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Zhang S, Jeffreys LN, Poddar H, Yu Y, Liu C, Patel K, Johannissen LO, Zhu L, Cliff MJ, Yan C, Schirò G, Weik M, Sakuma M, Levy CW, Leys D, Heyes DJ, Scrutton NS. Photocobilins integrate B 12 and bilin photochemistry for enzyme control. Nat Commun 2024; 15:2740. [PMID: 38548733 PMCID: PMC10979010 DOI: 10.1038/s41467-024-46995-1] [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: 05/18/2023] [Accepted: 03/17/2024] [Indexed: 04/01/2024] Open
Abstract
Photoreceptor proteins utilise chromophores to sense light and trigger a biological response. The discovery that adenosylcobalamin (or coenzyme B12) can act as a light-sensing chromophore heralded a new field of B12-photobiology. Although microbial genome analysis indicates that photoactive B12-binding domains form part of more complex protein architectures, regulating a range of molecular-cellular functions in response to light, experimental evidence is lacking. Here we identify and characterise a sub-family of multi-centre photoreceptors, termed photocobilins, that use B12 and biliverdin (BV) to sense light across the visible spectrum. Crystal structures reveal close juxtaposition of the B12 and BV chromophores, an arrangement that facilitates optical coupling. Light-triggered conversion of the B12 affects quaternary structure, in turn leading to light-activation of associated enzyme domains. The apparent widespread nature of photocobilins implies involvement in light regulation of a wider array of biochemical processes, and thus expands the scope for B12 photobiology. Their characterisation provides inspiration for the design of broad-spectrum optogenetic tools and next generation bio-photocatalysts.
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Affiliation(s)
- Shaowei Zhang
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China.
| | - Laura N Jeffreys
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Harshwardhan Poddar
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Yuqi Yu
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Chuanyang Liu
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
| | - Kaylee Patel
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Linus O Johannissen
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Lingyun Zhu
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
| | - Matthew J Cliff
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Cunyu Yan
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Giorgio Schirò
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Martin Weik
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Michiyo Sakuma
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Colin W Levy
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - David Leys
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Derren J Heyes
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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Ling J, Niu Y, Liu D, Li R, Ruan Y, Li X. Inhibition of algal blooms by residual antibiotics in aquatic environments: Design, screening, and validation of antibiotic alternatives. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167914. [PMID: 37858809 DOI: 10.1016/j.scitotenv.2023.167914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/14/2023] [Accepted: 10/16/2023] [Indexed: 10/21/2023]
Abstract
Water blooms frequently appear in the aquatic environment with global warming. However, traditional methods for treating water bloom usually require the addition of algaecides, which may lead to secondary environmental pollution problems in the water environment. To solve this problem, researchers have initiated efforts to harness pre-existing chemical substances within aquatic environments to regulate algal blooms, thereby pioneering novel avenues for water body management. Therefore, an integrated approach involving molecular docking, molecular dynamics simulations, three-dimensional quantitative structure-activity relationship (3D-QSAR), and toxicokinetics methods were utilized for the molecular modification of fluoroquinolone antibiotics, to design and screen fluoroquinolone substitutes with improved toxicity of cyanobacteria and green algae, functionality, and environmental friendliness. A total of 143 fluoroquinolone alternatives were designed in this study, and lomefloxacin-6 (LOM6) was found as the optimum alternative to lomefloxacin (LOM), with increased toxicity to cyanobacteria and green algae by 31 % and 72 %. Molecular docking of LOM before and after modification with seven other cyanobacterial and green algal photosynthetic proteins revealed that LOM6 exhibited varying degrees of increased toxicity towards 6 of these photosynthetic proteins, of which 2J96 protein increased the most (136.25 %). It shows that the residual LOM6 in the water environment has a certain inhibitory effect on the algae bloom. In addition, results showed that LOM6 had synergistic toxic effects on cyanobacteria and green algae with other pollutants residual in the aqueous environment, such as trichloroethyl phosphate, triethyl phosphate, perfluorononanoic acid, perfluorooctanoic acid. This indicates that LOM6 has better algal removal effectiveness in aqueous environments where organophosphate flame retardants and perfluorinated compounds exist together. In this paper, a novel method was developed to remove cyanobacteria and green algae in water environment and reduce the secondary pollution through theoretical simulation, which provides theoretical support for the control of water blooms.
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Affiliation(s)
- Jianglong Ling
- School of Public Health, Lanzhou University, Lanzhou 730000, China.
| | - Yong Niu
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Environmental Protection Key Laboratory for Lake Pollution Control, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Di Liu
- Center for Environmental Health Risk Assessment and Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Rui Li
- Center for Environmental Health Risk Assessment and Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Ye Ruan
- School of Public Health, Lanzhou University, Lanzhou 730000, China.
| | - Xixi Li
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Environmental Protection Key Laboratory for Lake Pollution Control, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's A1B 3X5, Canada.
