonzalez FJ, Matsuda H, Nair A, Abdala-Valencia H, Budinger GRS, Dong JT, Beitel GJ, Sporn PHS. Myeloid Zfhx3 Deficiency Protects Against Hypercapnia-induced Suppression of Host Defense Against Influenza A Virus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.28.530480. [PMID: 36909510 PMCID: PMC10002734 DOI: 10.1101/2023.02.28.530480] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Hypercapnia, elevation of the partial pressure of CO 2 in blood and tissues, is a risk factor for mortality in patients with severe acute and chronic lung diseases. We previously showed that hypercapnia inhibits multiple macrophage and neutrophil antimicrobial functions, and that elevated CO 2 increases the mortality of bacterial and viral pneumonia in mice. Here, we show that normoxic hypercapnia downregulates innate immune and antiviral gene programs in alveolar macrophages (AMØs). We also show that zinc finger homeobox 3 (Zfhx3), mammalian ortholog of zfh2, which mediates hypercapnic immune suppression in Drosophila , is expressed in mouse and human MØs. Deletion of Zfhx3 in the myeloid lineage blocked the suppressive effect of hypercapnia on immune gene expression in AMØs and decreased viral replication, inflammatory lung injury and mortality in hypercapnic mice infected with influenza A virus. Our results establish Zfhx3 as the first known mammalian mediator of CO 2 effects on immune gene expression and lay the basis for future studies to identify therapeutic targets to interrupt hypercapnic immunosuppression in patients with advanced lung diseases. Graphical abstract
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14
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Sharkey TD. The discovery of rubisco. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:510-519. [PMID: 35689795 DOI: 10.1093/jxb/erac254] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Rubisco is possibly the most important enzyme on Earth, certainly in terms of amount. This review describes the initial reports of ribulose 1,5-bisphosphate carboxylating activity. Discoveries of core concepts are described, including its quaternary structure, the requirement for post-translational modification, and its role as an oxygenase as well as a carboxylase. Finally, the requirement for numerous chaperonins for assembly of rubisco in plants is described.
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Affiliation(s)
- Thomas D Sharkey
- MSU-DOE Plant Research Laboratory, Plant Resilience Institute, and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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15
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Allophycocyanin A is a carbon dioxide receptor in the cyanobacterial phycobilisome. Nat Commun 2022; 13:5289. [PMID: 36075935 PMCID: PMC9458709 DOI: 10.1038/s41467-022-32925-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 08/24/2022] [Indexed: 11/10/2022] Open
Abstract
Light harvesting is fundamental for production of ATP and reducing equivalents for CO2 fixation during photosynthesis. However, electronic energy transfer (EET) through a photosystem can harm the photosynthetic apparatus when not balanced with CO2. Here, we show that CO2 binding to the light-harvesting complex modulates EET in photosynthetic cyanobacteria. More specifically, CO2 binding to the allophycocyanin alpha subunit of the light-harvesting complex regulates EET and its fluorescence quantum yield in the cyanobacterium Synechocystis sp. PCC 6803. CO2 binding decreases the inter-chromophore distance in the allophycocyanin trimer. The result is enhanced EET in vitro and in live cells. Our work identifies a direct target for CO2 in the cyanobacterial light-harvesting apparatus and provides insights into photosynthesis regulation. The transfer of electronic energy through a photosystem can harm the photosynthetic apparatus when not balanced with CO2 fixation. Here, the authors show that CO2 modulates electronic energy transfer in cyanobacteria by binding to and enhancing the activity of the light-harvesting complex.
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16
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Radi R. Interplay of carbon dioxide and peroxide metabolism in mammalian cells. J Biol Chem 2022; 298:102358. [PMID: 35961463 PMCID: PMC9485056 DOI: 10.1016/j.jbc.2022.102358] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 10/25/2022] Open
Abstract
The carbon dioxide/bicarbonate (CO2/HCO3-) molecular pair is ubiquitous in mammalian cells and tissues, mainly as a result of oxidative decarboxylation reactions that occur during intermediary metabolism. CO2 is in rapid equilibrium with HCO3-via the hydration reaction catalyzed by carbonic anhydrases. Far from being an inert compound in redox biology, CO2 enhances or redirects the reactivity of peroxides, modulating the velocity, extent, and type of one- and two-electron oxidation reactions mediated by hydrogen peroxide (H2O2) and peroxynitrite (ONOO-/ONOOH). Herein, we review the biochemical mechanisms by which CO2 engages in peroxide-dependent reactions, free radical production, redox signaling, and oxidative damage. First, we cover the metabolic formation of CO2 and its connection to peroxide formation and decomposition. Next, the reaction mechanisms, kinetics, and processes by which the CO2/peroxide interplay modulates mammalian cell redox biology are scrutinized in-depth. Importantly, CO2 also regulates gene expression related to redox and nitric oxide metabolism and as such influences oxidative and inflammatory processes. Accumulated biochemical evidence in vitro, in cellula, and in vivo unambiguously show that the CO2 and peroxide metabolic pathways are intertwined and together participate in key redox events in mammalian cells.
