1
|
Garric S, Ratin M, Marie D, Foulon V, Probert I, Rodriguez F, Six C. Impaired photoacclimation in a kleptoplastidic dinoflagellate reveals physiological limits of early stages of endosymbiosis. Curr Biol 2024; 34:3064-3076.e5. [PMID: 38936366 DOI: 10.1016/j.cub.2024.05.066] [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: 02/02/2024] [Revised: 04/02/2024] [Accepted: 05/29/2024] [Indexed: 06/29/2024]
Abstract
Dinophysis dinoflagellates are predators of Mesodinium ciliates, from which they retain only the plastids of cryptophyte origin. The absence of nuclear photosynthetic cryptophyte genes in Dinophysis raises intriguing physiological and evolutionary questions regarding the functional dynamics of these temporary kleptoplastids within a foreign cellular environment. In an experimental setup including two light conditions, the comparative analysis with Mesodinium rubrum and the cryptophyte Teleaulax amphioxeia revealed that Dinophysis acuminata possessed a smaller and less dynamic functional photosynthetic antenna for green light, a function performed by phycoerythrin. We showed that the lack of the cryptophyte nucleus prevented the synthesis of the phycoerythrin α subunit, thereby hindering the formation of a complete phycoerythrin in Dinophysis. In particular, biochemical analyses showed that Dinophysis acuminata synthesized a poorly stable, incomplete phycoerythrin composed of chromophorylated β subunits, with impaired performance. We show that, consequently, a continuous supply of new plastids is crucial for growth and effective photoacclimation in this organism. Transcriptome analyses revealed that all examined strains of Dinophysis spp. have acquired the cryptophyte pebA and pebB genes through horizontal gene transfer, suggesting a potential ability to synthesize the phycobilin pigments bound to the cryptophyte phycoerythrin. By emphasizing that a potential long-term acquisition of the cryptophyte plastid relies on establishing genetic independence for essential functions such as light harvesting, this study highlights the intricate molecular challenges inherent in the enslavement of organelles and the processes involved in the diversification of photosynthetic organisms through endosymbiosis.
Collapse
Affiliation(s)
- Sarah Garric
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR 7144, Adaptation et Diversité en Milieu Marin, group Ecology of Marine Plankton, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Morgane Ratin
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR 7144, Adaptation et Diversité en Milieu Marin, group Ecology of Marine Plankton, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Dominique Marie
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR 7144, Adaptation et Diversité en Milieu Marin, group Ecology of Marine Plankton, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Valentin Foulon
- Centre National de la Recherche Scientifique, UMR 6285 Laboratoire des Sciences et Techniques de l'information de la Communication et de la Connaissance (Lab-STICC), Technopole Brest-Iroise, Brest 29238, France
| | - Ian Probert
- Sorbonne Université, FR 2424, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Francisco Rodriguez
- Centro oceanográfico de Vigo (IEO-CSIC), Subida a Radio Faro 50, Vigo 36390, Spain
| | - Christophe Six
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR 7144, Adaptation et Diversité en Milieu Marin, group Ecology of Marine Plankton, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France.
| |
Collapse
|
2
|
Sato M, Kawaguchi T, Maeda K, Watanabe M, Ikeuchi M, Narikawa R, Watanabe S. Functional Modification of Cyanobacterial Phycobiliprotein and Phycobilisomes through Bilin Metabolism Control. ACS Synth Biol 2024. [PMID: 39038807 DOI: 10.1021/acssynbio.4c00094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Phycobilisomes (PBSs) are light-harvesting antenna complexes in cyanobacteria that adapt to diverse light environments through the use of phycobiliproteins within the PBS structures. Freshwater cyanobacteria, such as Synechococcus elongatus PCC 7942, thrive under red light because of the presence of phycocyanin (PC) and its chromophore, phycocyanobilin (PCB), in the PBS. Cyanobacteria in shorter-wavelength light environments such as green light, employ phycoerythrin paired with phycoerythrobilin (PEB) along with PC in the PBS. Synthetic biology studies have shown that PEB production can be achieved by expression of the heterologous PEB synthases 15,16-dihydrobiliverdin:ferredoxin oxidoreductase (PebA) and PEB:ferredoxin oxidoreductase (PebB), leading to PEB accumulation and cellular browning. This approach is genetically unstable, and the properties of the resulting PEB-bound PBS complexes remain uncharacterized. In this study, we engineered a novel strain of Synechococcus 7942 PEB1 with finely tuned control of PEB biosynthesis. PEB1 exhibited a reversible change in the color of the culture from green to brown and pink based on PebA and PebB induction levels. High induction led to complete PCB-to-PEB substitution, causing the disassembly of the PBS rod complex. In contrast, low induction levels of PebA and PebB resulted in the formation of a stable chimeric PBS complex with partial PCB-to-PEB substitution. This acclimation enabled efficient light harvesting in the green spectrum and energy transfer to the photosynthetic reaction center. These findings, which improve our understanding of PBS and highlight the structural importance of the bilin composition, provide a foundation for future studies on PBS adaptation in bioengineering, synthetic biology, and renewable energy.
Collapse
Affiliation(s)
- Mizuho Sato
- Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Takeshi Kawaguchi
- Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Kaisei Maeda
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Mai Watanabe
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Masahiko Ikeuchi
- Graduate School of Arts and Sciences, University of Tokyo, Tokyo 153-0041, Japan
| | - Rei Narikawa
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| |
Collapse
|
3
|
Hubáček M, Wey LT, Kourist R, Malihan-Yap L, Nikkanen L, Allahverdiyeva Y. Strong heterologous electron sink outcompetes alternative electron transport pathways in photosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39008444 DOI: 10.1111/tpj.16935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/27/2024] [Accepted: 07/03/2024] [Indexed: 07/17/2024]
Abstract
Improvement of photosynthesis requires a thorough understanding of electron partitioning under both natural and strong electron sink conditions. We applied a wide array of state-of-the-art biophysical and biochemical techniques to thoroughly investigate the fate of photosynthetic electrons in the engineered cyanobacterium Synechocystis sp. PCC 6803, a blueprint for photosynthetic biotechnology, expressing the heterologous gene for ene-reductase, YqjM. This recombinant enzyme catalyses the reduction of an exogenously added substrate into the desired product by utilising photosynthetically produced NAD(P)H, enabling whole-cell biotransformation. Through coupling the biotransformation reaction with biophysical measurements, we demonstrated that the strong artificial electron sink, outcompetes the natural electron valves, the flavodiiron protein-driven Mehler-like reaction and cyclic electron transport. These results show that ferredoxin-NAD(P)H-oxidoreductase is the preferred route for delivering photosynthetic electrons from reduced ferredoxin and the cellular NADPH/NADP+ ratio as a key factor in orchestrating photosynthetic electron flux. These insights are crucial for understanding molecular mechanisms of photosynthetic electron transport and harnessing photosynthesis for sustainable bioproduction by engineering the cellular source/sink balance. Furthermore, we conclude that identifying the bioenergetic bottleneck of a heterologous electron sink is a crucial prerequisite for targeted engineering of photosynthetic biotransformation platforms.
Collapse
Affiliation(s)
- Michal Hubáček
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Turku, 20014, Finland
| | - Laura T Wey
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Turku, 20014, Finland
| | - Robert Kourist
- Institute of Molecular Biotechnology, NAWI Graz, BioTechMed, Graz University of Technology, Graz, 8010, Austria
| | - Lenny Malihan-Yap
- Institute of Molecular Biotechnology, NAWI Graz, BioTechMed, Graz University of Technology, Graz, 8010, Austria
| | - Lauri Nikkanen
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Turku, 20014, Finland
| | - Yagut Allahverdiyeva
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Turku, 20014, Finland
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Schluchter WM, Babin CH, Liu X, Bieller A, Shen G, Alvey RM, Bryant DA. Loss of Biliverdin Reductase Increases Oxidative Stress in the Cyanobacterium Synechococcus sp. PCC 7002. Microorganisms 2023; 11:2593. [PMID: 37894251 PMCID: PMC10608806 DOI: 10.3390/microorganisms11102593] [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: 09/24/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Oxygenic photosynthesis requires metal-rich cofactors and electron-transfer components that can produce reactive oxygen species (ROS) that are highly toxic to cyanobacterial cells. Biliverdin reductase (BvdR) reduces biliverdin IXα to bilirubin, which is a potent scavenger of radicals and ROS. The enzyme is widespread in mammals but is also found in many cyanobacteria. We show that a previously described bvdR mutant of Synechocystis sp. PCC 6803 contained a secondary deletion mutation in the cpcB gene. The bvdR gene from Synechococcus sp. PCC 7002 was expressed in Escherichia coli, and recombinant BvdR was purified and shown to reduce biliverdin to bilirubin. The bvdR gene was successfully inactivated in Synechococcus sp. PCC 7002, a strain that is naturally much more tolerant of high light and ROS than Synechocystis sp. PCC 6803. The bvdR mutant strain, BR2, had lower total phycobiliprotein and chlorophyll levels than wild-type cells. As determined using whole-cell fluorescence at 77 K, the photosystem I levels were also lower than those in wild-type cells. The BR2 mutant had significantly higher ROS levels compared to wild-type cells after exposure to high light for 30 min. Together, these results suggest that bilirubin plays an important role as a scavenger for ROS in Synechococcus sp. PCC 7002. The oxidation of bilirubin by ROS could convert bilirubin to biliverdin IXα, and thus BvdR might be important for regenerating bilirubin. These results further suggest that BvdR is a key component of a scavenging cycle by which cyanobacteria protect themselves from the toxic ROS byproducts generated during oxygenic photosynthesis.
Collapse
Affiliation(s)
- Wendy M. Schluchter
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA; (C.H.B.); (X.L.); (A.B.)
| | - Courtney H. Babin
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA; (C.H.B.); (X.L.); (A.B.)
| | - Xindi Liu
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA; (C.H.B.); (X.L.); (A.B.)
| | - Amori Bieller
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA; (C.H.B.); (X.L.); (A.B.)
| | - Gaozhong Shen
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA (R.M.A.); (D.A.B.)
| | - Richard M. Alvey
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA (R.M.A.); (D.A.B.)
- Biology Department, Bloomington, Illinois Wesleyan University, Bloomington, IL 61702, USA
| | - Donald A. Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA (R.M.A.); (D.A.B.)
| |
Collapse
|
6
|
Frascogna F, Ledermann B, Hartmann J, Pérez Patallo E, Zeqiri F, Hofmann E, Frankenberg-Dinkel N. On the evolution of the plant phytochrome chromophore biosynthesis. PLANT PHYSIOLOGY 2023; 193:246-258. [PMID: 37311159 DOI: 10.1093/plphys/kiad327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/15/2023]
Abstract
Phytochromes are biliprotein photoreceptors present in plants, algae, certain bacteria, and fungi. Land plant phytochromes use phytochromobilin (PΦB) as the bilin chromophore. Phytochromes of streptophyte algae, the clade within which land plants evolved, employ phycocyanobilin (PCB), leading to a more blue-shifted absorption spectrum. Both chromophores are synthesized by ferredoxin-dependent bilin reductases (FDBRs) starting from biliverdin IXα (BV). In cyanobacteria and chlorophyta, BV is reduced to PCB by the FDBR phycocyanobilin:ferredoxin oxidoreductase (PcyA), whereas, in land plants, BV is reduced to PФB by phytochromobilin synthase (HY2). However, phylogenetic studies suggested the absence of any ortholog of PcyA in streptophyte algae and the presence of only PФB biosynthesis-related genes (HY2). The HY2 of the streptophyte alga Klebsormidium nitens (formerly Klebsormidium flaccidum) has already indirectly been indicated to participate in PCB biosynthesis. Here, we overexpressed and purified a His6-tagged variant of K. nitens HY2 (KflaHY2) in Escherichia coli. Employing anaerobic bilin reductase activity assays and coupled phytochrome assembly assays, we confirmed the product and identified intermediates of the reaction. Site-directed mutagenesis revealed 2 aspartate residues critical for catalysis. While it was not possible to convert KflaHY2 into a PΦB-producing enzyme by simply exchanging the catalytic pair, the biochemical investigation of 2 additional members of the HY2 lineage enabled us to define 2 distinct clades, the PCB-HY2 and the PΦB-HY2 clade. Overall, our study gives insight into the evolution of the HY2 lineage of FDBRs.
