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Discovery of the new alpha-glucosidase inhibitor with therapeutic potential in type 2 diabetes mellitus by a novel high-throughput virtual screening and free energy evaluation. J Mol Graph Model 2023; 121:108447. [PMID: 36913808 DOI: 10.1016/j.jmgm.2023.108447] [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: 12/15/2022] [Revised: 02/15/2023] [Accepted: 03/03/2023] [Indexed: 03/11/2023]
Abstract
Type 2 diabetes can cause a variety of complications, significantly affecting people's health. Given their ability to suppress carbohydrate digestion, alpha-glucosidase inhibitors are effective treatments for diabetes. However, the current approved glucosidase inhibitors' side effects of abdominal discomfort limit their use. We used the compound Pg3R from the natural fruit berry as a reference, screening against a large database of 22 million compounds to identify potential health-friendly alpha-glucosidase inhibitors. Ligand-based screening enables us to identify 3968 ligands that exhibit structural similarity compared to the natural compound. These lead hits were used for LeDock, and their binding free energies were evaluated by MM/GBSA. Among the top-scoring candidates, ZINC263584304 exhibited the strongest binding affinity to alpha-glucosidase, with a "low-fat" structural characteristic. Its recognition mechanism was further investigated by microsecond MD simulations and free energy landscapes, exhibiting novel conformational changes during the binding process. Our study provided a novel alpha-glucosidase inhibitor with the potential to treat type 2 diabetes.
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Molecular Insights into Substrate Binding of the Outer Membrane Enzyme OmpT. Catalysts 2023. [DOI: 10.3390/catal13020214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The enzyme OmpT of the outer membrane of Escherichia coli shows proteolytic activity and cleaves peptides and proteins. Using molecular dynamics simulations in a fully hydrated lipid bilayer on a time scale of hundreds of nanoseconds, we draw a detailed atomic picture of substrate recognition in the OmpT-holo enzyme complex. Hydrogen bonds and salt bridges are essential for maintaining the integrity of the active site and play a central role for OmpT in recognizing its substrate. Electrostatic interactions are critical at all stages from approaching the substrate to docking at the active site. Computational alanine scanning based on the Molecular Mechanics Generalized Born Surface Area (MM-GBSA) approach confirms the importance of multiple residues in the active site that form salt bridges. The substrate fluctuates along the axis of the β-barrel, which is associated with oscillations of the binding cleft formed by the residue pairs D210-H212 and D83-D85. Principal component analysis suggests that substrate and protein movements are correlated. We observe the transient presence of putative catalytic water molecules near the active site, which may be involved in the nucleophilic attack on the cleavable peptide bond of the substrate.
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Gong J, Zhang H, Zeng Y, Cheng Y, Sun X, Wang P. Combining BN-PAGE and microscopy techniques to investigate pigment-protein complexes and plastid transitions in citrus fruit. PLANT METHODS 2022; 18:124. [PMID: 36403000 PMCID: PMC9675244 DOI: 10.1186/s13007-022-00956-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 11/10/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Chlorophyll and carotenoids, the most widely distributed lipophilic pigments in plants, contribute to fruit coloration during development and ripening. These pigments are assembled with pigment-protein complexes localized at plastid membrane. Pigment-protein complexes are essential for multiple cellular processes, however, their identity and composition in fruit have yet to be characterized. RESULTS By using BN-PAGE technique in combination with microscopy, we studied pigment-protein complexes and plastid transformation in the purified plastids from the exocarp of citrus fruit. The discontinuous sucrose gradient centrifugation was used to isolate total plastids from kumquat fruit, and the purity of isolated plastids was assessed by microscopy observation and western blot analysis. The isolated plastids at different coloring stages were subjected to pigment autofluorescence observation, western blot, two-dimensional electrophoresis analysis and BN-PAGE assessment. Our results demonstrated that (i) chloroplasts differentiate into chromoplasts during fruit coloring, and this differentiation is accompanied with a decrease in the chlorophyll/carotenoid ratio; (ii) BN-PAGE analysis reveals the profiles of macromolecular protein complexes among different types of plastids in citrus fruit; and (iii) the degradation rate of chlorophyll-protein complexes varies during the transition from chloroplasts to chromoplasts, with the stability generally following the order of LHCII > PS II core > LHC I > PS I core. CONCLUSIONS Our optimized methods for both plastid separation and BN-PAGE assessment provide an opportunity for developing a better understanding of pigment-protein complexes and plastid transitions in plant fruit. These attempts also have the potential for expanding our knowledge on the sub-cellular level synchronism of protein changes and pigment metabolism during the transition from chloroplasts to chromoplasts.
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Affiliation(s)
- Jinli Gong
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- National R&D Centre for Citrus Preservation, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Hang Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- National R&D Centre for Citrus Preservation, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yunliu Zeng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- National R&D Centre for Citrus Preservation, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yunjiang Cheng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- National R&D Centre for Citrus Preservation, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xuepeng Sun
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.
| | - Pengwei Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
- National R&D Centre for Citrus Preservation, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, China.