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Affiliation(s)
- Rafael Radi
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
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17
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Grams RJ, Hsu KL. Catch your breath. Nat Chem Biol 2022; 18:686-687. [PMID: 35710618 DOI: 10.1038/s41589-022-01063-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- R Justin Grams
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Ku-Lung Hsu
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA. .,Department of Pharmacology, , University of Virginia School of Medicine, Charlottesville, VA, USA. .,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA. .,University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, USA.
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18
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Yang Y, Fischer NH, Oliveira MT, Hadaf GB, Liu J, Brock-Nannestad T, Diness F, Lee JW. Carbon dioxide enhances sulphur-selective conjugate addition reactions. Org Biomol Chem 2022; 20:4526-4533. [PMID: 35605989 DOI: 10.1039/d2ob00831a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sulphur-selective conjugate addition reactions play a central role in synthetic chemistry and chemical biology. A general tool for conjugate addition reactions should provide high selectivity in the presence of competing nucleophilic functional groups, namely nitrogen nucleophiles. We report CO2-mediated chemoselective S-Michael addition reactions where CO2 can reversibly control the reaction pHs, thus providing practical reaction conditions. The increased chemoselectivity for sulphur-alkylation products was ascribed to CO2 as a temporary and traceless protecting group for nitrogen nucleophiles, while CO2 efficiently provide higher conversion and selectivity sulphur nucleophiles on peptides and human serum albumin (HSA) with various electrophiles. This method offers simple reaction conditions for cysteine modification reactions when high chemoselectivity is required.
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Affiliation(s)
- Yang Yang
- Department of Chemistry, University of Copenhagen Universitetsparken 5, Copenhagen Ø, 2100, Denmark.
| | - Niklas Henrik Fischer
- Department of Chemistry, University of Copenhagen Universitetsparken 5, Copenhagen Ø, 2100, Denmark. .,Nanoscience Center, University of Copenhagen Universitetsparken 5, Copenhagen Ø, 2100, Denmark
| | - Maria Teresa Oliveira
- Department of Chemistry, University of Copenhagen Universitetsparken 5, Copenhagen Ø, 2100, Denmark. .,Nanoscience Center, University of Copenhagen Universitetsparken 5, Copenhagen Ø, 2100, Denmark
| | - Gul Barg Hadaf
- Department of Chemistry, University of Copenhagen Universitetsparken 5, Copenhagen Ø, 2100, Denmark.
| | - Jian Liu
- Department of Chemistry, University of Copenhagen Universitetsparken 5, Copenhagen Ø, 2100, Denmark.
| | - Theis Brock-Nannestad
- Department of Chemistry, University of Copenhagen Universitetsparken 5, Copenhagen Ø, 2100, Denmark.
| | - Frederik Diness
- Department of Chemistry, University of Copenhagen Universitetsparken 5, Copenhagen Ø, 2100, Denmark. .,Nanoscience Center, University of Copenhagen Universitetsparken 5, Copenhagen Ø, 2100, Denmark
| | - Ji-Woong Lee
- Department of Chemistry, University of Copenhagen Universitetsparken 5, Copenhagen Ø, 2100, Denmark. .,Nanoscience Center, University of Copenhagen Universitetsparken 5, Copenhagen Ø, 2100, Denmark
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19
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Pawloski W, Komiyama T, Kougentakis C, Majumdar A, Fushman D. Site-Specific Detection and Characterization of Ubiquitin Carbamylation. Biochemistry 2022; 61:712-721. [PMID: 35380792 PMCID: PMC9173829 DOI: 10.1021/acs.biochem.2c00085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The physiological consequences of varying in vivo CO2 levels point to a general mechanism for CO2 to influence cellular homeostasis beyond regulating pH. Aside from a few instances where CO2 has been observed to cause post-translational protein modification, by forming long-lived carbamates, little is known about how transitory and ubiquitous carbamylation events could induce a physiological response. Ubiquitin is a versatile protein involved in a multitude of cellular signaling pathways as polymeric chains of various lengths formed through one of the seven lysines or N-terminal amine. Unique polyubiquitin (polyUb) compositions present recognition signals for specific ubiquitin-receptors which enables this one protein to be involved in many different cellular processes. Advances in proteomic methods have allowed the capture and identification of protein carbamates in vivo, and Ub was found carbamylated at lysines K48 and K33. This was shown to negatively regulate ubiquitin-mediated signaling by inhibiting polyUb chain formation. Here, we expand upon these observations by characterizing the carbamylation susceptibility for all Ub amines simultaneously. Using NMR methods which directly probe 15N resonances, we determined carbamylation rates under various environmental conditions and related them to the intrinsic pKas. Our results show that the relatively low pKas for half of the Ub amines are correlated with enhanced susceptibility to carbamylation under physiological conditions. Two of these carbamylated amines, not observed by chemical capture, appear to be physiologically relevant post-translational modifications. These findings point to a mechanism for varying the levels of CO2 due to intracellular localization, cellular stresses, and metabolism to affect certain polyUb-mediated signaling pathways.