Collapse
Affiliation(s)
- Federica Frascogna
- Department of Microbiology, University of Kaiserslautern-Landau, Kaiserslautern 67663, Germany
| | - Benjamin Ledermann
- Department of Microbiology, University of Kaiserslautern-Landau, Kaiserslautern 67663, Germany
| | - Jana Hartmann
- Department of Microbiology, University of Kaiserslautern-Landau, Kaiserslautern 67663, Germany
| | - Eugenio Pérez Patallo
- Department of Microbiology, University of Kaiserslautern-Landau, Kaiserslautern 67663, Germany
| | - Fjoralba Zeqiri
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum 44780, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum 44780, Germany
| | | |
Collapse
|
7
|
Wang Y, Ferrinho S, Connaris H, Goss RJM. The Impact of Viral Infection on the Chemistries of the Earth's Most Abundant Photosynthesizes: Metabolically Talented Aquatic Cyanobacteria. Biomolecules 2023; 13:1218. [PMID: 37627283 PMCID: PMC10452541 DOI: 10.3390/biom13081218] [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: 05/31/2023] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Cyanobacteria are the most abundant photosynthesizers on earth, and as such, they play a central role in marine metabolite generation, ocean nutrient cycling, and the control of planetary oxygen generation. Cyanobacteriophage infection exerts control on all of these critical processes of the planet, with the phage-ported homologs of genes linked to photosynthesis, catabolism, and secondary metabolism (marine metabolite generation). Here, we analyze the 153 fully sequenced cyanophages from the National Center for Biotechnology Information (NCBI) database and the 45 auxiliary metabolic genes (AMGs) that they deliver into their hosts. Most of these AMGs are homologs of those found within cyanobacteria and play a key role in cyanobacterial metabolism-encoding proteins involved in photosynthesis, central carbon metabolism, phosphate metabolism, methylation, and cellular regulation. A greater understanding of cyanobacteriophage infection will pave the way to a better understanding of carbon fixation and nutrient cycling, as well as provide new tools for synthetic biology and alternative approaches for the use of cyanobacteria in biotechnology and sustainable manufacturing.
Collapse
Affiliation(s)
- Yunpeng Wang
- School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9AJ, UK; (S.F.); (H.C.)
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9SX, UK
| | - Scarlet Ferrinho
- School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9AJ, UK; (S.F.); (H.C.)
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9SX, UK
| | - Helen Connaris
- School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9AJ, UK; (S.F.); (H.C.)
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9SX, UK
| | - Rebecca J. M. Goss
- School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9AJ, UK; (S.F.); (H.C.)
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9SX, UK
| |
Collapse
|
8
|
Guo R, Wang S, Niu NN, Xu YL, Zhu JX, Scheer H, Noy D, Zhao KH. Dichromic Allophycocyanin Trimer Covering a Broad Spectral Range (550-660 nm). Chemistry 2023; 29:e202203367. [PMID: 36382427 DOI: 10.1002/chem.202203367] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/17/2022]
Abstract
Phycobilisomes, the light-harvesting complexes of cyanobacteria and red algae, are a resource for photosynthetic, photonic and fluorescence labeling elements. They cover an exceptionally broad spectral range, but the complex superstructure and assembly have been an obstacle. By replacing in Synechocystis sp. PCC 6803 the biliverdin reductases, we studied the role of chromophores in the assembly of the phycobilisome core. Introduction of the green-absorbing phycoerythrobilin instead of the red-absorbing phycocyanobilin inhibited aggregation. A novel, trimeric allophycocyanin (Dic-APC) was obtained. In the small (110 kDa) unit, the two chromophores, phycoerythrobilin and phytochromobilin, cover a wide spectral range (550 to 660 nm). Due to efficient energy transfer, it provides an efficient artificial light-harvesting element. Dic-APC was generated in vitro by using the contained core-linker, LC , for template-assisted purification and assembly. Labeling the linker provides a method for targeting Dic-APC.
Collapse
Affiliation(s)
- Rui Guo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Si Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Nan-Nan Niu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Ya-Li Xu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Jun-Xun Zhu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Hugo Scheer
- Department Biologie I, Universität München, Menzinger Str. 67, D-80638, München, Germany
| | - Dror Noy
- MIGAL-Galilee Research Institute S. Industrial Zone, Kiryat Shmona, Israel.,Faculty of Sciences and Technology, Tel-Hai Academic College, Upper Galilee, Israel
| | - Kai-Hong Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| |
Collapse
|
9
|
Joutsuka T, Nanasawa R, Igarashi K, Horie K, Sugishima M, Hagiwara Y, Wada K, Fukuyama K, Yano N, Mori S, Ostermann A, Kusaka K, Unno M. Neutron crystallography and quantum chemical analysis of bilin reductase PcyA mutants reveal substrate and catalytic residue protonation states. J Biol Chem 2022; 299:102763. [PMID: 36463961 PMCID: PMC9800206 DOI: 10.1016/j.jbc.2022.102763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/16/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022] Open
Abstract
PcyA, a ferredoxin-dependent bilin pigment reductase, catalyzes the site-specific reduction of the two vinyl groups of biliverdin (BV), producing phycocyanobilin. Previous neutron crystallography detected both the neutral BV and its protonated form (BVH+) in the wildtype (WT) PcyA-BV complex, and a nearby catalytic residue Asp105 was found to have two conformations (protonated and deprotonated). Semiempirical calculations have suggested that the protonation states of BV are reflected in the absorption spectrum of the WT PcyA-BV complex. In the previously determined absorption spectra of the PcyA D105N and I86D mutants, complexed with BV, a peak at 730 nm, observed in the WT, disappeared and increased, respectively. Here, we performed neutron crystallography and quantum chemical analysis of the D105N-BV and I86D-BV complexes to determine the protonation states of BV and the surrounding residues and study the correlation between the absorption spectra and protonation states around BV. Neutron structures elucidated that BV in the D105N mutant is in a neutral state, whereas that in the I86D mutant is dominantly in a protonated state. Glu76 and His88 showed different hydrogen bonding with surrounding residues compared with WT PcyA, further explaining why D105N and I86D have much lower activities for phycocyanobilin synthesis than the WT PcyA. Our quantum mechanics/molecular mechanics calculations of the absorption spectra showed that the spectral change in D105N arises from Glu76 deprotonation, consistent with the neutron structure. Collectively, our findings reveal more mechanistic details of bilin pigment biosynthesis.
Collapse
Affiliation(s)
- Tatsuya Joutsuka
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki, Japan,Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka-Tokai, Ibaraki, Japan,For correspondence: Tatsuya Joutsuka; Masaki Unno
| | - Ryota Nanasawa
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki, Japan
| | - Keisuke Igarashi
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki, Japan
| | - Kazuki Horie
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki, Japan
| | - Masakazu Sugishima
- Department of Medical Biochemistry, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Yoshinori Hagiwara
- Department of Biochemistry and Applied Chemistry, National Institute of Technology, Kurume College, Kurume, Fukuoka, Japan
| | - Kei Wada
- Department of Medical Sciences, University of Miyazaki, Miyazaki, Miyazaki, Japan
| | - Keiichi Fukuyama
- Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Naomine Yano
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka-Tokai, Ibaraki, Japan
| | - Seiji Mori
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki, Japan,Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka-Tokai, Ibaraki, Japan
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum (MLZ), Technical University Munich, Garching, Germany
| | - Katsuhiro Kusaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka-Tokai, Ibaraki, Japan
| | - Masaki Unno
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki, Japan,Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka-Tokai, Ibaraki, Japan,For correspondence: Tatsuya Joutsuka; Masaki Unno
| |
Collapse
|
10
|
Khani-Juyabad F, Mohammadi P, Zarrabi M. Insights from cyanobacterial genomic and transcriptomic analyses into adaptation strategies in terrestrial environments. Genomics 2022; 114:110438. [PMID: 35902068 DOI: 10.1016/j.ygeno.2022.110438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 07/11/2022] [Accepted: 07/24/2022] [Indexed: 11/26/2022]
Abstract
Phylogenomic analysis of Nostoc sp. MG11, a terrestrial cyanobacterium, and some terrestrial and freshwater Nostoc strains showed that the terrestrial strains grouped together in a distinctive clade, which reveals the effect of habitat on shaping Nostoc genomes. Terrestrial strains showed larger genomes and had higher predicted CDS contents than freshwater strains. Comparative genomic analysis demonstrated that genome expansion in the terrestrial Nostoc is supported by an increase in copy number of the core genes and acquisition of shared genes. Transcriptomic profiling analysis under desiccation stress revealed that Nostoc sp. MG11 protected its cell by induction of catalase, proteases, sucrose synthase, trehalose biosynthesis and maltodextrin utilization genes and maintained its normal metabolism during this condition by up-regulation of genes related to phycobilisomes and light reactions of photosynthesis, CO2 fixation and protein metabolism. These results provide insights into the strategies related to survival and adaptation of Nostoc strains to terrestrial environments.
Collapse
Affiliation(s)
- Fatemeh Khani-Juyabad
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Parisa Mohammadi
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran; Research Center for Applied Microbiology and Microbial Biotechnology, Alzahra University, Tehran, Iran.
| | - Mahbubeh Zarrabi
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| |
Collapse
|
11
|
Rockwell NC, Moreno MV, Martin SS, Lagarias JC. Protein-chromophore interactions controlling photoisomerization in red/green cyanobacteriochromes. Photochem Photobiol Sci 2022; 21:471-491. [PMID: 35411484 PMCID: PMC9609751 DOI: 10.1007/s43630-022-00213-3] [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] [Received: 01/31/2022] [Accepted: 03/21/2022] [Indexed: 10/18/2022]
Abstract
Photoreceptors in the phytochrome superfamily use 15,16-photoisomerization of a linear tetrapyrrole (bilin) chromophore to photoconvert between two states with distinct spectral and biochemical properties. Canonical phytochromes include master regulators of plant growth and development in which light signals trigger interconversion between a red-absorbing 15Z dark-adapted state and a metastable, far-red-absorbing 15E photoproduct state. Distantly related cyanobacteriochromes (CBCRs) carry out a diverse range of photoregulatory functions in cyanobacteria and exhibit considerable spectral diversity. One widespread CBCR subfamily typically exhibits a red-absorbing 15Z dark-adapted state similar to that of phytochrome that gives rise to a distinct green-absorbing 15E photoproduct. This red/green CBCR subfamily also includes red-inactive examples that fail to undergo photoconversion, providing an opportunity to study protein-chromophore interactions that either promote photoisomerization or block it. In this work, we identified a conserved lineage of red-inactive CBCRs. This enabled us to identify three substitutions sufficient to block photoisomerization in photoactive red/green CBCRs. The resulting red-inactive variants faithfully replicated the fluorescence and circular dichroism properties of naturally occurring examples. Converse substitutions restored photoconversion in naturally red-inactive CBCRs. This work thus identifies protein-chromophore interactions that control the fate of the excited-state population in red/green cyanobacteriochromes.
Collapse
Affiliation(s)
- Nathan C Rockwell
- Department of Molecular and Cellular Biology, University of California at Davis, Davis, CA, 95616, USA.
| | - Marcus V Moreno
- Department of Molecular and Cellular Biology, University of California at Davis, Davis, CA, 95616, USA
| | - Shelley S Martin
- Department of Molecular and Cellular Biology, University of California at Davis, Davis, CA, 95616, USA
| | - J Clark Lagarias
- Department of Molecular and Cellular Biology, University of California at Davis, Davis, CA, 95616, USA.
| |
Collapse
|
12
|
Singh N, Bhatla SC. Heme oxygenase-nitric oxide crosstalk-mediated iron homeostasis in plants under oxidative stress. Free Radic Biol Med 2022; 182:192-205. [PMID: 35247570 DOI: 10.1016/j.freeradbiomed.2022.02.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 12/22/2022]
Abstract
Plant growth under abiotic stress conditions significantly enhances intracellular generation of reactive oxygen species (ROS). Oxidative status of plant cells is directly affected by the modulation of iron homeostasis. Among mammals and plants, heme oxygenase-1 (HO-1) is a well-known antioxidant enzyme. It catalyzes oxygenation of heme, thereby producing Fe2+, CO and biliverdin as byproducts. The antioxidant potential of HO-1 is primarily due to its catalytic reaction byproducts. Biliverdin and bilirubin possess conjugated π-electrons which escalate the ability of these biomolecules to scavenge free radicals. CO also enhances the ROS scavenging ability of plants cells by upregulating catalase and peroxidase activity. Enhanced expression of HO-1 in plants under oxidative stress accompanies sequestration of iron in specialized iron storage proteins localized in plastids and mitochondria, namely ferritin for Fe3+ storage and frataxin for storage of Fe-S clusters, respectively. Nitric oxide (NO) crosstalks with HO-1 at multiple levels, more so in plants under oxidative stress, in order to maintain intracellular iron status. Formation of dinitrosyl-iron complexes (DNICs) significantly prevents Fenton reaction during oxidative stress. DNICs also release NO upon dissociation in target cells over long distance in plants. They also function as antioxidants against superoxide anions and lipidic free radicals. A number of NO-modulated transcription factors also facilitate iron homeostasis in plant cells. Plants facing oxidative stress exhibit modulation of lateral root formation by HO-1 through NO and auxin-dependent pathways. The present review provides an in-depth analysis of the structure-function relationship of HO-1 in plants and mammals, correlating them with their adaptive mechanisms of survival under stress.
