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Florencio-Santiago OI, Blas-Valdivia V, Serrano-Contreras JI, Rojas-Franco P, Escalona-Cardoso GN, Paniagua-Castro N, Franco-Colin M, Cano-Europa E. C-Phycoerythrin Prevents Chronic Kidney Disease-Induced Systemic Arterial Hypertension, Avoiding Oxidative Stress and Vascular Dysfunction in Remanent Functional Kidney. Mar Drugs 2024; 22:337. [PMID: 39195453 DOI: 10.3390/md22080337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 07/12/2024] [Accepted: 07/18/2024] [Indexed: 08/29/2024] Open
Abstract
Chronic kidney disease (CKD) is a burden in low- and middle-income countries, and a late diagnosis with systemic arterial hypertension (SAH) is the major complication of CKD. C-phycoerythrin (CPE) is a bioactive compound derived from Phormidium persicinum that presents anti-inflammatory and antioxidant effects in vitro and nephroprotective effects in vivo. In the current study, we determine the antihypertensive effect of CPE in a 5/6 nephrectomy-induced CKD model using twenty normotensives male Wistar rats, grouped into four groups (n = 5): sham; sham + CPE; 5/6 nephrectomy (NFx); and NFx + CPE. Treatment started a week post-surgery and continued for five weeks, with weekly hemodynamic evaluations. Following treatment, renal function, oxidative stress, and the expression of vascular dysfunction markers were assessed. The renal function analysis revealed CKD hyperfiltration, and the hemodynamic evaluation showed that SAH developed at the third week. AT1R upregulation and AT2R downregulation together with Mas1/p-Akt/p-eNOS axis were also observed. CPE treatment mitigated renal damage, preserved renal function, and prevented SAH with the modulation of the vasodilative AT1R, AT2R, and Mas1/pAKT/peNOS axis. This result reveals that CPE prevented CKD progression to SAH by avoiding oxidative stress and vascular dysfunction in the kidneys.
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Affiliation(s)
- Oscar Iván Florencio-Santiago
- Laboratorio de Metabolismo I, Departamento de Fisiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 07738, Mexico
| | - Vanesa Blas-Valdivia
- Laboratorio de Neurobiología, Departamento de Fisiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 07738, Mexico
| | - José Iván Serrano-Contreras
- Department of Metabolism, Digestion and Reproduction, Division of Digestive Diseases, Section of Nutrition, Faculty of Medicine, Hammersmith Campus, Imperial College London, London W12 0NN, UK
| | - Placido Rojas-Franco
- Laboratorio de Metabolismo I, Departamento de Fisiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 07738, Mexico
| | - Gerardo Norberto Escalona-Cardoso
- Laboratorio de Farmacología del Desarrollo, Departamento de Fisiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 07738, Mexico
| | - Norma Paniagua-Castro
- Laboratorio de Farmacología del Desarrollo, Departamento de Fisiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 07738, Mexico
| | - Margarita Franco-Colin
- Laboratorio de Metabolismo I, Departamento de Fisiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 07738, Mexico
| | - Edgar Cano-Europa
- Laboratorio de Metabolismo I, Departamento de Fisiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 07738, Mexico
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Patel SN, Sonani RR, Gupta GD, Singh NK, Kumar V, Madamwar D. Crystal structure analysis of phycoerythrin from marine cyanobacterium Halomicronema. J Biomol Struct Dyn 2022; 41:3752-3761. [PMID: 35354393 DOI: 10.1080/07391102.2022.2055647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Phycoerythrin (PE) is green light-absorbing pigment-protein that assists in efficient light harvesting in cyanobacteria and red-algae. PE in cyanobacteria stays less studied so far as compared to that in red algae. In this study, PE from marine cyanobacteria Halomicronema sp. R31DM is purified and subjected for its structural characterisation by X-ray crystallography in order to understand its light-harvesting characteristics. The crystal structure is solved to a resolution-limit of 2.21 Å with reasonable R-factors values, 0.16/0.21 (Rwork/ Rfree). PE forms hexamer of hetero-dimers made up of two peptide chains, α- and β-subunits containing 2 and 3 phycoerythrobilin (PEB) chromophores covalently attached to them, respectively. Geometry of five chromophores is analysed along with their relative position within the PE hexamer. Also, their interactions with the surrounding microenvironment are analysed. The plausible energy transfer pathways in hexamer structure have been predicted based on relative position and geometry of chromophores. This structure enriches the structural information of cyanobacterial PE in order to understand its light-harvesting capacity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Stuti N Patel