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Affiliation(s)
- Westley Pawloski
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland 20742, United States
| | - Teppei Komiyama
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland 20742, United States
| | - Christos Kougentakis
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ananya Majumdar
- Biomolecular NMR Center, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland 20742, United States
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20
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Trejo-Zambrano MI, Gómez-Bañuelos E, Andrade F. Redox-Mediated Carbamylation As a Hapten Model Applied to the Origin of Antibodies to Modified Proteins in Rheumatoid Arthritis. Antioxid Redox Signal 2022; 36:389-409. [PMID: 33906423 PMCID: PMC8982126 DOI: 10.1089/ars.2021.0064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 04/16/2021] [Indexed: 12/23/2022]
Abstract
Significance: The production of antibodies to posttranslationally modified antigens is a hallmark in rheumatoid arthritis (RA). In particular, the presence of citrullination-associated antibodies, targeting both citrullinating enzymes (the peptidylarginine deiminases [PADs]) and citrullinated antigens (anticitrullinated protein antibodies [ACPAs]), has suggested that dysregulated citrullination is relevant for disease pathogenesis. Antibodies to other protein modifications with physicochemical similarities to citrulline, such as carbamylated-lysine and acetylated-lysine, have also gained interest in RA, but their mechanistic relation to ACPAs remains unclear. Recent Advances: Recent studies using RA-derived monoclonal antibodies have found that ACPAs are cross-reactive to carbamylated and acetylated peptides, challenging our understanding of the implications of such cross-reactivity. Critical Issues: Analogous to the classic antibody response to chemically modified proteins, we examine the possibility that antibodies to modified proteins in RA are more likely to resemble antihapten antibodies rather than autoantibodies. This potential shift in the autoantibody paradigm in RA offers the opportunity to explore new mechanisms involved in the origin and cross-reactivity of pathogenic antibodies in RA. In contrast to citrullination, carbamylation is a chemical modification associated with oxidative stress, it is highly immunogenic, and is considered in the group of posttranslational modification-derived products. We discuss the possibility that carbamylated proteins are antigenic drivers of cross-reacting antihapten antibodies that further create the ACPA response, and that ACPAs may direct the production of antibodies to PAD enzymes. Future Directions: Understanding the complexity of autoantibodies in RA is critical to develop tools to clearly define their origin, identify drivers of disease propagation, and develop novel therapeutics. Antioxid. Redox Signal. 36, 389-409.
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Affiliation(s)
| | - Eduardo Gómez-Bañuelos
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Felipe Andrade
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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21
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Blake LI, Cann MJ. Carbon Dioxide and the Carbamate Post-Translational Modification. Front Mol Biosci 2022; 9:825706. [PMID: 35300111 PMCID: PMC8920986 DOI: 10.3389/fmolb.2022.825706] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/03/2022] [Indexed: 01/10/2023] Open
Abstract
Carbon dioxide is essential for life. It is at the beginning of every life process as a substrate of photosynthesis. It is at the end of every life process as the product of post-mortem decay. Therefore, it is not surprising that this gas regulates such diverse processes as cellular chemical reactions, transport, maintenance of the cellular environment, and behaviour. Carbon dioxide is a strategically important research target relevant to crop responses to environmental change, insect vector-borne disease and public health. However, we know little of carbon dioxide’s direct interactions with the cell. The carbamate post-translational modification, mediated by the nucleophilic attack by carbon dioxide on N-terminal α-amino groups or the lysine ɛ-amino groups, is one mechanism by which carbon dioxide might alter protein function to form part of a sensing and signalling mechanism. We detail known protein carbamates, including the history of their discovery. Further, we describe recent studies on new techniques to isolate this problematic post-translational modification.
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22
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Kryvenko V, Vadász I. Mechanisms of Hypercapnia-Induced Endoplasmic Reticulum Dysfunction. Front Physiol 2021; 12:735580. [PMID: 34867444 PMCID: PMC8640499 DOI: 10.3389/fphys.2021.735580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/27/2021] [Indexed: 01/16/2023] Open
Abstract
Protein transcription, translation, and folding occur continuously in every living cell and are essential for physiological functions. About one-third of all proteins of the cellular proteome interacts with the endoplasmic reticulum (ER). The ER is a large, dynamic cellular organelle that orchestrates synthesis, folding, and structural maturation of proteins, regulation of lipid metabolism and additionally functions as a calcium store. Recent evidence suggests that both acute and chronic hypercapnia (elevated levels of CO2) impair ER function by different mechanisms, leading to adaptive and maladaptive regulation of protein folding and maturation. In order to cope with ER stress, cells activate unfolded protein response (UPR) pathways. Initially, during the adaptive phase of ER stress, the UPR mainly functions to restore ER protein-folding homeostasis by decreasing protein synthesis and translation and by activation of ER-associated degradation (ERAD) and autophagy. However, if the initial UPR attempts for alleviating ER stress fail, a maladaptive response is triggered. In this review, we discuss the distinct mechanisms by which elevated CO2 levels affect these molecular pathways in the setting of acute and chronic pulmonary diseases associated with hypercapnia.