Collapse
Affiliation(s)
- Neha Singh
- Department of Botany, Gargi College, University of Delhi, India.
| | - Satish C Bhatla
- Laboratory of Plant Physiology and Biochemistry, Department of Botany, University of Delhi, Delhi, 110007, India.
| |
Collapse
|
13
|
Yang Y, Wang L, Che Z, Wang R, Cui R, Xu H, Chu S, Jiao Y, Zhang H, Yu D, Zhang D. Novel target sites for soybean yield enhancement by photosynthesis. JOURNAL OF PLANT PHYSIOLOGY 2022; 268:153580. [PMID: 34871989 DOI: 10.1016/j.jplph.2021.153580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 06/13/2023]
Abstract
Photosynthesis plays an important role in plant growth and development. Increasing photosynthetic rate is a main objective of improving crop productivity. Chlorophyll fluorescence is an effective method for quickly evaluating photosynthesis. In this study, four representative chlorophyll fluorescence parameters, that is, maximum quantum efficiency of photosystem II, quantum efficiency of PSII, photochemical quenching, and non-photochemical quenching, of 219 diverse soybean accessions were measured across three environments. The underlying genetic architecture was analyzed by genome-wide association study. Forty-eight SNPs were detected to associate with the four traits and explained 10.43-20.41% of the phenotypic variation. Nine candidate genes in the stable QTLs were predicted. Great differences in the expression levels of the candidate genes existed between the high photosynthetic efficiency accessions and low photosynthetic efficiency accessions. In all, we uncover 17 QTLs associated with photosynthesis-related traits and nine genes that may participate in the regulation of photosynthesis, which can provide references for revealing the genetic mechanism of photosynthesis. These QTLs and candidate genes will provide new targets for crop yield improvement through increasing photosynthesis.
Collapse
Affiliation(s)
- Yuming Yang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450006, China
| | - Li Wang
- National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210014, China
| | - Zhijun Che
- Ningxia University, Yinchuan, 750021, China
| | - Ruiyang Wang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450006, China
| | - Ruifang Cui
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450006, China
| | - Huanqing Xu
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450006, China
| | - Shanshan Chu
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450006, China
| | - Yongqing Jiao
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450006, China
| | - Hengyou Zhang
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, Chinese Academy of Sciences, Harbin, 150081, China
| | - Deyue Yu
- National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210014, China.
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450006, China.
| |
Collapse
|
14
|
Tang K, Beyer HM, Zurbriggen MD, Gärtner W. The Red Edge: Bilin-Binding Photoreceptors as Optogenetic Tools and Fluorescence Reporters. Chem Rev 2021; 121:14906-14956. [PMID: 34669383 PMCID: PMC8707292 DOI: 10.1021/acs.chemrev.1c00194] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Indexed: 12/15/2022]
Abstract
This review adds the bilin-binding phytochromes to the Chemical Reviews thematic issue "Optogenetics and Photopharmacology". The work is structured into two parts. We first outline the photochemistry of the covalently bound tetrapyrrole chromophore and summarize relevant spectroscopic, kinetic, biochemical, and physiological properties of the different families of phytochromes. Based on this knowledge, we then describe the engineering of phytochromes to further improve these chromoproteins as photoswitches and review their employment in an ever-growing number of different optogenetic applications. Most applications rely on the light-controlled complex formation between the plant photoreceptor PhyB and phytochrome-interacting factors (PIFs) or C-terminal light-regulated domains with enzymatic functions present in many bacterial and algal phytochromes. Phytochrome-based optogenetic tools are currently implemented in bacteria, yeast, plants, and animals to achieve light control of a wide range of biological activities. These cover the regulation of gene expression, protein transport into cell organelles, and the recruitment of phytochrome- or PIF-tagged proteins to membranes and other cellular compartments. This compilation illustrates the intrinsic advantages of phytochromes compared to other photoreceptor classes, e.g., their bidirectional dual-wavelength control enabling instant ON and OFF regulation. In particular, the long wavelength range of absorption and fluorescence within the "transparent window" makes phytochromes attractive for complex applications requiring deep tissue penetration or dual-wavelength control in combination with blue and UV light-sensing photoreceptors. In addition to the wide variability of applications employing natural and engineered phytochromes, we also discuss recent progress in the development of bilin-based fluorescent proteins.
Collapse
Affiliation(s)
- Kun Tang
- Institute
of Synthetic Biology, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Hannes M. Beyer
- Institute
of Synthetic Biology, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Matias D. Zurbriggen
- Institute
of Synthetic Biology and CEPLAS, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse
1, D-40225 Düsseldorf, Germany
| | - Wolfgang Gärtner
- Retired: Max Planck Institute
for Chemical Energy Conversion. At present: Institute for Analytical Chemistry, University
Leipzig, Linnéstrasse
3, 04103 Leipzig, Germany
| |
Collapse
|
15
|
Sakai K, Kondo Y, Fujioka H, Kamiya M, Aoki K, Goto Y. Near-infrared imaging in fission yeast using a genetically encoded phycocyanobilin biosynthesis system. J Cell Sci 2021; 134:273759. [PMID: 34806750 DOI: 10.1242/jcs.259315] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/09/2021] [Indexed: 11/20/2022] Open
Abstract
Near-infrared fluorescent protein (iRFP) is a bright and stable fluorescent protein with near-infrared excitation and emission maxima. Unlike the other conventional fluorescent proteins, iRFP requires biliverdin (BV) as a chromophore. Here, we report that phycocyanobilin (PCB) functions as a brighter chromophore for iRFP than BV, and that biosynthesis of PCB allows live-cell imaging with iRFP in the fission yeast Schizosaccharomyces pombe. We initially found that fission yeast cells did not produce BV and therefore did not show any iRFP fluorescence. The brightness of iRFP-PCB was higher than that of iRFP-BV both in vitro and in fission yeast. We introduced SynPCB2.1, a PCB biosynthesis system, into fission yeast, resulting in the brightest iRFP fluorescence. To make iRFP readily available in fission yeast, we developed an endogenous gene tagging system with iRFP and all-in-one integration plasmids carrying the iRFP-fused marker proteins together with SynPCB2.1. These tools not only enable the easy use of multiplexed live-cell imaging in fission yeast with a broader color palette, but also open the door to new opportunities for near-infrared fluorescence imaging in a wider range of living organisms. This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Keiichiro Sakai
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Yohei Kondo
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Hiroyoshi Fujioka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mako Kamiya
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kazuhiro Aoki
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Yuhei Goto
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| |
Collapse
|
16
|
Tomazic N, Overkamp KE, Wegner H, Gu B, Mahler F, Aras M, Keller S, Pierik AJ, Hofmann E, Frankenberg-Dinkel N. Exchange of a single amino acid residue in the cryptophyte phycobiliprotein lyase GtCPES expands its substrate specificity. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2021; 1862:148493. [PMID: 34537203 DOI: 10.1016/j.bbabio.2021.148493] [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: 06/02/2021] [Revised: 08/26/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
Cryptophytes are among the few eukaryotes employing phycobiliproteins (PBP) for light harvesting during oxygenic photosynthesis. In contrast to cyanobacterial PBP that are organized in membrane-associated phycobilisomes, those from cryptophytes are soluble within the chloroplast thylakoid lumen. Their light-harvesting capacity is due to covalent linkage of several open-chain tetrapyrrole chromophores (phycobilins). Guillardia theta utilizes the PBP phycoerythrin 545 with 15,16-dihydrobiliverdin (DHBV) in addition to phycoerythrobilin (PEB) as chromophores. The assembly of PBPs in cryptophytes involves the action of PBP-lyases as shown for cyanobacterial PBP. PBP-lyases facilitate the attachment of the chromophore in the right configuration and stereochemistry. Here we present the functional characterization of the eukaryotic S-type PBP lyase GtCPES. We show GtCPES-mediated transfer and covalent attachment of PEB to the conserved Cys82 of the acceptor PBP β-subunit (PmCpeB) of Prochlorococcus marinus MED4. On the basis of the previously solved crystal structure, the GtCPES binding pocket was investigated using site-directed mutagenesis. Thereby, amino acid residues involved in phycobilin binding and transfer were identified. Interestingly, exchange of a single amino acid residue Met67 to Ala extended the substrate specificity to phycocyanobilin (PCB), most likely by enlarging the substrate-binding pocket. Variant GtCPES_M67A binds both PEB and PCB forming a stable, colored complex in vitro and produced in Escherichia coli. GtCPES_M67A is able to mediate PCB transfer to Cys82 of PmCpeB. Based on these findings, we postulate that this single amino acid residue has a crucial role for bilin binding specificity of S-type phycoerythrin lyases but additional factors regulate handover to the target protein.
Collapse
Affiliation(s)
- Natascha Tomazic
- Microbiology, Faculty for Biology, Technische Universität Kaiserslautern (TUK), Germany
| | - Kristina E Overkamp
- Microbiology, Faculty for Biology, Technische Universität Kaiserslautern (TUK), Germany
| | - Helen Wegner
- Microbiology, Faculty for Biology, Technische Universität Kaiserslautern (TUK), Germany
| | - Bin Gu
- Microbiology, Faculty for Biology, Technische Universität Kaiserslautern (TUK), Germany
| | - Florian Mahler
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Germany
| | - Marco Aras
- Microbiology, Faculty for Biology, Technische Universität Kaiserslautern (TUK), Germany
| | - Sandro Keller
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Germany; Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Austria; Field of Excellence BioHealth, University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Antonio J Pierik
- Biochemistry, Faculty for Chemistry, Technische Universität Kaiserslautern (TUK), Germany
| | - Eckhard Hofmann
- Proteincrystallography, Faculty for Biology and Biotechnology, Ruhr-Universität Bochum, Germany
| | | |
Collapse
|
17
|
Montoya EJO, Dorion S, Atehortua-Garcés L, Rivoal J. Phycobilin heterologous production from the Rhodophyta Porphyridium cruentum. J Biotechnol 2021; 341:30-42. [PMID: 34500003 DOI: 10.1016/j.jbiotec.2021.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/30/2021] [Accepted: 09/02/2021] [Indexed: 11/19/2022]
Abstract
Phycobiliproteins are colored, active molecules with potential use in different industries. They are the union of proteins and bilins (Chromophores). The primary source of phycobiliproteins is algae; however, the traditional algae culture has production restrictions. The production in bacterial models can be a more efficient alternative to produce these molecules. However, the lack of knowledge in some steps of the phycobiliprotein metabolic pathway limits this alternative. Porphyridium cruentum is a single cell red alga with a high phycobiliprotein content. Its protein sequences were the basis for phycobilin production in this study. In this study, we cloned and characterized enzymes presumably involved in the chromophore production of P. cruentum. Using sequences obtained from its transcriptome, we characterized two cDNA sequences predicted to code respectively for a ferredoxin-dependent bilin reductase and a bilin lyase-isomerase. We expressed these enzymes in Escherichia coli to obtain in vivo evidence of their enzymatic activity on the substrate biliverdin IXα. Lastly, we analyzed them using thin-layer chromatography, spectrophotometry, and fluorescence spectroscopy. These experiments provided evidence of bilin modification. The expressed bilin lyase-isomerase did not show significant activity over the biliverdin molecule. On the contrary, the expressed ferredoxin-dependent bilin reductase showed activity over the biliverdin.
