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Article: Dysfunction of Chloroplast Protease Activity Mitigates

Ozawa, Shin-Ichiro / Zhang, Guoxian / Sakamoto, Wataru

2024 Volume 13, Issue 5

Abstract: Researchers have described protection mechanisms against the photoinhibition of photosystems under strong-light stress. Cyclic Electron Flow (CEF) mitigates electron acceptor-side limitation, and thus contributes to Photosystem I (PSI) protection. ... ...

Abstract	Researchers have described protection mechanisms against the photoinhibition of photosystems under strong-light stress. Cyclic Electron Flow (CEF) mitigates electron acceptor-side limitation, and thus contributes to Photosystem I (PSI) protection. Chloroplast protease removes damaged protein to assist with protein turn over, which contributes to the quality control of Photosystem II (PSII). The PGR5 protein is involved in PGR5-dependent CEF. The FTSH protein is a chloroplast protease which effectively degrades the damaged PSII reaction center subunit, D1 protein. To investigate how the PSI photoinhibition phenotype in
Language	English
Publishing date	2024-02-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704341-1
ISSN	2223-7747
ISSN	2223-7747
DOI	10.3390/plants13050606
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Article ; Online: Algal PETC-Pro171-Leu suppresses electron transfer in cytochrome b6f under acidic lumenal conditions.

Ozawa, Shin-Ichiro / Buchert, Felix / Reuys, Ruby / Hippler, Michael / Takahashi, Yuichiro

Plant physiology

2022 Volume 191, Issue 3, Page(s) 1803–1817

Abstract: Linear photosynthetic electron flow (LEF) produces NADPH and generates a proton electrochemical potential gradient across the thylakoid membrane to synthesize ATP, both of which are required for CO2 fixation. As cellular demand for ATP and NADPH varies, ... ...

Abstract	Linear photosynthetic electron flow (LEF) produces NADPH and generates a proton electrochemical potential gradient across the thylakoid membrane to synthesize ATP, both of which are required for CO2 fixation. As cellular demand for ATP and NADPH varies, cyclic electron flow (CEF) between Photosystem I and the cytochrome b6f complex (b6f) produces extra ATP. b6f regulates LEF and CEF via photosynthetic control, which is a pH-dependent b6f slowdown of plastoquinol oxidation at the lumenal site. This protection mechanism is triggered at more alkaline lumen pH in the pgr1 (proton gradient regulation 1) mutant of the vascular plant Arabidopsis (Arabidopsis thaliana), which contains a Pro194Leu substitution in the b6f Rieske Iron-sulfur protein Photosynthetic Electron Transfer C (PETC) subunit. In this work, we introduced the equivalent pgr1 mutation in the green alga Chlamydomonas reinhardtii to generate PETC-P171L. Consistent with the pgr1 phenotype, PETC-P171L displayed impaired NPQ induction along with slower photoautotrophic growth under high light conditions. Our data provide evidence that the ΔpH component in PETC-P171L depends on oxygen availability. Only under low oxygen conditions was the ΔpH component sufficient to trigger a phenotype in algal PETC-P171L where the mutant b6f was more restricted to oxidize the plastoquinol pool and showed diminished electron flow through the b6f complex. These results demonstrate that photosynthetic control of different stringency are established in C. reinhardtii depending on the cellular metabolism, and the lumen pH-sensitive PETC-P171L was generated to read out various associated effects.
MeSH term(s)	Cytochrome b6f Complex/genetics ; Cytochrome b6f Complex/metabolism ; Protons ; Electrons ; NADP/metabolism ; Electron Transport/physiology ; Photosynthesis/genetics ; Oxidation-Reduction ; Arabidopsis/genetics ; Arabidopsis/metabolism ; Adenosine Triphosphate/metabolism ; Oxygen/metabolism
Chemical Substances	Cytochrome b6f Complex (9035-40-9) ; Protons ; plastoquinol (3819-09-8) ; NADP (53-59-8) ; Adenosine Triphosphate (8L70Q75FXE) ; Oxygen (S88TT14065)
Language	English
Publishing date	2022-12-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	208914-2
ISSN	1532-2548 ; 0032-0889
ISSN (online)	1532-2548
ISSN	0032-0889
DOI	10.1093/plphys/kiac575
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Article ; Online: The stability of NPM1 oligomers regulated by acidic disordered regions controls the quality of liquid droplets.