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Affiliation(s)
- Vitalii Kryvenko
- Department of Internal Medicine, Justus Liebig University Giessen, Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Giessen, Germany.,The Cardio-Pulmonary Institute (CPI), Giessen, Germany
| | - István Vadász
- Department of Internal Medicine, Justus Liebig University Giessen, Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Giessen, Germany.,The Cardio-Pulmonary Institute (CPI), Giessen, Germany.,Institute for Lung Health (ILH), Giessen, Germany
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23
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Pramanik SK, Das A. Fluorescent probes for imaging bioactive species in subcellular organelles. Chem Commun (Camb) 2021; 57:12058-12073. [PMID: 34706371 DOI: 10.1039/d1cc04273d] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Luminescent molecular probes and nanoscale materials have become important tools in biosensing and bioimaging applications because of their high sensitivity, fast response, specificity, and methodological simplicity. In recent years, there has been a notable advancement in fluorescent probes that respond to the subtle changes in subcellular microenvironments (e.g., polarity, pH, and viscosity) or distribution of certain crucial biomarkers (e.g., reactive oxygen species, ions, amino acids, and enzymes). The dynamic fluctuations of these bio-molecules in subcellular microenvironments control cellular homeostasis, immunity, signal conduction, and metabolism. Their abnormal expressions are linked to various biological disorders and disease states. Thus, the real-time monitoring of such bioactive species is intimately linked to clinical diagnostics. Appropriately designed luminescent probes are ideally suited for desired organelle specificity, as well as for reporting intracellular changes in biochemicals/microenvironmental factors with the luminescence ON response. In this perspective, we review our recent work on the development of fluorescent probes for sensing and imaging within sub-cellular organelles. We have also discussed the design aspects for developing a prodrug with a fluorescent probe as an integral part of possible theranostic applications. An overview of the design principles, photophysical properties, detection mechanisms, current challenges, and potential future directions of fluorescent probes is presented in this feature article. We have also discussed the limitations and challenges of developing the solution platform for sensing technologies in clinical diagnostics.
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Affiliation(s)
- Sumit Kumar Pramanik
- CSIR-Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar, Gujarat, 364002, India.
| | - Amitva Das
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur, 741 246, West Bengal, India.
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24
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Crespi S, Vadivel D, Bellisario A, Dondi D. Computational Study of the Stability of Natural Amino Acid isomers. ORIGINS LIFE EVOL B 2021; 51:287-298. [PMID: 34739664 DOI: 10.1007/s11084-021-09615-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/10/2021] [Indexed: 10/19/2022]
Abstract
The secular debate on the origin of life on our planet represents one of the open challenges for the scientific community. In this endeavour, chemistry has a pivotal role in disclosing novel scenarios that allow us to understand how the formation of simple organic molecules would be possible in the early primitive geological ages of Earth. Amino acids play a crucial role in biological processes. They are known to be formed in experiments simulating primitive conditions and were found in meteoric samples retrieved throughout the years. Understanding their formation is a key step for prebiotic chemistry. Following this reasoning, we performed a computational investigation over 100'000 structural isomers of natural amino acids. The results we have found suggest that natural amino acids are among the most thermodynamically stable structures and, therefore, one of the most probable ones to be synthesised among their possible isomers.
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Affiliation(s)
- Stefano Crespi
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Dhanalakshmi Vadivel
- Dipartimento Di Chimica, Università Di Pavia, Via Taramelli 12, 27100, Pavia, Italy. .,Istituto Nazionale Di Fisica Nucleare (INFN), Via Bassi 6, 27100, Pavia, Italy.
| | - Alfredo Bellisario
- Department of Cell and Molecular Biology, Molecular Biophysics, Husargatan 3, 752 37, Uppsala, Sweden
| | - Daniele Dondi
- Dipartimento Di Chimica, Università Di Pavia, Via Taramelli 12, 27100, Pavia, Italy.,Istituto Nazionale Di Fisica Nucleare (INFN), Via Bassi 6, 27100, Pavia, Italy
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25
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Linthwaite VL, Pawloski W, Pegg HB, Townsend PD, Thomas MJ, So VKH, Brown AP, Hodgson DRW, Lorimer GH, Fushman D, Cann MJ. Ubiquitin is a carbon dioxide-binding protein. SCIENCE ADVANCES 2021; 7:eabi5507. [PMID: 34559559 PMCID: PMC8462908 DOI: 10.1126/sciadv.abi5507] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
The identification of CO2-binding proteins is crucial to understanding CO2-regulated molecular processes. CO2 can form a reversible posttranslational modification through carbamylation of neutral N-terminal α-amino or lysine ε-amino groups. We have previously developed triethyloxonium (TEO) ion as a chemical proteomics tool for covalent trapping of carbamates, and here, we deploy TEO to identify ubiquitin as a mammalian CO2-binding protein. We use 13C-NMR spectroscopy to demonstrate that CO2 forms carbamates on the ubiquitin N terminus and ε-amino groups of lysines 6, 33, 48, and 63. We demonstrate that biologically relevant pCO2 levels reduce ubiquitin conjugation at lysine-48 and down-regulate ubiquitin-dependent NF-κB pathway activation. Our results show that ubiquitin is a CO2-binding protein and demonstrates carbamylation as a viable mechanism by which mammalian cells can respond to fluctuating pCO2.