Collapse
Affiliation(s)
- Erika Juliana Obando Montoya
- Laboratorio de Biotecnología, Sede de Investigación Universitaria - SIU, Universidad de Antioquia, Carrera 53 # 61 - 30 - SIU. Torre 1 Laboratorio de 210, Medellín 050010, Colombia.
| | - Sonia Dorion
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke est, Montréal, QC H1X 2B2, Canada
| | - Lucía Atehortua-Garcés
- Laboratorio de Biotecnología, Sede de Investigación Universitaria - SIU, Universidad de Antioquia, Carrera 53 # 61 - 30 - SIU. Torre 1 Laboratorio de 210, Medellín 050010, Colombia
| | - Jean Rivoal
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke est, Montréal, QC H1X 2B2, Canada
| |
Collapse
|
18
|
Hu L, Liu P, Jin Z, Sun J, Weng Y, Chen P, Du S, Wei A, Li Y. A mutation in CsHY2 encoding a phytochromobilin (PΦB) synthase leads to an elongated hypocotyl 1(elh1) phenotype in cucumber (Cucumis sativus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2639-2652. [PMID: 34091695 DOI: 10.1007/s00122-021-03849-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/29/2021] [Indexed: 06/12/2023]
Abstract
The elongated hypocotyl1 (elh1) mutant in cucumber is due to a mutation in CsHY2, which is a homolog of the Arabidopsis HY2 encoding the phytochromobilin (PΦB) synthase for phytochrome biosynthesis Hypocotyl length is a critical determinant in establishing high quality seedlings for successful cucumber production, but knowledge on the molecular regulation of hypocotyl growth in cucumber is very limited. Here, we reported identification and characterization of a cucumber elongated hypocotyl 1 (elh1) mutant. We found that the longer hypocotyl in elh1 was due to longitudinal growth of hypocotyl cells. With fine mapping, the elh1 locus was delimited to a 20.9-kb region containing three annotated genes; only one polymorphism was identified in this region between two parental lines, which was a non-synonymous SNP (G28153633A) in the third exon of CsHY2 (CsGy1G030000) that encodes a phytochromobilin (PΦB) synthase. Uniqueness of the mutant allele at CsHY2 was verified in natural cucumber populations. Ectopic expression of CsHY2 in Arabidopsis hy2-1 long-hypocotyl mutant led to reduced hypocotyl length. The PΦB protein was targeted to the chloroplast. The expression levels of CsHY2 and five phytochrome genes CsPHYA1, CsPHYA2, CsPHYB, CsPHYC and CsPHYE were all significantly down-regulated while several cell elongation related genes were up-regulated in elh1 mutant compared to wild-type cucumber, which are correlated with dynamic hypocotyl elongation in the mutant. RNA-seq analysis in the WT and mutant revealed differentially expressed genes involved in porphyrin and chlorophyll metabolisms, cell elongation and plant hormone signal transduction pathways. This is the first report to characterize and clone the CsHY2 gene in cucumber. This work reveals the important of CsHY2 in regulating hypocotyl length and extends our understanding of the roles of CsHY2 in cucumber.
Collapse
Affiliation(s)
- Liangliang Hu
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Peng Liu
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhuoshuai Jin
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jing Sun
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yiqun Weng
- Horticulture Department, USDA-ARS Vegetable Crops Research Unit, University of Wisconsin, Madison, WI, 53706, USA
| | - Peng Chen
- College of Life Science, Northwest A & F University, Yangling, 712100, Shaanxi,, China
| | - Shengli Du
- Tianjin Vegetable Research Center, Tianjin, 300192, China
- National Key Laboratory of Vegetable Germplasm Innovation, Tianjin, 300192, China
| | - Aimin Wei
- Tianjin Vegetable Research Center, Tianjin, 300192, China.
- National Key Laboratory of Vegetable Germplasm Innovation, Tianjin, 300192, China.
| | - Yuhong Li
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| |
Collapse
|
19
|
Norena-Caro DA, Zuniga C, Pete AJ, Saemundsson SA, Donaldson MR, Adams AJ, Dooley KM, Zengler K, Benton MG. Analysis of the cyanobacterial amino acid metabolism with a precise genome-scale metabolic reconstruction of Anabaena sp. UTEX 2576. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
|
20
|
Makita Y, Suzuki S, Fushimi K, Shimada S, Suehisa A, Hirata M, Kuriyama T, Kurihara Y, Hamasaki H, Okubo-Kurihara E, Yoshitake K, Watanabe T, Sakuta M, Gojobori T, Sakami T, Narikawa R, Yamaguchi H, Kawachi M, Matsui M. Identification of a dual orange/far-red and blue light photoreceptor from an oceanic green picoplankton. Nat Commun 2021; 12:3593. [PMID: 34135337 PMCID: PMC8209157 DOI: 10.1038/s41467-021-23741-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 05/11/2021] [Indexed: 11/09/2022] Open
Abstract
Photoreceptors are conserved in green algae to land plants and regulate various developmental stages. In the ocean, blue light penetrates deeper than red light, and blue-light sensing is key to adapting to marine environments. Here, a search for blue-light photoreceptors in the marine metagenome uncover a chimeric gene composed of a phytochrome and a cryptochrome (Dualchrome1, DUC1) in a prasinophyte, Pycnococcus provasolii. DUC1 detects light within the orange/far-red and blue spectra, and acts as a dual photoreceptor. Analyses of its genome reveal the possible mechanisms of light adaptation. Genes for the light-harvesting complex (LHC) are duplicated and transcriptionally regulated under monochromatic orange/blue light, suggesting P. provasolii has acquired environmental adaptability to a wide range of light spectra and intensities.
Collapse
Affiliation(s)
- Yuko Makita
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Shigekatsu Suzuki
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Keiji Fushimi
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Saitama, Japan
| | - Setsuko Shimada
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Aya Suehisa
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Manami Hirata
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Tomoko Kuriyama
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Yukio Kurihara
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Hidefumi Hamasaki
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Yokohama City University, Kihara Institute for Biological Research, Yokohama, Japan
| | - Emiko Okubo-Kurihara
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Kazutoshi Yoshitake
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Tsuyoshi Watanabe
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Kushiro, Hokkaido, Japan
| | - Masaaki Sakuta
- Department of Biological Sciences, Ochanomizu University, Tokyo, Japan
| | - Takashi Gojobori
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Tomoko Sakami
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Minami-ise, Mie, Japan
| | - Rei Narikawa
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Saitama, Japan
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Haruyo Yamaguchi
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Masanobu Kawachi
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Minami Matsui
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan.
- Yokohama City University, Kihara Institute for Biological Research, Yokohama, Japan.
| |
Collapse
|
21
|
Koehl P, Delarue M, Orland H. Simultaneous Identification of Multiple Binding Sites in Proteins: A Statistical Mechanics Approach. J Phys Chem B 2021; 125:5052-5067. [PMID: 33973782 DOI: 10.1021/acs.jpcb.1c02658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present an extension of the Poisson-Boltzmann model in which the solute of interest is immersed in an assembly of self-orienting Langevin water dipoles, anions, cations, and hydrophobic molecules, all of variable densities. Interactions between charges are controlled by electrostatics, while hydrophobic interactions are modeled with a Yukawa potential. We impose steric constraints by assuming that the system is represented on a cubic lattice. We also assume incompressibility; i.e., all sites of the lattice are occupied. This model, which we refer to as the Hydrophobic Dipolar Poisson-Boltzmann Langevin (HDPBL) model, leads to a system of two equations whose solutions give the water dipole, salt, and hydrophobic molecule densities, all of them in the presence of the others in a self-consistent way. We use those to study the organization of the ions, cosolvent, and solvent molecules around proteins. In particular, peaks of densities are expected to reveal, simultaneously, the presence of compatible binding sites of different kinds on a protein. We have tested and validated the ability of HDPBL to detect pockets in proteins that bind to hydrophobic ligands, polar ligands, and charged small probes as well as to characterize the binding sites of lipids for membrane proteins.
Collapse
Affiliation(s)
- Patrice Koehl
- Department of Computer Science and Genome Center, University of California, Davis, California 95616, United States
| | - Marc Delarue
- Architecture et Dynamique des Macromolécules Biologiques, Département de Biologie Structurale et Chimie, UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France
| | - Henri Orland
- Institut de Physique Théorique, Université Paris-Saclay, CEA, 91191 Gif/Yvette Cedex, France
| |
Collapse
|
22
|
Lamparter T, Xue P, Elkurdi A, Kaeser G, Sauthof L, Scheerer P, Krauß N. Phytochromes in Agrobacterium fabrum. FRONTIERS IN PLANT SCIENCE 2021; 12:642801. [PMID: 33995441 PMCID: PMC8117939 DOI: 10.3389/fpls.2021.642801] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/18/2021] [Indexed: 05/31/2023]
Abstract
The focus of this review is on the phytochromes Agp1 and Agp2 of Agrobacterium fabrum. These are involved in regulation of conjugation, gene transfer into plants, and other effects. Since crystal structures of both phytochromes are known, the phytochrome system of A. fabrum provides a tool for following the entire signal transduction cascade starting from light induced conformational changes to protein interaction and the triggering of DNA transfer processes.
Collapse
Affiliation(s)
- Tilman Lamparter
- Botanical Institute, Karlsruhe Institute of Technology KIT, Karlsruhe, Germany
| | - Peng Xue
- Botanical Institute, Karlsruhe Institute of Technology KIT, Karlsruhe, Germany
| | - Afaf Elkurdi
- Botanical Institute, Karlsruhe Institute of Technology KIT, Karlsruhe, Germany
| | - Gero Kaeser
- Botanical Institute, Karlsruhe Institute of Technology KIT, Karlsruhe, Germany
| | - Luisa Sauthof
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Berlin, Germany
| | - Patrick Scheerer
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Berlin, Germany
| | - Norbert Krauß
- Botanical Institute, Karlsruhe Institute of Technology KIT, Karlsruhe, Germany
| |
Collapse
|
23
|
Current knowledge and recent advances in understanding metabolism of the model cyanobacterium Synechocystis sp. PCC 6803. Biosci Rep 2021; 40:222317. [PMID: 32149336 PMCID: PMC7133116 DOI: 10.1042/bsr20193325] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 02/06/2023] Open
Abstract
Cyanobacteria are key organisms in the global ecosystem, useful models for studying metabolic and physiological processes conserved in photosynthetic organisms, and potential renewable platforms for production of chemicals. Characterizing cyanobacterial metabolism and physiology is key to understanding their role in the environment and unlocking their potential for biotechnology applications. Many aspects of cyanobacterial biology differ from heterotrophic bacteria. For example, most cyanobacteria incorporate a series of internal thylakoid membranes where both oxygenic photosynthesis and respiration occur, while CO2 fixation takes place in specialized compartments termed carboxysomes. In this review, we provide a comprehensive summary of our knowledge on cyanobacterial physiology and the pathways in Synechocystis sp. PCC 6803 (Synechocystis) involved in biosynthesis of sugar-based metabolites, amino acids, nucleotides, lipids, cofactors, vitamins, isoprenoids, pigments and cell wall components, in addition to the proteins involved in metabolite transport. While some pathways are conserved between model cyanobacteria, such as Synechocystis, and model heterotrophic bacteria like Escherichia coli, many enzymes and/or pathways involved in the biosynthesis of key metabolites in cyanobacteria have not been completely characterized. These include pathways required for biosynthesis of chorismate and membrane lipids, nucleotides, several amino acids, vitamins and cofactors, and isoprenoids such as plastoquinone, carotenoids, and tocopherols. Moreover, our understanding of photorespiration, lipopolysaccharide assembly and transport, and degradation of lipids, sucrose, most vitamins and amino acids, and haem, is incomplete. We discuss tools that may aid our understanding of cyanobacterial metabolism, notably CyanoSource, a barcoded library of targeted Synechocystis mutants, which will significantly accelerate characterization of individual proteins.
Collapse
|
24
|
Seghiri R, Legrand J, Hsissou R, Essamri A. Comparative study of the impact of conventional and unconventional drying processes on phycobiliproteins from Arthrospira platensis. ALGAL RES 2021. [DOI: 10.1016/j.algal.2020.102165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
25
|
Baumschlager A, Khammash M. Synthetic Biological Approaches for Optogenetics and Tools for Transcriptional Light-Control in Bacteria. Adv Biol (Weinh) 2021; 5:e2000256. [PMID: 34028214 DOI: 10.1002/adbi.202000256] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 01/11/2021] [Indexed: 12/22/2022]
Abstract
Light has become established as a tool not only to visualize and investigate but also to steer biological systems. This review starts by discussing the unique features that make light such an effective control input in biology. It then gives an overview of how light-control came to progress, starting with photoactivatable compounds and leading up to current genetic implementations using optogenetic approaches. The review then zooms in on optogenetics, focusing on photosensitive proteins, which form the basis for optogenetic engineering using synthetic biological approaches. As the regulation of transcription provides a highly versatile means for steering diverse biological functions, the focus of this review then shifts to transcriptional light regulators, which are presented in the biotechnologically highly relevant model organism Escherichia coli.
