Article
Biochemistry & Molecular Biology
Haruki Kikuchi, Takafumi Yamashino, Shu Anami, Ryo Suzuki, Mamoru Sugita, Setsuyuki Aoki
Summary: In this study, we found that the moss PHK1 is diurnally regulated, interacting with HPt1 and HPt2 in the nucleus at night and expanding to nucleocytoplasmic in the day. These results suggest that PHK1 may play a crucial role in moss adaptation to light environment.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Microbiology
Neda Baseri, Shahin Najar-Peerayeh, Bita Bakhshi
Summary: The WalK-H364R mutation in VISA strain destabilized the protein and decreased interactions with other molecules, potentially contributing to VISA development. Downregulation of related genes was observed, supporting the impact of this mutation. This study highlights the importance of molecular modelling in uncovering the molecular mechanisms of VISA development.
Article
Microbiology
Jiawei Xing, Vadim M. Gumerov, Igor B. Zhulin
Summary: Photoactive yellow protein (PYP) is an evolutionarily novel domain family within the PAS superfamily, likely originating from Myxococcota and horizontally transferred to other bacterial phyla. It plays a key role in signal transduction pathways related to gene expression, motility, and biofilm formation. The conservation of certain residues in the PYP family suggests functional conservation, but there are also cases of potential neofunctionalization, such as a transition from light sensing to redox sensing. The study lays the foundation for further exploration of the signaling mechanisms and functional diversity of the PYP family.
JOURNAL OF BACTERIOLOGY
(2022)
Article
Parasitology
Maura Rojas-Pirela, Andrea Delgado, Yossmayer d. C. Rondon-Guerrero, Ana J. Caceres, Paul A. M. Michels, Juan Luis Concepcion, Wilfredo Quinones
Summary: PAS domains are a family of domains present in various prokaryotic and eukaryotic organisms. In Trypanosoma cruzi, the phosphoglycerate kinase (PGK) isoform TcPAS-PGK, which contains a PAS domain, was found to be localized in glycosomes and enriched mitochondrial fraction. The PAS domain plays an important regulatory role in the catalytic activity of PGK in T. cruzi.
EXPERIMENTAL PARASITOLOGY
(2023)
Article
Cell Biology
Shu Anami, Takafumi Yamashino, Ryo Suzuki, Kota Nakai, Kensuke Sato, Bowen Wu, Masashi Ryo, Mamoru Sugita, Setsuyuki Aoki
Summary: The study focused on the subcellular patterns of localization and interaction between PHKs and HPts in the moss Physcomitrella patens. It was found that PHKs are mainly localized and interact with HPts in the nucleus, which is a unique feature for plant HKs. Additionally, red light triggered interactions between PHKs and HPts in the cytoplasm, and light repressed the expression of certain genes.
Article
Multidisciplinary Sciences
Koji Kato, Ryo Nagao, Yoshifumi Ueno, Makio Yokono, Takehiro Suzuki, Tian-Yi Jiang, Naoshi Dohmae, Fusamichi Akita, Seiji Akimoto, Naoyuki Miyazaki, Jian-Ren Shen
Summary: This study provides insights into the tetrameric structure of PSI from a glaucophyte alga, revealing evolutionary changes in subunit composition and excitation-energy transfer.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Koji Kato, Tasuku Hamaguchi, Ryo Nagao, Keisuke Kawakami, Yoshifumi Ueno, Takehiro Suzuki, Hiroko Uchida, Akio Murakami, Yoshiki Nakajima, Makio Yokono, Seiji Akimoto, Naoshi Dohmae, Koji Yonekura, Jian-Ren Shen
Summary: By analyzing the structure of a PSI trimer from the ancient cyanobacterium Gloeobacter violaceus PCC 7421, we discovered two low-energy chlorophylls that are missing in this organism, shedding light on the evolutionary changes of low-energy chlorophylls in oxygenic photosynthetic organisms.
