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Moses D, Ginell GM, Holehouse AS, Sukenik S. Intrinsically disordered regions are poised to act as sensors of cellular chemistry. Trends Biochem Sci 2023; 48:1019-1034. [PMID: 37657994 PMCID: PMC10840941 DOI: 10.1016/j.tibs.2023.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 09/03/2023]
Abstract
Intrinsically disordered proteins and protein regions (IDRs) are abundant in eukaryotic proteomes and play a wide variety of essential roles. Instead of folding into a stable structure, IDRs exist in an ensemble of interconverting conformations whose structure is biased by sequence-dependent interactions. The absence of a stable 3D structure, combined with high solvent accessibility, means that IDR conformational biases are inherently sensitive to changes in their environment. Here, we argue that IDRs are ideally poised to act as sensors and actuators of cellular physicochemistry. We review the physical principles that underlie IDR sensitivity, the molecular mechanisms that translate this sensitivity to function, and recent studies where environmental sensing by IDRs may play a key role in their downstream function.
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Affiliation(s)
- David Moses
- Department of Chemistry and Biochemistry, University of California, Merced, CA, USA
| | - Garrett M Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA; Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA; Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO, USA.
| | - Shahar Sukenik
- Department of Chemistry and Biochemistry, University of California, Merced, CA, USA; Quantitative Systems Biology Program, University of California, Merced, CA, USA.
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2
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Launay H, Avilan L, Gérard C, Parsiegla G, Receveur-Brechot V, Gontero B, Carriere F. Location of the photosynthetic carbon metabolism in microcompartments and separated phases in microalgal cells. FEBS Lett 2023; 597:2853-2878. [PMID: 37827572 DOI: 10.1002/1873-3468.14754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/04/2023] [Accepted: 09/22/2023] [Indexed: 10/14/2023]
Abstract
Carbon acquisition, assimilation and storage in eukaryotic microalgae and cyanobacteria occur in multiple compartments that have been characterised by the location of the enzymes involved in these functions. These compartments can be delimited by bilayer membranes, such as the chloroplast, the lumen, the peroxisome, the mitochondria or monolayer membranes, such as lipid droplets or plastoglobules. They can also originate from liquid-liquid phase separation such as the pyrenoid. Multiple exchanges exist between the intracellular microcompartments, and these are reviewed for the CO2 concentration mechanism, the Calvin-Benson-Bassham cycle, the lipid metabolism and the cellular energetic balance. Progress in microscopy and spectroscopic methods opens new perspectives to characterise the molecular consequences of the location of the proteins involved, including intrinsically disordered proteins.
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Affiliation(s)
- Hélène Launay
- Aix Marseille Univ, CNRS, BIP, UMR7281, Marseille, France
| | - Luisana Avilan
- Aix Marseille Univ, CNRS, BIP, UMR7281, Marseille, France
| | - Cassy Gérard
- Aix Marseille Univ, CNRS, BIP, UMR7281, Marseille, France
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3
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Gérard C, Carrière F, Receveur-Bréchot V, Launay H, Gontero B. A Trajectory of Discovery: Metabolic Regulation by the Conditionally Disordered Chloroplast Protein, CP12. Biomolecules 2022; 12:biom12081047. [PMID: 36008940 PMCID: PMC9406205 DOI: 10.3390/biom12081047] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 11/25/2022] Open
Abstract
The chloroplast protein CP12, which is widespread in photosynthetic organisms, belongs to the intrinsically disordered proteins family. This small protein (80 amino acid residues long) presents a bias in its composition; it is enriched in charged amino acids, has a small number of hydrophobic residues, and has a high proportion of disorder-promoting residues. More precisely, CP12 is a conditionally disordered proteins (CDP) dependent upon the redox state of its four cysteine residues. During the day, reducing conditions prevail in the chloroplast, and CP12 is fully disordered. Under oxidizing conditions (night), its cysteine residues form two disulfide bridges that confer some stability to some structural elements. Like many CDPs, CP12 plays key roles, and its redox-dependent conditional disorder is important for the main function of CP12: the dark/light regulation of the Calvin-Benson-Bassham (CBB) cycle responsible for CO2 assimilation. Oxidized CP12 binds to glyceraldehyde-3-phosphate dehydrogenase and phosphoribulokinase and thereby inhibits their activity. However, recent studies reveal that CP12 may have other functions beyond the CBB cycle regulation. In this review, we report the discovery of this protein, its features as a disordered protein, and the many functions this small protein can have.