Collapse
Affiliation(s)
- Armin Baumschlager
- Department of Biosystems Science and Engineering (D-BSSE), ETH-Zürich, Mattenstrasse 26, Basel, 4058, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering (D-BSSE), ETH-Zürich, Mattenstrasse 26, Basel, 4058, Switzerland
| |
Collapse
|
26
|
Carrigee LA, Frick JP, Karty JA, Garczarek L, Partensky F, Schluchter WM. MpeV is a lyase isomerase that ligates a doubly linked phycourobilin on the β-subunit of phycoerythrin I and II in marine Synechococcus. J Biol Chem 2021; 296:100031. [PMID: 33154169 PMCID: PMC7948978 DOI: 10.1074/jbc.ra120.015289] [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: 07/18/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 11/06/2022] Open
Abstract
Synechococcus cyanobacteria are widespread in the marine environment, as the extensive pigment diversity within their light-harvesting phycobilisomes enables them to utilize various wavelengths of light for photosynthesis. The phycobilisomes of Synechococcus sp. RS9916 contain two forms of the protein phycoerythrin (PEI and PEII), each binding two chromophores, green-light absorbing phycoerythrobilin and blue-light absorbing phycourobilin. These chromophores are ligated to specific cysteines via bilin lyases, and some of these enzymes, called lyase isomerases, attach phycoerythrobilin and simultaneously isomerize it to phycourobilin. MpeV is a putative lyase isomerase whose role in PEI and PEII biosynthesis is not clear. We examined MpeV in RS9916 using recombinant protein expression, absorbance spectroscopy, and tandem mass spectrometry. Our results show that MpeV is the lyase isomerase that covalently attaches a doubly linked phycourobilin to two cysteine residues (C50, C61) on the β-subunit of both PEI (CpeB) and PEII (MpeB). MpeV activity requires that CpeB or MpeB is first chromophorylated by the lyase CpeS (which adds phycoerythrobilin to C82). Its activity is further enhanced by CpeZ (a homolog of a chaperone-like protein first characterized in Fremyella diplosiphon). MpeV showed no detectable activity on the α-subunits of PEI or PEII. The mechanism by which MpeV links the A and D rings of phycourobilin to C50 and C61 of CpeB was also explored using site-directed mutants, revealing that linkage at the A ring to C50 is a critical step in chromophore attachment, isomerization, and stability. These data provide novel insights into β-PE biosynthesis and advance our understanding of the mechanisms guiding lyase isomerases.
Collapse
Affiliation(s)
- Lyndsay A Carrigee
- Department of Biological Sciences, University of New Orleans, New Orleans, Louisiana, USA
| | - Jacob P Frick
- Department of Biological Sciences, University of New Orleans, New Orleans, Louisiana, USA
| | - Jonathan A Karty
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Laurence Garczarek
- Ecology of Marine Plankton (ECOMAP) Team, Station Biologique, Sorbonne Université & CNRS, UMR 7144, Roscoff, France
| | - Frédéric Partensky
- Ecology of Marine Plankton (ECOMAP) Team, Station Biologique, Sorbonne Université & CNRS, UMR 7144, Roscoff, France
| | - Wendy M Schluchter
- Department of Biological Sciences, University of New Orleans, New Orleans, Louisiana, USA.
| |
Collapse
|
27
|
Phytochromes and Cyanobacteriochromes: Photoreceptor Molecules Incorporating a Linear Tetrapyrrole Chromophore. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1293:167-187. [PMID: 33398813 DOI: 10.1007/978-981-15-8763-4_10] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this chapter, we summarize the molecular mechanisms of the linear tetrapyrrole-binding photoreceptors, phytochromes, and cyanobacteriochromes. We especially focus on the color-tuning mechanisms and conformational changes during the photoconversion process. Furthermore, we introduce current status of development of the optogenetic tools based on these molecules. Huge repertoire of these photoreceptors with diverse spectral properties would contribute to development of multiplex optogenetic regulation. Among them, the photoreceptors incorporating the biliverdin IXα chromophore is advantageous for in vivo optogenetics because this is intrinsic in the mammalian cells, and absorbs far-red light penetrating into deep mammalian tissues.
Collapse
|
28
|
Uda Y, Miura H, Goto Y, Yamamoto K, Mii Y, Kondo Y, Takada S, Aoki K. Improvement of Phycocyanobilin Synthesis for Genetically Encoded Phytochrome-Based Optogenetics. ACS Chem Biol 2020; 15:2896-2906. [PMID: 33164485 DOI: 10.1021/acschembio.0c00477] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Optogenetics is a powerful technique using photoresponsive proteins, and the light-inducible dimerization (LID) system, an optogenetic tool, allows to manipulate intracellular signaling pathways. One of the red/far-red responsive LID systems, phytochrome B (PhyB)-phytochrome interacting factor (PIF), has a unique property of controlling both association and dissociation by light on the second time scale, but PhyB requires a linear tetrapyrrole chromophore such as phycocyanobilin (PCB), and such chromophores are present only in higher plants and cyanobacteria. Here, we report that we further improved our previously developed PCB synthesis system (SynPCB) and successfully established a stable cell line containing a genetically encoded PhyB-PIF LID system. First, four genes responsible for PCB synthesis, namely, PcyA, HO1, Fd, and Fnr, were replaced with their counterparts derived from thermophilic cyanobacteria. Second, Fnr was truncated, followed by fusion with Fd to generate a chimeric protein, tFnr-Fd. Third, these genes were concatenated with P2A peptide cDNAs for polycistronic expression, resulting in an approximately 4-fold increase in PCB synthesis compared with the previous version. Finally, we incorporated the PhyB, PIF, and SynPCB system into drug inducible lentiviral and transposon vectors, which enabled us to induce PCB synthesis and the PhyB-PIF LID system by doxycycline treatment. These tools provide a new opportunity to advance our understanding of the causal relationship between intracellular signaling and cellular functions.
Collapse
Affiliation(s)
- Youichi Uda
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Haruko Miura
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Yuhei Goto
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Kei Yamamoto
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Yusuke Mii
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Yohei Kondo
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Shinji Takada
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Kazuhiro Aoki
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| |
Collapse
|
29
|
Sanfilippo JE, Garczarek L, Partensky F, Kehoe DM. Chromatic Acclimation in Cyanobacteria: A Diverse and Widespread Process for Optimizing Photosynthesis. Annu Rev Microbiol 2020; 73:407-433. [PMID: 31500538 DOI: 10.1146/annurev-micro-020518-115738] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chromatic acclimation (CA) encompasses a diverse set of molecular processes that involve the ability of cyanobacterial cells to sense ambient light colors and use this information to optimize photosynthetic light harvesting. The six known types of CA, which we propose naming CA1 through CA6, use a range of molecular mechanisms that likely evolved independently in distantly related lineages of the Cyanobacteria phylum. Together, these processes sense and respond to the majority of the photosynthetically relevant solar spectrum, suggesting that CA provides fitness advantages across a broad range of light color niches. The recent discoveries of several new CA types suggest that additional CA systems involving additional light colors and molecular mechanisms will be revealed in coming years. Here we provide a comprehensive overview of the currently known types of CA and summarize the molecular details that underpin CA regulation.
Collapse
Affiliation(s)
- Joseph E Sanfilippo
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08540, USA;
| | - Laurence Garczarek
- Adaptation et Diversité en Milieu Marin (AD2M), Station Biologique de Roscoff, CNRS UMR 7144, Sorbonne Université, 29680 Roscoff, France; ,
| | - Frédéric Partensky
- Adaptation et Diversité en Milieu Marin (AD2M), Station Biologique de Roscoff, CNRS UMR 7144, Sorbonne Université, 29680 Roscoff, France; ,
| | - David M Kehoe
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA;
| |
Collapse
|
30
|
Heidenreich KM, Richardson TL. Photopigment, Absorption, and Growth Responses of Marine Cryptophytes to Varying Spectral Irradiance. JOURNAL OF PHYCOLOGY 2020; 56:507-520. [PMID: 31876286 DOI: 10.1111/jpy.12962] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 12/07/2019] [Indexed: 06/10/2023]
Abstract
The underwater light field of lakes, estuaries, and oceans may vary greatly in spectral composition. Phytoplankton in these environments must contain pigments that absorb the available colors of light. If spectral quality changes, acclimation to the new spectral environment would confer an ecological advantage in terms of photosynthesis and growth. Here, we explored the capacity of eight marine cryptophytes to adjust pigmentation in response to changes in spectral irradiance and related effects on light absorption, photosynthetically useable radiation (PUR), and growth rate. The pigment composition of all species changed in some way in response to shifts in spectral irradiance, but not all pigment changes could be considered advantageous in the context of chromatic acclimation. For most species, absorption by chl-a and chl-c2 resulted in highest absorption in the blue region, highest PUR values for blue-light grown cells, and highest growth rates in blue light. The exception was Chroomonas mesostigmatica (CCMP 1168), which contains a high percentage of Cryptophyte-Phycocyanin (Cr-PC) 645, absorbs strongly in the orange-to-red region of the spectrum, and grew fastest under red light. The position and magnitude of the maximum and secondary absorption peak of Cr-PC 569, the phycobiliprotein pigment of Hemiselmis cryptochromatica, varied with spectral irradiance. The underlying cause remains unknown, but may represent a mechanism by which cryptophytes optimize photon capture.
Collapse
Affiliation(s)
- Kristin M Heidenreich
- Department of Biological Sciences and School of the Earth, Ocean & Environment, University of South Carolina, Columbia, South Carolina, 29208, USA
| | - Tammi L Richardson
- Department of Biological Sciences and School of the Earth, Ocean & Environment, University of South Carolina, Columbia, South Carolina, 29208, USA
| |
Collapse
|
31
|
Rockwell NC, Lagarias JC. Phytochrome evolution in 3D: deletion, duplication, and diversification. THE NEW PHYTOLOGIST 2020; 225:2283-2300. [PMID: 31595505 PMCID: PMC7028483 DOI: 10.1111/nph.16240] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 09/17/2019] [Indexed: 05/09/2023]
Abstract
Canonical plant phytochromes are master regulators of photomorphogenesis and the shade avoidance response. They are also part of a widespread superfamily of photoreceptors with diverse spectral and biochemical properties. Plant phytochromes belong to a clade including other phytochromes from glaucophyte, prasinophyte, and streptophyte algae (all members of the Archaeplastida) and those from cryptophyte algae. This is consistent with recent analyses supporting the existence of an AC (Archaeplastida + Cryptista) clade. AC phytochromes have been proposed to arise from ancestral cyanobacterial genes via endosymbiotic gene transfer (EGT), but most recent studies instead support multiple horizontal gene transfer (HGT) events to generate extant eukaryotic phytochromes. In principle, this scenario would be compared to the emerging understanding of early events in eukaryotic evolution to generate a coherent picture. Unfortunately, there is currently a major discrepancy between the evolution of phytochromes and the evolution of eukaryotes; phytochrome evolution is thus not a solved problem. We therefore examine phytochrome evolution in a broader context. Within this context, we can identify three important themes in phytochrome evolution: deletion, duplication, and diversification. These themes drive phytochrome evolution as organisms evolve in response to environmental challenges.
Collapse
|
32
|
Miyake K, Fushimi K, Kashimoto T, Maeda K, Ni-Ni-Win, Kimura H, Sugishima M, Ikeuchi M, Narikawa R. Functional diversification of two bilin reductases for light perception and harvesting in unique cyanobacterium Acaryochloris marina MBIC 11017. FEBS J 2020; 287:4016-4031. [PMID: 31995844 DOI: 10.1111/febs.15230] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/17/2019] [Accepted: 01/27/2020] [Indexed: 02/06/2023]
Abstract
Bilin pigments play important roles for both light perception and harvesting in cyanobacteria by binding to cyanobacteriochromes (CBCRs) and phycobilisomes (PBS), respectively. Among various cyanobacteria, Acaryochloris marina MBIC 11017 (A. marina 11017) exceptionally uses chlorophyll d as the main photosynthetic pigment absorbing longer wavelength light than the canonical pigment, chlorophyll a, indicating existence of a system to sense longer wavelength light than others. On the other hand, A. marina 11017 has the PBS apparatus to harvest short-wavelength orange light, similar to most cyanobacteria. Thus, A. marina 11017 might sense longer wavelength light and harvest shorter wavelength light by using bilin pigments. Phycocyanobilin (PCB) is the main bilin pigment of both systems. Phycocyanobilin:ferredoxin oxidoreductase (PcyA) catalyzes PCB synthesis from biliverdin via the intermediate 181 ,182 -dihydrobiliverdin (181 ,182 -DHBV), resulting in the stepwise shortening of the absorbing wavelengths. In this study, we found that A. marina 11017 exceptionally encodes two PcyA homologs, AmPcyAc and AmPcyAp. AmPcyAc is encoded on the main chromosome with most photoreceptor genes, whereas AmPcyAp is encoded on a plasmid with PBS-related genes. High accumulation of 181 ,182 -DHBV for extended periods was observed during the reaction catalyzed by AmPcyAc, whereas 181 ,182 -DHBV was transiently accumulated for a short period during the reaction catalyzed by AmPcyAp. CBCRs could sense longer wavelength far-red light through 181 ,182 -DHBV incorporation, whereas PBS could only harvest orange light through PCB incorporation, suggesting functional diversification of PcyA as AmPcyAc and AmPcyAp to provide 181 ,182 -DHBV and PCB to the light perception and harvesting systems, respectively.