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, Anand, India
| | - Ravi R Sonani
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland.,Radiation Biology and Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Gagan D Gupta
- Radiation Biology and Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Niraj Kumar Singh
- Shri A. N. Patel P. G. Institute of Science and Research, Sardar Patel University, Anand, India
| | - Vinay Kumar
- Radiation Biology and Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Datta Madamwar
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, Anand, India
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3
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Blas-Valdivia V, Rojas-Franco P, Serrano-Contreras JI, Sfriso AA, Garcia-Hernandez C, Franco-Colín M, Cano-Europa E. C-phycoerythrin from Phormidium persicinum Prevents Acute Kidney Injury by Attenuating Oxidative and Endoplasmic Reticulum Stress. Mar Drugs 2021; 19:md19110589. [PMID: 34822460 PMCID: PMC8624244 DOI: 10.3390/md19110589] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/16/2021] [Accepted: 10/16/2021] [Indexed: 12/18/2022] Open
Abstract
C-phycoerythrin (C-PE) is a phycobiliprotein that prevents oxidative stress and cell damage. The aim of this study was to evaluate whether C-PE also counteracts endoplasmic reticulum (ER) stress as a mechanism contributing to its nephroprotective activity. After C-PE was purified from Phormidium persicinum by using size exclusion chromatography, it was characterized by spectrometry and fluorometry. A mouse model of HgCl2-induced acute kidney injury (AKI) was used to assess the effect of C-PE treatment (at 25, 50, or 100 mg/kg of body weight) on oxidative stress, the redox environment, and renal damage. ER stress was examined with the same model and C-PE treatment at 100 mg/kg. C-PE diminished oxidative stress and cell damage in a dose-dependent manner by impeding the decrease in expression of nephrin and podocin normally caused by mercury intoxication. It reduced ER stress by preventing the activation of the inositol-requiring enzyme-1α (IRE1α) pathway and avoiding caspase-mediated cell death, while leaving the expression of protein kinase RNA-like ER kinase (PERK) and activating transcription factor 6α (ATF6α) pathways unmodified. Hence, C-PE exhibited a nephroprotective effect on HgCl2-induced AKI by reducing oxidative stress and ER stress.
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Affiliation(s)
- Vanessa Blas-Valdivia
- Laboratorio de Neurobiología, Departamento de Fisiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 07738, Mexico; (V.B.-V.); (C.G.-H.)
| | - Plácido Rojas-Franco
- Laboratorio de Metabolismo I, Departamento de Fisiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 07738, Mexico;
| | - Jose Ivan Serrano-Contreras
- Department of Metabolism, Digestion and Reproduction, Division of Systems Medicine, Section of Biomolecular Medicine, Faculty of Medicine, Imperial College London, South Kensington Campus, London SW7 2AZ, UK;
| | - Andrea Augusto Sfriso
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, 44121 Ferrara, Italy;
| | - Cristian Garcia-Hernandez
- Laboratorio de Neurobiología, Departamento de Fisiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 07738, Mexico; (V.B.-V.); (C.G.-H.)
- Laboratorio de Metabolismo I, Departamento de Fisiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 07738, Mexico;
| | - Margarita Franco-Colín
- Laboratorio de Metabolismo I, Departamento de Fisiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 07738, Mexico;
- Correspondence: (M.F.-C.); (E.C.-E.); Tel./Fax: +52-55-57-29-60-00 (ext. 52351) (M.F.-C. & E.C.-E.)
| | - Edgar Cano-Europa
- Laboratorio de Metabolismo I, Departamento de Fisiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 07738, Mexico;
- Correspondence: (M.F.-C.); (E.C.-E.); Tel./Fax: +52-55-57-29-60-00 (ext. 52351) (M.F.-C. & E.C.-E.)