Article
Chemistry, Multidisciplinary
Xiaohong Liu, Pengcheng Liu, Hongjie Li, Zhen Xu, Lu Jia, Yan Xia, Minling Yu, Wenqin Tang, Xiaolei Zhu, Chao Chen, Yuanlin Zhang, Eriko Nango, Rie Tanaka, Fangjia Luo, Koji Kato, Yoshiki Nakajima, Shunpei Kishi, Huaxin Yu, Naoki Matsubara, Shigeki Owada, Kensuke Tono, So Iwata, Long-Jiang Yu, Jian-Ren Shen, Jiangyun Wang
Summary: One of the key objectives in chemistry research is to observe atomic motion during reactions in real time. A team of researchers has developed a method to genetically encode a xanthone amino acid into a protein, allowing for high selective and quantum efficient photo-induced C-H bond transformation, and capturing the elusive excited-state intermediates responsible for precise C-H bond activation.
Article
Plant Sciences
Kohei Kagatani, Ryo Nagao, Jian-Ren Shen, Yumiko Yamano, Shinichi Takaichi, Seiji Akimoto
Summary: This article investigates the functions and excitation relaxation dynamics of diadinoxanthin and diatoxanthin in photosynthesis. The study finds that the absorption spectra shift to longer wavelengths and the lifetimes of the excited states decrease after converting diadinoxanthin to diatoxanthin.
PHOTOSYNTHESIS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Jing-Hua Chen, Weiwei Wang, Chen Wang, Tingyun Kuang, Jian-Ren Shen, Xing Zhang
Summary: This study reports the structure of the photosynthetic reaction center complex (RCC) in green sulfur bacteria, which consists of a RC core, two FMO trimers, and two new subunits. The structure reveals a new bacteriochlorophyll and provides insights into the energy transfer network within this photosynthetic apparatus.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Melinda Magyar, Gabor Sipka, Wenhui Han, Xingyue Li, Guangye Han, Jian-Ren Shen, Petar H. H. Lambrev, Gyozo Garab
Summary: By measuring the chlorophyll-a fluorescence transients produced by single-turnover saturating flashes, researchers identified the rate-limiting steps in the transition from dark to light of Photosystem II. They found that in samples treated with diuron, the first flash fully reduced the Q(A) quinone acceptor molecule but only generated an F-1 fluorescence transient.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Instruments & Instrumentation
Artoni Kevin R. Ang, Yasufumi Umena, Ayana Sato-Tomita, Naoya Shibayama, Naohisa Happo, Riho Marumi, Yuta Yamamoto, Koji Kimura, Naomi Kawamura, Yu Takano, Tomohiro Matsushita, Yuji C. Sasaki, Jian-Ren Shen, Kouichi Hayashi
Summary: X-ray fluorescence holography (XFH) is a powerful atomic resolution technique that directly images the local atomic structure of a target element in a material. The development of serial X-ray fluorescence holography allows for direct recording of hologram patterns before radiation damage occurs. This technique paves the way for future experiments on protein crystals to study the local atomic structures of their metal clusters.
JOURNAL OF SYNCHROTRON RADIATION
(2023)
Article
Multidisciplinary Sciences
Dan-Hong Li, Wenda Wang, Cuicui Zhou, Yan Zhang, Songhao Zhao, Yi-Ming Zhou, Rong-Yao Gao, Hai-Dan Yao, Li-Min Fu, Peng Wang, Jian-Ren Shen, Tingyun Kuang, Jian-Ping Zhang
Summary: The light-harvesting complex II (LHCII) of Bryopsis corticulans differs in chlorophyll and carotenoid compositions from that of spinach. Using time-resolved absorption spectroscopy, we investigated the ultrafast excitation dynamics of B-LHCII. Our results showed rapid photogeneration of Chl-Chl charge transfer (CT) species and revealed the transfer of singlet excitation between different chlorophyll and carotenoid molecules. The induction of Chl-Chl CT species by red-light excitation is a common occurrence for LHCIIs in light-harvesting form, as observed in S-LHCII.