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Patel SN, Sonani RR, Roy D, Singh NK, Subudhi S, Pabbi S, Madamwar D. Exploring the structural aspects and therapeutic perspectives of cyanobacterial phycobiliproteins. 3 Biotech 2022; 12:224. [PMID: 35975025 PMCID: PMC9375810 DOI: 10.1007/s13205-022-03284-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 07/28/2022] [Indexed: 11/01/2022] Open
Abstract
Phycobiliproteins (PBPs) of cyanobacteria and algae possess unique light harvesting capacity which expand the photosynthetically active region (PAR) and allow them to thrive in extreme niches where higher plants cannot. PBPs of cyanobacteria/algae vary in abundance, types, amino acid composition and in structure as a function of species and the habitat that they grow in. In the present review, the key aspects of structure, stability, and spectral properties of PBPs, and their correlation with ecological niche of cyanobacteria are discussed. Besides their role in light-harvesting, PBPs possess antioxidant, anti-aging, neuroprotective, hepatoprotective and anti-inflammatory properties, which can be used in therapeutics. Recent developments in therapeutic applications of PBPs are reviewed with special focus on 'route of PBPs administration' and 'therapeutic potential of PBP-derived peptide and chromophores'.
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Affiliation(s)
- Stuti N. Patel
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa, Anand, Gujarat 388421 India
- Post-Graduate Department of Biosciences, UGC-Centre of Advanced Study, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol, Anand, Gujarat 388315 India
- Present Address: Małopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Ravi R. Sonani
- Present Address: Małopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908 USA
| | - Diya Roy
- Centre for Conservation and Utilisation of Blue Green Algae (CCUBGA), Division of Microbiology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Niraj Kumar Singh
- Department of Biotechnology, Shree A. N. Patel PG Institute of Science and Research, Sardar Patel University, Anand, Gujarat 388001 India
- Present Address: Gujarat Biotechnology Research Centre (GBRC), Deaprtment of Science and Technology (DST), Government of Gujarat, Gandhinagar, Gujarat 382011 India
| | - Sanjukta Subudhi
- The Energy and Resources Institute Darbari Seth Block, India Habitat Centre, Lodi Road, New Delhi, 110003 India
| | - Sunil Pabbi
- Centre for Conservation and Utilisation of Blue Green Algae (CCUBGA), Division of Microbiology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Datta Madamwar
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa, Anand, Gujarat 388421 India
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Meng D, Zhang L, Wang Q, Zhang Y, Sun Y, Zhang H, Wang Z, Zhou Z, Yang R. Self-Assembly of Phycoerythrin with Oligochitosan by Electrostatic Interaction for Stabilization of Phycoerythrin. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:12818-12827. [PMID: 34669400 DOI: 10.1021/acs.jafc.1c05205] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Phycoerythrin (PE) is a natural water-soluble pigment protein with characteristic phycobilins and is sensitive to thermal and light environmental changes. In this study, PE was extracted from Porphyra haitanensis and PE-oligochitosan complexes (POC) were fabricated by a self-assembly approach. The effects of cationic oligochitosan on the binding interaction, structure, size distribution, and color stability of PE were evaluated. The stoichiometric number n was calculated to be 21.67 ± 2.65 (oligochitosan/PE) and the binding constant K was (6.47 ± 0.48) × 105 M-1. Cationic oligochitosan could electrostatically interact with PE and affect the PE structure by increasing the α-helix content. In addition, high concentrations of oligochitosan led to the formation of dense phycoerythrin protein granules. Moreover, at a reaction ratio of 20.0:1 (oligochitosan/PE), being approximately the predicted stoichiometric number n, the thermal stability (40-80 °C), natural light stability, and ultraviolet light irradiation (254 nm) stability of the POC were improved. This study provides an approach to reduce the susceptibility of PE upon environmental changes by forming a stable self-assembly complex, which will promote the application of PE as a natural pigment protein in food and chemical applications.
