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Yan X, White JC, He E, Peijnenburg WJGM, Zhang P, Qiu H. Temporal Dynamics of Copper-Based Nanopesticide Transfer and Subsequent Modulation of the Interplay Between Host and Microbiota Across Trophic Levels. ACS NANO 2024; 18:25552-25564. [PMID: 39171664 DOI: 10.1021/acsnano.4c06047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
During agricultural production, significant quantities of copper-based nanopesticides (CBNPs) may be released into terrestrial ecosystems through foliar spraying, thereby posing a potential risk of biological transmission via food chains. Consequently, we investigated the trophic transfer of two commonly available commercial CBNPs, Reap2000 (RP) and HolyCu (HC), in a plant-caterpillar terrestrial food chain and evaluated impacts on host microbiota. Upon foliar exposure (with 4 rounds of spraying, totaling 6.0 mg CBNPs per plant), leaf Cu accumulation levels were 726 ± 180 and 571 ± 121 mg kg-1 for RP and HC, respectively. HC exhibited less penetration through the cuticle compared to RP (RP: 55.5%; HC: 32.8%), possibly due to size exclusion limitations. While caterpillars accumulated higher amounts of RP, HC exhibited a slightly higher trophic transfer factor (TTF; RP: 0.69 ± 0.20; HC: 0.74 ± 0.17, p > 0.05) and was more likely to be transferred through the food chain. The application of RP promoted the dispersal of phyllosphere microbes and perturbed the original host intestinal microbiota, whereas the HC group was largely host-modulated (control: 65%; RP: 94%; HC: 34%). Integrating multiomics analyses and modeling approaches, we elucidated two pathways by which plants exert bottom-up control over caterpillar health. Beyond the direct transmission of phyllosphere microbes, the leaf microbiome recruited upon exposure to CBNPs further influenced the ingestion behavior and intestinal microbiota of caterpillars via altered leaf metabolites. Elevated Proteobacteria abundance benefited caterpillar growth with RP, while the reduction of Proteobacteria with HC increased the risk of lipid metabolism issues and gut disease. The recruited Bacteroidota in the RP phyllosphere proliferated more extensively into the caterpillar gut to enhance stress resistance. Overall, the gut microbes reshaped in RP caterpillars exerted a strong regulatory effect on host health. These findings expand our understanding of the dynamic transmission of host-microbiota interactions with foliar CBNPs exposure, and provide critical insight necessary to ensure the safety and sustainability of nanoenabled agricultural strategies.
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Affiliation(s)
- Xuchen Yan
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jason C White
- The Connecticut Agricultural Experiment Station, New Haven06511, Connecticut, United States
| | - Erkai He
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China
| | - Willie J G M Peijnenburg
- Center for the Safety of Substances and Products, National Institute of Public Health and the Environment, Bilthoven 3720BA, The Netherlands
- Institute of Environmental Sciences, Leiden University, Leiden 2300RA, The Netherlands
| | - Peng Zhang
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston B15 2TT, Birmingham, U.K
| | - Hao Qiu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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Xu E, Liu Y, Gu D, Zhan X, Li J, Zhou K, Zhang P, Zou Y. Molecular Mechanisms of Plant Responses to Copper: From Deficiency to Excess. Int J Mol Sci 2024; 25:6993. [PMID: 39000099 PMCID: PMC11240974 DOI: 10.3390/ijms25136993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/20/2024] [Accepted: 06/22/2024] [Indexed: 07/16/2024] Open
Abstract
Copper (Cu) is an essential nutrient for plant growth and development. This metal serves as a constituent element or enzyme cofactor that participates in many biochemical pathways and plays a key role in photosynthesis, respiration, ethylene sensing, and antioxidant systems. The physiological significance of Cu uptake and compartmentalization in plants has been underestimated, despite the importance of Cu in cellular metabolic processes. As a micronutrient, Cu has low cellular requirements in plants. However, its bioavailability may be significantly reduced in alkaline or organic matter-rich soils. Cu deficiency is a severe and widespread nutritional disorder that affects plants. In contrast, excessive levels of available Cu in soil can inhibit plant photosynthesis and induce cellular oxidative stress. This can affect plant productivity and potentially pose serious health risks to humans via bioaccumulation in the food chain. Plants have evolved mechanisms to strictly regulate Cu uptake, transport, and cellular homeostasis during long-term environmental adaptation. This review provides a comprehensive overview of the diverse functions of Cu chelators, chaperones, and transporters involved in Cu homeostasis and their regulatory mechanisms in plant responses to varying Cu availability conditions. Finally, we identified that future research needs to enhance our understanding of the mechanisms regulating Cu deficiency or stress in plants. This will pave the way for improving the Cu utilization efficiency and/or Cu tolerance of crops grown in alkaline or Cu-contaminated soils.