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Ghosh T, Mondal A, Vamsi Bharadwaj SV, Mishra S. A naturally fluorescent protein C-phycoerythrin and graphene oxide bio-composite as a selective fluorescence 'turn off/on' probe for DNA quantification and characterization. Int J Biol Macromol 2021; 185:644-653. [PMID: 34217741 DOI: 10.1016/j.ijbiomac.2021.06.201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 10/21/2022]
Abstract
Highly specific graphene-DNA interactions have been at the forefront of graphene-based sensor design for various analytes, including DNA itself. However, in addition to its detection, DNA also needs to be characterized according to its size and concentration in a sample, which is an additional analytical step. Designing a highly sensitive and selective DNA sensing and characterization platform is, thus, of great interest. The present study demonstrates that a bio-derived, naturally fluorescent protein C-phycoerythrin (CPE) - graphene oxide (GO) bio-composite can be used to detect dsDNA in nanomolar quantities efficiently via fluorescent "turn off/on" mechanism. Interaction with GO temporarily quenches CPE fluorescence in a dose-dependent manner. Analytical characterization indicates an indirect charge transfer with a corresponding loss of crystalline GO structure. The fluorescence is regained with the addition of DNA, while other biomolecules do not pose any hinderance in the detection process. The extent of regain is DNA length dependent, and the corresponding calibration curve successfully quantifies the size of an unknown DNA. The incubation time for detection is ~3-5 min. The bio-composite platform also works successfully in a complex biomolecule matrix and cell lysate. However, the presence of serum albumin poses a hinderance in the serum sample. Particle size analysis proves that CPE displacement from GO surface by the incoming DNA is the reason for the 'turn on' response, and that the sensing process is exclusive to dsDNA. This new platform could be an exciting and rapid DNA sensing and characterization tool.
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Affiliation(s)
- Tonmoy Ghosh
- Applied Phycology and Biotechnology Division, CSIR - Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar 364002, Gujarat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.
| | - Aniruddha Mondal
- Inorganic Materials and Catalysis Division, CSIR - Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar 364002, Gujarat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - S V Vamsi Bharadwaj
- Applied Phycology and Biotechnology Division, CSIR - Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar 364002, Gujarat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Sandhya Mishra
- Applied Phycology and Biotechnology Division, CSIR - Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar 364002, Gujarat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.
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5
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Sonani RR, Roszak AW, Ortmann de Percin Northumberland C, Madamwar D, Cogdell RJ. An improved crystal structure of C-phycoerythrin from the marine cyanobacterium Phormidium sp. A09DM. PHOTOSYNTHESIS RESEARCH 2018; 135:65-78. [PMID: 28918447 PMCID: PMC5783998 DOI: 10.1007/s11120-017-0443-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 09/08/2017] [Indexed: 06/07/2023]
Abstract
C-Phycoerythrin (PE) from Phormidium sp. A09DM has been crystallized using different conditions and its structure determined to atomic resolution (1.14 Å). In order for the pigment present, phycoerythrobilin (PEB), to function as an efficient light-harvesting molecule it must be held rigidly (Kupka and Scheer in Biochim Biophys Acta 1777:94-103, 2008) and, moreover, the different PEB molecules in PE must be arranged, relative to each other, so as to promote efficient energy transfer between them. This improved structure has allowed us to define in great detail the structure of the PEBs and their binding sites. These precise structural details will facilitate theoretical calculations of each PEB's spectroscopic properties. It was possible, however, to suggest a model for which chromophores contribute to the different regions of absorption spectrum and propose a tentative scheme for energy transfer. We show that some subtle differences in one of these PEB binding sites in two of the 12 subunits are caused by crystal contacts between neighboring hexamers in the crystal lattice. This explains some of the differences seen in previous lower resolution structures determined at two different pH values (Kumar et al. in Photosyn Res 129:17-28, 2016).
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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, 388315, India
| | - Aleksander W Roszak
- Institute of Molecular Cell an Systems Biology, University of Glasgow, 120 University Place, Glasgow, G12 8TA, UK.
| | | | - Datta Madamwar
- Post-Graduate Department of Biosciences, UGC-Centre of Advanced Study, Sardar Patel University, Vadtal Road, Satellite Campus, Bakrol, Anand, Gujarat, 388315, India.