Okuwaki, Mitsuru / Ozawa, Shin-Ichiro / Ebine, Shuhei / Juichi, Motoki / Umeki, Tadanobu / Niioka, Kazuki / Kikuchi, Taiyo / Tanaka, Nobutada

Journal of biochemistry

2023 Volume 174, Issue 5, Page(s) 461–476

Abstract: The nucleolus is a membrane-less nuclear body that typically forms through the process of liquid-liquid phase separation (LLPS) involving its components. NPM1 drives LLPS within the nucleolus and its oligomer formation and inter-oligomer interactions ... ...

Abstract	The nucleolus is a membrane-less nuclear body that typically forms through the process of liquid-liquid phase separation (LLPS) involving its components. NPM1 drives LLPS within the nucleolus and its oligomer formation and inter-oligomer interactions play a cooperative role in inducing LLPS. However, the molecular mechanism underlaying the regulation of liquid droplet quality formed by NPM1 remains poorly understood. In this study, we demonstrate that the N-terminal and central acidic residues within the intrinsically disordered regions (IDR) of NPM1 contribute to attenuating oligomer stability, although differences in the oligomer stability were observed only under stringent conditions. Furthermore, the impact of the IDRs is augmented by an increase in net negative charges resulting from phosphorylation within the IDRs. Significantly, we observed an increase in fluidity of liquid droplets formed by NPM1 with decreased oligomer stability. These results indicate that the difference in oligomer stability only observed biochemically under stringent conditions has a significant impact on liquid droplet quality formed by NPM1. Our findings provide new mechanistic insights into the regulation of nucleolar dynamics during the cell cycle.
MeSH term(s)	Protein Domains ; Cell Nucleolus/metabolism ; Nuclear Proteins/metabolism ; Intrinsically Disordered Proteins/analysis
Chemical Substances	Nuclear Proteins ; Intrinsically Disordered Proteins
Language	English
Publishing date	2023-08-02
Publishing country	England
Document type	Journal Article
ZDB-ID	218073-x
ISSN	1756-2651 ; 0021-924X
ISSN (online)	1756-2651
ISSN	0021-924X
DOI	10.1093/jb/mvad061
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Article ; Online: Two specific domains of the γ subunit of chloroplast F

Akiyama, Kentaro / Ozawa, Shin-Ichiro / Takahashi, Yuichiro / Yoshida, Keisuke / Suzuki, Toshiharu / Kondo, Kumiko / Wakabayashi, Ken-Ichi / Hisabori, Toru

Proceedings of the National Academy of Sciences of the United States of America

2023 Volume 120, Issue 6, Page(s) e2218187120

Abstract: Chloroplast ... ...

Abstract	Chloroplast F
MeSH term(s)	Chloroplast Proton-Translocating ATPases/genetics ; Chloroplast Proton-Translocating ATPases/metabolism ; Chloroplasts/metabolism ; Photosynthesis/genetics ; Oxidation-Reduction ; Adenosine Triphosphate/metabolism
Chemical Substances	Chloroplast Proton-Translocating ATPases (EC 3.6.3.-) ; Adenosine Triphosphate (8L70Q75FXE)
Language	English
Publishing date	2023-01-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2218187120
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Article: Phos-tag-based approach to study protein phosphorylation in the thylakoid membrane

Nishioka, Keiji / Kato, Yusuke / Ozawa, Shin-ichiro / Takahashi, Yuichiro / Sakamoto, Wataru

Photosynthesis research. 2021 Jan., v. 147, no. 1

2021

Abstract: Protein phosphorylation is a fundamental post-translational modification in all organisms. In photoautotrophic organisms, protein phosphorylation is essential for the fine-tuning of photosynthesis. The reversible phosphorylation of the photosystem II ( ... ...

