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Ando S, Tanaka R, Ito H. Activity examination of plant Mg-dechelatase and its bacterial homolog in plants and in vitro. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 215:109073. [PMID: 39182428 DOI: 10.1016/j.plaphy.2024.109073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 08/07/2024] [Accepted: 08/22/2024] [Indexed: 08/27/2024]
Abstract
Chlorophyll a serves as a photosynthetic pigment in plants. Its degradation is initiated by the extraction of the central Mg by the Mg-dechelatase enzyme, which is encoded by Stay-Green (SGR). Plant SGR is believed to be derived from bacterial SGR homolog obtained through horizontal gene transfer into photosynthetic eukaryotes. However, it is not known how the bacterial SGR homolog was modified to function in plants. To assess its adaptation mechanism in plants, a bacterial SGR homolog derived from the Anaerolineae bacterium SM23_63 was introduced into plants. It was found that the bacterial SGR homolog metabolized chlorophyll in plants. However, its chlorophyll catabolic activity was lower than that of plant SGR. Recombinant proteins of the bacterial SGR homolog exhibited higher activity than those of the plant SGR. The reduced chlorophyll catabolic activity of bacterial SGR homologs in plants may be associated with low hydrophobicity of the entrance to the catalytic site compared to that of plant SGR. This hinders the enzyme access to chlorophyll, which is localized in hydrophobic environments. This study offers insights into the molecular changes underlying the optimization of enzyme function.
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Affiliation(s)
- Saki Ando
- Graduate School of Environmental Science, Hokkaido University, N10 W5, Sapporo, 060-0810, Japan; Institute of Low Temperature Science, Hokkaido University, N19 W8, Sapporo, 060-0819, Japan
| | - Ryouichi Tanaka
- Institute of Low Temperature Science, Hokkaido University, N19 W8, Sapporo, 060-0819, Japan
| | - Hisashi Ito
- Institute of Low Temperature Science, Hokkaido University, N19 W8, Sapporo, 060-0819, Japan.
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2
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Sato S, Hirose M, Tanaka R, Ito H, Tamiaki H. In vitro demetalation of central magnesium in various chlorophyll derivatives using Mg-dechelatase homolog from the chloroflexi Anaerolineae. PHOTOSYNTHESIS RESEARCH 2024; 160:45-53. [PMID: 38530505 PMCID: PMC11006732 DOI: 10.1007/s11120-024-01088-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/26/2024] [Indexed: 03/28/2024]
Abstract
In the metabolic pathway of chlorophylls (Chls), an enzyme called STAY-GREEN or SGR catalyzes the removal of the central magnesium ion of Chls and their derivatives to their corresponding free bases, including pheophytins. The substrate specificity of SGR has been investigated through in vitro reactions using Chl-related molecules. However, information about the biochemical properties and reaction mechanisms of SGR and its substrate specificity remains elusive. In this study, we synthesized various Chl derivatives and investigated their in vitro dechelations using an SGR enzyme. Chl-a derivatives with the C3-vinyl group on the A-ring, which is commonly found as a substituent in natural substrates, and their analogs with ethyl, hydroxymethyl, formyl, and styryl groups at the C3-position were prepared as substrates. In vitro dechelatase reactions of these substrates were performed using an SGR enzyme derived from an Anaerolineae bacterium, allowing us to investigate their specificity. Reactivity was reduced for substrates with an electron-withdrawing formyl or sterically demanding styryl group at the C3-position. Furthermore, the Chl derivative with the C8-styryl group on the B-ring was less reactive for SGR dechelation than the C3-styryl substrate. These results indicate that the SGR enzyme recognizes substituents on the B-ring of substrates more than those on the A-ring.
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Affiliation(s)
- Soma Sato
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
- Graduate School of Environmental Science, Hokkaido University, N10 W5, Sapporo, 060-0810, Japan
- Institute of Low Temperature Science, Hokkaido University, N19 W8, Sapporo, 060-0819, Japan
| | - Mitsuaki Hirose
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
- Department of Science and Technology, Seikei University, Tokyo, 180-8633, Japan
| | - Ryouichi Tanaka
- Institute of Low Temperature Science, Hokkaido University, N19 W8, Sapporo, 060-0819, Japan
| | - Hisashi Ito
- Institute of Low Temperature Science, Hokkaido University, N19 W8, Sapporo, 060-0819, Japan
| | - Hitoshi Tamiaki
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan.