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Bag P, Schröder WP, Jansson S, Farci D. Solubilization Method for Isolation of Photosynthetic Mega- and Super-complexes from Conifer Thylakoids. Bio Protoc 2021; 11:e4144. [PMID: 34604449 DOI: 10.21769/bioprotoc.4144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 11/02/2022] Open
Abstract
Photosynthesis is the main process by which sunlight is harvested and converted into chemical energy and has been a focal point of fundamental research in plant biology for decades. In higher plants, the process takes place in the thylakoid membranes where the two photosystems (PSI and PSII) are located. In the past few decades, the evolution of biophysical and biochemical techniques allowed detailed studies of the thylakoid organization and the interaction between protein complexes and cofactors. These studies have mainly focused on model plants, such as Arabidopsis, pea, spinach, and tobacco, which are grown in climate chambers even though significant differences between indoor and outdoor growth conditions are present. In this manuscript, we present a new mild-solubilization procedure for use with "fragile" samples such as thylakoids from conifers growing outdoors. Here, the solubilization protocol is optimized with two detergents in two species, namely Norway spruce (Picea abies) and Scots pine (Pinus sylvestris). We have optimized the isolation and characterization of PSI and PSII multimeric mega- and super-complexes in a close-to-native condition by Blue-Native gel electrophoresis. Eventually, our protocol will not only help in the characterization of photosynthetic complexes from conifers but also in understanding winter adaptation.
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Affiliation(s)
- Pushan Bag
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Sweden
| | | | - Stefan Jansson
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Sweden
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PAP90, a novel rice protein plays a critical role in regulation of D1 protein stability of PSII. J Adv Res 2021; 30:197-211. [PMID: 34026296 PMCID: PMC8132209 DOI: 10.1016/j.jare.2020.11.008] [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: 07/08/2020] [Revised: 10/29/2020] [Accepted: 11/17/2020] [Indexed: 01/24/2023] Open
Abstract
Introduction Photosystem II (PSII) protein complex plays an essential role in the entire photosynthesis process. Various known and unknown protein factors are involved in the dynamics of the PSII complex that need to be characterized in crop plants for enhancing photosynthesis efficiency and productivity. Objectives The experiments were conducted to decipher the regulatory proteins involved in PSII dynamics of rice crop. Methods A novel rice regulatory protein PAP90 (PSII auxiliary protein ~90 kDa) was characterized by generating a loss-of-function mutant pap90. The mutation was characterized at molecular level followed by various experiments to analyze the morphological, physiological and biochemical processes of mutant under control and abiotic stresses. Results The pap90 mutant showed reduced photosynthesis due to D1 protein instability that subsequently causes inadequate accumulation of thylakoid membrane complexes, especially PSII and decreases PSII functional efficiency. Expression of OsFtsH family genes and proteins were induced in the mutant, which are known to play a key role in D1 protein degradation and turnover. The reduced D1 protein accumulation in the mutant increased the production of reactive oxygen species (ROS). The accumulation of ROS along with the increased activity of antioxidant enzymes and induced expression of stress-associated genes and proteins in pap90 mutant contributed to its water-limited stress tolerance ability. Conclusion We propose that PAP90 is a key auxiliary protein that interacts with D1 protein and maintains its stability, thereby promoting subsequent assembly of the PSII and associated membrane complexes.
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Koper K, Hwang SK, Wood M, Singh S, Cousins A, Kirchhoff H, Okita TW. The Rice Plastidial Phosphorylase Participates Directly in Both Sink and Source Processes. ACTA ACUST UNITED AC 2020; 62:125-142. [DOI: 10.1093/pcp/pcaa146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 11/11/2020] [Indexed: 12/19/2022]
Abstract
Abstract
The plastidial starch phosphorylase (Pho1) functions in starch metabolism. A distinctive structural feature of the higher Pho1 is a 50–82-amino-acid long peptide (L50–L82), which is absent in phosphorylases from non-plant organisms. To study the function of the rice Pho1 L80 peptide, we complemented a pho1− rice mutant (BMF136) with the wild-type Pho1 gene or with a Pho1 gene lacking the L80 region (Pho1ΔL80). While expression of Pho1 in BMF136 restored normal wild-type phenotype, the introduction of Pho1ΔL80 enhanced the growth rate and plant productivity above wild-type levels. Mass spectrometry analysis of proteins captured by anti-Pho1 showed the surprising presence of PsaC, the terminal electron acceptor/donor subunit of photosystem I (PSI). This unexpected interaction was substantiated by reciprocal immobilized protein pull-down assays of seedling extracts and supported by the presence of Pho1 on isolated PSI complexes resolved by blue-native gels. Spectrophotometric studies showed that Pho1ΔL80 plants exhibited modified PSI and enhanced CO2 assimilation properties. Collectively, these findings indicate that the higher plant Pho1 has dual roles as a potential modulator of source and sink processes.
