1
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Lecomte JTJ, Johnson EA. The globins of cyanobacteria and green algae: An update. Adv Microb Physiol 2024; 85:97-144. [PMID: 39059824 DOI: 10.1016/bs.ampbs.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
The globin superfamily of proteins is ancient and diverse. Regular assessments based on the increasing number of available genome sequences have elaborated on a complex evolutionary history. In this review, we present a summary of a decade of advances in characterising the globins of cyanobacteria and green algae. The focus is on haem-containing globins with an emphasis on recent experimental developments, which reinforce links to nitrogen metabolism and nitrosative stress response in addition to dioxygen management. Mention is made of globins that do not bind haem to provide an encompassing view of the superfamily and perspective on the field. It is reiterated that an effort toward phenotypical and in-vivo characterisation is needed to elucidate the many roles that these versatile proteins fulfil in oxygenic photosynthetic microbes. It is also proposed that globins from oxygenic organisms are promising proteins for applications in the biotechnology arena.
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Affiliation(s)
- Juliette T J Lecomte
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States.
| | - Eric A Johnson
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
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2
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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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3
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Liu R, Zhen ZH, Li W, Ge B, Qin S. How can Phycobilisome, the unique light harvesting system in certain algae working highly efficiently: The connection in between structures and functions. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 186:39-52. [PMID: 38030044 DOI: 10.1016/j.pbiomolbio.2023.11.005] [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: 07/11/2023] [Revised: 11/02/2023] [Accepted: 11/23/2023] [Indexed: 12/01/2023]
Abstract
Algae, which are ubiquitous in ecosystems, have evolved a variety of light-harvesting complexes to better adapt to diverse habitats. Phycobilisomes/phycobiliproteins, unique to cyanobacteria, red algae, and certain cryptomonads, compensate for the lack of chlorophyll absorption, allowing algae to capture and efficiently transfer light energy in aquatic environments. With the advancement of microscopy and spectroscopy, the structure and energy transfer processes of increasingly complex phycobilisomes have been elucidated, providing us with a vivid portrait of the dynamic adaptation of their structures to the light environment in which algae thrive: 1) Cyanobacteria living on the surface of the water use short, small phycobilisomes to absorb red-orange light and reduce the damage from blue-violet light via multiple methods; 2) Large red algae inhabiting the depths of the ocean have evolved long and dense phycobilisomes containing phycoerythrin to capture the feeble blue-green light; 3) In far-red light environments such as caves, algae use special allophycocyanin cores to optimally utilize the far-red light; 4) When the environment shifts, algae can adjust the length, composition and density of their rods to better adapt; 5) By carefully designing the position of the pigments, phycobilisomes can transfer light energy to the reaction center with nearly 100% efficiency via three energy transfer processes.
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Affiliation(s)
- Runze Liu
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China; University of Chinese Academy of Sciences, Beijing, 100000, China
| | - Zhang-He Zhen
- Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Wenjun Li
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China
| | - Baosheng Ge
- China University of Petroleum (HUADONG), Qingdao, Shandong, 266580, China
| | - Song Qin
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China.
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4
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Krohn I, Menanteau‐Ledouble S, Hageskal G, Astafyeva Y, Jouannais P, Nielsen JL, Pizzol M, Wentzel A, Streit WR. Health benefits of microalgae and their microbiomes. Microb Biotechnol 2022; 15:1966-1983. [PMID: 35644921 PMCID: PMC9249335 DOI: 10.1111/1751-7915.14082] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 12/16/2022] Open
Abstract
Microalgae comprise a phylogenetically very diverse group of photosynthetic unicellular pro‐ and eukaryotic organisms growing in marine and other aquatic environments. While they are well explored for the generation of biofuels, their potential as a source of antimicrobial and prebiotic substances have recently received increasing interest. Within this framework, microalgae may offer solutions to the societal challenge we face, concerning the lack of antibiotics treating the growing level of antimicrobial resistant bacteria and fungi in clinical settings. While the vast majority of microalgae and their associated microbiota remain unstudied, they may be a fascinating and rewarding source for novel and more sustainable antimicrobials and alternative molecules and compounds. In this review, we present an overview of the current knowledge on health benefits of microalgae and their associated microbiota. Finally, we describe remaining issues and limitation, and suggest several promising research potentials that should be given attention.