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Affiliation(s)
- Demei Meng
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Technology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Liqun Zhang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Technology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Qiaoe Wang
- Beijing Key Lab of Plant Resource Research and Development, Beijing Technology and Business University, Beijing 100048, China
| | - Yidan Zhang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Technology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Yifei Sun
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Technology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Haili Zhang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Technology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Zhiwei Wang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Technology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Zhongkai Zhou
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Technology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Rui Yang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Technology, Tianjin University of Science & Technology, Tianjin 300457, China
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Lee PT, Huang J, Huang CY, Liu ZX, Yeh HY, Huang HT, Chen LL, Nan FH, Lee MC. Phycoerythrin from Colaconema sp. Has Immunostimulatory Effects on the Whiteleg Shrimp Litopenaeus vannamei and Increases Resistance to Vibrio parahaemolyticus and White Spot Syndrome Virus. Animals (Basel) 2021; 11:ani11082371. [PMID: 34438826 PMCID: PMC8388644 DOI: 10.3390/ani11082371] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/07/2021] [Accepted: 08/09/2021] [Indexed: 12/04/2022] Open
Abstract
Simple Summary In this study, we found that phycoerythrin from Colaconema sp. can differentially stimulate the immune response of whiteleg shrimp in vitro and in vivo and could potentially be used as an immunomodulator in shrimp culture. Abstract We investigated whether phycoerythrin (PE), a pigment sourced from marine algae, could act as an immunomodulatory agent in whiteleg shrimp (Litopenaeus vannamei). To this end, PE was extracted and purified from a PE-rich macroalgae, Colaconema sp. Our in vitro analysis demonstrated that PE enhanced prophenoloxidase and phagocytosis activity but inhibited the production of reactive oxygen species in hemocytes. Additionally, the PE signal could be detected using an in vivo imaging system after its injection into the ventral sinus of the cephalothorax of whiteleg shrimp. The expression profiles of fourteen immune-related genes were monitored in hemocytes from whiteleg shrimp injected with 0.30 μg of PE per gram of body weight, and crustin, lysozyme, penaiedin 4, and anti-lipopolysaccharide factor showed up-regulated post-stimulation. The induction of immune genes and enhancement of innate immune parameters by PE may explain the higher survival rates for shrimp that received different doses of PE prior to being challenged with Vibrio parahaemolyticus or white spot syndrome virus compared to controls. Combined, these results show that PE from Colaconema sp. can differentially stimulate the immune response of whiteleg shrimp in vitro and in vivo and could potentially be used as an immunomodulator in shrimp culture.
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Affiliation(s)
- Po-Tsang Lee
- Department of Aquaculture, National Taiwan Ocean University, Keelung City 20224, Taiwan; (P.-T.L.); (J.H.); (C.-Y.H.); (Z.-X.L.); (H.-Y.Y.); (H.-T.H.); (F.-H.N.)
| | - Jing Huang
- Department of Aquaculture, National Taiwan Ocean University, Keelung City 20224, Taiwan; (P.-T.L.); (J.H.); (C.-Y.H.); (Z.-X.L.); (H.-Y.Y.); (H.-T.H.); (F.-H.N.)
| | - Chin-Yi Huang
- Department of Aquaculture, National Taiwan Ocean University, Keelung City 20224, Taiwan; (P.-T.L.); (J.H.); (C.-Y.H.); (Z.-X.L.); (H.-Y.Y.); (H.-T.H.); (F.-H.N.)
| | - Zi-Xuan Liu
- Department of Aquaculture, National Taiwan Ocean University, Keelung City 20224, Taiwan; (P.-T.L.); (J.H.); (C.-Y.H.); (Z.-X.L.); (H.-Y.Y.); (H.-T.H.); (F.-H.N.)
| | - Han-Yang Yeh
- Department of Aquaculture, National Taiwan Ocean University, Keelung City 20224, Taiwan; (P.-T.L.); (J.H.); (C.-Y.H.); (Z.-X.L.); (H.-Y.Y.); (H.-T.H.); (F.-H.N.)
| | - Huai-Ting Huang
- Department of Aquaculture, National Taiwan Ocean University, Keelung City 20224, Taiwan; (P.-T.L.); (J.H.); (C.-Y.H.); (Z.-X.L.); (H.-Y.Y.); (H.-T.H.); (F.-H.N.)
| | - Li-Li Chen
- Institute of Marine Biology, National Taiwan Ocean University, Keelung City 20224, Taiwan;
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung City 20224, Taiwan
| | - Fan-Hua Nan
- Department of Aquaculture, National Taiwan Ocean University, Keelung City 20224, Taiwan; (P.-T.L.); (J.H.); (C.-Y.H.); (Z.-X.L.); (H.-Y.Y.); (H.-T.H.); (F.-H.N.)
- Center of Excellence for Ocean Engineering, National Taiwan Ocean University, Keelung City 20224, Taiwan
| | - Meng-Chou Lee
- Department of Aquaculture, National Taiwan Ocean University, Keelung City 20224, Taiwan; (P.-T.L.); (J.H.); (C.-Y.H.); (Z.-X.L.); (H.-Y.Y.); (H.-T.H.); (F.-H.N.)