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Affiliation(s)
- Kaan Koper
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Seon-Kap Hwang
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Magnus Wood
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Salvinder Singh
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam 785013, India
| | - Asaph Cousins
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Helmut Kirchhoff
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Thomas W Okita
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
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Zhang Y, Zhong X, Su S, Huang G. Discovery of Novel Prebiotic Carbohydrates and Sugar Mimics of BlMsmE, a Solute-Binding Protein of the ABC Transporter from Bacillus licheniformis. J Phys Chem B 2020; 124:9996-10006. [DOI: 10.1021/acs.jpcb.0c05583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yubo Zhang
- Department of Food Science, Foshan University, Foshan 528231, China
| | - Xianfeng Zhong
- Department of Food Science, Foshan University, Foshan 528231, China
| | - Siyun Su
- Department of Food Science, Foshan University, Foshan 528231, China
| | - Guidong Huang
- Department of Food Science, Foshan University, Foshan 528231, China
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Yang P, Li Y, He C, Yan J, Zhang W, Li X, Xiang F, Zuo Z, Li X, Zhu Y, Liu X, Zhao X. Phenotype and TMT-based quantitative proteomics analysis of Brassica napus reveals new insight into chlorophyll synthesis and chloroplast structure. J Proteomics 2019; 214:103621. [PMID: 31863931 DOI: 10.1016/j.jprot.2019.103621] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/27/2019] [Accepted: 12/13/2019] [Indexed: 12/20/2022]
Abstract
The conversion of light energy into chemical energy in leaves is very important for plant growth and development. During this process, chlorophylls and their derivatives are indispensable as their fundamental role in the energy absorption and transduction activities. Chlorophyll variation mutants are important materials for studying chlorophyll metabolism, chloroplast biogenesis, photosynthesis and related physiological processes. Here, a chlorophyll-reduced mutant (crm1) was isolated from ethyl methanesulfonate (EMS) mutagenized Brassica napus. Compared to wild type, crm1 showed yellow leaves, reduced chlorophyll content, fewer thylakoid stacks and retarded growth. Quantitative mass spectrometry analysis with Tandem Mass Tag (TMT) isobaric labeling showed that totally 4575 proteins were identified from the chloroplast of Brassica napus leaves, and 466 of which displayed differential accumulations between wild type and crm1. The differential abundance proteins were found to be involved in chlorophyll metabolism, photosynthesis, phagosome and proteasome. Our results suggest that the decreased abundance of chlorophyll biosynthetic enzymes, proteins involved in photosynthesis might account for the reduced chlorophyll content, impaired thylakoid structure, and reduction of plant productivity. The increased abundance of proteins involved in phagosome and proteasome pathways might allow plants to adapt the proteome to environmental conditions to ensure growth and survival due to chlorophyll reduction. BIOLOGICAL SIGNIFICANCE: Photosynthesis, which consists of light and dark reactions, is fundamental to biomass production. Chloroplast is regarded as the main site for photosynthesis. During photosynthesis, the pigment chlorophyll is essential for light harvesting and energy transfer. This work provides new insights into protein expression patterns, and enables the identification of many attractive candidates for investigation of chlorophyll biosynthesis, chloroplast structure and photosynthesis in Brassica napus. These findings may be applied to improve the photosynthetic efficiency by genetic engineering in crops.
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Affiliation(s)
- Piao Yang
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China; Shenzhen Institute, Hunan University, Shenzhen 518057, China
| | - Yaxing Li
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chongsheng He
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China
| | - Jindong Yan
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China; Shenzhen Institute, Hunan University, Shenzhen 518057, China
| | - Wei Zhang
- Hunan Agricultural University, College of Agronnomy, Changsha, Hunan 410128, China
| | - Xin Li
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China; Shenzhen Institute, Hunan University, Shenzhen 518057, China
| | - Fujiang Xiang
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China; Shenzhen Institute, Hunan University, Shenzhen 518057, China
| | - Zecheng Zuo
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xinmei Li
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China; Shenzhen Institute, Hunan University, Shenzhen 518057, China
| | - Yonghua Zhu
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China
| | - Xuanming Liu
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China; Shenzhen Institute, Hunan University, Shenzhen 518057, China.
| | - Xiaoying Zhao
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China; Shenzhen Institute, Hunan University, Shenzhen 518057, China.
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Li J, Yang J, Zhu B, Xie G. Overexpressing OsFBN1 enhances plastoglobule formation, reduces grain-filling percent and jasmonate levels under heat stress in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 285:230-238. [PMID: 31203888 DOI: 10.1016/j.plantsci.2019.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/06/2019] [Accepted: 05/08/2019] [Indexed: 06/09/2023]
Abstract
In higher plants, Fibrillins (FBNs) constitute a conserved plastid-lipid-associated (PAPs) protein family and modulate the metabolite transport and lipid metabolism in plastids of dicot species. However, FBNs have not functionally characterized in monocot species. In this study, the function of rice fibrillin 1 (OsFBN1) was investigated. The subcellular localization assay showed that the N-terminal chloroplast transport peptide (CTP) could facilitate the import of OsFBN1 into chloroplast. OsFBN1 specifically bound C18- and C20- fatty acids in vitro. Overexpressing OsFBN1 increased the tiller number but decreased the panicle length, grain-filling percent and JA levels compared to the wild type and RNAi silencing lines under heat stress. In addition, the overexpressing lines had more plastoglobules (PGs) than the wild type and RNAi silencing lines under both normal and heat stress conditions. Moreover, overexpressing OsFBN1 affected the transcription levels of OsAOS2 in JA synthesis, OsTHF1, OsABC1K7 and OsPsaE in thylakoid stability and photosynthesis, OsABC1-4 and OsSPS2 in ubiquinone-metabolism, OsHDR, OsDXR, and OsFPPS in isoprenoid metabolism. Collectively, these findings suggest the essential role of rice OsFBN1 in PG formation and lipid metabolism in chloroplasts, which coordinately regulate the growth and grain filling of the overexpressing lines under heat stress.