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Affiliation(s)
- Ines Krohn
- Department of Microbiology and Biotechnology University of Hamburg Hamburg Germany
| | | | - Gunhild Hageskal
- Department of Biotechnology and Nanomedicine SINTEF Industry Trondheim Norway
| | - Yekaterina Astafyeva
- Department of Microbiology and Biotechnology University of Hamburg Hamburg Germany
| | | | - Jeppe Lund Nielsen
- Department for Chemistry and Bioscience Aalborg University Aalborg Denmark
| | - Massimo Pizzol
- Department of Planning Aalborg University Aalborg Denmark
| | - Alexander Wentzel
- Department of Biotechnology and Nanomedicine SINTEF Industry Trondheim Norway
| | - Wolfgang R. Streit
- Department of Microbiology and Biotechnology University of Hamburg Hamburg Germany
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5
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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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6
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Li M, Du M, Sun R, Zhang W, Hou Y, Li Y. Application of a 2D-QSAR with a sine normalization method for the biodegradation of fluoroquinolones to poison cyanobacteria. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:11302-11316. [PMID: 33118068 DOI: 10.1007/s11356-020-11366-y] [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: 06/12/2020] [Accepted: 10/21/2020] [Indexed: 06/11/2023]
Abstract
Cyanobacteria are photosynthetic autotrophic aquatic prokaryotes. One of the methods for controlling cyanobacterial blooms is to destroy the phycobiliproteins required for photosynthesis. In this study, to improve the biodegradation of the fluoroquinolones through inhibit cyanobacteria, the molecular docking scores of 32 fluoroquinolones (FQs) with four categories of phycobiliproteins from cyanobacteria were calculated after sine normalization to characterize the binding ability between them. A two-dimensional quantitative structure-activity relationship (2D-QSAR) model was constructed based on the comprehensive scores. Danofloxacin (DAN) with the highest comprehensive score was chosen for molecular modification. When docking with four categories of phycobiliproteins from cyanobacteria, the docking values of DAN-11 and DAN-16 were increased up to 35.75%. Moreover, their functional characteristics and environmentally friendly predictive values were improved. When the DAN-11 and DAN-16 molecules docked with the other cyanobacterial phycobiliproteins, indicating that the designed DAN derivatives had general applicability to poison cyanobacteria, the weak interaction forces might increase the binding ability between the DAN derivatives and the receptor phycobiliprotein compared with the target molecule.
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Affiliation(s)
- Minghao Li
- The Moe Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing, 102206, China
| | - Meijin Du
- The Moe Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing, 102206, China
| | - Ruihao Sun
- The Moe Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing, 102206, China
| | - Wenhui Zhang
- The Moe Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing, 102206, China
| | - Yilin Hou
- The Moe Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing, 102206, China
| | - Yu Li
- The Moe Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing, 102206, China.
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7
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Dagnino-Leone J, Figueroa M, Uribe E, Hinrichs MV, Ortiz-López D, Martínez-Oyanedel J, Bunster M. Biosynthesis and characterization of a recombinant eukaryotic allophycocyanin using prokaryotic accessory enzymes. Microbiologyopen 2020; 9:e989. [PMID: 31970933 PMCID: PMC7066465 DOI: 10.1002/mbo3.989] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/18/2019] [Accepted: 12/18/2019] [Indexed: 12/03/2022] Open
Abstract
Phycobiliproteins (PBPs) are colored fluorescent proteins present in cyanobacteria, red alga, and cryptophyta. These proteins have many potential uses in biotechnology going from food colorants to medical applications. Allophycocyanin, the simplest PBP, is a heterodimer of αβ subunits that oligomerizes as a trimer (αβ)3. Each subunit contains a phycocyanobilin, bound to a cysteine residue, which is responsible for its spectroscopic properties. In this article, we are reporting the expression of recombinant allophycocyanin (rAPC) from the eukaryotic red algae Agarophyton chilensis in Escherichia coli, using prokaryotic accessory enzymes to obtain a fully functional rAPC. Three duet vectors were used to include coding sequences of α and β subunits from A. chilensis and accessorial enzymes (heterodimeric lyase cpc S/U, heme oxygenase 1, phycocyanobilin oxidoreductase) from cyanobacteria Arthrospira maxima. rAPC was purified using several chromatographic steps. The characterization of the pure rAPC indicates very similar spectroscopic properties, λmaxAbs, λmaxEm, fluorescence lifetime, and chromophorylation degree, with native allophycocyanin (nAPC) from A. chilensis. This method, to produce high‐quality recombinant allophycocyanin, can be used to express and characterize other macroalga phycobiliproteins, to be used for biotechnological or biomedical purposes.