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Affiliation(s)
| | - Wes Pawloski
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Hamish B. Pegg
- Department of Biosciences, Durham University, Durham DH1 3LE, UK
| | | | | | - Victor K. H. So
- Department of Biosciences, Durham University, Durham DH1 3LE, UK
| | - Adrian P. Brown
- Department of Biosciences, Durham University, Durham DH1 3LE, UK
| | - David R. W. Hodgson
- Department of Chemistry, Durham University, Durham DH1 3LE, UK
- Biophysical Sciences Institute, Durham University, Durham DH1 3LE, UK
| | - George H. Lorimer
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Martin J. Cann
- Department of Biosciences, Durham University, Durham DH1 3LE, UK
- Biophysical Sciences Institute, Durham University, Durham DH1 3LE, UK
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26
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Baloğlu E, Mairbäurl H. In Search of a Sensor: How Does CO 2 Regulate Alveolar Ion Transport? Am J Respir Cell Mol Biol 2021; 65:571-572. [PMID: 34348088 PMCID: PMC8641802 DOI: 10.1165/rcmb.2021-0270ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Affiliation(s)
- Emel Baloğlu
- Acibadem Mehmet Ali Aydinlar University School of Medicine, Department of Pharmacology , Istanbul, Turkey
| | - Heimo Mairbäurl
- University Hospital Heidelberg, 27178, Translational Pneumology and Translational Lung Research Center Heidelberg (TLRC) German Center for Lung Research (DZL) Im Neuenheimer Feld 156, Heidelberg, Germany;
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27
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Phelan DE, Mota C, Lai C, Kierans SJ, Cummins EP. Carbon dioxide-dependent signal transduction in mammalian systems. Interface Focus 2021; 11:20200033. [PMID: 33633832 PMCID: PMC7898142 DOI: 10.1098/rsfs.2020.0033] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2020] [Indexed: 12/15/2022] Open
Abstract
Carbon dioxide (CO2) is a fundamental physiological gas known to profoundly influence the behaviour and health of millions of species within the plant and animal kingdoms in particular. A recent Royal Society meeting on the topic of 'Carbon dioxide detection in biological systems' was extremely revealing in terms of the multitude of roles that different levels of CO2 play in influencing plants and animals alike. While outstanding research has been performed by leading researchers in the area of plant biology, neuronal sensing, cell signalling, gas transport, inflammation, lung function and clinical medicine, there is still much to be learned about CO2-dependent sensing and signalling. Notably, while several key signal transduction pathways and nodes of activity have been identified in plants and animals respectively, the precise wiring and sensitivity of these pathways to CO2 remains to be fully elucidated. In this article, we will give an overview of the literature relating to CO2-dependent signal transduction in mammalian systems. We will highlight the main signal transduction hubs through which CO2-dependent signalling is elicited with a view to better understanding the complex physiological response to CO2 in mammalian systems. The main topics of discussion in this article relate to how changes in CO2 influence cellular function through modulation of signal transduction networks influenced by pH, mitochondrial function, adenylate cyclase, calcium, transcriptional regulators, the adenosine monophosphate-activated protein kinase pathway and direct CO2-dependent protein modifications. While each of these topics will be discussed independently, there is evidence of significant cross-talk between these signal transduction pathways as they respond to changes in CO2. In considering these core hubs of CO2-dependent signal transduction, we hope to delineate common elements and identify areas in which future research could be best directed.
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Affiliation(s)
- D. E. Phelan
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - C. Mota
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - C. Lai
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - S. J. Kierans
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - E. P. Cummins
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
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28
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Dale N. CO 2 sensing by connexin26 and its role in the control of breathing. Interface Focus 2021; 11:20200029. [PMID: 33633831 PMCID: PMC7898151 DOI: 10.1098/rsfs.2020.0029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2020] [Indexed: 12/14/2022] Open
Abstract
Breathing is essential to provide the O2 required for metabolism and to remove its inevitable CO2 by-product. The rate and depth of breathing is controlled to regulate the excretion of CO2 to maintain the pH of arterial blood at physiological values. A widespread consensus is that chemosensory cells in the carotid body and brainstem measure blood and tissue pH and adjust the rate of breathing to ensure its homeostatic regulation. In this review, I shall consider the evidence that underlies this consensus and highlight historical data indicating that direct sensing of CO2 also plays a significant role in the regulation of breathing. I shall then review work from my laboratory that provides a molecular mechanism for the direct detection of CO2 via the gap junction protein connexin26 (Cx26) and demonstrates the contribution of this mechanism to the chemosensory regulation of breathing. As there are many pathological mutations of Cx26 in humans, I shall discuss which of these alter the CO2 sensitivity of Cx26 and the extent to which these mutations could affect human breathing. I finish by discussing the evolution of the CO2 sensitivity of Cx26 and its link to the evolution of amniotes.