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4
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Bezerra RP, Conniff AS, Uversky VN. Comparative study of structures and functional motifs in lectins from the commercially important photosynthetic microorganisms. Biochimie 2022; 201:63-74. [PMID: 35839918 DOI: 10.1016/j.biochi.2022.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/17/2022] [Accepted: 07/08/2022] [Indexed: 11/26/2022]
Abstract
Photosynthetic microorganisms, specifically cyanobacteria and microalgae, can synthesize a vast array of biologically active molecules, such as lectins, that have great potential for various biotechnological and biomedical applications. However, since the structures of these proteins are not well established, likely due to the presence of intrinsically disordered regions, our ability to better understand their functionality is hampered. We embarked on a study of the carbohydrate recognition domain (CRD), intrinsically disordered regions (IDRs), amino acidic composition, as well as and functional motifs in lectins from cyanobacteria of the genus Arthrospira and microalgae Chlorella and Dunaliella genus using a combination of bioinformatics techniques. This search revealed the presence of five distinctive CRD types differently distributed between the genera. Most CRDs displayed a group-specific distribution, except to C. sorokiniana possessing distinctive CRD probably due to its specific lifestyle. We also found that all CRDs contain short IDRs. Bacterial lectin of Arthrospira prokarionte showed lower intrinsic disorder and proline content when compared to the lectins from the eukaryotic microalgae (Chlorella and Dunaliella). Among the important functions predicted in all lectins were several specific motifs, which directly interacts with proteins involved in the cell-cycle control and which may be used for pharmaceutical purposes. Since the aforementioned properties of each type of lectin were investigated in silico, they need experimental confirmation. The results of our study provide an overview of the distribution of CRD, IDRs, and functional motifs within lectin from the commercially important microalgae.
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Affiliation(s)
- Raquel P Bezerra
- Department of Morphology and Animal Physiology, Federal Rural University of Pernambuco-UFRPE, Dom Manoel de Medeiros Ave, Recife, PE, 52171-900, Brazil.
| | - Amanda S Conniff
- Department of Medical Engineering, Morsani College of Medicine and College of Engineering, University of South Florida, Tampa, FL, 33612, USA.
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
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5
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Abstract
Abstract Signaling pathways allow cells to detect and respond to a wide variety of chemical (e.g. Ca2+ or chemokine proteins) and physical stimuli (e.g., sheer stress, light). Together, these pathways form an extensive communication network that regulates basic cell activities and coordinates the function of multiple cells or tissues. The process of cell signaling imposes many demands on the proteins that comprise these pathways, including the abilities to form active and inactive states, and to engage in multiple protein interactions. Furthermore, successful signaling often requires amplifying the signal, regulating or tuning the response to the signal, combining information sourced from multiple pathways, all while ensuring fidelity of the process. This sensitivity, adaptability, and tunability are possible, in part, due to the inclusion of intrinsically disordered regions in many proteins involved in cell signaling. The goal of this collection is to highlight the many roles of intrinsic disorder in cell signaling. Following an overview of resources that can be used to study intrinsically disordered proteins, this review highlights the critical role of intrinsically disordered proteins for signaling in widely diverse organisms (animals, plants, bacteria, fungi), in every category of cell signaling pathway (autocrine, juxtacrine, intracrine, paracrine, and endocrine) and at each stage (ligand, receptor, transducer, effector, terminator) in the cell signaling process. Thus, a cell signaling pathway cannot be fully described without understanding how intrinsically disordered protein regions contribute to its function. The ubiquitous presence of intrinsic disorder in different stages of diverse cell signaling pathways suggest that more mechanisms by which disorder modulates intra- and inter-cell signals remain to be discovered. Graphical abstract ![]()
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Affiliation(s)
- Sarah E Bondos
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX, 77843, USA.
