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Hughes J, Winkler A. New Insight Into Phytochromes: Connecting Structure to Function. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:153-183. [PMID: 39038250 DOI: 10.1146/annurev-arplant-070623-110636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Red and far-red light-sensing phytochromes are widespread in nature, occurring in plants, algae, fungi, and prokaryotes. Despite at least a billion years of evolution, their photosensory modules remain structurally and functionally similar. Conversely, nature has found remarkably different ways of transmitting light signals from the photosensor to diverse physiological responses. We summarize key features of phytochrome structure and function and discuss how these are correlated, from how the bilin environment affects the chromophore to how light induces cellular signals. Recent advances in the structural characterization of bacterial and plant phytochromes have resulted in paradigm changes in phytochrome research that we discuss in the context of present-day knowledge. Finally, we highlight questions that remain to be answered and suggest some of the benefits of understanding phytochrome structure and function.
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Affiliation(s)
- Jon Hughes
- Department of Plant Physiology, Justus Liebig University, Giessen, Germany;
- Department of Physics, Free University of Berlin, Berlin, Germany
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, Graz, Austria;
- BioTechMed-Graz, Graz, Austria
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2
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Ko YJ, Lee ME, Cho BH, Kim M, Hyeon JE, Han JH, Han SO. Bioproduction of porphyrins, phycobilins, and their proteins using microbial cell factories: engineering, metabolic regulations, challenges, and perspectives. Crit Rev Biotechnol 2024; 44:373-387. [PMID: 36775664 DOI: 10.1080/07388551.2023.2168512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/21/2022] [Accepted: 01/03/2023] [Indexed: 02/14/2023]
Abstract
Porphyrins, phycobilins, and their proteins have abundant π-electrons and strongly absorb visible light, some of which bind a metal ion in the center. Because of the structural and optical properties, they not only play critical roles as an essential component in natural systems but also have attracted much attention as a high value specialty chemical in various fields, including renewable energy, cosmetics, medicines, and foods. However, their commercial application seems to be still limited because the market price of porphyrins and phycobilins is generally expensive to apply them easily. Furthermore, their petroleum-based chemical synthesis is energy-intensive and emits a pollutant. Recently, to replace petroleum-based production, many studies on the bioproduction of metalloporphyrins, including Zn-porphyrin, Co-porphyrin, and heme, porphyrin derivatives including chlorophyll, biliverdin, and phycobilins, and their proteins including hemoproteins, phycobiliproteins, and phytochromes from renewable carbon sources using microbial cell factories have been reported. This review outlines recent advances in the bioproduction of porphyrins, phycobilins, and their proteins using microbial cell factories developed by various microbial biotechnology techniques, provides well-organized information on metabolic regulations of the porphyrin metabolism, and then critically discusses challenges and future perspectives. Through these, it is expected to be able to achieve possible solutions and insights and to develop an outstanding platform to be applied to the industry in future research.
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Affiliation(s)
- Young Jin Ko
- Department of Biotechnology, Korea University, Seoul, Republic of Korea
- Institute of Life Science and Natural Resources, Korea University, Seoul, Korea
| | - Myeong-Eun Lee
- Department of Biotechnology, Korea University, Seoul, Republic of Korea
| | - Byeong-Hyeon Cho
- Department of Biotechnology, Korea University, Seoul, Republic of Korea
| | - Minhye Kim
- Department of Biotechnology, Korea University, Seoul, Republic of Korea
| | - Jeong Eun Hyeon
- Department of Next Generation Applied Sciences, The Graduate School of Sungshin University, Seoul, Korea
- Department of Food Science and Biotechnology, College of Knowledge-Based Services Engineering, Sungshin Women's University, Seoul, Korea
| | - Joo Hee Han
- Department of Next Generation Applied Sciences, The Graduate School of Sungshin University, Seoul, Korea
- Department of Food Science and Biotechnology, College of Knowledge-Based Services Engineering, Sungshin Women's University, Seoul, Korea
| | - Sung Ok Han
- Department of Biotechnology, Korea University, Seoul, Republic of Korea
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Braslavsky SE. Outstanding women scientists who have broadened the knowledge on biological photoreceptors-II. Photochem Photobiol Sci 2024; 23:757-761. [PMID: 38446404 DOI: 10.1007/s43630-024-00551-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/08/2024] [Indexed: 03/07/2024]
Abstract
This part II is a continuation of the article published in Photochemical and Photobiological Sciences (2023) 22, 2799-2815, https://doi.org/10.1007/s43630-023-00487-1 , which should be considered a work in progress. Now, two female scientists who have worked on different aspects of chronobiology, plus a younger colleague who recently and too prematurely died, are incorporated to the list of outstanding women who have expanded the knowledge in the field of biological photoreceptors.