Article
Biochemistry & Molecular Biology
Shota Shimizu, Haruya Ogawa, Naoki Tsuboshita, Takehiro Suzuki, Koji Kato, Yoshiki Nakajima, Naoshi Dohmae, Jian-Ren Shen, Ryo Nagao
Summary: In this study, we successfully purified PSI-monomer-PBS and PSI-dimer-PBS supercomplexes from iron-deficient cyanobacterium. This suggests that the binding between CpcL and PSI becomes tighter under iron deficiency, resulting in the formation of these two supercomplexes.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2023)
Article
Plant Sciences
Ryo Nagao, Yoshifumi Ueno, Miyu Furutani, Koji Kato, Jian-Ren Shen, Seiji Akimoto
Summary: LHCs play a crucial role in capturing light energy and transferring it to photosystem cores in oxygenic photosynthetic organisms. In this study, three types of preparations from the red alga Cyanidium caldarium were purified and examined. The results indicate that the expression, function, and structure of red algal PSI-LHCI supercomplexes are affected by the binding of LHCIs to PSI.
PHOTOSYNTHESIS RESEARCH
(2023)
Article
Plant Sciences
Ryo Nagao, Haruya Ogawa, Naoki Tsuboshita, Koji Kato, Reona Toyofuku, Tatsuya Tomo, Jian-Ren Shen
Summary: This study successfully isolated and characterized PSI monomers containing chlorophyll d and compared their properties with PSI trimers from A. marina. The polypeptide composition of the monomer was consistent with that of the trimer, but the absorption and fluorescence emission spectra were different, suggesting different formations of low-energy chlorophylls d between the two types of PSI cores. Based on these findings, the location of low-energy chlorophyll d in A. marina PSIs is discussed.
PHOTOSYNTHESIS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Ryo Nagao, Koji Kato, Tasuku Hamaguchi, Yoshifumi Ueno, Naoki Tsuboshita, Shota Shimizu, Miyu Furutani, Shigeki Ehira, Yoshiki Nakajima, Keisuke Kawakami, Takehiro Suzuki, Naoshi Dohmae, Seiji Akimoto, Koji Yonekura, Jian-Ren Shen
Summary: By using cryo-EM, the authors determined the structure of a PSI monomer associated with six IsiA proteins in Anabaena, providing insights into the diversity and functions of IsiAs. IsiAs are expressed in cyanobacteria under iron-deficient conditions, and the binding properties and functional roles of IsiAs in PSI were still unknown in Anabaena. The cryo-EM structure of a PSI-IsiA supercomplex isolated from iron-deficient Anabaena revealed the association of six IsiA subunits with a PSI core monomer, and the absence of a PsaL subunit due to the occupation of its position by the C-terminal domain of IsiA2.
NATURE COMMUNICATIONS
(2023)
Article
Plant Sciences
Parveen Akhtar, Fanny Balog-Vig, Wenhui Han, Xingyue Li, Guangye Han, Jian-Ren Shen, Petar H. Lambrev
Summary: The spatial separation of photosystems I and II (PSI and PSII) is crucial for maintaining an efficient flow of excitation energy in photosynthesis. Unlike plant chloroplasts, cyanobacterial thylakoids do not form tightly appressed grana stacks, allowing energy spillover from PSII to PSI. Studies have shown that this spillover can reach a quantum yield of up to 40% in certain systems. These findings support the model of coexistence of laterally separated microdomains of PSI and PSII in cyanobacterial cells, as well as energetically connected domains between the two photosystems.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Plant Sciences
Song Zhang, Kailu Tang, Qiujing Yan, Xingyue Li, Liangliang Shen, Wenda Wang, Yi-Kun He, Tingyun Kuang, Guangye Han, Jian-Ren Shen, Xing Zhang
Summary: This article describes the structure of a photosystem I supercomplex in the moss Physcomitrium patens, revealing the assembly process mediated by Lhcb9 and providing important information on energy transfer pathways.
Article
Multidisciplinary Sciences
Orion Farr, Nil Gaudu, Gregoire Danger, Michael J. Russell, Daniel Ferry, Wolfgang Nitschke, Simon Duval
Summary: The shared coordination geometries between metal ions in reactive minerals and enzymatic metal cofactors suggest a similarity in mechanisms and evolution between biological metabolism and non-biological chemical mineralogy. By simulating the oxidation reaction of reactive minerals in the presence of seawater, we found that methane oxidation yields not only methanol but also other organic compounds. This discovery reveals a previously unidentified carbon cycling mechanism in modern and ancient environments, and provides insights into the synthesis of organic compounds necessary for the emergence of life.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2023)