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.,Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, Russia, 142290
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Bae JW, Park M, Lee CS, Kwon WS. Proteomic profiling of cryopreserved Trichormus variabilis using various cryoprotectants. Cryobiology 2021; 104:23-31. [PMID: 34808109 DOI: 10.1016/j.cryobiol.2021.11.175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 10/25/2021] [Accepted: 11/18/2021] [Indexed: 11/25/2022]
Abstract
Algae, which may be unicellular or multicellular, can carry out photosynthesis just like plants as they effectively utilize light energy. They contain various physiologically active substances and are, therefore, widely used commercially to produce healthy food and feed additives, cosmetics, and energy supplements. For useful applications, the cryopreservation technique has been used in various fields. Recently, to develop suitable cryopreservation methods for algal applications, various studies have been performed. However, adequate investigations have not been conducted to understand the mechanism underlying algal cryopreservation at the molecular level. Therefore, this study examined the profile alteration of the proteome using cryopreservation with various cryoprotectants (CPAs). Trichormus variabilis was cultured and then cryopreserved with 10% dimethyl sulfoxide, methanol, and glycerol, after which, proteome profiling was done. Finally, signaling pathway search was performed, and a new signaling pathway was established based on differentially expressed proteins. As a result, the expression levels of 17 proteins were observed. Additionally, it was confirmed that the differentially expressed proteins were related to 16 signaling pathways and that they were capable of interacting with each other. The findings suggest that the differentially expressed proteins may be applied as biomarkers for algal cryopreservation and to understand the mechanism underlying T. variabilis cryopreservation. Moreover, it is anticipated that the results from this study would be useful in selecting suitable CPAs and in upgrading the cryopreservation techniques.
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Affiliation(s)
- Jeong-Won Bae
- Department of Animal Science and Biotechnology, Kyungpook National University, Sangju, Gyeongsangbuk-do, 37224, Republic of Korea
| | - Mirye Park
- Protist Research Team, Microbial Research Department, Nakdonggang National Institute of Biological Resources, Sangju, 37242, Republic of Korea
| | - Chang Soo Lee
- Protist Research Team, Microbial Research Department, Nakdonggang National Institute of Biological Resources, Sangju, 37242, Republic of Korea.
| | - Woo-Sung Kwon
- Department of Animal Science and Biotechnology, Kyungpook National University, Sangju, Gyeongsangbuk-do, 37224, Republic of Korea.
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Launay H, Shao H, Bornet O, Cantrelle FX, Lebrun R, Receveur-Brechot V, Gontero B. Flexibility of Oxidized and Reduced States of the Chloroplast Regulatory Protein CP12 in Isolation and in Cell Extracts. Biomolecules 2021; 11:biom11050701. [PMID: 34066751 PMCID: PMC8151241 DOI: 10.3390/biom11050701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 12/12/2022] Open
Abstract
In the chloroplast, Calvin–Benson–Bassham enzymes are active in the reducing environment created in the light by electrons from the photosystems. In the dark, these enzymes are inhibited, mainly caused by oxidation of key regulatory cysteine residues. CP12 is a small protein that plays a role in this regulation with four cysteine residues that undergo a redox transition. Using amide-proton exchange with solvent, measured by nuclear magnetic resonance (NMR) and mass-spectrometry, we confirmed that reduced CP12 is intrinsically disordered. Using real-time NMR, we showed that the oxidation of the two disulfide bridges is simultaneous. In oxidized CP12, the C23–C31 pair is in a region that undergoes a conformational exchange in the NMR-intermediate timescale. The C66–C75 pair is in the C-terminus that folds into a stable helical turn. We confirmed that these structural states exist in a physiologically relevant environment: a cell extract from Chlamydomonas reinhardtii. Consistent with these structural equilibria, the reduction is slower for the C66–C75 pair than for the C23–C31 pair. The redox mid-potentials for the two cysteine pairs differ and are similar to those found for glyceraldehyde 3-phosphate dehydrogenase and phosphoribulokinase, consistent with the regulatory role of CP12.
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Affiliation(s)
- Helene Launay
- Aix Marseille Univ, CNRS, BIP, UMR7281, F-13402 Marseille, France; (H.S.); (V.R.-B.)