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Affiliation(s)
- Nicholas Dale
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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29
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Schuster J, Mahler HC, Joerg S, Kamuju V, Huwyler J, Mathaes R. Stability of monoclonal antibodies after simulated subcutaneous administration. J Pharm Sci 2021; 110:2386-2394. [PMID: 33722546 DOI: 10.1016/j.xphs.2021.03.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Changes in the environment from the drug product to the human physiology might lead to physical and/or chemical modifications of the protein drug, such as in vivo aggregation and fragmentation. Although subcutaneous (SC) injection is a common route of administration for therapeutic proteins, knowledge on in vivo stability in the SC tissue is limited. In this study, we developed a physiologic in vitro model simulating the SC environment in patients. We assessed the stability of two monoclonal antibodies (mAbs) in four different protein-free fluids under physiologic conditions. We monitored protein stability over two weeks using a range of analytical methods, in analogy to testing purposes of a drug product. Both mAbs showed an increase of protein aggregates, fragments, and acidic species. mAb1 was consistently more stable in this in vitro model than mAb2, highlighting the importance of comparing the stability of different mAbs under physiologic conditions. Throughout the study, both mAbs were substantially less stable in bicarbonate buffers as compared to phosphate-buffered saline. In summary, our developed model was able to differentiate stability between molecules. Bicarbonate buffers were more suitable compared to phosphate-buffered saline in regards to simulating the in vivo conditions and evaluating protein liabilities.
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Affiliation(s)
- Joachim Schuster
- Lonza Pharma and Biotech, Drug Product Services, Hochbergerstr. 60A, 4057 Basel, Switzerland; Division of Pharmaceutical Technology, University of Basel, Pharmacenter, Basel, Switzerland
| | - Hanns-Christian Mahler
- Lonza Pharma and Biotech, Drug Product Services, Hochbergerstr. 60A, 4057 Basel, Switzerland
| | - Susanne Joerg
- Lonza Pharma and Biotech, Drug Product Services, Hochbergerstr. 60A, 4057 Basel, Switzerland
| | - Vinay Kamuju
- Lonza Pharma and Biotech, Drug Product Services, Hochbergerstr. 60A, 4057 Basel, Switzerland
| | - Joerg Huwyler
- Division of Pharmaceutical Technology, University of Basel, Pharmacenter, Basel, Switzerland
| | - Roman Mathaes
- Lonza Pharma and Biotech, Drug Product Services, Hochbergerstr. 60A, 4057 Basel, Switzerland.
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30
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Changing the residues interaction pattern as a universal mechanism for enzyme inactivation and denaturation in supercritical CO2. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114884] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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31
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Linthwaite VL, Cann MJ. A methodology for carbamate post-translational modification discovery and its application in Escherichia coli. Interface Focus 2021; 11:20200028. [PMID: 33633830 DOI: 10.1098/rsfs.2020.0028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2020] [Indexed: 11/12/2022] Open
Abstract
Carbon dioxide can influence cell phenotypes through the modulation of signalling pathways. CO2 regulates cellular processes as diverse as metabolism, cellular homeostasis, chemosensing and pathogenesis. This diversity of regulated processes suggests a broadly conserved mechanism for CO2 interactions with diverse cellular targets. CO2 is generally unreactive but can interact with neutral amines on protein under normal intracellular conditions to form a carbamate post-translational modification (PTM). We have previously demonstrated the presence of this PTM in a subset of protein produced by the model plant species Arabidopsis thaliana. Here, we describe a detailed methodology for identifying new carbamate PTMs in an extracted soluble proteome under biologically relevant conditions. We apply this methodology to the soluble proteome of the model prokaryote Escherichia coli and identify new carbamate PTMs. The application of this methodology, therefore, supports the hypothesis that the carbamate PTM is both more widespread in biology than previously suspected and may represent a broadly relevant mechanism for CO2-protein interactions.
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Affiliation(s)
| | - Martin J Cann
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
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32
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Casalino-Matsuda SM, Berdnikovs S, Wang N, Nair A, Gates KL, Beitel GJ, Sporn PHS. Hypercapnia selectively modulates LPS-induced changes in innate immune and DNA replication-related gene transcription in the macrophage. Interface Focus 2021; 11:20200039. [PMID: 33633835 DOI: 10.1098/rsfs.2020.0039] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2020] [Indexed: 12/14/2022] Open
Abstract
Hypercapnia, the elevation of CO2 in blood and tissues, commonly occurs in severe acute and chronic respiratory diseases and is associated with increased risk of death. Recent studies have shown that hypercapnia inhibits expression of select innate immune genes and suppresses host defence against bacterial and viral pneumonia in mice. In the current study, we evaluated the effect of culture under conditions of hypercapnia (20% CO2) versus normocapnia (5% CO2), both with normoxia, on global gene transcription in human THP-1 and mouse RAW 264.7 macrophages stimulated with lipopolysaccharide (LPS). We found that hypercapnia selectively downregulated transcription of LPS-induced genes associated with innate immunity, antiviral response, type I interferon signalling, cytokine signalling and other inflammatory pathways in both human and mouse macrophages. Simultaneously, hypercapnia increased expression of LPS-downregulated genes associated with mitosis, DNA replication and DNA repair. These CO2-induced changes in macrophage gene expression help explain hypercapnic suppression of antibacterial and antiviral host defence in mice and reveal a mechanism that may underlie, at least in part, the high mortality of patients with severe lung disease and hypercapnia.