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Affiliation(s)
- Jorge Dagnino-Leone
- Departamento de Bioquímica y Biología Molecular, Universidad de Concepción, Concepción, Chile
| | - Maximiliano Figueroa
- Departamento de Bioquímica y Biología Molecular, Universidad de Concepción, Concepción, Chile
| | - Elena Uribe
- Departamento de Bioquímica y Biología Molecular, Universidad de Concepción, Concepción, Chile
| | - María Victoria Hinrichs
- Departamento de Bioquímica y Biología Molecular, Universidad de Concepción, Concepción, Chile
| | - Diego Ortiz-López
- Departamento de Bioquímica y Biología Molecular, Universidad de Concepción, Concepción, Chile
| | - José Martínez-Oyanedel
- Departamento de Bioquímica y Biología Molecular, Universidad de Concepción, Concepción, Chile
| | - Marta Bunster
- Departamento de Bioquímica y Biología Molecular, Universidad de Concepción, Concepción, Chile
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8
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Preparation, characterization of food grade phycobiliproteins from Porphyra haitanensis and the application in liposome-meat system. Lebensm Wiss Technol 2017. [DOI: 10.1016/j.lwt.2016.12.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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9
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Kannaujiya VK, Sinha RP. Detection of Free Thiols and Fluorescence Response of Phycoerythrin Chromophore after Ultraviolet-B Radiation Stress. J Fluoresc 2016; 27:561-567. [PMID: 27858299 DOI: 10.1007/s10895-016-1983-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 11/09/2016] [Indexed: 11/29/2022]
Abstract
The chemistry of thiol-chromophore linkage plays a central role in the nature of fluorescence of phycoerythrin (PE). Interaction of thiol and chromophore is crucial for the energy transfer, redox signal and inhibition of oxidative damage. In the present investigation the effects of ultraviolet-B radiation on an emission fluorescence intensity and wavelength shift in PE due to interaction between thiol and chromophore by remarkable strategy of detection technique was studied. Purification of PE was done by using a gel permeation and ion exchange chromatography that yielded a quite high purity index (6.40) in a monomeric (αβ) form. UV-B radiation accelerated the quenching efficiency (24.9 ± 1.52%) by reducing fluorescence emission intensity of thiol linked chromophore after 240 min of UV-B exposure. However, after blocking of transiently released free thiol by N-ethylmaleimide, quenching efficiency was increased (36.8 ± 2.80%) with marked emission wavelength shift towards shorter wavelengths up to 562 nm as compared to 575 nm in control. Emission fluorescence of free thiol was at maximum after 240 min that was detected specifically by monobromobimane (mBrB) molecular probe. The association/dissociation of bilin chromophore was analyzed by SDS- and Native-PAGE that also indicated a complete reduction in emission fluorescence. Our work clearly shows an early detection of free thiols and relative interaction with chromophore after UV-B radiation which might play a significant role in structural and functional integrity of terminal PE.
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Affiliation(s)
- Vinod K Kannaujiya
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, 221005, India
| | - Rajeshwar P Sinha
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, 221005, India.