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung City 20224, Taiwan
- Center of Excellence for Ocean Engineering, National Taiwan Ocean University, Keelung City 20224, Taiwan
- Correspondence: ; Tel.: +886-22462-2192 (ext. 5239) or +886-978-586-589; Fax: +886-22463-5441
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Abstract
Phycobilisomes (PBSs) are extremely large chromophore-protein complexes on the stromal side of the thylakoid membrane in cyanobacteria and red algae. The main function of PBSs is light harvesting, and they serve as antennas and transfer the absorbed energy to the reaction centers of two photosynthetic systems (photosystems I and II). PBSs are composed of phycobiliproteins and linker proteins. How phycobiliproteins and linkers are organized in PBSs and how light energy is efficiently harvested and transferred in PBSs are the fundamental questions in the study of photosynthesis. In this review, the structures of the red algae Griffithsia pacifica and Porphyridium purpureum are discussed in detail, along with the functions of linker proteins in phycobiliprotein assembly and in fine-tuning the energy state of chromophores.
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Affiliation(s)
- Sen-Fang Sui
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China;
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Ghosh T, Mishra S. Studies on Extraction and Stability of C-Phycoerythrin From a Marine Cyanobacterium. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.00102] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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Sonani RR, Rastogi RP, Singh NK, Thadani J, Patel PJ, Kumar J, Tiwari AK, Devkar RV, Madamwar D. Phycoerythrin averts intracellular ROS generation and physiological functional decline in eukaryotes under oxidative stress. PROTOPLASMA 2017; 254:849-862. [PMID: 27335008 DOI: 10.1007/s00709-016-0996-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 06/08/2016] [Indexed: 06/06/2023]
Abstract
In vitro antioxidant virtue and life-prolonging effect of phycoerythrin (PE; a pigment protein isolated from Phormidium sp. A09DM) have been revealed in our previous reports (Sonani et al. in Age 36:9717, 2014a; Sonani et al. in Process Biochem 49:1757-1766, 2014b). It has been hypothesized that the PE expands life span of Caenorhabditis elegans (bears large resemblance with human aging pathways) due to its antioxidant virtue. This hypothesis is tested in present study by checking the effect of PE on intracellular reactive oxygen species (ROS) generation and associated physiological deformities using mouse and human skin fibroblasts, C. elegans, and Drosophila melanogaster Oregon R + and by divulging PE's structural attributes responsible for its antioxidant asset. PE treatment displayed noteworthy decrease of 67, 48, and 77 % in ROS level in mouse fibroblast (3T3-L1), human fibroblast, and C. elegans N2, respectively, arisen under chemical-induced oxidative stress. PE treatment delayed the development of paraquat-induced Alzheimer phenotype by 14.5 % in C. elegans CL4176. Furthermore, PE improved the locomotion of D. melanogaster Oregon R + under oxidative stress with simultaneous up-regulation in super-oxide dismutase and catalase activities. The existence of 52 Glu + Asp + His + Thr residues (having metal ion sequestration capacity), 5 phycoerythrobilin chromophores (potential electron exchangers) in PE's primary structure, and significant hydrophobic patches on the surface of its α- and β-subunits are supposed to collectively contribute in the antioxidant virtues of PE. Altogether, results support the hypothesis that it is the PE's antioxidant asset, which is responsible for its life-prolonging effect and thus could be exploited in the therapeutics of ROS-associated abnormalities including aging and neurodegeneration in eukaryotes.
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Affiliation(s)
- Ravi R Sonani
- Post-Graduate Department of Biosciences, UGC-Centre of Advanced Study, Sardar Patel University, Vadtal Road, Satellite Campus, Bakrol, Anand, Gujarat, 388 315, India
- Commission of Atomic and Alternative Energy, Institute of Biology and Technology of Saclay, 91191, Gif/Yvette, France
| | - Rajesh P Rastogi
- Post-Graduate Department of Biosciences, UGC-Centre of Advanced Study, Sardar Patel University, Vadtal Road, Satellite Campus, Bakrol, Anand, Gujarat, 388 315, India
| | - Niraj K Singh
- Department of Biotechnology, Shri A. N. Patel PG Institute, Anand, Gujarat, 388001, India
| | - Jaymesh Thadani
- Division of Phytotherapeutics and Metabolic Endocrinology, Department of Zoology, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, 390002, India
| | - Puja J Patel
- Department of Biotechnology, Shri A. N. Patel PG Institute, Anand, Gujarat, 388001, India
| | - Jitendra Kumar
- The Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA, 94945, USA.