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Affiliation(s)
- Jiajia Li
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
| | - Jun Yang
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
| | - Bohua Zhu
- Agricultural Technology Extension Center of Wuhan City, Wuhan, Hubei 430016, China.
| | - Guosheng Xie
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
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Luo A, Li X, Zhang X, Zhan H, Du H, Zhang Y, Peng X. Identification of AtHsp90.6 involved in early embryogenesis and its structure prediction by molecular dynamics simulations. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190219. [PMID: 31218061 PMCID: PMC6550000 DOI: 10.1098/rsos.190219] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 04/02/2019] [Indexed: 05/29/2023]
Abstract
Heat-shock protein of 90 kDa (Hsp90) is a key molecular chaperone involved in folding the synthesized protein and controlling protein quality. Conformational dynamics coupled to ATPase activity in N-terminal domain is essential for Hsp90's function. However, the relevant process is still largely unknown in plant Hsp90s, especially those required for plant embryogenesis which is inextricably tied up with human survival. Here, AtHsp90.6, a member of Hsp90 family in Arabidopsis, was firstly identified as a protein essential for embryogenesis. Thus we modelled AtHsp90.6 in its functionally closed 'lid-down' and open 'lid-up' states, exploring the nucleotide binding mechanism in these two states. Free energy landscape and electrostatic potential analysis revealed the switching mechanism between these two states. Collectively, this study quantitatively analysed the conformational changes of AtHsp90.6 bound to ATP or ADP. This result may help us understand the mechanism of action of AtHsp90.6 in future.
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Affiliation(s)
- An Luo
- College of Life Science, Yangtze University, Jingzhou 434023, People's Republic of China
| | - Xinbo Li
- College of Life Science, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, People's Republic of China
- Center for Tissue Engineering and Regenerative Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430072, People's Republic of China
| | - Xuecheng Zhang
- College of Life Science, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, People's Republic of China
| | - Huadong Zhan
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai, 200234, People's Republic of China
| | - Hewei Du
- College of Life Science, Yangtze University, Jingzhou 434023, People's Republic of China
| | - Yubo Zhang
- Department of Food Science, Foshan University, Foshan 528231, People's Republic of China
| | - Xiongbo Peng
- College of Life Science, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, People's Republic of China
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Zhao J, Xu J, Chen B, Cui W, Zhou Z, Song X, Chen Z, Zheng H, Lin L, Peng J, Lu Y, Deng Z, Chen J, Yan F. Characterization of Proteins Involved in Chloroplast Targeting Disturbed by Rice Stripe Virus by Novel Protoplast⁻Chloroplast Proteomics. Int J Mol Sci 2019; 20:E253. [PMID: 30634635 PMCID: PMC6358847 DOI: 10.3390/ijms20020253] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/19/2018] [Accepted: 01/06/2019] [Indexed: 12/21/2022] Open
Abstract
Rice stripe virus (RSV) is one of the most devastating viral pathogens in rice and can also cause the general chlorosis symptom in Nicotiana benthamiana plants. The chloroplast changes associated with chlorosis symptom suggest that RSV interrupts normal chloroplast functions. Although the change of proteins of the whole cell or inside the chloroplast in response to RSV infection have been revealed by proteomics, the mechanisms resulted in chloroplast-related symptoms and the crucial factors remain to be elucidated. RSV infection caused the malformation of chloroplast structure and a global reduction of chloroplast membrane protein complexes in N. benthamiana plants. Here, both the protoplast proteome and the chloroplast proteome were acquired simultaneously upon RSV infection, and the proteins in each fraction were analyzed. In the protoplasts, 1128 proteins were identified, among which 494 proteins presented significant changes during RSV; meanwhile, 659 proteins were identified from the chloroplasts, and 279 of these chloroplast proteins presented significant change. According to the label-free LC⁻MS/MS data, 66 nucleus-encoded chloroplast-related proteins (ChRPs), which only reduced in chloroplast but not in the whole protoplast, were identified, indicating that these nuclear-encoded ChRPswere not transported to chloroplasts during RSV infection. Gene ontology (GO) enrichment analysis confirmed that RSV infection changed the biological process of protein targeting to chloroplast, where 3 crucial ChRPs (K4CSN4, K4CR23, and K4BXN9) were involved in the regulation of protein targeting into chloroplast. In addition to these 3 proteins, 41 among the 63 candidate proteins were characterized to have chloroplast transit peptides. These results indicated that RSV infection changed the biological process of protein targeting into chloroplast and the location of ChRPs through crucial protein factors, which illuminated a new layer of RSV⁻host interaction that might contribute to the symptom development.