- Correspondence: (H.L.); (B.G.)
| | - Hui Shao
- Aix Marseille Univ, CNRS, BIP, UMR7281, F-13402 Marseille, France; (H.S.); (V.R.-B.)
| | - Olivier Bornet
- NMR Platform, Institut de Microbiologie de la Méditerranée, Aix Marseille Univ, F-13009 Marseille, France;
| | - Francois-Xavier Cantrelle
- CNRS, ERL9002, Integrative Structural Biology, Univ. Lille, F-59658 Lille, France;
- U1167, INSERM, CHU Lille, Institut Pasteur de Lille, F-59019 Lille, France
| | - Regine Lebrun
- Plate-forme Protéomique, Marseille Protéomique (MaP), IMM FR 3479, 31 Chemin Joseph Aiguier, F-13009 Marseille, France;
| | | | - Brigitte Gontero
- Aix Marseille Univ, CNRS, BIP, UMR7281, F-13402 Marseille, France; (H.S.); (V.R.-B.)
- Correspondence: (H.L.); (B.G.)
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8
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Pikula K, Kirichenko K, Vakhniuk I, Kalantzi OI, Kholodov A, Orlova T, Markina Z, Tsatsakis A, Golokhvast K. Aquatic toxicity of particulate matter emitted by five electroplating processes in two marine microalgae species. Toxicol Rep 2021; 8:880-887. [PMID: 33981588 PMCID: PMC8085665 DOI: 10.1016/j.toxrep.2021.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/17/2021] [Accepted: 04/13/2021] [Indexed: 11/28/2022] Open
Abstract
Electroplating is a widely used group of industrial processes that make a metal coating on a solid substrate. Our previous research studied the concentrations, characteristics, and chemical composition of nano- and microparticles emitted during different electroplating processes. The objective of this study was to evaluate the environmental toxicity of particulate matter obtained from five different electrochemical processes. We collected airborne particle samples formed during aluminum cleaning, aluminum etching, chemical degreasing, nonferrous metals etching, and nickel plating. The toxicity of the particles was evaluated by the standard microalgae growth rate inhibition test. Additionally, we evaluated membrane potential and cell size changes in the microalgae H. akashiwo and P. purpureum exposed to the obtained suspensions of electroplating particles. The findings of this research demonstrate that the aquatic toxicity of electroplating emissions significantly varies between different industrial processes and mostly depends on particle chemical composition and solubility rather than the number of insoluble particles. The sample from an aluminum cleaning workshop was significantly more toxic for both microalgae species compared to the other samples and demonstrated dose and time-dependent toxicity. The samples obtained during chemical degreasing and nonferrous metals etching processes induced depolarization of microalgal cell membranes, demonstrated the potential of chronic toxicity, and stimulated the growth rate of microalgae after 72 h of exposure. Moreover, the sample from a nonferrous metals etching workshop revealed hormetic dose-response toxicity in H. akashiwo, which can lead to harmful algal blooms in the environment.
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Affiliation(s)
- Konstantin Pikula
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources, Saint-Petersburg, 190000, Russia
- Far Eastern Federal University, Vladivostok, 690922, Russia
| | - Konstantin Kirichenko
- Far Eastern Federal University, Vladivostok, 690922, Russia
- Siberian Federal Scientific Center of Agrobiotechnologies of the Russian Academy of Sciences, SFSCA RAS, 630501, Krasnoobsk, Novosibirsk region, Russia
| | - Igor Vakhniuk
- Far Eastern Federal University, Vladivostok, 690922, Russia
- Siberian Federal Scientific Center of Agrobiotechnologies of the Russian Academy of Sciences, SFSCA RAS, 630501, Krasnoobsk, Novosibirsk region, Russia
| | | | - Aleksei Kholodov
- Far East Geological Institute, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, 690022, Russia
| | - Tatiana Orlova
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 690041, Vladivostok, Russia
| | - Zhanna Markina
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 690041, Vladivostok, Russia
| | - Aristidis Tsatsakis
- Laboratory of Toxicology and Forensic Sciences, Medical School, University of Crete, 71003 Heraklion, Greece
- Department of Analytical and Forensic Medical Toxicology, Sechenov University, 119991 Moscow, Russia
| | - Kirill Golokhvast
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources, Saint-Petersburg, 190000, Russia
- Far Eastern Federal University, Vladivostok, 690922, Russia