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Affiliation(s)
- Ending Xu
- Anhui Province Key Laboratory of Rice Germplasm Innovation and Molecular Improvement, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Yuanyuan Liu
- Department of Biochemistry & Molecular Biology, College of Life Science, Nanjing Agriculture University, Nanjing 210095, China
| | - Dongfang Gu
- Anhui Province Key Laboratory of Rice Germplasm Innovation and Molecular Improvement, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xinchun Zhan
- Anhui Province Key Laboratory of Rice Germplasm Innovation and Molecular Improvement, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Jiyu Li
- Institute of Horticultural Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Kunneng Zhou
- Anhui Province Key Laboratory of Rice Germplasm Innovation and Molecular Improvement, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Peijiang Zhang
- Anhui Province Key Laboratory of Rice Germplasm Innovation and Molecular Improvement, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Yu Zou
- Anhui Province Key Laboratory of Rice Germplasm Innovation and Molecular Improvement, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
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Kovalenko I, Kholina E, Fedorov V, Khruschev S, Vasyuchenko E, Meerovich G, Strakhovskaya M. Interaction of Methylene Blue with Severe Acute Respiratory Syndrome Coronavirus 2 Envelope Revealed by Molecular Modeling. Int J Mol Sci 2023; 24:15909. [PMID: 37958892 PMCID: PMC10650479 DOI: 10.3390/ijms242115909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/24/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023] Open
Abstract
Methylene blue has multiple antiviral properties against Severe Acute Respiratory Syndrome-related Coronavirus 2 (SARS-CoV-2). The ability of methylene blue to inhibit different stages of the virus life cycle, both in light-independent and photodynamic processes, is used in clinical practice. At the same time, the molecular aspects of the interactions of methylene blue with molecular components of coronaviruses are not fully understood. Here, we use Brownian dynamics to identify methylene blue binding sites on the SARS-CoV-2 envelope. The local lipid and protein composition of the coronavirus envelope plays a crucial role in the binding of this cationic dye. Viral structures targeted by methylene blue include the S and E proteins and negatively charged lipids. We compare the obtained results with known experimental data on the antiviral effects of methylene blue to elucidate the molecular basis of its activity against coronaviruses.
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Affiliation(s)
- Ilya Kovalenko
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia; (I.K.); (E.K.); (V.F.); (S.K.); (E.V.)
- Scientific and Educational Mathematical Center «Sofia Kovalevskaya Northwestern Center for Mathematical Research», Pskov State University, Pskov 180000, Russia
| | - Ekaterina Kholina
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia; (I.K.); (E.K.); (V.F.); (S.K.); (E.V.)
| | - Vladimir Fedorov
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia; (I.K.); (E.K.); (V.F.); (S.K.); (E.V.)
| | - Sergei Khruschev
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia; (I.K.); (E.K.); (V.F.); (S.K.); (E.V.)
| | - Ekaterina Vasyuchenko
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia; (I.K.); (E.K.); (V.F.); (S.K.); (E.V.)
| | - Gennady Meerovich
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Moscow 119991, Russia
- Institute for Physics and Engineering in Biomedicine, National Research Nuclear University “MEPHI”, Moscow 115409, Russia
| | - Marina Strakhovskaya
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia; (I.K.); (E.K.); (V.F.); (S.K.); (E.V.)
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Zhu Y, Zhu S, Zhang F, Zhao Z, Christensen MJ, Nan Z, Zhang X. Transcriptomic Analyses Reveals Molecular Regulation of Photosynthesis by Epichloë endophyte in Achnatherum inebrians under Blumeria graminis Infection. J Fungi (Basel) 2022; 8:1201. [PMID: 36422022 PMCID: PMC9695909 DOI: 10.3390/jof8111201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/10/2022] [Accepted: 11/10/2022] [Indexed: 09/24/2023] Open
Abstract
Photosynthesis is essential for the growth of all green plants, and the presence of an Epichloë endophyte enhances the photosynthesis of Achnatherum inebrians (drunken horse grass, DHG), including when it is under attack by fungal pathogens. However, few studies have examined the mechanism of the increased photosynthetic activity at the molecular level of A. inebrians when it is under pathogen stress. The present study investigated the effects of the presence of the Epichloë endophyte on the net photosynthetic rate, intercellular CO2 concentration, stomatal conductance, and transpiration rate of DHG plants under a Blumeria graminis infection condition, and we compared the transcriptomes using RNA sequencing. The results showed that the photosynthetic rate of Epichloë endophyte-infected (E+) plants was higher under the B. graminis infection condition, and also without this pathogen, when it was compared with Epichloë endophyte-free (E-) plants. The E+ plants uninfected with B. graminis had 15 up-regulated unigenes that are involved in photosynthesis which were compared to the E- plants that were uninfected with this pathogen. This suggests that the presence of an Epichloë endophyte up-regulates the genes that are involved in the process of photosynthesis.