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Affiliation(s)
- Jinping Zhao
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
- Texas A&M University AgriLife Research Center at Dallas, Dallas, TX 75252, USA.
| | - Jingjing Xu
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
- School of Biotechnology, Jiangnan University, Wuxi 214122, China.
| | - Binghua Chen
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
- Institute of Plant Virology, Ningbo University, Ningbo 315211, China.
- Center of Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China.
| | - Weijun Cui
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
- Institute of Plant Virology, Ningbo University, Ningbo 315211, China.
| | - Zhongjing Zhou
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Xijiao Song
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Zhuo Chen
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
- Center of Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China.
| | - Hongying Zheng
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
- Institute of Plant Virology, Ningbo University, Ningbo 315211, China.
| | - Lin Lin
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
- Institute of Plant Virology, Ningbo University, Ningbo 315211, China.
| | - Jiejun Peng
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
- Institute of Plant Virology, Ningbo University, Ningbo 315211, China.
| | - Yuwen Lu
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
- Institute of Plant Virology, Ningbo University, Ningbo 315211, China.
| | - Zhiping Deng
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Jianping Chen
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
- Institute of Plant Virology, Ningbo University, Ningbo 315211, China.
| | - Fei Yan
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
- Institute of Plant Virology, Ningbo University, Ningbo 315211, China.
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12
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Zhong XF, Zhang YB, Huang GD, Ouyang YZ, Liao DJ, Peng JW, Huang WZ. Proteomic analysis of stachyose contribution to the growth of Lactobacillus acidophilus CICC22162. Food Funct 2018; 9:2979-2988. [DOI: 10.1039/c8fo00528a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Stachyose is a functional oligosaccharide, acting as a potential prebiotic for colonic fermentation.
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Affiliation(s)
- Xian-feng Zhong
- Department of Food Science
- Foshan University
- Foshan 528231
- China
- Foshan Engineering Research Center for Brewing Technology
| | - Yu-bo Zhang
- Department of Food Science
- Foshan University
- Foshan 528231
- China
- Foshan Engineering Research Center for Brewing Technology
| | - Gui-dong Huang
- Department of Food Science
- Foshan University
- Foshan 528231
- China
- Foshan Engineering Research Center for Brewing Technology
| | - Yong-zhong Ouyang
- School of Environmental and Chemical Engineering
- Foshan University
- Foshan 528231
- China
| | | | - Jia-wei Peng
- Department of Food Science
- Foshan University
- Foshan 528231
- China
- Foshan Engineering Research Center for Brewing Technology
| | - Wei-zhi Huang
- Department of Food Science
- Foshan University
- Foshan 528231
- China
- Foshan Engineering Research Center for Brewing Technology
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13
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Wang Y, Xu C, Li K, Cai X, Wu M, Chen G. Fe deficiency induced changes in rice (Oryza sativa L.) thylakoids. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:1380-1388. [PMID: 27783241 DOI: 10.1007/s11356-016-7900-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 10/11/2016] [Indexed: 06/06/2023]
Abstract
Iron deficiency is an important abiotic stress that limits productivity of crops all over the world. We selected a hybrid rice (Oryza sativa L.), LYPJ, which is super high-yield and widely cultured in China, to investigate changes in the components and structure of thylakoid membranes and photosynthetic performance in response to iron deficiency. Our results demonstrated that photosystem I (PSI) is the primary target for iron deficiency, while the changes in photosystem II (PSII) are important for rebuilding a balance in disrupted energy utilization and dissipation caused by differential degradation of photosynthetic components. The result of immunoblot analysis suggested that the core subunit PsaA declined drastically, while PsbA remained relatively stable. Furthermore, several organizational changes of the photosynthetic apparatus were found by BN-PAGE, including a marked decrease in the PSI core complexes, the Cytb 6 /f complex, and the trimeric form of the LHCII antenna, consistent with the observed unstacking grana. The fluorescence induction analysis indicated a descending PSII activity with energy dissipation enhanced markedly. In addition, we proposed that the crippled CO2 assimilation could be compensated by the enhanced of phosphoenolpyruvate carboxylase (PEPC), which is suggested by the decreased ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and photosynthetic efficiency.
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Affiliation(s)
- Yuwen Wang
- Jiangsu Key Laboratory of Biodiversity and Biotechnology, Life Sciences College, Nanjing Normal University, Nanjing, 210023, China
| | - Chao Xu
- Jiangsu Key Laboratory of Biodiversity and Biotechnology, Life Sciences College, Nanjing Normal University, Nanjing, 210023, China
| | - Kang Li
- Jiangsu Key Laboratory of Biodiversity and Biotechnology, Life Sciences College, Nanjing Normal University, Nanjing, 210023, China
| | - Xiaojie Cai
- Jiangsu Key Laboratory of Biodiversity and Biotechnology, Life Sciences College, Nanjing Normal University, Nanjing, 210023, China
| | - Min Wu
- Jiangsu Key Laboratory of Biodiversity and Biotechnology, Life Sciences College, Nanjing Normal University, Nanjing, 210023, China
- Zijin College, Nanjing University of Science and Technology, Nanjing, 210023, China
| | - Guoxiang Chen
- Jiangsu Key Laboratory of Biodiversity and Biotechnology, Life Sciences College, Nanjing Normal University, Nanjing, 210023, China.