Abstract	Protein phosphorylation is a fundamental post-translational modification in all organisms. In photoautotrophic organisms, protein phosphorylation is essential for the fine-tuning of photosynthesis. The reversible phosphorylation of the photosystem II (PSII) core and the light-harvesting complex of PSII (LHCII) contribute to the regulation of photosynthetic activities. Besides the phosphorylation of these major proteins, recent phosphoproteomic analyses have revealed that several proteins are phosphorylated in the thylakoid membrane. In this study, we utilized the Phos-tag technology for a comprehensive assessment of protein phosphorylation in the thylakoid membrane of Arabidopsis. Phos-tag SDS-PAGE enables the mobility shift of phosphorylated proteins compared with their non-phosphorylated isoform, thus differentiating phosphorylated proteins from their non-phosphorylated isoforms. We extrapolated this technique to two-dimensional (2D) SDS-PAGE for detecting protein phosphorylation in the thylakoid membrane. Thylakoid proteins were separated in the first dimension by conventional SDS-PAGE and in the second dimension by Phos-tag SDS-PAGE. In addition to the isolation of major phosphorylated photosynthesis-related proteins, 2D Phos-tag SDS-PAGE enabled the detection of several minor phosphorylated proteins in the thylakoid membrane. The analysis of the thylakoid kinase mutants demonstrated that light-dependent protein phosphorylation was mainly restricted to the phosphorylation of the PSII core and LHCII proteins. Furthermore, we assessed the phosphorylation states of the structural domains of the thylakoid membrane, grana core, grana margin, and stroma lamella. Overall, these results demonstrated that Phos-tag SDS-PAGE is a useful biochemical tool for studying in vivo protein phosphorylation in the thylakoid membrane protein.
Keywords	Arabidopsis ; grana ; light harvesting complex ; membrane proteins ; photosystem II ; polyacrylamide gel electrophoresis ; post-translational modification ; protein phosphorylation ; research ; thylakoids
Language	English
Dates of publication	2021-01
Size	p. 107-124.
Publishing place	Springer Netherlands
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	1475688-2
ISSN	1573-5079 ; 0166-8595
ISSN (online)	1573-5079
ISSN	0166-8595
DOI	10.1007/s11120-020-00803-1
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Article ; Online: Structure-based virtual screening for novel chymase inhibitors by in silico fragment mapping.

Ozawa, Shin-Ichiro / Takahashi, Miki / Yamaotsu, Noriyuki / Hirono, Shuichi

Journal of molecular graphics & modelling

2019 Volume 89, Page(s) 102–108

Abstract: The term chymase refers to a family of chymotrypsin-like serine proteases stored within the secretory granules of mast cells. Recently, a variety of small molecule inhibitors for chymase have been developed with a primary focus on the treatment of ... ...

Abstract	The term chymase refers to a family of chymotrypsin-like serine proteases stored within the secretory granules of mast cells. Recently, a variety of small molecule inhibitors for chymase have been developed with a primary focus on the treatment of cardiovascular diseases. Despite the expected therapeutic benefit of these chymase inhibitors, they have not been used clinically. Here, we attempted to identify new chymase inhibitors using a multistep structure-based virtual screening protocol combined with our knowledge-based in silico fragment mapping technique. The mapping procedure identified fragments with novel modes of interaction at the oxyanion hole of chymase. Next, we constructed a three-dimensional (3D) pharmacophore model and retrieved eight candidate chymase inhibitors from a commercial database that included approximately five million compounds. This selection was achieved using a multistep virtual screening protocol, which combined a 3D pharmacophore-based search, docking calculations, and analyses of binding free energy. One of the eight compounds exhibited concentration-dependent chymase inhibitory activity, which could be further optimized to develop more potent chymase inhibitors.
MeSH term(s)	Chymases/antagonists & inhibitors ; Chymases/chemistry ; Drug Discovery ; Humans ; Ligands ; Molecular Conformation ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Molecular Structure ; Quantitative Structure-Activity Relationship ; Serine Proteinase Inhibitors/chemistry ; Serine Proteinase Inhibitors/pharmacology
Chemical Substances	Ligands ; Serine Proteinase Inhibitors ; Chymases (EC 3.4.21.39)
Language	English
Publishing date	2019-03-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1396450-1
ISSN	1873-4243 ; 1093-3263
ISSN (online)	1873-4243
ISSN	1093-3263
DOI	10.1016/j.jmgm.2019.03.011
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Article ; Online: Phos-tag-based approach to study protein phosphorylation in the thylakoid membrane.