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Affiliation(s)
- Yue Zhu
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Shibo Zhu
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Fang Zhang
- Jiayuguan Municipal Bureau of Agriculture and Rural Affairs, Jiayuguan 735100, China
| | - Zhenrui Zhao
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Michael J. Christensen
- Retired Scientist from Grasslands Research Centre, Private Bag 11-008, Palmerston North 4442, New Zealand
| | - Zhibiao Nan
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Xingxu Zhang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
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Riznichenko GY, Belyaeva NE, Kovalenko IB, Antal TK, Goryachev SN, Maslakov AS, Plyusnina TY, Fedorov VA, Khruschev SS, Yakovleva OV, Rubin AB. Mathematical Simulation of Electron Transport in the Primary Photosynthetic Processes. BIOCHEMISTRY (MOSCOW) 2022; 87:1065-1083. [DOI: 10.1134/s0006297922100017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Riznichenko GY, Antal TK, Belyaeva NE, Khruschev SS, Kovalenko IB, Maslakov AS, Plyusnina TY, Fedorov VA, Rubin AB. Molecular, Brownian, kinetic and stochastic models of the processes in photosynthetic membrane of green plants and microalgae. Biophys Rev 2022; 14:985-1004. [PMID: 36124262 PMCID: PMC9481862 DOI: 10.1007/s12551-022-00988-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/25/2022] [Indexed: 10/15/2022] Open
Abstract
The paper presents the results of recent work at the Department of Biophysics of the Biological Faculty, Lomonosov Moscow State University on the kinetic and multiparticle modeling of processes in the photosynthetic membrane. The detailed kinetic models and the rule-based kinetic Monte Carlo models allow to reproduce the fluorescence induction curves and redox transformations of the photoactive pigment P700 in the time range from 100 ns to dozens of seconds and make it possible to reveal the role of individual carriers in their formation for different types of photosynthetic organisms under different illumination regimes, in the presence of inhibitors, under stress conditions. The fitting of the model curves to the experimental data quantifies the reaction rate constants that cannot be directly measured experimentally, including the non-radiative thermal relaxation reactions. We use the direct multiparticle models to explicitly describe the interactions of mobile photosynthetic carrier proteins with multienzyme complexes both in solution and in the biomembrane interior. An analysis of these models reveals the role of diffusion and electrostatic factors in the regulation of electron transport, the influence of ionic strength and pH of the cellular environment on the rate of electron transport reactions between carrier proteins. To describe the conformational intramolecular processes of formation of the final complex, in which the actual electron transfer occurs, we use the methods of molecular dynamics. The results obtained using kinetic and molecular models supplement our knowledge of the mechanisms of organization of the photosynthetic electron transport processes at the cellular and molecular levels.