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Affiliation(s)
- Silvia E Braslavsky
- Max Planck Institute for Chemical Energy Conversion, 45410, Mülheim an der Ruhr, Germany.
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Alexiev U, Rühl E. Visualization of Nanocarriers and Drugs in Cells and Tissue. Handb Exp Pharmacol 2024; 284:153-189. [PMID: 37566121 DOI: 10.1007/164_2023_684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
In this chapter, the visualization of nanocarriers and drugs in cells and tissue is reviewed. This topic is tightly connected to modern drug delivery, which relies on nanoscopic drug formulation approaches and the ability to probe nanoparticulate systems selectively in cells and tissue using advanced spectroscopic and microscopic techniques. We first give an overview of the breadth of this research field. Then, we mainly focus on topical drug delivery to the skin and discuss selected visualization techniques from spectromicroscopy, such as scanning transmission X-ray microscopy and fluorescence lifetime imaging. These techniques rely on the sensitive and quantitative detection of the topically applied drug delivery systems and active substances, either by exploiting their molecular properties or by introducing environmentally sensitive probes that facilitate their detection.
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Affiliation(s)
- Ulrike Alexiev
- Fachbereich Physik, Freie Universität Berlin, Berlin, Germany.
| | - Eckart Rühl
- Physikalische Chemie, Freie Universität Berlin, Berlin, Germany.
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Balke J, Díaz Gutiérrez P, Rafaluk-Mohr T, Proksch J, Koksch B, Alexiev U. Osmolytes Modulate Photoactivation of Phytochrome: Probing Protein Hydration. Molecules 2023; 28:6121. [PMID: 37630372 PMCID: PMC10457786 DOI: 10.3390/molecules28166121] [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: 06/13/2023] [Revised: 07/23/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
Phytochromes are bistable red/far-red light-responsive photoreceptor proteins found in plants, fungi, and bacteria. Light-activation of the prototypical phytochrome Cph1 from the cyanobacterium Synechocystis sp. PCC 6803 allows photoisomerization of the bilin chromophore in the photosensory module and a subsequent series of intermediate states leading from the red absorbing Pr to the far-red-absorbing Pfr state. We show here via osmotic and hydrostatic pressure-based measurements that hydration of the photoreceptor modulates the photoconversion kinetics in a controlled manner. While small osmolytes like sucrose accelerate Pfr formation, large polymer osmolytes like PEG 4000 delay the formation of Pfr. Thus, we hypothesize that an influx of mobile water into the photosensory domain is necessary for proceeding to the Pfr state. We suggest that protein hydration changes are a molecular event that occurs during photoconversion to Pfr, in addition to light activation, ultrafast electric field changes, photoisomerization, proton release and uptake, and the major conformational change leading to signal transmission, or simultaneously with one of these events. Moreover, we discuss this finding in light of the use of Cph1-PGP as a hydration sensor, e.g., for the characterization of novel hydrogel biomaterials.