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Affiliation(s)
- S Marina Casalino-Matsuda
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Sergejs Berdnikovs
- Division of Allergy-Immunology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Naizhen Wang
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Aisha Nair
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Khalilah L Gates
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Greg J Beitel
- Department of Molecular Biosciences, Weinberg College of Arts and Sciences, Northwestern University, Evanston, IL 60208, USA
| | - Peter H S Sporn
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.,Medical Service, Jesse Brown Veterans Affairs Medical Center, Chicago, IL 60612, USA
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33
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van de Wiel J, Meigh L, Bhandare A, Cook J, Nijjar S, Huckstepp R, Dale N. Connexin26 mediates CO 2-dependent regulation of breathing via glial cells of the medulla oblongata. Commun Biol 2020; 3:521. [PMID: 32958814 PMCID: PMC7505967 DOI: 10.1038/s42003-020-01248-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 08/21/2020] [Indexed: 01/12/2023] Open
Abstract
Breathing is highly sensitive to the PCO2 of arterial blood. Although CO2 is detected via the proxy of pH, CO2 acting directly via Cx26 may also contribute to the regulation of breathing. Here we exploit our knowledge of the structural motif of CO2-binding to Cx26 to devise a dominant negative subunit (Cx26DN) that removes the CO2-sensitivity from endogenously expressed wild type Cx26. Expression of Cx26DN in glial cells of a circumscribed region of the mouse medulla - the caudal parapyramidal area - reduced the adaptive change in tidal volume and minute ventilation by approximately 30% at 6% inspired CO2. As central chemosensors mediate about 70% of the total response to hypercapnia, CO2-sensing via Cx26 in the caudal parapyramidal area contributed about 45% of the centrally-mediated ventilatory response to CO2. Our data unequivocally link the direct sensing of CO2 to the chemosensory control of breathing and demonstrates that CO2-binding to Cx26 is a key transduction step in this fundamental process.
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Affiliation(s)
| | - Louise Meigh
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Amol Bhandare
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Jonathan Cook
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Sarbjit Nijjar
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Robert Huckstepp
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Nicholas Dale
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
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34
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Schuster J, Mahler HC, Koulov A, Joerg S, Racher A, Huwyler J, Detampel P, Mathaes R. Tracking the physical stability of fluorescent-labeled mAbs under physiologic in vitro conditions in human serum and PBS. Eur J Pharm Biopharm 2020; 152:193-201. [DOI: 10.1016/j.ejpb.2020.04.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/18/2020] [Accepted: 04/22/2020] [Indexed: 02/08/2023]
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35
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Chernyshev A, Braggins T. Investigation of Temporal Apparent C4 Sugar Change in Manuka Honey. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:4261-4267. [PMID: 32159341 DOI: 10.1021/acs.jafc.9b06965] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
New Zealand manuka honeys are known for their propensity to increase apparent C4 sugar content during storage. Depending on the particular storage regime and the initial content of dihydroxyacetone (DHA) in honey, the ready-to-market product often fails the C4 sugar test because of the above phenomenon. We have used DHA labeled with a radioactive 14C isotope in a set of honeys subject to an incubation experiment. These honeys were analyzed for DHA, methylglyoxal (MG), hydroxymethylfurfural (HMF), apparent C4 sugars, and 14C scintillation counts over a period of 18 months. The major conclusion of this experiment is that neither DHA nor MG is responsible for the δ13C shift in the honey protein extract. There must be some other yet unknown substance of manuka honey, which binds to the protein and causes negative δ13C shift. One identified candidate for such a binding is carbon dioxide.
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Affiliation(s)
- Anatoly Chernyshev
- Analytica Laboratories Ltd., Ruakura Research Centre, 10 Bisley Rd, Hamilton 3240, New Zealand
| | - Terry Braggins
- Analytica Laboratories Ltd., Ruakura Research Centre, 10 Bisley Rd, Hamilton 3240, New Zealand
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36
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Pagliano E. Versatile derivatization for GC-MS and LC-MS: alkylation with trialkyloxonium tetrafluoroborates for inorganic anions, chemical warfare agent degradation products, organic acids, and proteomic analysis. Anal Bioanal Chem 2020; 412:1963-1971. [PMID: 31915869 DOI: 10.1007/s00216-019-02299-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/04/2019] [Accepted: 11/21/2019] [Indexed: 10/25/2022]
Abstract
Analytical chemists resort to derivatization for improving the detection performance of certain categories of analytes. Within this context, alkylation reactions are regarded as an important asset for many methods based on GC-MS and LC-MS. Trialkyloxonium tetrafluoroborates (R[Formula: see text][BF4]-) are powerful alkylating agents with ionic liquid properties: they are nonvolatile salts soluble in water which are easier and safer to handle with respect to common alkylating agents like diazomethane. R[Formula: see text][BF4]- can perform the alkylation in both organic and aqueous media at pH conditions ranging from acidic to alkaline. Recent analytical applications of trialkyloxonium derivatizations include the high-precision determination of inorganic anions in complex matrices, the qualitative confirmation of chemical warfare agent degradation products in soils, the profiling of carboxylic acids in urine, and the detection of protein post-translational modifications induced by carbon dioxide. The common denominator for all methods presented can be found in the simplicity of the alkylation protocol which, in most of the cases, requires a single step addition of the reagent directly to the sample. Graphical Abstract Alkylation with trialkyloxonium salts for GC-MS and LC-MS analysis.