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Affiliation(s)
- Galina Yu. Riznichenko
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1/12, 119234 Moscow, Russia
| | - Taras K. Antal
- Laboratory of Integrated Environmental Research, Pskov State University, Lenin Sq. 2, 180000 Pskov, Russia
| | - Natalia E. Belyaeva
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1/12, 119234 Moscow, Russia
| | - Sergey S. Khruschev
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1/12, 119234 Moscow, Russia
| | - Ilya B. Kovalenko
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1/12, 119234 Moscow, Russia
| | - Alexey S. Maslakov
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1/12, 119234 Moscow, Russia
| | - Tatyana Yu Plyusnina
- Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1/12, 119234 Moscow, Russia
| | - Vladimir A. Fedorov
- Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1/12, 119234 Moscow, Russia
| | - Andrey B. Rubin
- Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1/12, 119234 Moscow, Russia
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Fedorov V, Kholina E, Khruschev S, Kovalenko I, Rubin A, Strakhovskaya M. Electrostatic Map of the SARS-CoV-2 Virion Specifies Binding Sites of the Antiviral Cationic Photosensitizer. Int J Mol Sci 2022; 23:7304. [PMID: 35806316 PMCID: PMC9266743 DOI: 10.3390/ijms23137304] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 06/26/2022] [Accepted: 06/28/2022] [Indexed: 02/04/2023] Open
Abstract
Electrostatics is an important part of virus life. Understanding the detailed distribution of charges over the surface of a virus is important to predict its interactions with host cells, antibodies, drugs, and different materials. Using a coarse-grained model of the entire viral envelope developed by D. Korkin and S.-J. Marrink's scientific groups, we created an electrostatic map of the external surface of SARS-CoV-2 and found a highly heterogeneous distribution of the electrostatic potential field of the viral envelope. Numerous negative patches originate mainly from negatively charged lipid domains in the viral membrane and negatively charged areas on the "stalks" of the spike (S) proteins. Membrane (M) and envelope (E) proteins with the total positive charge tend to colocalize with the negatively charged lipids. In the E protein pentamer exposed to the outer surface, negatively charged glutamate residues and surrounding lipids form a negative electrostatic potential ring around the channel entrance. We simulated the interaction of the antiviral octacationic photosensitizer octakis(cholinyl)zinc phthalocyanine with the surface structures of the entire model virion using the Brownian dynamics computational method implemented in ProKSim software (version r661). All mentioned negatively charged envelope components attracted the photosensitizer molecules and are thus potential targets for reactive oxygen generated in photosensitized reactions.
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Affiliation(s)
- Vladimir Fedorov
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (E.K.); (S.K.); (I.K.); (A.R.); (M.S.)
| | - Ekaterina Kholina
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (E.K.); (S.K.); (I.K.); (A.R.); (M.S.)
| | - Sergei Khruschev
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (E.K.); (S.K.); (I.K.); (A.R.); (M.S.)
| | - Ilya Kovalenko
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (E.K.); (S.K.); (I.K.); (A.R.); (M.S.)
- Federal Scientific and Clinical Center of Specialized Types of Medical Care and Medical Technologies, Federal Medical and Biological Agency of Russia, 115682 Moscow, Russia
| | - Andrew Rubin
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (E.K.); (S.K.); (I.K.); (A.R.); (M.S.)
| | - Marina Strakhovskaya
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (E.K.); (S.K.); (I.K.); (A.R.); (M.S.)
- Federal Scientific and Clinical Center of Specialized Types of Medical Care and Medical Technologies, Federal Medical and Biological Agency of Russia, 115682 Moscow, Russia
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Lan Y, Zhang K, Wang Y, Wu J, Lin M, Yan H, Xiang Y. Comparative analysis of the stellacyanins (SCs) family and focus on drought resistance of PtSC18 in Populus trichocarpa. Gene 2021; 813:146106. [PMID: 34953936 DOI: 10.1016/j.gene.2021.146106] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/28/2021] [Accepted: 11/16/2021] [Indexed: 11/18/2022]
Abstract
Stellacyanin (SC) is a type I (blue) copper protein, which plays a crucial role in plant growth and stress response. However, the comprehensive analysis and functional research of SCs in the woody plant is still lacking. Here, a total of 74 SCs were collected and identified from Arabidopsis, papaya, grape, rice and poplar. Bioinformatics was used to analyze the gene structure, protein structure and evolutionary relationship of 74 genes, especially 19 SCs in Populus trichocarpa. Based on the RNA-seq data, expression pattern of SCs in poplar under cold, high temperature, drought and salt stress were further analyzed. Subsequently, a key candidate gene PtSC18 that strongly responded to drought stress was screened. Subcellular localization experiment exhibited that PtSC18 was localized in the nucleus and plasma membrane. Overexpression of PtSC18 enhanced drought tolerance of transgenic Arabidopsis by improving water retention and reducing oxidative damage. Measurements of physiological indicators, including chlorophyll, H2O2, malondialdehyde content, peroxidase and catalase enzyme activities and electrical conductivity, all supported this conclusion. More importantly, PtSC18 enhanced the expression of some stress-related genes in transgenic Arabidopsis. Overall, our results lay a foundation for understanding the structure and function of PtSCs and provide useful gene resources for breeding through genetic engineering.
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Affiliation(s)
- Yangang Lan
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Kaimei Zhang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Yamei Wang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Jing Wu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Miao Lin
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Hanwei Yan
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China.
| | - Yan Xiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China.