- Siberian Federal Scientific Center of Agrobiotechnologies of the Russian Academy of Sciences, SFSCA RAS, 630501, Krasnoobsk, Novosibirsk region, Russia
- Pacific Geographical Institute, Far Eastern Branch of the Russian Academy of Sciences, 690041, Vladivostok, Russia
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9
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Shao H, Huang W, Avilan L, Receveur-Bréchot V, Puppo C, Puppo R, Lebrun R, Gontero B, Launay H. A new type of flexible CP12 protein in the marine diatom Thalassiosira pseudonana. Cell Commun Signal 2021; 19:38. [PMID: 33761918 PMCID: PMC7992989 DOI: 10.1186/s12964-021-00718-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/09/2021] [Indexed: 12/11/2022] Open
Abstract
Background CP12 is a small chloroplast protein that is widespread in various photosynthetic organisms and is an actor of the redox signaling pathway involved in the regulation of the Calvin Benson Bassham (CBB) cycle. The gene encoding this protein is conserved in many diatoms, but the protein has been overlooked in these organisms, despite their ecological importance and their complex and still enigmatic evolutionary background. Methods A combination of biochemical, bioinformatics and biophysical methods including electrospray ionization-mass spectrometry, circular dichroism, nuclear magnetic resonance spectroscopy and small X ray scattering, was used to characterize a diatom CP12. Results Here, we demonstrate that CP12 is expressed in the marine diatom Thalassiosira pseudonana constitutively in dark-treated and in continuous light-treated cells as well as in all growth phases. This CP12 similarly to its homologues in other species has some features of intrinsically disorder protein family: it behaves abnormally under gel electrophoresis and size exclusion chromatography, has a high net charge and a bias amino acid composition. By contrast, unlike other known CP12 proteins that are monomers, this protein is a dimer as suggested by native electrospray ionization-mass spectrometry and small angle X-ray scattering. In addition, small angle X-ray scattering revealed that this CP12 is an elongated cylinder with kinks. Circular dichroism spectra indicated that CP12 has a high content of α-helices, and nuclear magnetic resonance spectroscopy suggested that these helices are unstable and dynamic within a millisecond timescale. Together with in silico predictions, these results suggest that T. pseudonana CP12 has both coiled coil and disordered regions. Conclusions These findings bring new insights into the large family of dynamic proteins containing disordered regions, thus increasing the diversity of known CP12 proteins. As it is a protein that is more abundant in many stresses, it is not devoted to one metabolism and in particular, it is not specific to carbon metabolism. This raises questions about the role of this protein in addition to the well-established regulation of the CBB cycle. Choregraphy of metabolism by CP12 proteins in Viridiplantae and Heterokonta. While the monomeric CP12 in Viridiplantae is involved in carbon assimilation, regulating phosphoribulokinase (PRK) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) through the formation of a ternary complex, in Heterokonta studied so far, the dimeric CP12 is associated with Ferredoxin-NADP reductase (FNR) and GAPDH. The Viridiplantae CP12 can bind metal ions and can be a chaperone, the Heterokonta CP12 is more abundant in all stresses (C, N, Si, P limited conditions) and is not specific to a metabolism. ![]()
Video Abstract
Supplementary Information The online version contains supplementary material available at 10.1186/s12964-021-00718-x.
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Affiliation(s)
- Hui Shao
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France
| | - Wenmin Huang
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France.,Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Luisana Avilan
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France.,Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | | | - Carine Puppo
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France
| | - Rémy Puppo
- CNRS FR 3479, Plate-Forme Protéomique de L'Institut de Microbiologie de La Méditerranée (IMM), Aix Marseille Univ, 13009, Marseille, France
| | - Régine Lebrun
- CNRS FR 3479, Plate-Forme Protéomique de L'Institut de Microbiologie de La Méditerranée (IMM), Aix Marseille Univ, 13009, Marseille, France
| | - Brigitte Gontero
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France.
| | - Hélène Launay
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France.