- DBT-PU-IPLS Programme, Department of Botany/Biotechnology, Patna University, Patna, Bihar, 800005, India.
| | - Anand K Tiwari
- School of Biological Sciences and Biotechnology, Indian Institute of Advanced Research, Koba, Gandhinagar, Gujarat, 382007, India.
| | - Ranjitsinh V Devkar
- Division of Phytotherapeutics and Metabolic Endocrinology, Department of Zoology, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, 390002, India.
| | - Datta Madamwar
- Post-Graduate Department of Biosciences, UGC-Centre of Advanced Study, Sardar Patel University, Vadtal Road, Satellite Campus, Bakrol, Anand, Gujarat, 388 315, India.
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Echenique-Subiabre I, Dalle C, Duval C, Heath MW, Couté A, Wood SA, Humbert JF, Quiblier C. Application of a spectrofluorimetric tool (bbe BenthoTorch) for monitoring potentially toxic benthic cyanobacteria in rivers. WATER RESEARCH 2016; 101:341-350. [PMID: 27286469 DOI: 10.1016/j.watres.2016.05.081] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 05/24/2016] [Accepted: 05/25/2016] [Indexed: 05/12/2023]
Abstract
Over the last decade reports of animal poisoning following accidental consumption of neurotoxin-producing benthic cyanobacteria (mainly Phormidium spp.) have increased. There is a need for rapid and cost-effective tools to survey benthic cyanobacteria. In this study we assessed the performance of the BenthoTorch, a fluorometric probe that provides in situ estimations of cyanobacteria, diatoms and green algae biomass in biofilms. Biofilms (n = 288) were analysed from two rivers in France and eight in New Zealand. Correlations between chlorophyll-a measured using the BenthoTorch and spectrophotometry were higher for thin (<2 mm) compared to thick (>2 mm) biofilms (r(2) = 0.58 and 0.27 respectively; p < 0.001). When cyanobacteria represented less than 50% of the total biomass (based on biovolumes), microscopic and BenthoTorch compositional estimations were significantly correlated (r(2) = 0.53, p < 0.001). Conversely, there was no correlation when cyanobacteria exceeded 50% of the total biomass. Under this scenario diatoms were overestimated. Our results suggest that the observed biases occur because the BenthoTorch only measures the upper biofilm layer and it underestimates the biomass of phycoerythrin-containing cyanobacteria. To improve the performance of this sensor and render it a useful tool for a rapid evaluation of benthic cyanobacterial biomass in rivers, we propose that: (i) the algorithms based on the LEDs responses currently available on this tool need revision, (ii) new excitation wavelengths should be included that allow the fingerprints of phycoerythrin-containing cyanobacteria to be discriminated, and (iii) a sensor that penetrates the biofilms is needed to obtain more accurate estimates of cyanobacterial biomass.
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Affiliation(s)
- Isidora Echenique-Subiabre
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245), Muséum National d'Histoire Naturelle, CNRS, Case 39, 57 Rue Cuvier, 75005, Paris, France; INRA, IEES Paris, Université Pierre et Marie Curie (UPMC), 4 Place Jussieu, 75005, Paris, France
| | - Caroline Dalle
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245), Muséum National d'Histoire Naturelle, CNRS, Case 39, 57 Rue Cuvier, 75005, Paris, France
| | - Charlotte Duval
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245), Muséum National d'Histoire Naturelle, CNRS, Case 39, 57 Rue Cuvier, 75005, Paris, France
| | - Mark W Heath
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Alain Couté
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245), Muséum National d'Histoire Naturelle, CNRS, Case 39, 57 Rue Cuvier, 75005, Paris, France
| | - Susanna A Wood
- Cawthron Institute, Private Bag 2, 7001, Nelson, New Zealand; Environmental Research Institute, University of Waikato, Private Bag 3105, 3240 Hamilton, New Zealand
| | - Jean-François Humbert
- INRA, IEES Paris, Université Pierre et Marie Curie (UPMC), 4 Place Jussieu, 75005, Paris, France
| | - Catherine Quiblier
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245), Muséum National d'Histoire Naturelle, CNRS, Case 39, 57 Rue Cuvier, 75005, Paris, France; Université Paris Diderot, 5 Rue T. Mann, 75013, Paris, France.