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Castell C, Rodríguez-Lumbreras LA, Hervás M, Fernández-Recio J, Navarro JA. New Insights into the Evolution of the Electron Transfer from Cytochrome f to Photosystem I in the Green and Red Branches of Photosynthetic Eukaryotes. PLANT & CELL PHYSIOLOGY 2021; 62:1082-1093. [PMID: 33772595 PMCID: PMC8557733 DOI: 10.1093/pcp/pcab044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/15/2021] [Indexed: 05/11/2023]
Abstract
In cyanobacteria and most green algae of the eukaryotic green lineage, the copper-protein plastocyanin (Pc) alternatively replaces the heme-protein cytochrome c6 (Cc6) as the soluble electron carrier from cytochrome f (Cf) to photosystem I (PSI). The functional and structural equivalence of 'green' Pc and Cc6 has been well established, representing an example of convergent evolution of two unrelated proteins. However, plants only produce Pc, despite having evolved from green algae. On the other hand, Cc6 is the only soluble donor available in most species of the red lineage of photosynthetic organisms, which includes, among others, red algae and diatoms. Interestingly, Pc genes have been identified in oceanic diatoms, probably acquired by horizontal gene transfer from green algae. However, the mechanisms that regulate the expression of a functional Pc in diatoms are still unclear. In the green eukaryotic lineage, the transfer of electrons from Cf to PSI has been characterized in depth. The conclusion is that in the green lineage, this process involves strong electrostatic interactions between partners, which ensure a high affinity and an efficient electron transfer (ET) at the cost of limiting the turnover of the process. In the red lineage, recent kinetic and structural modeling data suggest a different strategy, based on weaker electrostatic interactions between partners, with lower affinity and less efficient ET, but favoring instead the protein exchange and the turnover of the process. Finally, in diatoms the interaction of the acquired green-type Pc with both Cf and PSI may not yet be optimized.
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Affiliation(s)
- Carmen Castell
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, cicCartuja, Sevilla, Spain
| | - Luis A Rodríguez-Lumbreras
- Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC—Universidad de La Rioja—Gobierno de La Rioja, Logroño, Spain
| | - Manuel Hervás
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, cicCartuja, Sevilla, Spain
| | - Juan Fernández-Recio
- Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC—Universidad de La Rioja—Gobierno de La Rioja, Logroño, Spain
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What Binds Cationic Photosensitizers Better: Brownian Dynamics Reveals Key Interaction Sites on Spike Proteins of SARS-CoV, MERS-CoV, and SARS-CoV-2. Viruses 2021; 13:v13081615. [PMID: 34452480 PMCID: PMC8402653 DOI: 10.3390/v13081615] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 12/17/2022] Open
Abstract
We compared the electrostatic properties of the spike proteins (S-proteins) of three coronaviruses, SARS-CoV, MERS-CoV, and SARS-CoV-2, and their interactions with photosensitizers (PSs), octacationic octakis(cholinyl)zinc phthalocyanine (Zn-PcChol8+) and monocationic methylene blue (MB). We found a major common PS binding site at the connection of the S-protein stalk and head. The molecules of Zn-PcChol8+ and MB also form electrostatic encounter complexes with large area of negative electrostatic potential at the head of the S-protein of SARS-CoV-2, between fusion protein and heptad repeat 1 domain. The top of the SARS-CoV spike head demonstrates a notable area of electrostatic contacts with Zn-PcChol8+ and MB that corresponds to the N-terminal domain. The S-protein protomers of SARS-CoV-2 in “open” and “closed” conformations demonstrate different ability to attract PS molecules. In contrast with Zn-PcChol8+, MB possesses the ability to penetrate inside the pocket formed as a result of SARS-CoV-2 receptor binding domain transition into the “open” state. The existence of binding site for cationic PSs common to the S-proteins of SARS-CoV, SARS-CoV-2, and MERS-CoV creates prospects for the wide use of this type of PSs to combat the spread of coronaviruses.