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10
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Neira JL, Rizzuti B, Jiménez-Alesanco A, Palomino-Schätzlein M, Abián O, Velázquez-Campoy A, Iovanna JL. A Phosphorylation-Induced Switch in the Nuclear Localization Sequence of the Intrinsically Disordered NUPR1 Hampers Binding to Importin. Biomolecules 2020; 10:E1313. [PMID: 32933064 DOI: 10.3390/biom10091313] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 09/05/2020] [Accepted: 09/09/2020] [Indexed: 12/24/2022] Open
Abstract
Several carrier proteins are involved in protein transport from the cytoplasm to the nucleus in eukaryotic cells. One of those is importin α, of which there are several human isoforms; among them, importin α3 (Impα3) has a high flexibility. The protein NUPR1, a nuclear protein involved in the cell-stress response and cell cycle regulation, is an intrinsically disordered protein (IDP) that has a nuclear localization sequence (NLS) to allow for nuclear translocation. NUPR1 does localize through the whole cell. In this work, we studied the affinity of the isolated wild-type NLS region (residues 54–74) of NUPR1 towards Impα3 and several mutants of the NLS region by using several biophysical techniques and molecular docking approaches. The NLS region of NUPR1 interacted with Impα3, opening the way to model the nuclear translocation of disordered proteins. All the isolated NLS peptides were disordered. They bound to Impα3 with low micromolar affinity (1.7–27 μM). Binding was hampered by removal of either Lys65 or Lys69 residues, indicating that positive charges were important; furthermore, binding decreased when Thr68 was phosphorylated. The peptide phosphorylated at Thr68, as well as four phospho-mimetic peptides (all containing the Thr68Glu mutation), showed the presence of a sequential NN(i,i + 1) nuclear Overhauser effect (NOE) in the 2D-1H-NMR (two-dimensional–proton NMR) spectra, indicating the presence of turn-like conformations. Thus, the phosphorylation of Thr68 modulates the binding of NUPR1 to Impα3 by a conformational, entropy-driven switch from a random-coil conformation to a turn-like structure.
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11
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Kim SY, Stessman DJ, Wright DA, Spalding MH, Huber SC, Ort DR. Arabidopsis plants expressing only the redox-regulated Rca-α isoform have constrained photosynthesis and plant growth. Plant J 2020; 103:2250-2262. [PMID: 32593186 DOI: 10.1111/tpj.14897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
Rubisco activase (Rca) facilitates the release of sugar-phosphate inhibitors from the active sites of Rubisco and thereby plays a central role in initiating and sustaining Rubisco activation. In Arabidopsis, alternative splicing of a single Rca gene results in two Rca isoforms, Rca-α and Rca-β. Redox modulation of Rca-α regulates the function of Rca-α and Rca-β acting together to control Rubisco activation. Although Arabidopsis Rca-α alone less effectively activates Rubisco in vitro, it is not known how CO2 assimilation and plant growth are impacted. Here, we show that two independent transgenic Arabidopsis lines expressing Rca-α in the absence of Rca-β ('Rca-α only' lines) grew more slowly in various light conditions, especially under low light or fluctuating light intensity, and in a short day photoperiod compared to wildtype. Photosynthetic induction was slower in the Rca-α only lines, and they maintained a lower rate of CO2 assimilation during both photoperiod types. Our findings suggest Rca oligomers composed of Rca-α only are less effective in initiating and sustaining the activation of Rubisco than when Rca-β is also present. Currently there are no examples of any plant species that naturally express Rca-α only but numerous examples of species expressing Rca-β only. That Rca-α exists in most plant species, including many C3 and C4 food and bioenergy crops, implies its presence is adaptive under some circumstances.