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14
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Zhang Y. Understanding the impact of Fc glycosylation on its conformational changes by molecular dynamics simulations and bioinformatics. MOLECULAR BIOSYSTEMS 2016; 11:3415-24. [PMID: 26507522 DOI: 10.1039/c5mb00602c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
N-linked glycosylation of Fc at N297 plays an important role in its effector function, aberrance of which would cause disease pathogenesis. Here, we performed all-atom molecular dynamics simulations to explore the effects of Fc glycosylation on its dynamics behaviors. Firstly, equilibrium simulations suggested that Fc deglycosylation was able to induce residual flexibility in its CH2 domain. Besides, the free energy landscape revealed three minimum energy wells in deglycosylated Fc, representing its "open", "semi-closed" and "closed" states. However, we could only observe the "open" state of glycosylated Fc. Supportively, principal component analysis emphasized the prominent motion of delyclosylated Fc and dynamically depicted how it changed from the "open" state to its "closed" state. Secondly, we studied the recognition mechanism of the Fc binding to its partners. Energy decomposition analysis identified key residues of Fc to recognize its two partners P13 and P34. Evidently, electrostatic potential surfaces showed that electrostatic attraction helped to stabilize the interaction between Fc and its partners. Also, relative binding free energies explained different binding affinities in Fc-P13 and Fc-P34. Collectively, these results together provided the structural basis for understanding conformational changes of deglycosylated Fc and the recognition mechanism of the Fc binding to its partners.
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Affiliation(s)
- Yubo Zhang
- Biological New Drug Research Institute, Innovative Pharmaceuticals, Guangdong, China.
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15
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Zhang Y, Ding Y. Molecular dynamics simulation and bioinformatics study on chloroplast stromal ridge complex from rice (Oryza sativa L.). BMC Bioinformatics 2016; 17:28. [PMID: 26753869 PMCID: PMC4709881 DOI: 10.1186/s12859-016-0877-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 01/04/2016] [Indexed: 11/29/2022] Open
Abstract
Background Rice (Oryza sativa L.) is one of the most important cereal crops in the world and its yield is closely related to the photosynthesis efficiency. The chloroplast stromal ridge complex consisting of PsaC-PsaD-PsaE plays an important role in plant photosynthesis, which has been a subject of many studies. Till now, the recognition mechanism between PsaC and PsaD in rice is still not fully understood. Results Here, we present the interaction features of OsPsaC and OsPsaD by molecular dynamics simulations and bioinformatics. Firstly, we identified interacting residues in the OsPsaC-OsPsaD complex during simulations. Significantly, important hydrogen bonds were observed in residue pairs R19-E103, D47-K62, R53-E63, Y81-R20, Y81-R61 and L26-V105. Free energy calculations suggested two salt bridges R19-E103 and D47-K62 were essential to maintain the OsPsaC-OsPsaD interaction. Supportively, electrostatic potentials surfaces of OsPsaD exhibited electrostatic attraction helped to stabilize the residue pairs R19-E103 and D47-K62. In particular, the importance of R19 was further verified by two 500 ns CG-MD simulations. Secondly, this study compared the stromal ridge complex in rice with that in other organisms. Notably, alignments of amino acids showed these two salt bridges R19-E103 and D47-K62 also existed in other organisms. Electrostatic potentials surfaces and X-ray structural analysis strongly suggested the stromal ridge complex in other organisms adopted a similar and general recognition mechanism. Conclusions These results together provided structure basis and dynamics behavior to understand recognition and assembly of the stromal ridge complex in rice. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0877-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yubo Zhang
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, People's Republic of China.
| | - Yi Ding
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, People's Republic of China.
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16
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Semenihin AV, Zolotareva OK. CARBONIC ANHYDRASE ACTIVITY OF INTEGRAL-FUNCTIONAL COMPLEXES OF THYLAKOID MEMBRANES OF SPINACH CHLOROPLASTS. UKRAINIAN BIOCHEMICAL JOURNAL 2015; 87:47-56. [PMID: 26502699 DOI: 10.15407/ubj87.03.047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Isolated thylakoid membranes were disrupted by treatment with nonionic detergents digitonin or dodecyl maltoside. Solubilized polypeptide complexes were separated by native gel charge shift electrophoresis. The position of ATP-synthase complex and its isolated catalytic part (CF1) within gel was determined using the color reaction for ATPase activity. Due to the presence of cytochromes, the red band in unstained gels corresponded to the cytochrome b6f complex. Localization of the cytochrome b6f complex, ATP synthase and coupling CF1 in the native gel was confirmed by their subunit composition determined after SDS-electrophoretic analysis. Carbonic anhydrase (CA) activity in polypeptide zones of PS II, cytochrome b6f complex, and ATP-synthase CF1 was identified in native gels using indicator bromothymol blue. CA activity of isolated CF1 in solution was determined by infrared gas analysis as the rate of bicarbonate dehydration. The water-soluble acetazolamide, an inhibitor of CA, unlike lipophilic ethoxyzolamide inhibited CA activity of CF1 Thus, it was shown for the first time that ATP-synthase has a component which is capable of catalyzing the interconversion of forms of carbonic acid associated with proton exchange. The data obtained suggest the presence of multiple forms of carbonic anhydrase in the thylakoid membranes of spinach chloroplasts and confirm their involvement in the proton transfer to the ATP synthase.