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Ling N, Li W, Xu G, Qi Z, Ji C, Liu X, Cui D, Sun Y. Transcriptomic sequencing reveals the response of Dunaliella salina to copper stress via the increased photosynthesis and carbon mechanism. Mol Omics 2021; 17:769-782. [PMID: 34254634 DOI: 10.1039/d1mo00125f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Copper (Cu) is one of the essential microelements for plants and algae. It can stimulate growth and photosynthesis at low concentration but inhibit them at higher concentration. The knowledge of molecular response mechanisms to copper stress in green algae is still limited. The responses of the green algae Dunaliella salina to Cu stress were studied using the physiochemical indexes and RNA-seq analysis. The physiochemical indexes such as growth rate, the content of chlorophyll and soluble sugar, photosynthesis and peroxidase activity were all changed in D. salina under Cu stress. In addition, a total of 3799 differentially expressed genes (DEGs) were identified between the control and Cu-treated group. Among these, 2350 unigenes were up-regulated whereas 1449 were down-regulated. Here, the DEGs encoding proteins relevant to photosynthesis, carbon assimilation and carbohydrate mechanism were significantly up-regulated in the Cu-treated group. In addition, the unigenes encoding proteins involved in the antioxidant system and heat shock proteins were also up-regulated, and these were consistent with the expression patterns based on TPM (transcripts per million) values. This study shows that the enhanced growth and photosynthesis and carbon mechanism in D. salina can be triggered by copper, which will lay a firm foundation for future breeding and carotenoid production, further highlighting the underlying application of D. salina as a functional food.
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Affiliation(s)
- Na Ling
- Engineering Research Center for Natural Anticancer Drugs, Ministry of Education, Harbin University of Commerce, Harbin, Heilongjiang 150076, China. and Engineering Research Center for Medicines, Harbin University of Commerce, Harbin, Heilongjiang 150076, China.
| | - Weilu Li
- Engineering Research Center for Natural Anticancer Drugs, Ministry of Education, Harbin University of Commerce, Harbin, Heilongjiang 150076, China.
| | - Guiguo Xu
- Engineering Research Center for Natural Anticancer Drugs, Ministry of Education, Harbin University of Commerce, Harbin, Heilongjiang 150076, China.
| | - Zheng Qi
- Engineering Research Center for Natural Anticancer Drugs, Ministry of Education, Harbin University of Commerce, Harbin, Heilongjiang 150076, China. and Engineering Research Center for Medicines, Harbin University of Commerce, Harbin, Heilongjiang 150076, China.
| | - Chenfeng Ji
- Engineering Research Center for Natural Anticancer Drugs, Ministry of Education, Harbin University of Commerce, Harbin, Heilongjiang 150076, China. and Engineering Research Center for Medicines, Harbin University of Commerce, Harbin, Heilongjiang 150076, China.
| | - Xiaorui Liu
- Engineering Research Center for Natural Anticancer Drugs, Ministry of Education, Harbin University of Commerce, Harbin, Heilongjiang 150076, China.
| | - Di Cui
- Engineering Research Center for Natural Anticancer Drugs, Ministry of Education, Harbin University of Commerce, Harbin, Heilongjiang 150076, China.
| | - Yuan Sun
- Engineering Research Center for Natural Anticancer Drugs, Ministry of Education, Harbin University of Commerce, Harbin, Heilongjiang 150076, China. and Engineering Research Center for Medicines, Harbin University of Commerce, Harbin, Heilongjiang 150076, China.
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12
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Sharshov K, Solomatina M, Kurskaya O, Kovalenko I, Kholina E, Fedorov V, Meerovich G, Rubin A, Strakhovskaya M. The Photosensitizer Octakis(cholinyl)zinc Phthalocyanine with Ability to Bind to a Model Spike Protein Leads to a Loss of SARS-CoV-2 Infectivity In Vitro When Exposed to Far-Red LED. Viruses 2021; 13:643. [PMID: 33918615 PMCID: PMC8068984 DOI: 10.3390/v13040643] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 12/17/2022] Open
Abstract
Photodynamic inactivation of pathogenic microorganisms can be successfully used to eradicate pathogens in localized lesions, infected liquid media, and on various surfaces. This technique utilizes the photosensitizer (PS), light, and molecular oxygen to produce reactive oxygen species that kill pathogens. Here, we used the PS, water soluble octakis(cholinyl)zinc phthalocyanine (Zn-PcChol8+), to inactivate an initial 4.75-5.00 IgTCID50/mL titer of SARS-CoV-2, thereby preventing viral infection when tested in Vero E6 cell cultures. Zn-PcChol8+ in a minimally studied concentration, 1 µM and LED 3.75 J/cm2, completely destroyed the infectivity of SARS-CoV-2. To detect possible PS binding sites on the envelope of SARS-CoV-2, we analyzed electrostatic potential and simulated binding of Zn-PcChol8+ to the spike protein of this coronavirus by means of Brownian dynamics software, ProKSim (Protein Kinetics Simulator). Most of the Zn-PcChol8+ molecules formed clusters at the upper half of the stalk within a vast area of negative electrostatic potential. Positioning of the PS on the surface of the spike protein at a distance of no more than 10 nm from the viral membrane may be favorable for the oxidative damage. The high sensitivity of SARS-CoV-2 to photodynamic inactivation by Zn-PcChol8+ is discussed with respect to the application of this PS to control the spread of COVID-19.