| | - Richard J Cogdell
- Institute of Molecular Cell an Systems Biology, University of Glasgow, 120 University Place, Glasgow, G12 8TA, UK
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Patel SN, Sonani RR, Jakharia K, Bhastana B, Patel HM, Chaubey MG, Singh NK, Madamwar D. Antioxidant activity and associated structural attributes of Halomicronema phycoerythrin. Int J Biol Macromol 2018; 111:359-369. [PMID: 29307804 DOI: 10.1016/j.ijbiomac.2017.12.170] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 12/28/2017] [Accepted: 12/31/2017] [Indexed: 11/25/2022]
Abstract
In the present study, blue light absorbing pigment protein phycoerythrin (PE) is purified up to molecular grade purity from marine Halomicronema sp. R31DM. The purification method is based on the use of non-ionic detergent Triton-X 100 in ammonium sulphate precipitation. The purified PE is characterized for its antioxidant activity in vitro and in vivo. PE is noted to show substantial in vitro antioxidant activity probed by various biochemical assays. The PE moderated rise in the intracellular-ROS (reactive oxygen species) in wild type Caenorhabditis elegans upon heat and oxidative stress. Further, the antioxidant asset of PE is noted an expedient in averting the ROS associated abnormalities, i.e. impaired physiological behaviour (health span) and aging in C. elegans. The structural attributes of PE contributing to its antioxidant virtue are analysed; the presence of ample residues having antioxidant activity and chromophore-PEB in PE are identified as a source of its antioxidant activity. Furthermore, the stability of PE is assessed under three physico-chemical stresses, temperature, pH and oxidative stress.
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Affiliation(s)
- Stuti N Patel
- Post-Graduate Department of Biosciences, UGC-Centre of Advanced Study, Satellite Campus, Vadtal Road, Sardar Patel University, Bakrol, Anand 388315, Gujarat, India
| | - Ravi R Sonani
- Post-Graduate Department of Biosciences, UGC-Centre of Advanced Study, Satellite Campus, Vadtal Road, Sardar Patel University, Bakrol, Anand 388315, Gujarat, India; School of Sciences, P. P. Savani University, Dhamdod, Kosamba 394125, Gujarat, India.
| | - Kinnari Jakharia
- Post-Graduate Department of Biosciences, UGC-Centre of Advanced Study, Satellite Campus, Vadtal Road, Sardar Patel University, Bakrol, Anand 388315, Gujarat, India
| | - Bela Bhastana
- Post-Graduate Department of Biosciences, UGC-Centre of Advanced Study, Satellite Campus, Vadtal Road, Sardar Patel University, Bakrol, Anand 388315, Gujarat, India
| | - Hiral M Patel
- Post-Graduate Department of Biosciences, UGC-Centre of Advanced Study, Satellite Campus, Vadtal Road, Sardar Patel University, Bakrol, Anand 388315, Gujarat, India
| | - Mukesh G Chaubey
- Department of Biotechnology, Shree A. N. Patel PG Institute, Anand 388001, Gujarat, India
| | - Niraj K Singh
- Department of Biotechnology, Shree A. N. Patel PG Institute, Anand 388001, Gujarat, India
| | - Datta Madamwar
- Post-Graduate Department of Biosciences, UGC-Centre of Advanced Study, Satellite Campus, Vadtal Road, Sardar Patel University, Bakrol, Anand 388315, Gujarat, India.
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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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Kumar V, Sonani RR, Sharma M, Gupta GD, Madamwar D. Crystal structure analysis of C-phycoerythrin from marine cyanobacterium Phormidium sp. A09DM. PHOTOSYNTHESIS RESEARCH 2016; 129:17-28. [PMID: 27068646 DOI: 10.1007/s11120-016-0259-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 03/31/2016] [Indexed: 05/22/2023]
Abstract
The role of unique sequence features of C-phycoerythrin, isolated from Phormidium sp. A09DM, has been investigated by crystallographic studies. Two conserved indels (i.e. inserts or deletions) are found in the β-subunit of Phormidium phycoerythrin that are distinctive characteristics of large number of cyanobacterial sequences. The identified signatures are a two-residue deletion from position 21 and a nine-residue insertion at position 146. Crystals of Phormidium phycoerythrin were obtained at pH values of 5 and 8.5, and structures have been resolved to high precision at 1.95 and 2.1 Å resolution, respectively. In both the structures, heterodimers of α- and β- subunits assemble as hexamers. The 7-residue insertion at position 146 significantly reduces solvent exposure of π-conjugated A-C rings of a phycoerythrobilin (PEB) chromophore, and can influence energy absorption and energy transfer characteristics. The structural analyses (with 12-fold redundancy) suggest that protein micro-environment alone dictates the conformation of bound chromophores. The low- and high-energy absorbing chromophores are identified based on A-B ring coplanarity. The spatial distribution of these is found to be similar to that observed in R-phycoerythrin, suggesting the direction of energy transfer from outer-surface of hexamer to inner-hollow cavity in the Phormidium protein. The crystal structures also reveal that a commonly observed Hydrogen-bonding network in phycobiliproteins, involving chromophore bound to α-subunit and amino acid at position 73 of β-subunit, may not be essential for structural and functional integrity of C-phycoerythrin orthologs. In solution, the protein displays slight red shift and decrease in fluorescence emission at acidic pH. The mechanism for which may be static and correlates with the proximity of +ve electric field of Arg148 to the C-ring of a PEB chromophore.