Nishioka, Keiji / Kato, Yusuke / Ozawa, Shin-Ichiro / Takahashi, Yuichiro / Sakamoto, Wataru

Photosynthesis research

2020 Volume 147, Issue 1, Page(s) 107–124

Abstract	Protein phosphorylation is a fundamental post-translational modification in all organisms. In photoautotrophic organisms, protein phosphorylation is essential for the fine-tuning of photosynthesis. The reversible phosphorylation of the photosystem II (PSII) core and the light-harvesting complex of PSII (LHCII) contribute to the regulation of photosynthetic activities. Besides the phosphorylation of these major proteins, recent phosphoproteomic analyses have revealed that several proteins are phosphorylated in the thylakoid membrane. In this study, we utilized the Phos-tag technology for a comprehensive assessment of protein phosphorylation in the thylakoid membrane of Arabidopsis. Phos-tag SDS-PAGE enables the mobility shift of phosphorylated proteins compared with their non-phosphorylated isoform, thus differentiating phosphorylated proteins from their non-phosphorylated isoforms. We extrapolated this technique to two-dimensional (2D) SDS-PAGE for detecting protein phosphorylation in the thylakoid membrane. Thylakoid proteins were separated in the first dimension by conventional SDS-PAGE and in the second dimension by Phos-tag SDS-PAGE. In addition to the isolation of major phosphorylated photosynthesis-related proteins, 2D Phos-tag SDS-PAGE enabled the detection of several minor phosphorylated proteins in the thylakoid membrane. The analysis of the thylakoid kinase mutants demonstrated that light-dependent protein phosphorylation was mainly restricted to the phosphorylation of the PSII core and LHCII proteins. Furthermore, we assessed the phosphorylation states of the structural domains of the thylakoid membrane, grana core, grana margin, and stroma lamella. Overall, these results demonstrated that Phos-tag SDS-PAGE is a useful biochemical tool for studying in vivo protein phosphorylation in the thylakoid membrane protein.
MeSH term(s)	Arabidopsis/enzymology ; Arabidopsis/genetics ; Arabidopsis/physiology ; Arabidopsis/radiation effects ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Chromatography, Liquid ; Electrophoresis, Gel, Two-Dimensional ; Electrophoresis, Polyacrylamide Gel ; Light-Harvesting Protein Complexes/metabolism ; Mutation ; Phosphorylation ; Photosynthesis ; Photosystem II Protein Complex/metabolism ; Protein Isoforms ; Protein Kinases/genetics ; Protein Kinases/metabolism ; Protein-Serine-Threonine Kinases/genetics ; Protein-Serine-Threonine Kinases/metabolism ; Pyridines ; Tandem Mass Spectrometry ; Thylakoids/metabolism
Chemical Substances	1,3-bis(bis(pyridin-2-ylmethyl)amino)propan-2-ol ; Arabidopsis Proteins ; Light-Harvesting Protein Complexes ; Photosystem II Protein Complex ; Protein Isoforms ; Pyridines ; Protein Kinases (EC 2.7.-) ; Protein-Serine-Threonine Kinases (EC 2.7.11.1) ; STN7 protein, Arabidopsis (EC 2.7.11.1) ; STN8 protein, Arabidopsis (EC 2.7.11.1)
Language	English
Publishing date	2020-12-02
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1475688-2
ISSN	1573-5079 ; 0166-8595
ISSN (online)	1573-5079
ISSN	0166-8595
DOI	10.1007/s11120-020-00803-1
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Article ; Online: Chloroplast ATP synthase biogenesis requires peripheral stalk subunits AtpF and ATPG and stabilization of atpE mRNA by OPR protein MDE1.