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Affiliation(s)
- Enea Pagliano
- National Research Council Canada, 1200 Montreal Road, K1A 0R6, Ottawa, Ontario, Canada.
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37
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Schuster J, Koulov A, Mahler HC, Detampel P, Huwyler J, Singh S, Mathaes R. In Vivo Stability of Therapeutic Proteins. Pharm Res 2020; 37:23. [DOI: 10.1007/s11095-019-2689-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/16/2019] [Indexed: 01/05/2023]
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38
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Qin W, Yang F, Wang C. Chemoproteomic profiling of protein-metabolite interactions. Curr Opin Chem Biol 2019; 54:28-36. [PMID: 31812894 DOI: 10.1016/j.cbpa.2019.11.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 10/23/2019] [Accepted: 11/03/2019] [Indexed: 12/29/2022]
Abstract
Small molecule metabolites play important roles in regulating protein functions, which are acted through either covalent non-enzymatic post-translational modifications or non-covalent binding interactions. Chemical proteomic strategies can help delineate global landscapes of cellular protein-metabolite interactions and provide molecular insights about their mechanisms of action. In this review, we summarized the recent progress in developments and applications of chemoproteomic strategies to profile protein-metabolite interactions.
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Affiliation(s)
- Wei Qin
- Synthetic and Functional Biomolecules Center, Peking University, Beijing, China; Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Fan Yang
- Synthetic and Functional Biomolecules Center, Peking University, Beijing, China; Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China; College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Chu Wang
- Synthetic and Functional Biomolecules Center, Peking University, Beijing, China; Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
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39
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Cummins EP, Strowitzki MJ, Taylor CT. Mechanisms and Consequences of Oxygen and Carbon Dioxide Sensing in Mammals. Physiol Rev 2019; 100:463-488. [PMID: 31539306 DOI: 10.1152/physrev.00003.2019] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Molecular oxygen (O2) and carbon dioxide (CO2) are the primary gaseous substrate and product of oxidative phosphorylation in respiring organisms, respectively. Variance in the levels of either of these gasses outside of the physiological range presents a serious threat to cell, tissue, and organism survival. Therefore, it is essential that endogenous levels are monitored and kept at appropriate concentrations to maintain a state of homeostasis. Higher organisms such as mammals have evolved mechanisms to sense O2 and CO2 both in the circulation and in individual cells and elicit appropriate corrective responses to promote adaptation to commonly encountered conditions such as hypoxia and hypercapnia. These can be acute and transient nontranscriptional responses, which typically occur at the level of whole animal physiology or more sustained transcriptional responses, which promote chronic adaptation. In this review, we discuss the mechanisms by which mammals sense changes in O2 and CO2 and elicit adaptive responses to maintain homeostasis. We also discuss crosstalk between these pathways and how they may represent targets for therapeutic intervention in a range of pathological states.
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Affiliation(s)
- Eoin P Cummins
- UCD Conway Institute, Systems Biology Ireland and the School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Moritz J Strowitzki
- UCD Conway Institute, Systems Biology Ireland and the School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Cormac T Taylor
- UCD Conway Institute, Systems Biology Ireland and the School of Medicine, University College Dublin, Belfield, Dublin, Ireland
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40
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van Groesen E, Lohans CT, Brem J, Aertker KMJ, Claridge TDW, Schofield CJ. 19 F NMR Monitoring of Reversible Protein Post-Translational Modifications: Class D β-Lactamase Carbamylation and Inhibition. Chemistry 2019; 25:11837-11841. [PMID: 31310409 PMCID: PMC6771976 DOI: 10.1002/chem.201902529] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/11/2019] [Indexed: 11/05/2022]
Abstract
Bacterial production of β‐lactamases with carbapenemase activity is a global health threat. The active sites of class D carbapenemases such as OXA‐48, which is of major clinical importance, uniquely contain a carbamylated lysine residue which is essential for catalysis. Although there is significant interest in characterizing this post‐translational modification, and it is a promising inhibition target, protein carbamylation is challenging to monitor in solution. We report the use of 19F NMR spectroscopy to monitor the carbamylation state of 19F‐labelled OXA‐48. This method was used to investigate the interactions of OXA‐48 with clinically used serine β‐lactamase inhibitors, including avibactam and vaborbactam. Crystallographic studies on 19F‐labelled OXA‐48 provide a structural rationale for the sensitivity of the 19F label to active site interactions. The overall results demonstrate the use of 19F NMR to monitor reversible covalent post‐translational modifications.
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Affiliation(s)
- Emma van Groesen
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Christopher T Lohans
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK.,Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Jürgen Brem
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
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