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Affiliation(s)
- Jens Balke
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Paula Díaz Gutiérrez
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Timm Rafaluk-Mohr
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Jonas Proksch
- Department of Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry–Organic Chemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany; (J.P.); (B.K.)
| | - Beate Koksch
- Department of Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry–Organic Chemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany; (J.P.); (B.K.)
| | - Ulrike Alexiev
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
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Insights into the Structures of Bilirubin and Biliverdin from Vibrational and Electronic Circular Dichroism: History and Perspectives. Molecules 2023; 28:molecules28062564. [PMID: 36985535 PMCID: PMC10054127 DOI: 10.3390/molecules28062564] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023] Open
Abstract
In this work we review research activities on a few of the most relevant structural aspects of bilirubin (BR) and biliverdin (BV). Special attention is paid to the exocyclic C=C bonds being in mostly Z rather than E configurations, and to the overall conformation being essentially different for BR and BV due to the presence or absence of the double C=C bond at C-10. In both cases, racemic mixtures of each compound of either M or P configuration are present in achiral solutions; however, imbalance between the two configurations may be easily achieved. In particular, results based on chiroptical spectroscopies, both electronic and vibrational circular dichroism (ECD and VCD) methods, are presented for chirally derivatized BR and BV molecules. Finally, we review deracemization experiments monitored with ECD data from our lab for BR in the presence of serum albumin and anesthetic compounds.
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Sadeghi M, Balke J, Rafaluk-Mohr T, Alexiev U. Long-Distance Protonation-Conformation Coupling in Phytochrome Species. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238395. [PMID: 36500486 PMCID: PMC9737838 DOI: 10.3390/molecules27238395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/25/2022] [Accepted: 11/27/2022] [Indexed: 12/04/2022]
Abstract
Phytochromes are biological red/far-red light sensors found in many organisms. The connection between photoconversion and the cellular output signal involves light-mediated global structural changes in the interaction between the photosensory module (PAS-GAF-PHY, PGP) and the C-terminal transmitter (output) module. We recently showed a direct correlation of chromophore deprotonation with pH-dependent conformational changes in the various domains of the prototypical phytochrome Cph1 PGP. These results suggested that the transient phycocyanobilin (PCB) chromophore deprotonation is closely associated with a higher protein mobility both in proximal and distal protein sites, implying a causal relationship that might be important for the global large-scale protein rearrangements. Here, we investigate the prototypical biliverdin (BV)-binding phytochrome Agp1. The structural changes at various positions in Agp1 PGP were investigated as a function of pH using picosecond time-resolved fluorescence anisotropy and site-directed fluorescence labeling of cysteine variants of Agp1 PGP. We show that the direct correlation of chromophore deprotonation with pH-dependent conformational changes does not occur in Agp1. Together with the absence of long-range effects between the PHY domain and chromophore pKa, in contrast to the findings in Cph1, our results imply phytochrome species-specific correlations between transient chromophore deprotonation and intramolecular signal transduction.
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Conserved histidine and tyrosine determine spectral responses through the water network in Deinococcus radiodurans phytochrome. PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES : OFFICIAL JOURNAL OF THE EUROPEAN PHOTOCHEMISTRY ASSOCIATION AND THE EUROPEAN SOCIETY FOR PHOTOBIOLOGY 2022; 21:1975-1989. [PMID: 35906527 DOI: 10.1007/s43630-022-00272-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/12/2022] [Indexed: 10/16/2022]
Abstract
Phytochromes are red light-sensing photoreceptor proteins that bind a bilin chromophore. Here, we investigate the role of a conserved histidine (H260) and tyrosine (Y263) in the chromophore-binding domain (CBD) of Deinococcus radiodurans phytochrome (DrBphP). Using crystallography, we show that in the H260A variant, the missing imidazole side chain leads to increased water content in the binding pocket. On the other hand, Y263F mutation reduces the water occupancy around the chromophore. Together, these changes in water coordination alter the protonation and spectroscopic properties of the biliverdin. These results pinpoint the importance of this conserved histidine and tyrosine, and the related water network, for the function and applications of phytochromes.
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