Chaux, Frédéric / Jarrige, Domitille / Rodrigues-Azevedo, Marcio / Bujaldon, Sandrine / Caspari, Oliver D / Ozawa, Shin-Ichiro / Drapier, Dominique / Vallon, Olivier / Choquet, Yves / de Vitry, Catherine

The Plant journal : for cell and molecular biology

2023 Volume 116, Issue 6, Page(s) 1582–1599

Abstract: Chloroplast ATP synthase contains subunits of plastid and nuclear genetic origin. To investigate the coordinated biogenesis of this complex, we isolated novel ATP synthase mutants in the green alga Chlamydomonas reinhardtii by screening for high light ... ...

Abstract	Chloroplast ATP synthase contains subunits of plastid and nuclear genetic origin. To investigate the coordinated biogenesis of this complex, we isolated novel ATP synthase mutants in the green alga Chlamydomonas reinhardtii by screening for high light sensitivity. We report here the characterization of mutants affecting the two peripheral stalk subunits b and b', encoded respectively by the atpF and ATPG genes, and of three independent mutants which identify the nuclear factor MDE1, required to stabilize the chloroplast-encoded atpE mRNA. Whole-genome sequencing revealed a transposon insertion in the 3'UTR of ATPG while mass spectrometry shows a small accumulation of functional ATP synthase in this knock-down ATPG mutant. In contrast, knock-out ATPG mutants, obtained by CRISPR-Cas9 gene editing, fully prevent ATP synthase function and accumulation, as also observed in an atpF frame-shift mutant. Crossing ATP synthase mutants with the ftsh1-1 mutant of the major thylakoid protease identifies AtpH as an FTSH substrate, and shows that FTSH significantly contributes to the concerted accumulation of ATP synthase subunits. In mde1 mutants, the absence of atpE transcript fully prevents ATP synthase biogenesis and photosynthesis. Using chimeric atpE genes to rescue atpE transcript accumulation, we demonstrate that MDE1, a novel octotricopeptide repeat (OPR) protein, genetically targets the atpE 5'UTR. In the perspective of the primary endosymbiosis (~1.5 Gy), the recruitment of MDE1 to its atpE target exemplifies a nucleus/chloroplast interplay that evolved rather recently, in the ancestor of the CS clade of Chlorophyceae, ~300 My ago.
MeSH term(s)	Chloroplast Proton-Translocating ATPases/genetics ; Chloroplast Proton-Translocating ATPases/metabolism ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Chlamydomonas reinhardtii/genetics ; Chlamydomonas reinhardtii/metabolism ; Chloroplasts/genetics ; Chloroplasts/metabolism ; Adenosine Triphosphate/metabolism
Chemical Substances	Chloroplast Proton-Translocating ATPases (EC 3.6.3.-) ; RNA, Messenger ; Adenosine Triphosphate (8L70Q75FXE)
Language	English
Publishing date	2023-10-12
Publishing country	England
Document type	Journal Article
ZDB-ID	1088037-9
ISSN	1365-313X ; 0960-7412
ISSN (online)	1365-313X
ISSN	0960-7412
DOI	10.1111/tpj.16448
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Article ; Online: Characterization of tryptophan oxidation affecting D1 degradation by FtsH in the photosystem II quality control of chloroplasts.

Kato, Yusuke / Kuroda, Hiroshi / Ozawa, Shin-Ichiro / Saito, Keisuke / Dogra, Vivek / Scholz, Martin / Zhang, Guoxian / de Vitry, Catherine / Ishikita, Hiroshi / Kim, Chanhong / Hippler, Michael / Takahashi, Yuichiro / Sakamoto, Wataru

eLife

2023 Volume 12

Abstract: Photosynthesis is one of the most important reactions for sustaining our environment. Photosystem II (PSII) is the initial site of photosynthetic electron transfer by water oxidation. Light in excess, however, causes the simultaneous production of ... ...