Collapse
Affiliation(s)
- Keita Miyake
- Graduate School of Integrated Science and Technology, Shizuoka University, Japan
| | - Keiji Fushimi
- Graduate School of Integrated Science and Technology, Shizuoka University, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Tomonori Kashimoto
- Graduate School of Integrated Science and Technology, Shizuoka University, Japan
| | - Kaisei Maeda
- Graduate School of Arts and Sciences, University of Tokyo, Japan
| | - Ni-Ni-Win
- Graduate School of Arts and Sciences, University of Tokyo, Japan
| | - Hiroyuki Kimura
- Graduate School of Integrated Science and Technology, Shizuoka University, Japan.,Research Institute of Green Science and Technology, Shizuoka University, Japan
| | - Masakazu Sugishima
- Department of Medical Biochemistry, Kurume University School of Medicine, Japan
| | - Masahiko Ikeuchi
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kawaguchi, Japan.,Graduate School of Arts and Sciences, University of Tokyo, Japan
| | - Rei Narikawa
- Graduate School of Integrated Science and Technology, Shizuoka University, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kawaguchi, Japan.,Research Institute of Green Science and Technology, Shizuoka University, Japan
| |
Collapse
|
33
|
Sugishima M, Wada K, Fukuyama K, Yamamoto K. Crystal structure of phytochromobilin synthase in complex with biliverdin IXα, a key enzyme in the biosynthesis of phytochrome. J Biol Chem 2020; 295:771-782. [PMID: 31822504 DOI: 10.1074/jbc.ra119.011431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/08/2019] [Indexed: 11/06/2022] Open
Abstract
Phytochromobilin (PΦB) is a red/far-red light sensory pigment in plant phytochrome. PΦB synthase is a ferredoxin-dependent bilin reductase (FDBR) that catalyzes the site-specific reduction of bilins, which are sensory and photosynthesis pigments, and produces PΦB from biliverdin, a heme-derived linear tetrapyrrole pigment. Here, we determined the crystal structure of tomato PΦB synthase in complex with biliverdin at 1.95 Å resolution. The overall structure of tomato PΦB synthase was similar to those of other FDBRs, except for the addition of a long C-terminal loop and short helices. The structure further revealed that the C-terminal loop is part of the biliverdin-binding pocket and that two basic residues in the C-terminal loop form salt bridges with the propionate groups of biliverdin. This suggested that the C-terminal loop is involved in the interaction with ferredoxin and biliverdin. The configuration of biliverdin bound to tomato PΦB synthase differed from that of biliverdin bound to other FDBRs, and its orientation in PΦB synthase was inverted relative to its orientation in the other FDBRs. Structural and enzymatic analyses disclosed that two aspartic acid residues, Asp-123 and Asp-263, form hydrogen bonds with water molecules and are essential for the site-specific A-ring reduction of biliverdin. On the basis of these observations and enzymatic assays with a V121A PΦB synthase variant, we propose the following mechanistic product release mechanism: PΦB synthase-catalyzed stereospecific reduction produces 2(R)-PΦB, which when bound to PΦB synthase collides with the side chain of Val-121, releasing 2(R)-PΦB from the synthase.
Collapse
Affiliation(s)
- Masakazu Sugishima
- Department of Medical Biochemistry, Kurume University School of Medicine, Kurume, Fukuoka 830-0011, Japan
| | - Kei Wada
- Department of Medical Sciences, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Keiichi Fukuyama
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
| | - Ken Yamamoto
- Department of Medical Biochemistry, Kurume University School of Medicine, Kurume, Fukuoka 830-0011, Japan
| |
Collapse
|
34
|
Sugishima M, Wada K, Fukuyama K, Yamamoto K. Crystal structure of phytochromobilin synthase in complex with biliverdin IXα, a key enzyme in the biosynthesis of phytochrome. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49934-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
|
35
|
Sommerkamp JA, Frankenberg-Dinkel N, Hofmann E. Crystal structure of the first eukaryotic bilin reductase GtPEBB reveals a flipped binding mode of dihydrobiliverdin. J Biol Chem 2019; 294:13889-13901. [PMID: 31366727 PMCID: PMC6755814 DOI: 10.1074/jbc.ra119.009306] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/26/2019] [Indexed: 01/11/2023] Open
Abstract
Phycobilins are light-harvesting pigments of cyanobacteria, red algae, and cryptophytes. The biosynthesis of phycoerythrobilin (PEB) is catalyzed by the subsequent action of two ferredoxin-dependent bilin reductases (FDBRs). Although 15,16-dihydrobiliverdin (DHBV):ferredoxin oxidoreductase (PebA) catalyzes the two-electron reduction of biliverdin IXα to 15,16-DHBV, PEB:ferredoxin oxidoreductase (PebB) reduces this intermediate further to PEB. Interestingly, marine viruses encode the FDBR PebS combining both activities within one enzyme. Although PebA and PebS share a canonical fold with similar substrate-binding pockets, the structural determinants for the stereo- and regiospecific modification of their tetrapyrrole substrates are incompletely understood, also because of the lack of a PebB structure. Here, we solved the X-ray crystal structures of both substrate-free and -bound PEBB from the cryptophyte Guillardia theta at 1.90 and 1.65 Å, respectively. The structures of PEBB exhibit the typical α/β/α-sandwich fold. Interestingly, the open-chain tetrapyrrole substrate DHBV is bound in an unexpected flipped orientation within the canonical FDBR active site. Biochemical analyses of the WT enzyme and active site variants identified two central aspartate residues Asp-99 and Asp-219 as essential for catalytic activity. In addition, the conserved Arg-215 plays a critical role in substrate specificity, binding orientation, and active site integrity. Because these critical residues are conserved within certain FDBRs displaying A-ring reduction activity, we propose that they present a conserved mechanism for this reaction. The flipped substrate-binding mode indicates that two-electron reducing FDBRs utilize the same primary site within the binding pocket and that substrate orientation is the determinant for A- or D-ring regiospecificity.
Collapse
Affiliation(s)
- Johannes A Sommerkamp
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Nicole Frankenberg-Dinkel
- Department of Biology, Microbiology, Technical University Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| |
Collapse
|
36
|
Aras M, Hartmann V, Hartmann J, Nowaczyk MM, Frankenberg-Dinkel N. Proximity channeling during cyanobacterial phycoerythrobilin synthesis. FEBS J 2019; 287:284-294. [PMID: 31319014 DOI: 10.1111/febs.15003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/17/2019] [Accepted: 07/16/2019] [Indexed: 11/30/2022]
Abstract
Substrate channeling is a widespread mechanism in metabolic pathways to avoid decomposition of unstable intermediates, competing reactions, and to accelerate catalytic turnover. During the biosynthesis of light-harvesting phycobilins in cyanobacteria, two members of the ferredoxin-dependent bilin reductases are involved in the reduction of the open-chain tetrapyrrole biliverdin IXα to the pink pigment phycoerythrobilin. The first reaction is catalyzed by 15,16-dihydrobiliverdin:ferredoxin oxidoreductase and produces the unstable intermediate 15,16-dihydrobiliverdin (DHBV). This intermediate is subsequently converted by phycoerythrobilin:ferredoxin oxidoreductase to the final product phycoerythrobilin. Although substrate channeling has been postulated already a decade ago, detailed experimental evidence was missing. Using a new on-column assay employing immobilized enzyme in combination with UV-Vis and fluorescence spectroscopy revealed that both enzymes transiently interact and that transfer of the intermediate is facilitated by a significantly higher binding affinity of DHBV toward phycoerythrobilin:ferredoxin oxidoreductase. Concluding from the presented data, the intermediate DHBV is transferred via proximity channeling.
Collapse
Affiliation(s)
- Marco Aras
- Fachbereich Biologie, Abteilung für Mikrobiologie, Technische Universität Kaiserslautern, Germany
| | - Volker Hartmann
- Cyanobakterielle Membranprotein Komplexe, Fakultät für Biologie und Biotechnologie, Ruhr-Universität Bochum, Germany
| | - Jana Hartmann
- Fachbereich Biologie, Abteilung für Mikrobiologie, Technische Universität Kaiserslautern, Germany
| | - Marc M Nowaczyk
- Cyanobakterielle Membranprotein Komplexe, Fakultät für Biologie und Biotechnologie, Ruhr-Universität Bochum, Germany
| | | |
Collapse
|
37
|
Castillo-Hair SM, Baerman EA, Fujita M, Igoshin OA, Tabor JJ. Optogenetic control of Bacillus subtilis gene expression. Nat Commun 2019; 10:3099. [PMID: 31308373 PMCID: PMC6629627 DOI: 10.1038/s41467-019-10906-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 06/07/2019] [Indexed: 01/27/2023] Open
Abstract
The Gram-positive bacterium Bacillus subtilis exhibits complex spatial and temporal gene expression signals. Although optogenetic tools are ideal for studying such processes, none has been engineered for this organism. Here, we port a cyanobacterial light sensor pathway comprising the green/red photoreversible two-component system CcaSR, two metabolic enzymes for production of the chromophore phycocyanobilin (PCB), and an output promoter to control transcription of a gene of interest into B. subtilis. Following an initial non-functional design, we optimize expression of pathway genes, enhance PCB production via a translational fusion of the biosynthetic enzymes, engineer a strong chimeric output promoter, and increase dynamic range with a miniaturized photosensor kinase. Our final design exhibits over 70-fold activation and rapid response dynamics, making it well-suited to studying a wide range of gene regulatory processes. In addition, the synthetic biology methods we develop to port this pathway should make B. subtilis easier to engineer in the future.
Collapse
Affiliation(s)
| | - Elliot A Baerman
- Department of Biosciences, Rice University, 6100 Main St., Houston, TX, 77005, USA
| | - Masaya Fujita
- Department of Biology and Biochemistry, University of Houston, 4800 Calhoun Rd., Houston, TX, 77004, USA
| | - Oleg A Igoshin
- Department of Bioengineering, Rice University, 6100 Main St., Houston, TX, 77005, USA
- Department of Biosciences, Rice University, 6100 Main St., Houston, TX, 77005, USA
- Center for Theoretical Biophysics, Rice University, 6100 Main St., Houston, TX, 77005, USA
| | - Jeffrey J Tabor
- Department of Bioengineering, Rice University, 6100 Main St., Houston, TX, 77005, USA.
- Department of Biosciences, Rice University, 6100 Main St., Houston, TX, 77005, USA.
| |
Collapse
|
38
|
Sun D, Zang X, Guo Y, Xiao D, Cao X, Liu Z, Zhang F, Jin Y, Shi J, Wang Z, Li R, Yangzong Z. Cloning of pcB and pcA Gene from Gracilariopsis lemaneiformis and Expression of a Fluorescent Phycocyanin in Heterologous Host. Genes (Basel) 2019; 10:genes10050322. [PMID: 31035529 PMCID: PMC6562448 DOI: 10.3390/genes10050322] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/16/2019] [Accepted: 04/18/2019] [Indexed: 11/16/2022] Open
Abstract
In order to study the assembly mechanism of phycocyanin in red algae, the apo-phycocyanin genes (pcB and pcA) were cloned from Gracilariopsis lemaneiformis. The full length of phycocyanin β-subunit (pcB) contained 519 nucleotides encoding a protein of 172 amino acids, and the full length of phycocyanin α-subunit(pcA) contained 489 nucleotides encoding a protein of 162 amino acids. Expression vector pACYCDuet-pcB-pcA was constructed and transformed into E. coli BL21 with pET-ho-pcyA (containing ho and pcyA gene to synthesize phycocyanobilin). The recombinant strain showed fluorescence activity, indicating the expression of optically active phycocyanin in E. coli. To further investigate the possible binding sites between phycocyanobilin and apo-phycocyanin, Cys-82 and Cys-153 of the β subunit and the Cys-84 of the α subunit were respectively mutated, and four mutants were obtained. All mutant strains had lower fluorescence intensity than the non-mutant strains, which indicated that these mutation sites could be the active binding sites between apo-phycocyanin and phycocyanobilin (PCB). This research provides a supplement for the comprehensive understanding of the assembly mechanism of optically active phycocyanin in red algae.