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Campos N, Torné JM, Bleda MJ, Manich A, Urreta I, Montalbán IA, Castañón S, Moncalean P, Santos M. Proteomic and transcriptomic analysis of rice tranglutaminase and chloroplast-related proteins. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 229:142-153. [PMID: 25443841 DOI: 10.1016/j.plantsci.2014.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 09/08/2014] [Accepted: 09/09/2014] [Indexed: 05/09/2023]
Abstract
The recently cloned rice transglutaminase gene (tgo) is the second plant transglutaminase identified to date (Campos et al. Plant Sci. 205-206 (2013) 97-110). Similarly to its counterpart in maize (tgz), this rice TGase was localized in the chloroplast, although in this case not exclusively. To further characterise plastidial tgo functionality, proteomic and transcriptomic studies were carried out to identify possible TGO-related proteins. Some LHCII antenna proteins were identified as TGO related using an in vitro proteomic approach, as well as ATPase and some PSII core proteins by mass spectrometry. To study the relationship between TGO and other plastidial proteins, a transcriptomic in vivo Dynamic Array (Fluidigm™) was used to analyse the mRNA expression of 30 plastidial genes with respect to that of tgo, in rice plants subjected to different periods of continuous illumination. The results indicated a gene-dependent tendency in the expression pattern that was related to tgo expression and to the illumination cycle. For certain genes, including tgo, significant differences between treatments, principally at the initiation and/or at the end of the illumination period, connected with the day/night cycling of gene expression, were observed. The tgo expression was especially related to plastidial proteins involved in photoprotection and the thylakoid electrochemical gradient.
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Affiliation(s)
- N Campos
- Molecular Genetics Department, Centre for Research in Agricultural Genomics: CRAG (Consorci CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra, 08193 Barcelona, Spain.
| | - J M Torné
- Molecular Genetics Department, Centre for Research in Agricultural Genomics: CRAG (Consorci CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra, 08193 Barcelona, Spain.
| | - M J Bleda
- Institute of Advanced Chemistry of Catalonia IQAC, CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain.
| | - A Manich
- Department of Chemical and Surfactants Technology, Institute of Advanced Chemistry of Catalonia IQAC, CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain.
| | - I Urreta
- Biotechnology Department, Neiker-Tecnalia, Arkaute, Vitoria, Campus Agroalimentario de Arkaute, Aptdo.46, E-01080 Vitoria-Gasteiz, Araba, Spain.
| | - I A Montalbán
- Biotechnology Department, Neiker-Tecnalia, Arkaute, Campus Agroalimentario de Arkaute Apto 46, E-01080, Vitoria-Gasteiz, Araba, Spain.
| | - S Castañón
- Biotechnology Department, Neiker-Tecnalia, Arkaute, Campus Agroalimentario de Arkaute, Aptdo.46, E-01080 Vitoria-Gasteiz, Araba, Spain.
| | - P Moncalean
- Biotechnology Department, Neiker-Tecnalia, Arkaute, Campus Agroalimentario de Arkaute, Apto 46, E-01080 Vitoria-Gasteiz, Araba, Spain.
| | - M Santos
- Molecular Genetics Department, Centre for Research in Agricultural Genomics: CRAG (Consorci CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra, 08193 Barcelona, Spain.
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Wang Y, Zhang J, Yu J, Jiang X, Sun L, Wu M, Chen G, Lv C. Photosynthetic changes of flag leaves during senescence stage in super high-yield hybrid rice LYPJ grown in field condition. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 82:194-201. [PMID: 24976603 DOI: 10.1016/j.plaphy.2014.06.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 06/10/2014] [Indexed: 06/03/2023]
Abstract
Photosynthetic activities and thylakoid membrane protein patterns as well as the ultrastructure of chloroplasts in flag leaves were investigated during the senescence processes in high-yield hybrid rice LYPJ under field condition. The earlier decrease of PS I activity than PS II in LYPJ was primarily due to the significant degradation of PS I chlorophyll-protein complex. The degradation rate for each chlorophyll-protein complex was different and the order for the stability of thylakoid membrane complexes during flag leaf senescence in rice LYPJ was: LHCII > OEC > PSII core antenna > PSII core > PSI core > LHCI, which was partly supported by the BN-PAGE gel combined with immunoblot analysis. A decrease in the chlorophyll a/b ratio at the senescence stage was observed to coincide with stability of the LHCII subunits. Ultrastructural investigations revealed that the chloroplasts have large loosen stacking grana without interconnecting stroma thylakoids during the senescence processes. It was hypothesized that the stability of grana thylakoids harboring the major LHCII under high radiation condition in summer might played a key role in the dissipation of excess light energy. This alternative strategy would protect photosynthetic apparatus from photodamage and might be causally related to the high yield of this rice cultivar.