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10
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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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11
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Purwar N, Tenboer J, Tripathi S, Schmidt M. Spectroscopic studies of model photo-receptors: validation of a nanosecond time-resolved micro-spectrophotometer design using photoactive yellow protein and α-phycoerythrocyanin. Int J Mol Sci 2013; 14:18881-98. [PMID: 24065094 PMCID: PMC3794812 DOI: 10.3390/ijms140918881] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 08/27/2013] [Accepted: 09/02/2013] [Indexed: 12/01/2022] Open
Abstract
Time-resolved spectroscopic experiments have been performed with protein in solution and in crystalline form using a newly designed microspectrophotometer. The time-resolution of these experiments can be as good as two nanoseconds (ns), which is the minimal response time of the image intensifier used. With the current setup, the effective time-resolution is about seven ns, determined mainly by the pulse duration of the nanosecond laser. The amount of protein required is small, on the order of 100 nanograms. Bleaching, which is an undesirable effect common to photoreceptor proteins, is minimized by using a millisecond shutter to avoid extensive exposure to the probing light. We investigate two model photoreceptors, photoactive yellow protein (PYP), and α-phycoerythrocyanin (α-PEC), on different time scales and at different temperatures. Relaxation times obtained from kinetic time-series of difference absorption spectra collected from PYP are consistent with previous results. The comparison with these results validates the capability of this spectrophotometer to deliver high quality time-resolved absorption spectra.
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Affiliation(s)
- Namrta Purwar
- Department of Physics, University of Wisconsin-Milwaukee, 1900 E. Kenwood Blvd., Milwaukee, WI 53211, USA.
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12
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Gao X, Wei TD, Zhang N, Xie BB, Su HN, Zhang XY, Chen XL, Zhou BC, Wang ZX, Wu JW, Zhang YZ. Molecular insights into the terminal energy acceptor in cyanobacterial phycobilisome. Mol Microbiol 2012; 85:907-15. [PMID: 22758351 DOI: 10.1111/j.1365-2958.2012.08152.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The linker protein L(CM) (ApcE) is postulated as the major component of the phycobilisome terminal energy acceptor (TEA) transferring excitation energy from the phycobilisome to photosystem II. L(CM) is the only phycobilin-attached linker protein in the cyanobacterial phycobilisome through auto-chromophorylation. However, the underlying mechanism for the auto-chromophorylation of L(CM) and the detailed molecular architecture of TEA is still unclear. Here, we demonstrate that the N-terminal phycobiliprotein-like domain of L(CM) (Pfam00502, LP502) can specifically recognize phycocyanobilin (PCB) by itself. Biochemical assays indicated that PCB binds into the same pocket in LP502 as that in the allophycocyanin α-subunit and that Ser152 and Asp155 play a vital role in LP502 auto-chromophorylation. By carefully conducting computational simulations, we arrived at a rational model of the PCB-LP502 complex structure that was supported by extensive mutational studies. In the PCB-LP502 complex, PCB binds into a deep pocket of LP502 with a distorted conformation, and Ser152 and Asp155 form several hydrogen bonds to PCB fixing the PCB Ring A and Ring D. Finally, based on our results, the dipoles and dipole-dipole interactions in TEA are analysed and a molecular structure for TEA is proposed, which gives new insights into the energy transformation mechanism of cyanobacterial phycobilisome.
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Affiliation(s)
- Xiang Gao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
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13
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Alvey RM, Biswas A, Schluchter WM, Bryant DA. Attachment of noncognate chromophores to CpcA of Synechocystis sp. PCC 6803 and Synechococcus sp. PCC 7002 by heterologous expression in Escherichia coli. Biochemistry 2011; 50:4890-902. [PMID: 21553904 DOI: 10.1021/bi200307s] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Many cyanobacteria use brilliantly pigmented, multisubunit macromolecular structures known as phycobilisomes as antenna to enhance light harvesting for photosynthesis. Recent studies have defined the enzymes that synthesize phycobilin chromophores as well as many of the phycobilin lyase enzymes that attach these chromophores to their cognate apoproteins. The ability of the phycocyanin α-subunit (CpcA) to bind alternative linear tetrapyrrole chromophores was examined through the use of a heterologous expression system in Escherichia coli. E. coli strains produced phycocyanobilin, phytochromobilin, or phycoerythrobilin when they expressed 3Z-phycocyanobilin:ferredoxin oxidoreductase (PcyA), 3Z-phytochromobilin:ferredoxin oxidoreductase (HY2) from Arabidopsis thaliana, or phycoerythrobilin synthase (PebS) from the myovirus P-SSM4, respectively. CpcA from Synechocystis sp. PCC 6803 or Synechococcus sp. PCC 7002 was coexpressed in these strains with the phycocyanin α-subunit phycocyanobilin lyase, CpcE/CpcF, or the phycoerythrocyanin α-subunit phycocyanobilin isomerizing lyase, PecE/PecF, from Noctoc sp. PCC 7120. Both lyases were capable of attaching three different linear tetrapyrrole chromophores to CpcA; thus, up to six different CpcA variants, each with a unique chromophore, could be produced with this system. One of these chromophores, denoted phytoviolobilin, has not yet been observed naturally. The recombinant proteins had unexpected and potentially useful properties, which included very high fluorescence quantum yields and photochemical activity. Chimeric lyases PecE/CpcF and CpcE/PecF were used to show that the isomerizing activity that converts phycocyanobilin to phycoviolobilin resides with PecF and not PecE. Finally, spectroscopic properties of recombinant phycocyanin R-PCIII, in which the CpcA subunits carry a phycoerythrobilin chromophore, are described.