Collapse
Affiliation(s)
- Deguang Sun
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao 266003, Shandong, China.
| | - Xiaonan Zang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao 266003, Shandong, China.
| | - Yalin Guo
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao 266003, Shandong, China.
| | - Dongfang Xiao
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao 266003, Shandong, China.
| | - Xuexue Cao
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao 266003, Shandong, China.
| | - Zhu Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao 266003, Shandong, China.
| | - Feng Zhang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao 266003, Shandong, China.
| | - Yuming Jin
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao 266003, Shandong, China.
| | - Jiawei Shi
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao 266003, Shandong, China.
| | - Zhendong Wang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao 266003, Shandong, China.
| | - Rui Li
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao 266003, Shandong, China.
| | - Zhaxi Yangzong
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao 266003, Shandong, China.
| |
Collapse
|
39
|
Sugishima M, Wada K, Unno M, Fukuyama K. Bilin-metabolizing enzymes: site-specific reductions catalyzed by two different type of enzymes. Curr Opin Struct Biol 2019; 59:73-80. [PMID: 30954759 DOI: 10.1016/j.sbi.2019.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 01/09/2019] [Accepted: 03/04/2019] [Indexed: 02/05/2023]
Abstract
In mammals, the green heme metabolite biliverdin is converted to a yellow anti-oxidant by NAD(P)H-dependent biliverdin reductase (BVR), whereas in O2-dependent photosynthetic organisms it is converted to photosynthetic or light-sensing pigments by ferredoxin-dependent bilin reductases (FDBRs). In NADP+-bound and biliverdin-bound BVR-A, two biliverdins are stacked at the binding cleft; one is positioned to accept hydride from NADPH, and the other appears to donate a proton to the first biliverdin through a neighboring arginine residue. During the FDBR-catalyzed reaction, electrons and protons are supplied to bilins from ferredoxin and from FDBRs and waters bound within FDBRs, respectively. Thus, the protonation sites of bilin and catalytic residues are important for the analysis of site-specific reduction. The neutron structure of FDBR sheds light on this issue.
Collapse
Affiliation(s)
- Masakazu Sugishima
- Department of Medical Biochemistry, Kurume University School of Medicine, Fukuoka 830-0011, Japan.
| | - Kei Wada
- Department of Medical Sciences, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Masaki Unno
- Graduate School of Science and Engineering, Ibaraki University, Ibaraki 316-8511, Japan
| | - Keiichi Fukuyama
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
| |
Collapse
|
40
|
Cai Y, Si W, Huang W, Chen P, Shao J, Dong X. Organic Dye Based Nanoparticles for Cancer Phototheranostics. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1704247. [PMID: 29611290 DOI: 10.1002/smll.201704247] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/03/2018] [Indexed: 06/08/2023]
Abstract
Phototheranostics, which simultaneously combines photodynamic and/or photothermal therapy with deep-tissue diagnostic imaging, is a promising strategy for the diagnosis and treatment of cancers. Organic dyes with the merits of strong near-infrared absorbance, high photo-to-radical and/or photothermal conversion efficiency, great biocompatibility, ready chemical structure fine-tuning capability, and easy metabolism, have been demonstrated as attractive candidates for clinical phototheranostics. These organic dyes can be further designed and fabricated into nanoparticles (NPs) using various strategies. Compared to free molecules, these NPs can be equipped with multiple synergistic functions and show longer lifetime in blood circulation and passive tumor-targeting property via the enhanced permeability and retention effect. In this article, the recent progress of organic dye-based NPs for cancer phototheranostic applications is summarized, which extends the anticancer arsenal and holds promise for clinical uses in the near future.
Collapse
Affiliation(s)
- Yu Cai
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital Medical School of Nanjing University, No 30 Zhongyang Road, Nanjing, 210008, China
| | - Weili Si
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), Nanjing, 211800, China
| | - Wei Huang
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), Nanjing, 211800, China
- Shaanxi Institute of Flexible Electronics (SIFE), Northwestern Polytechnical University (NPU), 127 West Youyi Road, Xi'an, 710072, China
| | - Peng Chen
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459, Singapore
| | - Jinjun Shao
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), Nanjing, 211800, China
| | - Xiaochen Dong
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), Nanjing, 211800, China
| |
Collapse
|
41
|
Iijima E, Gleeson MP, Unno M, Mori S. QM/MM Investigation for Protonation States in a Bilin Reductase PcyA-Biliverdin IXα Complex. Chemphyschem 2018; 19:1809-1813. [PMID: 29732737 DOI: 10.1002/cphc.201800031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Indexed: 02/28/2024]
Abstract
Herein we report quantum mechanical/molecular mechanical (QM/MM) studies to investigate the most probable protonation states of active site amino acids and bound substrate based on a recently reported neutron diffraction structure of phycocyanobilin:ferredoxin oxidoreductase (PcyA) by Unno et al. This structure was considered to be bound in its initial state of biliverdin IXα (BV), which has the C-pyrrole ring in the deprotonated state. The protonation state of BV suggested by neutron and spectroscopic studies is a stable, two-electron reduced complex with a bound hydronium ion. Several ambiguities in the neutron structure were observed which prompted a further theoretical analysis of the structure. This structural investigation provides new understanding of the PcyA and BV protonation states not previously reported in the literature. Our calculations suggest that the hydronium ion (H3 O+ ) is energetically unfavorable, preferentially protonating the neighboring His88 residue and that the C-ring of BV is not protonated.
Collapse
Affiliation(s)
- Eri Iijima
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito 310-8512 and Hitachi 316-8511, Ibaraki, Japan
| | - M Paul Gleeson
- Department of Biomedical Engineering, Faculty of Engineering, King Mongkut's institute of Technology Ladkrabang, Thailand
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10903, Thailand
| | - Masaki Unno
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito 310-8512 and Hitachi 316-8511, Ibaraki, Japan
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka, 319-1106, Japan
| | - Seiji Mori
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito 310-8512 and Hitachi 316-8511, Ibaraki, Japan
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka, 319-1106, Japan
| |
Collapse
|
42
|
Stiefelmaier J, Ledermann B, Sorg M, Banek A, Geib D, Ulber R, Frankenberg-Dinkel N. Pink bacteria-Production of the pink chromophore phycoerythrobilin with Escherichia coli. J Biotechnol 2018; 274:47-53. [PMID: 29549003 DOI: 10.1016/j.jbiotec.2018.03.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/01/2018] [Accepted: 03/11/2018] [Indexed: 11/29/2022]
Abstract
Phycoerythrobilin (PEB) is an open-chain tetrapyrrole derived from heme and plays an important role as light-harvesting pigment in the phycobiliproteins of cyanobacteria and red algae. Furthermore, PEB can also function as an antioxidant with potential use as a natural acid stable food colorant. PEB is not commercially available and large, pure quantities can only be obtained by laborious methanolysis of red algae followed by liquid chromatography. Here we describe an improved method for high yield production and purification of PEB in Escherichia coli via heterologous expression where the two required enzymes heme oxygenase and PEB synthase subsequently convert the substrate heme provided by the host cell. Experiments in shaking flasks resulted in the highest product yield of 680.23 ± 42.75 μg PEB per g cell dry weight, by induction with 0.1 mM IPTG. Scale-up to batch-operated fermentation in a 2 L bioreactor reached product concentrations up to 5.02 mg PEB L-1 by adjustment of aeration, induction time, media composition and supplementation of precursors. A further approach included separation of PEB from developed foam above the culture. This enabled continuous product collection during cultivation and simplified product purification. Produced PEB was validated via UV-vis spectroscopy, high pressure liquid chromatography and mass spectrometry.
Collapse
Affiliation(s)
- Judith Stiefelmaier
- Lehrgebiet Bioverfahrenstechnik, Technische Universität Kaiserslautern, Gottlieb-Daimler-Straße 49, 67663 Kaiserslautern, Germany.
| | - Benjamin Ledermann
- Abteilung für Mikrobiologie, Technische Universität Kaiserslautern, Erwin-Schroedinger-Straße 56, 67663 Kaiserslautern, Germany.
| | - Michael Sorg
- Lehrgebiet Bioverfahrenstechnik, Technische Universität Kaiserslautern, Gottlieb-Daimler-Straße 49, 67663 Kaiserslautern, Germany.
| | - Angela Banek
- Lehrgebiet Bioverfahrenstechnik, Technische Universität Kaiserslautern, Gottlieb-Daimler-Straße 49, 67663 Kaiserslautern, Germany; Abteilung für Mikrobiologie, Technische Universität Kaiserslautern, Erwin-Schroedinger-Straße 56, 67663 Kaiserslautern, Germany.
| | - Doris Geib
- Lehrgebiet Bioverfahrenstechnik, Technische Universität Kaiserslautern, Gottlieb-Daimler-Straße 49, 67663 Kaiserslautern, Germany.
| | - Roland Ulber
- Lehrgebiet Bioverfahrenstechnik, Technische Universität Kaiserslautern, Gottlieb-Daimler-Straße 49, 67663 Kaiserslautern, Germany.
| | - Nicole Frankenberg-Dinkel
- Abteilung für Mikrobiologie, Technische Universität Kaiserslautern, Erwin-Schroedinger-Straße 56, 67663 Kaiserslautern, Germany.
| |
Collapse
|
43
|
Mahawar L, Shekhawat GS. Haem oxygenase: A functionally diverse enzyme of photosynthetic organisms and its role in phytochrome chromophore biosynthesis, cellular signalling and defence mechanisms. PLANT, CELL & ENVIRONMENT 2018; 41:483-500. [PMID: 29220548 DOI: 10.1111/pce.13116] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 05/26/2017] [Accepted: 11/23/2017] [Indexed: 05/08/2023]
Abstract
Haem oxygenase (HO) is a universal enzyme that catalyses stereospecific cleavage of haem to BV IX α and liberates Fe+2 ion and CO as by-product. Beside haem degradation, it has important functions in plants that include cellular defence, stomatal regulation, iron mobilization, phytochrome chromophore synthesis, and lateral root formation. Phytochromes are an extended family of photoreceptors with a molecular mass of 250 kDa and occur as a dimer made up of 2 equivalent subunits of 125 kDa each. Each subunit is made of two components: the chromophore, a light-capturing pigment molecule and the apoprotein. Biosynthesis of phytochrome (phy) chromophore includes the oxidative splitting of haem to biliverdin IX by an enzyme HO, which is the decisive step in the biosynthesis. In photosynthetic organisms, BVα is reduced to 3Z PΦB by a ferredoxin-dependent PΦB synthase that finally isomerised to PΦB. The synthesized PΦB assembles with the phytochrome apoprotein in the cytoplasm to generate holophytochrome. Thus, necessary for photomorphogenesis in plants, which has confirmed from the genetic studies, conducted on Arabidopsis thaliana and pea. Besides the phytochrome chromophore synthesis, the review also emphasises on the current advances conducted in plant HO implying its developmental and defensive role.
Collapse
Affiliation(s)
- Lovely Mahawar
- Department of Botany, Jai Narain Vyas University, Jodhpur, 342001, India
| | | |
Collapse
|
44
|
Kyriakakis P, Catanho M, Hoffner N, Thavarajah W, Hu VJ, Chao SS, Hsu A, Pham V, Naghavian L, Dozier LE, Patrick GN, Coleman TP. Biosynthesis of Orthogonal Molecules Using Ferredoxin and Ferredoxin-NADP + Reductase Systems Enables Genetically Encoded PhyB Optogenetics. ACS Synth Biol 2018; 7:706-717. [PMID: 29301067 PMCID: PMC5820651 DOI: 10.1021/acssynbio.7b00413] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Transplanting metabolic reactions from one species into another has many uses as a research tool with applications ranging from optogenetics to crop production. Ferredoxin (Fd), the enzyme that most often supplies electrons to these reactions, is often overlooked when transplanting enzymes from one species to another because most cells already contain endogenous Fd. However, we have shown that the production of chromophores used in Phytochrome B (PhyB) optogenetics is greatly enhanced in mammalian cells by expressing bacterial and plant Fds with ferredoxin-NADP+ reductases (FNR). We delineated the rate limiting factors and found that the main metabolic precursor, heme, was not the primary limiting factor for producing either the cyanobacterial or plant chromophores, phycocyanobilin or phytochromobilin, respectively. In fact, Fd is limiting, followed by Fd+FNR and finally heme. Using these findings, we optimized the PCB production system and combined it with a tissue penetrating red/far-red sensing PhyB optogenetic gene switch in animal cells. We further characterized this system in several mammalian cell lines using red and far-red light. Importantly, we found that the light-switchable gene system remains active for several hours upon illumination, even with a short light pulse, and requires very small amounts of light for maximal activation. Boosting chromophore production by matching metabolic pathways with specific ferredoxin systems will enable the unparalleled use of the many PhyB optogenetic tools and has broader implications for optimizing synthetic metabolic pathways.