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Affiliation(s)
- Vinay Kumar
- Protein Crystallography Section, Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, 400085, India.
| | - Ravi R Sonani
- BRD School of Biosciences, Sardar Patel University, Vadtal Road, Satellite Campus, Post Box No-39, Vallabh Vidyanagar, 388120, India
| | - Mahima Sharma
- Protein Crystallography Section, Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Gagan D Gupta
- Protein Crystallography Section, Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Datta Madamwar
- BRD School of Biosciences, Sardar Patel University, Vadtal Road, Satellite Campus, Post Box No-39, Vallabh Vidyanagar, 388120, India.
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Kumar A, Ghosh B, Poswal HK, Pandey KK, Hosur MV, Dwivedi A, Makde RD, Sharma SM. Protein crystallography beamline (PX-BL21) at Indus-2 synchrotron. JOURNAL OF SYNCHROTRON RADIATION 2016; 23:629-634. [PMID: 26917153 DOI: 10.1107/s160057751600076x] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 01/14/2016] [Indexed: 06/05/2023]
Abstract
The protein crystallography beamline (PX-BL21), installed at the 1.5 T bending-magnet port at the Indian synchrotron (Indus-2), is now available to users. The beamline can be used for X-ray diffraction measurements on a single crystal of macromolecules such as proteins, nucleic acids and their complexes. PX-BL21 has a working energy range of 5-20 keV for accessing the absorption edges of heavy elements commonly used for phasing. A double-crystal monochromator [Si(111) and Si(220)] and a pair of rhodium-coated X-ray mirrors are used for beam monochromatization and manipulation, respectively. This beamline is equipped with a single-axis goniometer, Rayonix MX225 CCD detector, fluorescence detector, cryogenic sample cooler and automated sample changer. Additional user facilities include a workstation for on-site data processing and a biochemistry laboratory for sample preparation. In this article the beamline, other facilities and some recent scientific results are briefly described.
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Affiliation(s)
- Ashwani Kumar
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Center, Trombay, Mumbai, India
| | - Biplab Ghosh
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Center, Trombay, Mumbai, India
| | - H K Poswal
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Center, Trombay, Mumbai, India
| | - K K Pandey
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Center, Trombay, Mumbai, India
| | - M V Hosur
- Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
| | - Abhilash Dwivedi
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Center, Trombay, Mumbai, India
| | - Ravindra D Makde
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Center, Trombay, Mumbai, India
| | - Surinder M Sharma
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Center, Trombay, Mumbai, India
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Gupta GD, Sonani RR, Sharma M, Patel K, Rastogi RP, Madamwar D, Kumar V. Crystal structure analysis of phycocyanin from chromatically adapted Phormidium rubidum A09DM. RSC Adv 2016. [DOI: 10.1039/c6ra12493c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Structural and sequence analyses of Phormidium phycocyanin revealed three co-evolving residues that determine the conformation of a phycocyanobilin chromophore believed to play role in alternate pathways for intra and inter-rod energy transfer.
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Affiliation(s)
- Gagan Deep Gupta
- Protein Crystallography Section
- Solid State Physics Division
- Bhabha Atomic Research Centre (BARC)
- Mumbai 400085
- India
| | - Ravi R. Sonani
- Post-Graduate Department of Biosciences
- UGC-Centre of Advanced Study
- Sardar Patel University
- Anand
- India
| | - Mahima Sharma
- Protein Crystallography Section
- Solid State Physics Division
- Bhabha Atomic Research Centre (BARC)
- Mumbai 400085
- India
| | - Krishna Patel
- Post-Graduate Department of Biosciences
- UGC-Centre of Advanced Study
- Sardar Patel University
- Anand
- India
| | - Rajesh P. Rastogi
- Post-Graduate Department of Biosciences
- UGC-Centre of Advanced Study
- Sardar Patel University
- Anand
- India
| | - Datta Madamwar
- Post-Graduate Department of Biosciences
- UGC-Centre of Advanced Study
- Sardar Patel University
- Anand
- India
| | - Vinay Kumar
- Protein Crystallography Section
- Solid State Physics Division
- Bhabha Atomic Research Centre (BARC)
- Mumbai 400085
- India
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11
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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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