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Dey D, Nishijima M, Tanaka R, Kurisu G, Tanaka H, Ito H. Crystal structure and reaction mechanism of a bacterial Mg-dechelatase homolog from the Chloroflexi Anaerolineae. Protein Sci 2022; 31:e4430. [PMID: 36173179 PMCID: PMC9514216 DOI: 10.1002/pro.4430] [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: 07/04/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/05/2022]
Abstract
Chlorophyll degradation plays a myriad of physiological roles in photosynthetic organisms, including acclimation to light environment and nutrient remobilization during senescence. Mg extraction from chlorophyll a is the first and committed step of the chlorophyll degradation pathway. This reaction is catalyzed by the Mg-dechelatase enzyme encoded by Stay-Green (SGR). The reaction mechanism of SGR protein remains elusive since metal ion extraction from organic molecules is not a common enzymatic reaction. Additionally, experimentally derived structural information about SGR or its homologs has not yet been reported. In this study, the crystal structure of the SGR homolog from Anaerolineae bacterium was determined using the molecular replacement method at 1.85 Å resolution. Our previous study showed that three residues-H32, D34, and D62 are essential for the catalytic activity of the enzyme. Biochemical analysis involving mutants of D34 residue further strengthened its importance in the functioning of the dechelatase. Docking simulation also revealed the interaction between the D34 side chain and central Mg ion of chlorophyll a. Structural analysis showed the arrangement of D34/H32/D62 in the form of a catalytic triad that is generally found in hydrolases. The probable reaction mechanism suggests that deprotonated D34 side chain coordinates and destabilizes Mg, resulting in Mg extraction. Besides, H32 possibly acts as a general base catalyst and D62 facilitates H32 to be a better proton acceptor. Taken together, the reaction mechanism of SGR partially mirrors the one observed in hydrolases.
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Affiliation(s)
- Debayan Dey
- Graduate School of Life ScienceHokkaido UniversitySapporoJapan
- Institute of Low Temperature ScienceHokkaido UniversitySapporoJapan
| | | | - Ryouichi Tanaka
- Institute of Low Temperature ScienceHokkaido UniversitySapporoJapan
| | - Genji Kurisu
- Institute for Protein ResearchOsaka UniversitySuitaJapan
| | - Hideaki Tanaka
- Institute for Protein ResearchOsaka UniversitySuitaJapan
| | - Hisashi Ito
- Institute of Low Temperature ScienceHokkaido UniversitySapporoJapan
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Schumacher I, Menghini D, Ovinnikov S, Hauenstein M, Fankhauser N, Zipfel C, Hörtensteiner S, Aubry S. Evolution of chlorophyll degradation is associated with plant transition to land. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1473-1488. [PMID: 34931727 PMCID: PMC9306834 DOI: 10.1111/tpj.15645] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/09/2021] [Accepted: 12/15/2021] [Indexed: 05/27/2023]
Abstract
Chlorophyll, the central pigment of photosynthesis, is highly photo‐active and degraded enzymatically during leaf senescence. Merging comparative genomics and metabolomics, we evaluate the extent to which the chlorophyll detoxification pathway has evolved in Viridiplantae. We argue that cytosolic detoxification of phyllobilins in particular was a critical process to the green lineage’s transition to land.
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Affiliation(s)
- Isabel Schumacher
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Damian Menghini
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Serguei Ovinnikov
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Mareike Hauenstein
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Niklaus Fankhauser
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Cyril Zipfel
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Stefan Hörtensteiner
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Sylvain Aubry
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
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Research Progress in the Interconversion, Turnover and Degradation of Chlorophyll. Cells 2021; 10:cells10113134. [PMID: 34831365 PMCID: PMC8621299 DOI: 10.3390/cells10113134] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/06/2021] [Accepted: 11/08/2021] [Indexed: 01/01/2023] Open
Abstract
Chlorophylls (Chls, Chl a and Chl b) are tetrapyrrole molecules essential for photosynthetic light harvesting and energy transduction in plants. Once formed, Chls are noncovalently bound to photosynthetic proteins on the thylakoid membrane. In contrast, they are dismantled from photosystems in response to environmental changes or developmental processes; thus, they undergo interconversion, turnover, and degradation. In the last twenty years, fruitful research progress has been achieved on these Chl metabolic processes. The discovery of new metabolic pathways has been accompanied by the identification of enzymes associated with biochemical steps. This article reviews recent progress in the analysis of the Chl cycle, turnover and degradation pathways and the involved enzymes. In addition, open questions regarding these pathways that require further investigation are also suggested.