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Affiliation(s)
- Richard M Alvey
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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14
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Chen X, Zhang L, Zhang L, Wang J, Liu H, Bu Y. Proton-Regulated Electron Transfers from Tyrosine to Tryptophan in Proteins: Through-Bond Mechanism versus Long-Range Hopping Mechanism. J Phys Chem B 2009; 113:16681-8. [DOI: 10.1021/jp9077689] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Xiaohua Chen
- Center for Modeling & Simulation Chemistry, Institute of Theoretical Chemistry, Shandong University, Jinan 250100, P. R. China
| | - Laibin Zhang
- Center for Modeling & Simulation Chemistry, Institute of Theoretical Chemistry, Shandong University, Jinan 250100, P. R. China
| | - Liang Zhang
- Center for Modeling & Simulation Chemistry, Institute of Theoretical Chemistry, Shandong University, Jinan 250100, P. R. China
| | - Jun Wang
- Center for Modeling & Simulation Chemistry, Institute of Theoretical Chemistry, Shandong University, Jinan 250100, P. R. China
| | - Haiying Liu
- Center for Modeling & Simulation Chemistry, Institute of Theoretical Chemistry, Shandong University, Jinan 250100, P. R. China
| | - Yuxiang Bu
- Center for Modeling & Simulation Chemistry, Institute of Theoretical Chemistry, Shandong University, Jinan 250100, P. R. China
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Bourgeois D, Weik M. Kinetic protein crystallography: a tool to watch proteins in action. CRYSTALLOGR REV 2009. [DOI: 10.1080/08893110802604868] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Dines M, Sendersky E, David L, Schwarz R, Adir N. Structural, functional, and mutational analysis of the NblA protein provides insight into possible modes of interaction with the phycobilisome. J Biol Chem 2008; 283:30330-40. [PMID: 18718907 DOI: 10.1074/jbc.m804241200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The enormous macromolecular phycobilisome antenna complex (>4 MDa) in cyanobacteria and red algae undergoes controlled degradation during certain forms of nutrient starvation. The NblA protein (approximately 6 kDa) has been identified as an essential component in this process. We have used structural, biochemical, and genetic methods to obtain molecular details on the mode of action of the NblA protein. We have determined the three-dimensional structure of the NblA protein from both the thermophilic cyanobacterium Thermosynechococcus vulcanus and the mesophilic cyanobacterium Synechococcus elongatus sp. PCC 7942. The NblA monomer has a helix-loop-helix motif which dimerizes into an open, four-helical bundle, identical to the previously determined NblA structure from Anabaena. Previous studies indicated that mutations to NblA residues near the C terminus impaired its binding to phycobilisome proteins in vitro, whereas the only mutation known to affect NblA function in vivo is located near the protein N terminus. We performed random mutagenesis of the S. elongatus nblA gene which enabled the identification of four additional amino acids crucial for NblA function in vivo. This data shows that essential amino acids are not confined to the protein termini. We also show that expression of the Anabaena nblA gene complements phycobilisome degradation in an S. elongatus NblA-null mutant despite the low homology between NblAs of these cyanobacteria. We propose that the NblA interacts with the phycobilisome via "structural mimicry" due to similarity in structural motifs found in all phycobiliproteins. This suggestion leads to a new model for the mode of NblA action which involves the entire NblA protein.