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Affiliation(s)
- Kirill Sharshov
- Federal Research Center of Fundamental and Translational Medicine (CFTM), 630117 Novosibirsk, Russia; (K.S.); (M.S.); (O.K.)
| | - Mariya Solomatina
- Federal Research Center of Fundamental and Translational Medicine (CFTM), 630117 Novosibirsk, Russia; (K.S.); (M.S.); (O.K.)
| | - Olga Kurskaya
- Federal Research Center of Fundamental and Translational Medicine (CFTM), 630117 Novosibirsk, Russia; (K.S.); (M.S.); (O.K.)
| | - Ilya Kovalenko
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (I.K.); (E.K.); (V.F.); (A.R.)
- Federal Scientific and Clinical Center of Specialized Types of Medical Care and Medical Technologies of the Federal Medical and Biological Agency of Russia, 115682 Moscow, Russia
| | - Ekaterina Kholina
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (I.K.); (E.K.); (V.F.); (A.R.)
| | - Vladimir Fedorov
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (I.K.); (E.K.); (V.F.); (A.R.)
| | - Gennady Meerovich
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 119991 Moscow, Russia;
- Institute of Physics and Engineering in Biomedicine, National Research Nuclear University “MEPHI”, 115409 Moscow, Russia
| | - Andrew Rubin
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (I.K.); (E.K.); (V.F.); (A.R.)
| | - Marina Strakhovskaya
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (I.K.); (E.K.); (V.F.); (A.R.)
- Federal Scientific and Clinical Center of Specialized Types of Medical Care and Medical Technologies of the Federal Medical and Biological Agency of Russia, 115682 Moscow, Russia
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13
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Sarewicz M, Pintscher S, Pietras R, Borek A, Bujnowicz Ł, Hanke G, Cramer WA, Finazzi G, Osyczka A. Catalytic Reactions and Energy Conservation in the Cytochrome bc1 and b6f Complexes of Energy-Transducing Membranes. Chem Rev 2021; 121:2020-2108. [PMID: 33464892 PMCID: PMC7908018 DOI: 10.1021/acs.chemrev.0c00712] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Indexed: 12/16/2022]
Abstract
This review focuses on key components of respiratory and photosynthetic energy-transduction systems: the cytochrome bc1 and b6f (Cytbc1/b6f) membranous multisubunit homodimeric complexes. These remarkable molecular machines catalyze electron transfer from membranous quinones to water-soluble electron carriers (such as cytochromes c or plastocyanin), coupling electron flow to proton translocation across the energy-transducing membrane and contributing to the generation of a transmembrane electrochemical potential gradient, which powers cellular metabolism in the majority of living organisms. Cytsbc1/b6f share many similarities but also have significant differences. While decades of research have provided extensive knowledge on these enzymes, several important aspects of their molecular mechanisms remain to be elucidated. We summarize a broad range of structural, mechanistic, and physiological aspects required for function of Cytbc1/b6f, combining textbook fundamentals with new intriguing concepts that have emerged from more recent studies. The discussion covers but is not limited to (i) mechanisms of energy-conserving bifurcation of electron pathway and energy-wasting superoxide generation at the quinol oxidation site, (ii) the mechanism by which semiquinone is stabilized at the quinone reduction site, (iii) interactions with substrates and specific inhibitors, (iv) intermonomer electron transfer and the role of a dimeric complex, and (v) higher levels of organization and regulation that involve Cytsbc1/b6f. In addressing these topics, we point out existing uncertainties and controversies, which, as suggested, will drive further research in this field.
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Affiliation(s)
- Marcin Sarewicz
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Sebastian Pintscher
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Rafał Pietras
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Arkadiusz Borek
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Łukasz Bujnowicz
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Guy Hanke
- School
of Biological and Chemical Sciences, Queen
Mary University of London, London E1 4NS, U.K.