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Anwer K, Rahman S, Sonani RR, Khan FI, Islam A, Madamwar D, Ahmad F, Hassan MI. Probing pH sensitivity of αC-phycoerythrin and its natural truncant: A comparative study. Int J Biol Macromol 2016; 86:18-27. [DOI: 10.1016/j.ijbiomac.2016.01.046] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/09/2016] [Accepted: 01/13/2016] [Indexed: 12/13/2022]
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Sonani RR, Sharma M, Gupta GD, Kumar V, Madamwar D. Phormidium phycoerythrin forms hexamers in crystals: a crystallographic study. Acta Crystallogr F Struct Biol Commun 2015; 71:998-1004. [PMID: 26249689 PMCID: PMC4528931 DOI: 10.1107/s2053230x15010134] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 05/25/2015] [Indexed: 11/10/2022] Open
Abstract
The crystallographic analysis of a marine cyanobacterium (Phormidium sp. A09DM) phycoerythrin (PE) that shows distinct sequence features compared with known PE structures from cyanobacteria and red algae is reported. Phormidium PE was crystallized using the sitting-drop vapour-diffusion method with ammonium sulfate as a precipitant. Diffraction data were collected on the protein crystallography beamline at the Indus-2 synchrotron. The crystals diffracted to about 2.1 Å resolution at 100 K. The crystals, with an apparent hexagonal morphology, belonged to space group P1, with unit-cell parameters a = 108.3, b = 108.4 Å, c = 116.6 Å, α = 78.94, β = 82.50, γ = 60.34°. The molecular-replacement solution confirmed the presence of 12 αβ monomers in the P1 cell. The Phormidium PE elutes as an (αβ)3 trimer of αβ monomers from a molecular-sieve column and exists as [(αβ)3]2 hexamers in the crystal lattice. Unlike red algal PE proteins, the hexamers of Phormidium PE do not form higher-order structures in the crystals. The existence of only one characteristic visual absorption band at 564 nm suggests the presence of phycoerythrobilin chromophores, and the absence of any other types of bilins, in the Phormidium PE assembly.
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Affiliation(s)
- Ravi Raghav Sonani
- BRD School of Biosciences, Sardar Patel University, Post Box No. 39, Satellite Campus, Vadtal Road, Vallabh Vidyanagar 388 120, India
| | - Mahima Sharma
- Protein Crystallography Section, Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Gagan Deep Gupta
- Protein Crystallography Section, Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Vinay Kumar
- Protein Crystallography Section, Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Datta Madamwar
- BRD School of Biosciences, Sardar Patel University, Post Box No. 39, Satellite Campus, Vadtal Road, Vallabh Vidyanagar 388 120, India
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12
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Singh NK, Sonani RR, Rastogi RP, Madamwar D. The phycobilisomes: an early requisite for efficient photosynthesis in cyanobacteria. EXCLI JOURNAL 2015; 14:268-89. [PMID: 26417362 PMCID: PMC4553884 DOI: 10.17179/excli2014-723] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 01/16/2015] [Indexed: 01/26/2023]
Abstract
Cyanobacteria trap light energy by arrays of pigment molecules termed “phycobilisomes (PBSs)”, organized proximal to "reaction centers" at which chlorophyll perform the energy transduction steps with highest quantum efficiency. PBSs, composed of sequential assembly of various chromophorylated phycobiliproteins (PBPs), as well as nonchromophoric, basic and hydrophobic polypeptides called linkers. Atomic resolution structure of PBP is a heterodimer of two structurally related polypeptides but distinct specialised polypeptides- a and ß, made up of seven alpha-helices each which played a crucial step in evolution of PBPs. PBPs carry out various light dependent responses such as complementary chromatic adaptation. The aim of this review is to summarize and discuss the recent progress in this field and to highlight the new and the questions that remain unresolved.
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Affiliation(s)
- Niraj Kumar Singh
- Shri A. N. Patel PG Institute (M. B. Patel Science College Campus), Anand, Sardargunj, Anand - 388001, Gujarat, India
| | - Ravi Raghav Sonani
- BRD School of Biosciences, Sardar Patel Maidan, Vadtal Road, Post Box No. 39, Sardar Patel University, Vallabh Vidyanagar 388 120, Anand, Gujarat, India
| | - Rajesh Prasad Rastogi
- BRD School of Biosciences, Sardar Patel Maidan, Vadtal Road, Post Box No. 39, Sardar Patel University, Vallabh Vidyanagar 388 120, Anand, Gujarat, India
| | - Datta Madamwar
- BRD School of Biosciences, Sardar Patel Maidan, Vadtal Road, Post Box No. 39, Sardar Patel University, Vallabh Vidyanagar 388 120, Anand, Gujarat, India
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Rastogi RP, Sonani RR, Patel AB, Madamwar D. Occurrence of a functionally stable photoharvesting single peptide allophycocyanin α-subunit (16.4 kDa) in the cyanobacterium Nostoc sp. R76DM. RSC Adv 2015. [DOI: 10.1039/c5ra14508b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
We report the occurrence of a functionally stable single peptide APC α-subunit in cyanobacterium Nostoc sp. R76DM.