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Affiliation(s)
- Monica Dines
- Schulich Faculty of Chemistry and Institute of Catalysis, Science, and Technology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel
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Hahn J, Strauss HM, Schmieder P. Heteronuclear NMR Investigation on the Structure and Dynamics of the Chromophore Binding Pocket of the Cyanobacterial Phytochrome Cph1. J Am Chem Soc 2008; 130:11170-8. [DOI: 10.1021/ja8031086] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Janina Hahn
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, D-13125 Berlin, Germany
| | - Holger M. Strauss
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, D-13125 Berlin, Germany
| | - Peter Schmieder
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, D-13125 Berlin, Germany
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Narikawa R, Fukushima Y, Ishizuka T, Itoh S, Ikeuchi M. A novel photoactive GAF domain of cyanobacteriochrome AnPixJ that shows reversible green/red photoconversion. J Mol Biol 2008; 380:844-55. [PMID: 18571200 DOI: 10.1016/j.jmb.2008.05.035] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2008] [Revised: 05/12/2008] [Accepted: 05/14/2008] [Indexed: 01/08/2023]
Abstract
We report the discovery of a novel cyanobacteriochrome, the green/red photoreceptor AnPixJ (All1069), isolated from the heterocyst-forming cyanobacterium Anabaena (Nostoc) sp. PCC 7120. Cyanobacteriochromes are a recently emerging tetrapyrrole-based photoreceptor superfamily that are distantly related to the conventional red/far-red photoreceptor phytochromes (Phys). The chromophore-binding domains of AnPixJ produced in cyanobacterial and Escherichia coli cells both showed a reversible and full photoconversion between a green-absorbing form (lambda(max)=543 nm) and a red-absorbing form (lambda(max)=648 nm). Denaturation analysis revealed that the green-absorbing form and the red-absorbing form covalently ligated phycocyanobilin with E-configuration and Z-configuration at the C15C16 double bond, respectively. Time-resolved spectral analysis showed the formation of the first intermediate state peaking at 680 nm from the dark-stable red-absorbing form. This step resembles the first photoconversion step from the red-absorbing form to the red-shifted lumi-R intermediate state of the Phys. These results suggest that the Pr of AnPixJ is almost equivalent to that of the Phys and starts a primary photoreaction with Z-to-E isomerization in a mechanism similar to that in the Phys, but is finally photoconverted to the unique green-absorbing form.
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Affiliation(s)
- Rei Narikawa
- Department of Life Sciences Biology, Graduate School of Art and Sciences, University of Tokyo, Komaba, Meguro, Tokyo 153-0041, Japan
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Bourgeois D, Schotte F, Brunori M, Vallone B. Time-resolved methods in biophysics. 6. Time-resolved Laue crystallography as a tool to investigate photo-activated protein dynamics. Photochem Photobiol Sci 2007; 6:1047-56. [PMID: 17914477 DOI: 10.1039/b704249c] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
When polychromatic X-rays are shined onto crystalline material, they generate a Laue diffraction pattern. At third generation synchrotron radiation sources, a single X-ray pulse of approximately 100 ps duration is enough to produce interpretable Laue data from biomolecular crystals. Thus, by initiating biological turnover in a crystalline protein, structural changes along the reaction pathway may be filmed by ultra-fast Laue diffraction. Using laser-light as a trigger, transient species in photosensitive macromolecules can be captured at near atomic resolution with sub-nanosecond time-resolution. Such pump-probe Laue experiments have now reached an outstanding level of sophistication and have found a domain of excellence in the investigation of light-sensitive proteins undergoing cyclic photo-reactions and producing stiff crystals. The main theoretical concepts of Laue diffraction and the challenges associated with time-resolved experiments on biological crystals are recalled. The recent advances in the design of experiments are presented in terms of instrumental choices, data collection strategy and data processing, and some of the inherent difficulties of the method are highlighted. The discussion is based on the example of myoglobin, a protein that has traversed the whole history of pump-probe Laue diffraction, and for which a massive amount of data have provided considerable insight into the understanding of protein dynamics.
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Affiliation(s)
- Dominique Bourgeois
- IBS, Institut de Biologie Structurale Jean-Pierre Ebel, CEA, CNRS, Université Joseph Fourier, 41 rue Jules Horowitz, F-38027, Grenoble, France.
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