Abstract	Photosynthesis is one of the most important reactions for sustaining our environment. Photosystem II (PSII) is the initial site of photosynthetic electron transfer by water oxidation. Light in excess, however, causes the simultaneous production of reactive oxygen species (ROS), leading to photo-oxidative damage in PSII. To maintain photosynthetic activity, the PSII reaction center protein D1, which is the primary target of unavoidable photo-oxidative damage, is efficiently degraded by FtsH protease. In PSII subunits, photo-oxidative modifications of several amino acids such as Trp have been indeed documented, whereas the linkage between such modifications and D1 degradation remains elusive. Here, we show that an oxidative post-translational modification of Trp residue at the N-terminal tail of D1 is correlated with D1 degradation by FtsH during high-light stress. We revealed that
MeSH term(s)	Photosystem II Protein Complex/genetics ; Tryptophan/metabolism ; Arabidopsis Proteins/metabolism ; Light ; Chloroplasts/metabolism ; Arabidopsis/genetics ; Arabidopsis/metabolism ; Metalloendopeptidases/metabolism
Chemical Substances	Photosystem II Protein Complex ; Tryptophan (8DUH1N11BX) ; Arabidopsis Proteins ; FtsH protein, Arabidopsis (EC 3.4.24.-) ; Metalloendopeptidases (EC 3.4.24.-)
Language	English
Publishing date	2023-11-21
Publishing country	England
Document type	Journal Article
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.88822
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Article ; Online: The photosystem I assembly apparatus consisting of Ycf3-Y3IP1 and Ycf4 modules.

Nellaepalli, Sreedhar / Ozawa, Shin-Ichiro / Kuroda, Hiroshi / Takahashi, Yuichiro

Nature communications

2018 Volume 9, Issue 1, Page(s) 2439

Abstract: In oxygenic photosynthesis, light energy is converted into redox energy by two photosystems (PSI and PSII). PSI forms one of the largest multiprotein complexes in thylakoid membranes consisting of a core complex, peripheral light-harvesting complexes ( ... ...

Abstract	In oxygenic photosynthesis, light energy is converted into redox energy by two photosystems (PSI and PSII). PSI forms one of the largest multiprotein complexes in thylakoid membranes consisting of a core complex, peripheral light-harvesting complexes (LHCIs) and cofactors. Although the high-resolution structure of the PSI-LHCI complex has been determined, the assembly process remains unclear due to the rapid nature of the assembly process. Here we show that two conserved chloroplast-encoded auxiliary factors, Ycf3 and Ycf4, form modules that mediate PSI assembly. The first module consists of the tetratricopeptide repeat protein Ycf3 and its interacting partner, Y3IP1, and mainly facilitates the assembly of reaction center subunits. The second module consists of oligomeric Ycf4 and facilitates the integration of peripheral PSI subunits and LHCIs into the PSI reaction center subcomplex. We reveal that these two modules are major mediators of the PSI-LHCI assembly process.
MeSH term(s)	Chlamydomonas reinhardtii/physiology ; Light-Harvesting Protein Complexes/metabolism ; Photosynthesis/physiology ; Photosystem I Protein Complex/chemistry ; Photosystem I Protein Complex/isolation & purification ; Photosystem I Protein Complex/metabolism ; Plants, Genetically Modified ; Protozoan Proteins/chemistry ; Protozoan Proteins/isolation & purification ; Protozoan Proteins/metabolism ; Spectrum Analysis ; Thylakoids/metabolism
Chemical Substances	Light-Harvesting Protein Complexes ; Photosystem I Protein Complex ; Protozoan Proteins ; Ycf3 protein, Chlamydomonas reinhardtii ; Ycf4 protein, Chlamydomonas reinhardtii
Language	English
Publishing date	2018-06-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2041-1723
ISSN (online)	2041-1723
DOI	10.1038/s41467-018-04823-3
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