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Dey D, Dhar D, Fortunato H, Obata D, Tanaka A, Tanaka R, Basu S, Ito H. Insights into the structure and function of the rate-limiting enzyme of chlorophyll degradation through analysis of a bacterial Mg-dechelatase homolog. Comput Struct Biotechnol J 2021; 19:5333-5347. [PMID: 34745453 PMCID: PMC8531759 DOI: 10.1016/j.csbj.2021.09.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 12/13/2022] Open
Abstract
The Mg-dechelatase enzyme encoded by the Stay-Green (SGR) gene catalyzes Mg2+ dechelation from chlorophyll a. This reaction is the first committed step of chlorophyll degradation pathway in plants and is thus indispensable for the process of leaf senescence. There is no structural information available for this or its related enzymes. This study aims to provide insights into the structure and reaction mechanism of the enzyme through biochemical and computational analysis of an SGR homolog from the Chloroflexi Anaerolineae (AbSGR-h). Recombinant AbSGR-h with its intact sequence and those with mutations were overexpressed in Escherichia coli and their Mg-dechelatase activity were compared. Two aspartates - D34 and D62 were found to be essential for catalysis, while R26, Y28, T29 and D114 were responsible for structural maintenance. Gel filtration analysis of the recombinant AbSGR-h indicates that it forms a homo-oligomer. The three-dimensional structure of AbSGR-h was predicted by a deep learning-based method, which was evaluated by protein structure quality evaluation programs while structural stability of wild-type and mutant forms were investigated through molecular dynamics simulations. Furthermore, in concordance with the results of enzyme assay, molecular docking concluded the significance of D34 in ligand interaction. By combining biochemical analysis and computational prediction, this study unveils the detailed structural characteristics of the enzyme, including the probable pocket of interaction and the residues of structural and functional importance. It also serves as a basis for further studies on Mg-dechelatase such as elucidation of its reaction mechanism or inhibitor screening.
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Affiliation(s)
- Debayan Dey
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan.,Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan
| | - Dipanjana Dhar
- Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan.,Department of Natural History Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Helena Fortunato
- Department of Natural History Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Daichi Obata
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan
| | - Ayumi Tanaka
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan
| | - Ryouichi Tanaka
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan
| | - Soumalee Basu
- Department of Microbiology, University of Calcutta, Kolkata 700019, India
| | - Hisashi Ito
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan
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Fukura K, Tanaka A, Tanaka R, Ito H. Enrichment of chlorophyll catabolic enzymes in grana margins and their cooperation in catabolic reactions. JOURNAL OF PLANT PHYSIOLOGY 2021; 266:153535. [PMID: 34607178 DOI: 10.1016/j.jplph.2021.153535] [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: 08/19/2021] [Revised: 09/22/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
During leaf senescence, chlorophyll a and b are degraded through several enzymatic reactions, including chlorophyll b reductase, 7-hydroxymethyl chlorophyll a reductase, and Mg-dechelatase. Considering that the intermediates of the chlorophyll breakdown pathway are highly photoreactive, cooperative and efficient reactions of chlorophyll metabolic enzymes may protect chloroplasts from potential photo-oxidative damage. Here, we investigated the sub-organellar localization and cooperative reactions of the enzymes involved in the chlorophyll breakdown pathway by the fractionation of thylakoid membranes and enzymatic assays using recombinant proteins. We found that these enzymes were enriched in the grana margin fraction. Furthermore, we found that chlorophyll b reductase and Mg-dechelatase efficiently catabolized chlorophylls bound to the chlorophyll-protein complexes when these two enzymes were mixed. These results suggest that the co-localization of chlorophyll catabolic enzymes enables efficient chlorophyll breakdown. The results from this study highlight a key step forward in the investigation of the photosystem breakdown process.