Collapse
Affiliation(s)
- Phillip Kyriakakis
- Department
of Bioengineering, University of California, San Diego, 9500 Gilman
Drive, La Jolla, California 92093-0412, United States
| | - Marianne Catanho
- Department
of Bioengineering, University of California, San Diego, 9500 Gilman
Drive, La Jolla, California 92093-0412, United States
| | - Nicole Hoffner
- Neurosciences
Graduate Program, University of California, San Diego, 9500 Gilman
Drive, La Jolla, California 92093-0412, United States
| | - Walter Thavarajah
- Department
of Bioengineering, University of California, San Diego, 9500 Gilman
Drive, La Jolla, California 92093-0412, United States
| | - Vincent J. Hu
- Department
of Bioengineering, University of California, San Diego, 9500 Gilman
Drive, La Jolla, California 92093-0412, United States
| | - Syh-Shiuan Chao
- Frank
H. Better School of Medicine, Quinnipiac University, 370 Bassett Road, North Haven, Connecticut 06473, United States
| | - Athena Hsu
- School
of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412, United States
| | - Vivian Pham
- Roy J. and
Lucille A. Carver College of Medicine, University of Iowa, 451 Newton Road, Iowa City, Iowa 52242, United States
| | - Ladan Naghavian
- Department
of Bioengineering, University of California, San Diego, 9500 Gilman
Drive, La Jolla, California 92093-0412, United States
| | - Lara E. Dozier
- Section
of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093-0347, United States
| | - Gentry N. Patrick
- Section
of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093-0347, United States
| | - Todd P. Coleman
- Department
of Bioengineering, University of California, San Diego, 9500 Gilman
Drive, La Jolla, California 92093-0412, United States
| |
Collapse
|
45
|
Kuai B, Chen J, Hörtensteiner S. The biochemistry and molecular biology of chlorophyll breakdown. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:751-767. [PMID: 28992212 DOI: 10.1093/jxb/erx322] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Chlorophyll breakdown is one of the most obvious signs of leaf senescence and fruit ripening. The resulting yellowing of leaves can be observed every autumn, and the color change of fruits indicates their ripening state. During these processes, chlorophyll is broken down in a multistep pathway, now termed the 'PAO/phyllobilin' pathway, acknowledging the core enzymatic breakdown step catalysed by pheophorbide a oxygenase, which determines the basic linear tetrapyrrole structure of the products of breakdown that are now called 'phyllobilins'. This review provides an update on the PAO/phyllobilin pathway, and focuses on recent biochemical and molecular progress in understanding phyllobilin-modifying reactions as the basis for phyllobilin diversity, on the evolutionary diversity of the pathway, and on the transcriptional regulation of the pathway genes.
Collapse
Affiliation(s)
- Benke Kuai
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Junyi Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Stefan Hörtensteiner
- Institute of Plant and Microbial Biology, University of Zurich, Zollikerstrasse, Zurich, Switzerland
| |
Collapse
|
46
|
Ledermann B, Schwan M, Sommerkamp JA, Hofmann E, Béjà O, Frankenberg-Dinkel N. Evolution and molecular mechanism of four-electron reducing ferredoxin-dependent bilin reductases from oceanic phages. FEBS J 2017; 285:339-356. [PMID: 29156487 DOI: 10.1111/febs.14341] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/06/2017] [Accepted: 11/16/2017] [Indexed: 01/17/2023]
Abstract
Ferredoxin-dependent bilin reductases (FDBRs) are a class of enzymes reducing the heme metabolite biliverdin IXα (BV) to form open-chain tetrapyrroles used for light-perception and light-harvesting in photosynthetic organisms. Thus far, seven FDBR families have been identified, each catalysing a distinct reaction and either transferring two or four electrons from ferredoxin onto the substrate. The newest addition to the family is PcyX, originally identified from metagenomics data derived from phage. Phylogenetically, PcyA is the closest relative catalysing the reduction of BV to phycocyanobilin. PcyX, however, converts the same substrate to phycoerythrobilin, resembling the reaction catalysed by cyanophage PebS. Within this study, we aimed at understanding the evolution of catalytic activities within FDBRs using PcyX as an example. Additional members of the PcyX clade and a remote member of the PcyA family were investigated to gain insights into catalysis. Biochemical data in combination with the PcyX crystal structure revealed that a conserved aspartate-histidine pair is critical for activity. Interestingly, the same residues are part of a catalytic Asp-His-Glu triad in PcyA, including an additional Glu. While this Glu residue is replaced by Asp in PcyX, it is not involved in catalysis. Substitution back to a Glu failed to convert PcyX to a PcyA. Therefore, the change in regiospecificity is not only caused by individual catalytic amino acid residues. Rather the combination of the architecture of the active site with the positioning of the substrate triggers specific proton transfer yielding the individual phycobilin products. ENZYMES Suggested EC number for PcyX: 1.3.7.6 DATABASES: The PcyX X-ray structure was deposited in the PDB with the accession code 5OWG.
Collapse
Affiliation(s)
- Benjamin Ledermann
- Department of Biology, Microbiology, Technical University Kaiserslautern, Germany
| | - Meike Schwan
- Department of Biology, Microbiology, Technical University Kaiserslautern, Germany
| | - Johannes A Sommerkamp
- Protein Crystallography, Faculty for Biology and Biotechnology, Ruhr University Bochum, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Faculty for Biology and Biotechnology, Ruhr University Bochum, Germany
| | - Oded Béjà
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | | |
Collapse
|
47
|
Duanmu D, Rockwell NC, Lagarias JC. Algal light sensing and photoacclimation in aquatic environments. PLANT, CELL & ENVIRONMENT 2017; 40:2558-2570. [PMID: 28245058 PMCID: PMC5705019 DOI: 10.1111/pce.12943] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 02/13/2017] [Accepted: 02/15/2017] [Indexed: 05/05/2023]
Abstract
Anoxygenic photosynthetic prokaryotes arose in ancient oceans ~3.5 billion years ago. The evolution of oxygenic photosynthesis by cyanobacteria followed soon after, enabling eukaryogenesis and the evolution of complex life. The Archaeplastida lineage dates back ~1.5 billion years to the domestication of a cyanobacterium. Eukaryotic algae have subsequently radiated throughout oceanic/freshwater/terrestrial environments, adopting distinctive morphological and developmental strategies for adaptation to diverse light environments. Descendants of the ancestral photosynthetic alga remain challenged by a typical diurnally fluctuating light supply ranging from ~0 to ~2000 μE m-2 s-1 . Such extreme changes in light intensity and variations in light quality have driven the evolution of novel photoreceptors, light-harvesting complexes and photoprotective mechanisms in photosynthetic eukaryotes. This minireview focuses on algal light sensors, highlighting the unexpected roles for linear tetrapyrroles (bilins) in the maintenance of functional chloroplasts in chlorophytes, sister species to streptophyte algae and land plants.
Collapse
Affiliation(s)
- Deqiang Duanmu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Corresponding authors: Deqiang Duanmu, State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China. Tel:+86-27-87282101; Fax:+86-27-87282469; ; J. Clark Lagarias, Department of Molecular and Cellular Biology, University of California, Davis CA 95616. Tel: 530-752-1865; Fax: 530-752-3085;
| | - Nathan C. Rockwell
- Department of Molecular and Cellular Biology, University of California, Davis CA 95616
| | - J. Clark Lagarias
- Department of Molecular and Cellular Biology, University of California, Davis CA 95616
- Corresponding authors: Deqiang Duanmu, State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China. Tel:+86-27-87282101; Fax:+86-27-87282469; ; J. Clark Lagarias, Department of Molecular and Cellular Biology, University of California, Davis CA 95616. Tel: 530-752-1865; Fax: 530-752-3085;
| |
Collapse
|
48
|
Mancini JA, Kodali G, Jiang J, Reddy KR, Lindsey JS, Bryant DA, Dutton PL, Moser CC. Multi-step excitation energy transfer engineered in genetic fusions of natural and synthetic light-harvesting proteins. J R Soc Interface 2017; 14:rsif.2016.0896. [PMID: 28179548 DOI: 10.1098/rsif.2016.0896] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/16/2017] [Indexed: 11/12/2022] Open
Abstract
Synthetic proteins designed and constructed from first principles with minimal reference to the sequence of any natural protein have proven robust and extraordinarily adaptable for engineering a range of functions. Here for the first time we describe the expression and genetic fusion of a natural photosynthetic light-harvesting subunit with a synthetic protein designed for light energy capture and multi-step transfer. We demonstrate excitation energy transfer from the bilin of the CpcA subunit (phycocyanin α subunit) of the cyanobacterial photosynthetic light-harvesting phycobilisome to synthetic four-helix-bundle proteins accommodating sites that specifically bind a variety of selected photoactive tetrapyrroles positioned to enhance energy transfer by relay. The examination of combinations of different bilin, chlorin and bacteriochlorin cofactors has led to identification of the preconditions for directing energy from the bilin light-harvesting antenna into synthetic protein-cofactor constructs that can be customized for light-activated chemistry in the cell.
Collapse
Affiliation(s)
- Joshua A Mancini
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Goutham Kodali
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jianbing Jiang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | | | - Jonathan S Lindsey
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - P Leslie Dutton
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher C Moser
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
49
|
Efficient synthesis of phycocyanobilin in mammalian cells for optogenetic control of cell signaling. Proc Natl Acad Sci U S A 2017; 114:11962-11967. [PMID: 29078307 DOI: 10.1073/pnas.1707190114] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Optogenetics is a powerful tool to precisely manipulate cell signaling in space and time. For example, protein activity can be regulated by several light-induced dimerization (LID) systems. Among them, the phytochrome B (PhyB)-phytochrome-interacting factor (PIF) system is the only available LID system controlled by red and far-red lights. However, the PhyB-PIF system requires phycocyanobilin (PCB) or phytochromobilin as a chromophore, which must be artificially added to mammalian cells. Here, we report an expression vector that coexpresses HO1 and PcyA with Ferredoxin and Ferredoxin-NADP+ reductase for the efficient synthesis of PCB in the mitochondria of mammalian cells. An even higher intracellular PCB concentration was achieved by the depletion of biliverdin reductase A, which degrades PCB. The PCB synthesis and PhyB-PIF systems allowed us to optogenetically regulate intracellular signaling without any external supply of chromophores. Thus, we have provided a practical method for developing a fully genetically encoded PhyB-PIF system, which paves the way for its application to a living animal.
Collapse
|
50
|
Rockwell NC, Martin SS, Li FW, Mathews S, Lagarias JC. The phycocyanobilin chromophore of streptophyte algal phytochromes is synthesized by HY2. THE NEW PHYTOLOGIST 2017; 214:1145-1157. [PMID: 28106912 PMCID: PMC5388591 DOI: 10.1111/nph.14422] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 12/04/2016] [Indexed: 05/11/2023]
Abstract
Land plant phytochromes perceive red and far-red light to control growth and development, using the linear tetrapyrrole (bilin) chromophore phytochromobilin (PΦB). Phytochromes from streptophyte algae, sister species to land plants, instead use phycocyanobilin (PCB). PCB and PΦB are synthesized by different ferredoxin-dependent bilin reductases (FDBRs): PΦB is synthesized by HY2, whereas PCB is synthesized by PcyA. The pathway for PCB biosynthesis in streptophyte algae is unknown. We used phylogenetic analysis and heterologous reconstitution of bilin biosynthesis to investigate bilin biosynthesis in streptophyte algae. Phylogenetic results suggest that PcyA is present in chlorophytes and prasinophytes but absent in streptophytes. A system reconstituting bilin biosynthesis in Escherichia coli was modified to utilize HY2 from the streptophyte alga Klebsormidium flaccidum (KflaHY2). The resulting bilin was incorporated into model cyanobacterial photoreceptors and into phytochrome from the early-diverging streptophyte alga Mesostigma viride (MvirPHY1). All photoreceptors tested incorporate PCB rather than PΦB, indicating that KflaHY2 is sufficient for PCB synthesis without any other algal protein. MvirPHY1 exhibits a red-far-red photocycle similar to those seen in other streptophyte algal phytochromes. These results demonstrate that streptophyte algae use HY2 to synthesize PCB, consistent with the hypothesis that PΦB synthesis arose late in HY2 evolution.
Collapse
Affiliation(s)
- Nathan C. Rockwell
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Shelley S. Martin
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Fay-Wei Li
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Sarah Mathews
- CSIRO National Research Collections Australia, Australian National Herbarium, Canberra, ACT, 2601, Australia
| | - J. Clark Lagarias
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| |
Collapse
|