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Affiliation(s)
- Sang Yeol Kim
- US Department of Agriculture/Agricultural Research Service, Urbana, IL, 61801, USA
- Department of Plant Biology, University of Illinois, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA
| | - Dan J Stessman
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - David A Wright
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Martin H Spalding
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Steven C Huber
- US Department of Agriculture/Agricultural Research Service, Urbana, IL, 61801, USA
- Department of Plant Biology, University of Illinois, Urbana, IL, 61801, USA
| | - Donald R Ort
- Department of Plant Biology, University of Illinois, Urbana, IL, 61801, USA
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
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Pikula K, Mintcheva N, Kulinich SA, Zakharenko A, Markina Z, Chaika V, Orlova T, Mezhuev Y, Kokkinakis E, Tsatsakis A, Golokhvast K. Aquatic toxicity and mode of action of CdS and ZnS nanoparticles in four microalgae species. Environ Res 2020; 186:109513. [PMID: 32305679 DOI: 10.1016/j.envres.2020.109513] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/09/2020] [Accepted: 04/09/2020] [Indexed: 06/11/2023]
Abstract
This study reports the differences in toxic action between cadmium sulfide (CdS) and zinc sulfide (ZnS) nanoparticles (NPs) prepared by recently developed xanthate-mediated method. The aquatic toxicity of the synthesized NPs on four marine microalgae species was explored. Growth rate, esterase activity, membrane potential, and morphological changes of microalgae cells were evaluated using flow cytometry and optical microscopy. CdS and ZnS NPs demonstrated similar level of general toxicity and growth-rate inhibition to all used microalgae species, except the red algae P. purpureum. More specifically, CdS NPs caused higher inhibition of growth rate for C. muelleri and P. purpureum, while ZnS NPs were more toxic for A. ussuriensis and H. akashiwo species. Our findings suggest that the sensitivity of different microalgae species to CdS and ZnS NPs depends on the chemical composition of NPs and their ability to interact with the components of microalgal cell-wall. The red microalga was highly resistant to ZnS NPs most likely due to the presence of phycoerythrin proteins in the outer membrane bound Zn2+ cations defending their cells from further toxic influence. The treatment with CdS NPs caused morphological changes and biochemical disorder in all tested microalgae species. The toxicity of CdS NPs is based on their higher photoactivity under visible light irradiation and lower dissociation in water, which allows them to generate more reactive oxygen species and create a higher risk of oxidative stress to aquatic organisms. The results of this study contribute to our understanding of the parameters affecting the aquatic toxicity of semiconductor NPs and provide a basis for further investigations.
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Affiliation(s)
- Konstantin Pikula
- Far Eastern Federal University, Vladivostok, 690950, Russian Federation; N.I. Vavilov All-Russian Research Institute of Plant Genetic Resources, Saint Petersburg, 190121, Russian Federation.
| | - Neli Mintcheva
- Research Institute of Science and Technology, Tokai University, Hiratsuka, Kanagawa, 259-1292, Japan; Department of Chemistry, University of Mining and Geology, Sofia, 1700, Bulgaria
| | - Sergei A Kulinich
- Far Eastern Federal University, Vladivostok, 690950, Russian Federation; Research Institute of Science and Technology, Tokai University, Hiratsuka, Kanagawa, 259-1292, Japan; Department of Mechanical Engineering, Tokai University, Hiratsuka, Kanagawa, 259-1292, Japan
| | - Alexander Zakharenko
- Far Eastern Federal University, Vladivostok, 690950, Russian Federation; N.I. Vavilov All-Russian Research Institute of Plant Genetic Resources, Saint Petersburg, 190121, Russian Federation
| | - Zhanna Markina
- Far Eastern Federal University, Vladivostok, 690950, Russian Federation; A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, 690014, Russian Federation
| | - Vladimir Chaika
- Far Eastern Federal University, Vladivostok, 690950, Russian Federation
| | - Tatiana Orlova
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, 690014, Russian Federation
| | - Yaroslav Mezhuev
- Mendeleev University of Chemical Technology of Russia, Moscow, 125047, Russian Federation
| | - Emmanouil Kokkinakis
- Laboratory of Toxicology, School of Medicine, University of Crete, Heraklion, 71003, Greece
| | - Aristidis Tsatsakis
- Laboratory of Toxicology, School of Medicine, University of Crete, Heraklion, 71003, Greece; I.M. Sechenov First Moscow State Medical University, Moscow, 119048, Russian Federation
| | - Kirill Golokhvast
- Far Eastern Federal University, Vladivostok, 690950, Russian Federation; N.I. Vavilov All-Russian Research Institute of Plant Genetic Resources, Saint Petersburg, 190121, Russian Federation; Pacific Geographical Institute FEB RAS, Vladivostok, 690014, Russian Federation
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13
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Affiliation(s)
- Inmaculada Yruela
- Group of Computational and Structural Biology, Estación Experimental de Aula Dei (EEAD-CSIC), Avda. Montañana 1005, 50059, Zaragoza, Spain; Group of Biochemistry, Biophysics and Computational Biology (BIFI-Unizar) Joint Unit to CSIC, Spain.
| | - José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202, Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50018, Zaragoza, Spain.
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