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Affiliation(s)
- Yuwen Wang
- Jiangsu Key Laboratory of Biodiversity and Biotechnology, Life Sciences College, Nanjing Normal University, Nanjing 210023, China
| | - Jingjing Zhang
- Jiangsu Key Laboratory of Biodiversity and Biotechnology, Life Sciences College, Nanjing Normal University, Nanjing 210023, China
| | - Jing Yu
- Jiangsu Key Laboratory of Biodiversity and Biotechnology, Life Sciences College, Nanjing Normal University, Nanjing 210023, China
| | - Xiaohan Jiang
- Jiangsu Key Laboratory of Biodiversity and Biotechnology, Life Sciences College, Nanjing Normal University, Nanjing 210023, China
| | - Lingang Sun
- Jiangsu Key Laboratory of Biodiversity and Biotechnology, Life Sciences College, Nanjing Normal University, Nanjing 210023, China
| | - Min Wu
- Jiangsu Key Laboratory of Biodiversity and Biotechnology, Life Sciences College, Nanjing Normal University, Nanjing 210023, China; Zijin College, Nanjing University of Science and Technology, Nanjing 210023, China
| | - Guoxiang Chen
- Jiangsu Key Laboratory of Biodiversity and Biotechnology, Life Sciences College, Nanjing Normal University, Nanjing 210023, China.
| | - Chuangen Lv
- Institute of Food and Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
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19
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Photosynthetic responses of Oryza sativa L. seedlings to cadmium stress: physiological, biochemical and ultrastructural analyses. Biometals 2014; 27:389-401. [DOI: 10.1007/s10534-014-9720-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 02/12/2014] [Indexed: 10/25/2022]
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20
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Behrens C, Blume C, Senkler M, Eubel H, Peterhänsel C, Braun HP. The 'protein complex proteome' of chloroplasts in Arabidopsis thaliana. J Proteomics 2013; 91:73-83. [PMID: 23851315 DOI: 10.1016/j.jprot.2013.07.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 06/19/2013] [Accepted: 07/02/2013] [Indexed: 01/30/2023]
Abstract
UNLABELLED Here, a first GelMap of the chloroplast "protein complex proteome" of Arabidopsis thaliana is presented. The GelMap software tool allows assigning multiple proteins to gel spots, thereby taking advantage of the high sensitivity of state-of-the-art mass spectrometry systems. Furthermore, the software allows functional annotation of all identified proteins. If applied to a 2D blue native (BN)/SDS gel, GelMap can selectively display protein complexes of low abundance. For the chloroplast GelMap, highly purified organelles were separated by 2D BN/SDS PAGE and spots were automatically detected using Delta 2D software. Within 287 spots, a total of 1841 proteins were identified (on average 6.4 proteins per spot), representing a set of 436 non redundant proteins. Most of these proteins form part of protein complexes. The quality of the map is reflected by its inclusion of a more or less complete set of protein complexes described for chloroplasts in the literature. The GelMap is publically available at www.gelmap.de/arabidopsis-chloro and may be used as a resource for identifying novel protein complexes within any of its functional categories. BIOLOGICAL SIGNIFICANCE The chloroplast GelMap represents a data resource for the definition of protein complexes in the model plant A. thaliana. It should be useful for in depth understanding of chloroplast biochemistry, as illustrated by the discovery of so far unknown protein complexes. The GelMap is publically available at www.gelmap.de/arabidopsis-chloro.
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Affiliation(s)
- Christof Behrens
- Institute of Plant Genetics, Faculty of Natural Sciences, Leibniz Universität Hannover, Herrenhäuser Str. 2, D-30419 Hannover, Germany
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Kang Z, Li G, Huang J, Niu X, Zou H, Zang G, Wenwen Y, Wang G. Photosynthetic and physiological analysis of the rice high-chlorophyll mutant (Gc). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2012; 60:81-7. [PMID: 22922107 DOI: 10.1016/j.plaphy.2012.07.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 07/16/2012] [Indexed: 05/26/2023]
Abstract
Chlorophyll (Chl) molecules are essential for harvesting light energy in photosynthesis. A rice high-chlorophyll mutant (Gc) with significantly increased Chl b was identified previously in Zhenshan 97B (Oryza sativa indica). However, the mechanism underlying this higher Chl b content and its effects on photosynthetic efficiency are still unclear. Immunoblot and blue native polyacrylamide gel electrophoresis (BN-PAGE) with a second dimension electrophoresis followed by the matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) analysis showed that a few core proteins of photosystem I (PSI) and photosystem II (PSII), and light-harvesting complex II (LHCII) proteins were overexpressed in the mutant plants. Remarkable differences in chloroplast ultrastructure were observed between the wild-type and mutant plants, with the latter having more highly stacked and larger grana. Chl florescence analysis demonstrated that Gc had markedly increased quantum efficiency of photosystem II (ΦPSII), photochemical quenching (qP), non-photochemical quenching (qN) and electron transport rate (ETR). This morphological and physiological adaptation might confer a higher photosynthetic capacity in Gc than the wild-type.
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Affiliation(s)
- Zhenhui Kang
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400030, China
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