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Affiliation(s)
- Rajesh P. Rastogi
- BRD School of Biosciences
- Sardar Patel University
- Vallabh Vidyanagar 388120
- India
| | - Ravi R. Sonani
- BRD School of Biosciences
- Sardar Patel University
- Vallabh Vidyanagar 388120
- India
| | - Avani B. Patel
- BRD School of Biosciences
- Sardar Patel University
- Vallabh Vidyanagar 388120
- India
| | - Datta Madamwar
- BRD School of Biosciences
- Sardar Patel University
- Vallabh Vidyanagar 388120
- India
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14
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Sonani RR, Rastogi RP, Joshi M, Madamwar D. A stable and functional single peptide phycoerythrin (15.45 kDa) from Lyngbya sp. A09DM. Int J Biol Macromol 2014; 74:29-35. [PMID: 25485942 DOI: 10.1016/j.ijbiomac.2014.11.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 11/25/2014] [Accepted: 11/27/2014] [Indexed: 12/23/2022]
Abstract
A functional and stable truncated-phycoerythrin (T-PE) was found as a result of spontaneous in vitro truncation. Truncation was noticed to occur during storage of purified native-phycoerythrin (N-PE) isolated from Lyngbya sp. A09DM. SDS and native-PAGE analysis revealed the truncation of N-PE, containing α (19.0 kDa)--and β (21.5 kDa)--subunits to the only single peptide of ∼15.45 kDa (T-PE). The peptide mass fingerprinting (PMF) and MS/MS analysis indicated that T-PE is the part of α-subunit of N-PE. UV-visible absorption peak of N-PE was found to split into two peaks (540 and 565 nm) after truncation, suggesting the alterations in its folded state. The emission spectra of both N-PE and T-PE show the emission band centered at 581 nm (upon excitation at 559 nm) suggested the maintenance of fluorescence even after significant truncation. Urea-induced denaturation and Gibbs-free energy (ΔGD°) calculations suggested that the folding and structural stability of T-PE was almost similar to that of N-PE. Presented bunch of evidences revealed the truncation in N-PE without perturbing its folding, structural stability and functionality (fluorescence), and thereby suggested its applicability in fluorescence based biomedical techniques where smaller fluorescence molecules are more preferable.
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Affiliation(s)
- Ravi Raghav Sonani
- BRD School of Biosciences, Sardar Patel University, Vadtal Road, Satellite Campus, Post Box No. 39, Vallabh Vidyanagar 388120, Gujarat, India.
| | - Rajesh Prasad Rastogi
- BRD School of Biosciences, Sardar Patel University, Vadtal Road, Satellite Campus, Post Box No. 39, Vallabh Vidyanagar 388120, Gujarat, India.
| | - Meghna Joshi
- BRD School of Biosciences, Sardar Patel University, Vadtal Road, Satellite Campus, Post Box No. 39, Vallabh Vidyanagar 388120, Gujarat, India
| | - Datta Madamwar
- BRD School of Biosciences, Sardar Patel University, Vadtal Road, Satellite Campus, Post Box No. 39, Vallabh Vidyanagar 388120, Gujarat, India.
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15
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Anwer K, Parmar A, Rahman S, Kaushal A, Madamwar D, Islam A, Hassan MI, Ahmad F. Folding and stability studies on C-PE and its natural N-terminal truncant. Arch Biochem Biophys 2014; 545:9-21. [PMID: 24434005 DOI: 10.1016/j.abb.2014.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 01/03/2014] [Accepted: 01/07/2014] [Indexed: 10/25/2022]
Abstract
The conformational and functional state of biliproteins can be determined by optical properties of the covalently linked chromophores. α-Subunit of most of the phycoerythrin contains 164 residues. Recently determined crystal structure of the naturally truncated form of α-subunit of cyanobacterial phycoerythrin (Tr-αC-PE) lacks 31 N-terminal residues present in its full length form (FL-αC-PE). This provides an opportunity to investigate the structure-function relationship between these two natural forms. We measured guanidinium chloride (GdmCl)-induced denaturation curves of FL-αC-PE and Tr-αC-PE proteins, followed by observing changes in absorbance at 565nm, fluorescence at 350 and 573nm, and circular dichroism at 222nm. The denaturation curve of each protein was analyzed for ΔGD(∘), the value of Gibbs free energy change on denaturation (ΔGD) in the absence of GdmCl. The main conclusions of the this study are: (i) GdmCl-induced denaturation (native state↔denatured state) of FL-αC-PE and Tr-αC-PE is reversible and follows a two-state mechanism, (ii) FL-αC-PE is 1.4kcalmol(-1) more stable than Tr-αC-PE, (iii) truncation of 31-residue long fragment that contains two α-helices, does not alter the 3-D structure of the remaining protein polypeptide chain, protein-chromophore interaction, and (iv) amino acid sequence of Tr-αC-PE determines the functional structure of the phycoerythrin.