| | - William A. Cramer
- Department
of Biological Sciences, Purdue University, West Lafayette, Indiana 47907 United States
| | - Giovanni Finazzi
- Laboratoire
de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National Recherche Scientifique,
Commissariat Energie Atomique et Energies Alternatives, Institut National
Recherche l’agriculture, l’alimentation et l’environnement, 38054 Grenoble Cedex 9, France
| | - Artur Osyczka
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
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14
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Gideon DA, Nirusimhan V, Manoj KM. Are plastocyanin and ferredoxin specific electron carriers or generic redox capacitors? Classical and murburn perspectives on two photosynthetic proteins. J Biomol Struct Dyn 2020; 40:1995-2009. [PMID: 33073701 DOI: 10.1080/07391102.2020.1835715] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
In the light reaction of oxygenic photosynthesis, plastocyanin (PC) and ferredoxins (Fd) are small/diffusible redox-active proteins playing key roles in electron transfer/transport phenomena. In the Z-scheme mechanistic purview, they are considered as specific affinity binding-based electron-relay agents, linking the functions of Cytochrome b6f (Cyt. b6f), Photosystem I (PS I) and Fd:NADPH oxidoreductase (FNR). The murburn explanation for photolytic photophosphorylation deems PC/Fd as generic 'redox capacitors', temporally accepting and releasing one-electron equivalents in reaction milieu. Herein, we explore the two theories with respect to structural, distributional and functional aspects of PC/Fd. Amino acid residues located on the surface loci of key patches of PC/Fd vary in electrostatic/contour (topography) signatures. Crystal structures of four different complexes each of Cyt.f-PC and Fd-FNR show little conservation in the contact-surfaces, thereby discrediting 'affinity binding-based electron transfers (ET)' as an evolutionary logic. Further, thermodynamic and kinetic data of wildtype and mutant proteins interactions do not align with Z-scheme. Furthermore, micromolar physiological concentrations of PC and the non-conducive architecture of chloroplasts render the classical model untenable. In the murburn model, as PC is optional, the observation that plants lacking PC survive and grow is justified. Further, the low physiological concentration/distribution of PC in chloroplast lumen/stroma is supported by murburn equilibriums, as higher concentrations would limit electron transfers. Thus, structural evidence, interactive dynamics with redox partners and physiological distribution/role of PC/Fd support the murburn perspective that these proteins serve as generic redox-capacitors in chloroplasts.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Daniel Andrew Gideon
- Department of Biochemistry, Satyamjayatu: The Science & Ethics Foundation, Palakkad, India.,Department of Biotechnology and Bioinformatics, Bishop Heber College (Autonomous), Tiruchirappalli, India
| | - Vijay Nirusimhan
- Department of Biotechnology and Bioinformatics, Bishop Heber College (Autonomous), Tiruchirappalli, India
| | - Kelath Murali Manoj
- Department of Biochemistry, Satyamjayatu: The Science & Ethics Foundation, Palakkad, India
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15
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Riznichenko GY, Belyaeva NE, Diakonova AN, Kovalenko IB, Maslakov AS, Antal TK, Goryachev SN, Plyusnina TY, Fedorov VA, Khruschev SS, Rubin AB. Models of Photosynthetic Electron Transport. Biophysics (Nagoya-shi) 2020. [DOI: 10.1134/s0006350920050152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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16
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Riznichenk G, Kovalenko I, Fedorov V, Khruschev S, Rubin A. Photosynthetic Electron Transfer by Dint of Protein Mobile Carriers. Multi-particle Brownian and Molecular Modeling. EPJ WEB OF CONFERENCES 2019. [DOI: 10.1051/epjconf/201922403008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The paper presents the review of works on modeling the interaction of photosynthetic proteins using the multiparticle Brownian dynamics method developed at the Department of Biophysics, Biological Faculty, Lomonosov Moscow State University. The method describes the displacement of individual macromolecules – mobile electron carriers, and their electrostatic interactions between each other and with pigment-protein complexes embedded in photosynthetic membrane. Three-dimensional models of the protein molecules were constructed on the basis of the data from the Protein Data Bank. We applied the Brownian methods coupled to molecular dynamic simulations to reveal the role of electrostatic interactions and conformational motions in the transfer of an electron from the cytochrome complex Cyt b6f) membrane we developed the model which combines events of proteins Pc diffusion along the thylakoid membrane, electrostatic interactions of Pc with the membrane charges, formation of Pc super-complexes with multienzyme complexes of Photosystem I and to the molecule of the mobile carrier plastocyanin (Pc) in plants, green algae and cyanic bacteria. Taking into account the interior of photosynthetic membrane we developed the model which combines events of proteins Pc diffusion along the thylakoid membrane, electrostatic interactions of Pc with the membrane charges, formation of Pc super-complexes with multienzyme complexes of Photosystem I and Cyt b6f, embedded in photosynthetic membrane, electron transfer and complex dissociation. Multiparticle Brownian simulation method can be used to consider the processes of protein interactions in subcellular systems in order to clarify the role of individual stages and the biophysical mechanisms of these processes.
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