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Affiliation(s)
- Koki Fukura
- Graduate School of Life Science, Hokkaido University, N10 W8, Sapporo, 060-0810, Japan; Institute of Low Temperature Science, Hokkaido University, N19 W8, Sapporo, 060-0819, Japan
| | - Ayumi Tanaka
- Institute of Low Temperature Science, Hokkaido University, N19 W8, Sapporo, 060-0819, Japan
| | - Ryouichi Tanaka
- Institute of Low Temperature Science, Hokkaido University, N19 W8, Sapporo, 060-0819, Japan
| | - Hisashi Ito
- Institute of Low Temperature Science, Hokkaido University, N19 W8, Sapporo, 060-0819, Japan.
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Yang M, Zhu S, Jiao B, Duan M, Meng Q, Ma N, Lv W. SlSGRL, a tomato SGR-like protein, promotes chlorophyll degradation downstream of the ABA signaling pathway. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 157:316-327. [PMID: 33166770 DOI: 10.1016/j.plaphy.2020.10.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 10/25/2020] [Indexed: 05/25/2023]
Abstract
Chlorophyll (chl) degradation plays a vital role during green plant growth and development, including nutrient metabolism, fruit and seed maturation, and phototoxic detoxification. STAY-GREEN (SGR) is a plant-specific regulator involved in chl degradation. Previous studies showed that SlSGR1 functioned in chl degradation and lycopene accumulation during fruit ripening of tomato (Solanum lycopersicum). However, little is known about SlSGR-LIKE (SlSGRL) gene, which is a homolog of SlSGR1. We cloned the SlSGRL gene and created transgenic tomato plants overexpressing (OE) SlSGRL. Expression analysis showed that SlSGRL was up-regulated by abscisic acid (ABA). Our data showed that SlSGRL-OE lines exhibited earlier leaf yellowing than wild-type (WT) lines under ABA treatment. Yeast two-hybrid (Y2H) assay revealed that SlSGRL interacted with pheophytin pheophorbide hydrolase (SlPPH) and light-harvesting complex a2 (SlLHCa2) to promote the chl degradation. Further analysis demonstrated that ABA-INSENSITIVE5 (SlABI5) and SlABI5-LIKE regulated SlSGRL expression by directly binding to the sequence (-611 to -582) of the SlSGRL promoter that included an ABRE cis-element. We proposed that SlSGRL, which was regulated by SlABI5/SlABI5-LIKE, mainly acted in ABA-induced chl degradation via interacting with SlPPH and SlLHCa2.
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Affiliation(s)
- Minmin Yang
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Daizong Street, Tai'an 271018, Shandong, PR China.
| | - Shaobo Zhu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Daizong Street, Tai'an 271018, Shandong, PR China.
| | - Baozhen Jiao
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Daizong Street, Tai'an 271018, Shandong, PR China.
| | - Ming Duan
- Experimental and Teaching Center, Shanxi Agricultural University, Jinzhong 030801, Shanxi, PR China.
| | - Qingwei Meng
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Daizong Street, Tai'an 271018, Shandong, PR China.
| | - Nana Ma
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Daizong Street, Tai'an 271018, Shandong, PR China.
| | - Wei Lv
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Daizong Street, Tai'an 271018, Shandong, PR China.
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Scossa F, Fernie AR. The evolution of metabolism: How to test evolutionary hypotheses at the genomic level. Comput Struct Biotechnol J 2020; 18:482-500. [PMID: 32180906 PMCID: PMC7063335 DOI: 10.1016/j.csbj.2020.02.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 01/21/2023] Open
Abstract
The origin of primordial metabolism and its expansion to form the metabolic networks extant today represent excellent systems to study the impact of natural selection and the potential adaptive role of novel compounds. Here we present the current hypotheses made on the origin of life and ancestral metabolism and present the theories and mechanisms by which the large chemical diversity of plants might have emerged along evolution. In particular, we provide a survey of statistical methods that can be used to detect signatures of selection at the gene and population level, and discuss potential and limits of these methods for investigating patterns of molecular adaptation in plant metabolism.
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), Via Ardeatina 546, 00178 Rome, Italy
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
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