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Affiliation(s)
- Khalid Anwer
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia (Central University), Jamia Nagar, New Delhi 110 025, India
| | - Asha Parmar
- BRD School of Biosciences, Sardar Patel University, Vallabh Vidyanagar, Gujarat 388 120, India
| | - Safikur Rahman
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia (Central University), Jamia Nagar, New Delhi 110 025, India
| | - Avani Kaushal
- BRD School of Biosciences, Sardar Patel University, Vallabh Vidyanagar, Gujarat 388 120, India
| | - Datta Madamwar
- BRD School of Biosciences, Sardar Patel University, Vallabh Vidyanagar, Gujarat 388 120, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia (Central University), Jamia Nagar, New Delhi 110 025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia (Central University), Jamia Nagar, New Delhi 110 025, India.
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia (Central University), Jamia Nagar, New Delhi 110 025, India
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Anwer K, Sonani R, Madamwar D, Singh P, Khan F, Bisetty K, Ahmad F, Hassan MI. Role of N-terminal residues on folding and stability of C-phycoerythrin: simulation and urea-induced denaturation studies. J Biomol Struct Dyn 2013; 33:121-33. [PMID: 24279700 DOI: 10.1080/07391102.2013.855144] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The conformational state of biliproteins can be determined by optical properties of the covalently linked chromophores. Recently determined crystal structure of truncated form of α-subunit of cyanobacterial phycoerythrin (αC-PE) from Phormidium tenue provides a new insight into the structure-function relationship of αC-PE. To compare their stabilities, we have measured urea-induced denaturation transitions of the full length αC-PE (FL-αC-PE) and truncated αC-PE (Tr-αC-PE) followed by observing changes in absorbance at 565 nm, fluorescence at 350 and 573 nm, and circular dichroism at 222 nm as a function of [urea], the molar concentration of urea. The transition curve of each protein was analyzed for ΔG(D)(0), the value of Gibbs free energy change on denaturation (ΔG(D)) in the absence of urea; m, the slope (=∂∆G(D)/∂[urea]), and C(m), the midpoint of the denaturation curve, i.e. [urea] at which ΔG(D) = 0. A difference of about 10% in ΔG(D)(0) observed between FL-αC-PE and Tr-αC-PE, suggests that the two proteins are almost equally stable, and the natural deletion of 31 residues from the N-terminal side of the full length protein does not alter its stability. Furthermore, normalization of probes shows that the urea-induced denaturation of both the proteins is a two-state process. Folding of both structural variants (Tr-αC-PE and FL-αC-PE) of P. tenue were also studied using molecular dynamics simulations at 300 K. The results show clearly that the stability of the proteins is evenly distributed over the whole structure indicating no significant role of N-terminal residues in the stability of both proteins.
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Affiliation(s)
- Khalid Anwer
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia (A Central University) , Jamia Nagar, New Delhi 110 025 , India
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17
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Parmar A, Singh NK, Kaushal A, Madamwar D. Characterization of an intact phycoerythrin and its cleaved 14kDa functional subunit from marine cyanobacterium Phormidium sp. A27DM. Process Biochem 2011. [DOI: 10.1016/j.procbio.2011.06.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Parmar A, Singh NK, Kaushal A, Sonawala S, Madamwar D. Purification, characterization and comparison of phycoerythrins from three different marine cyanobacterial cultures. BIORESOURCE TECHNOLOGY 2011; 102:1795-802. [PMID: 20889334 DOI: 10.1016/j.biortech.2010.09.025] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 08/25/2010] [Accepted: 09/07/2010] [Indexed: 05/16/2023]
Abstract
The present study is focused on purification, characterization and comparison of phycoerythrins from three different marine cyanobacterial cultures--hormidium sp. A27 DM, Lyngbya sp. A09 DM and Halomicronema sp. A32 DM. 'Phycoerythrin' was successfully purified and characterized. On SDS-PAGE, the PE purified from all three young cultures showed four bands--corresponding to α and β subunits of each of PE-I and PE-II. However, phycoerythrin purified after prolonged growth of Phormidium sp. A27 DM and Halomicronema sp. A32DM showed only one band corresponding to 14 kDa whereas Lyngbya sp. A09 DM continued to produce uncleaved phycoerythrin. The absorption spectra of purified PEs from all the three young and old cultures showed variations however the fluorescence studies of the purified PEs in all cases gave the emission spectra at around 580 nm. The described work is of great importance to understand the role of phycoerythrin in adapting cyanobacteria to stress conditions.
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Affiliation(s)
- Asha Parmar
- BRD School of Biosciences, Sardar Patel Maidan, Vadtal Road, Satellite Campus, Post Box No. 39, Sardar Patel University, Vallabh Vidyanagar 388 120, Anand, Gujarat, India.
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