Article
Biotechnology & Applied Microbiology
Shu-Yan Wang, Xin Li, Shu-Guang Wang, Peng-Fei Xia
Summary: Cyanobacteria have the potential to convert atmospheric carbon dioxide into biofuels, chemicals, and food. However, the development of genome-editing tools for cyanobacteria has been slower compared to other microbial chassis. In this study, we successfully adapted base editing using the CRISPR-Cas system for cyanobacteria, enabling precise and efficient genome editing. We demonstrated multiplex base editing in a model cyanobacterium and manipulated the glycogen metabolic pathway to enhance the production of chemicals and food from carbon dioxide. This work represents the first report of base editing in cyanobacteria and provides a paradigm for using CRISPR-Cas systems in bacteria, with the potential to accelerate metabolic engineering and synthetic biology to address global climate change.
METABOLIC ENGINEERING
(2023)
Article
Multidisciplinary Sciences
Ryohei Kobayashi, Hiroshi Ueno, Kei-ichi Okazaki, Hiroyuki Noji
Summary: IF1 is a natural inhibitor protein that blocks the catalysis and rotation of mitochondrial FoF1 ATP synthase. It inhibits ATP hydrolysis by F-1, but this inhibition is relieved under ATP synthesis conditions. The study shows that IF1-inhibited F-1 is activated only when F-1 rotates in the clockwise direction, explaining the condition-dependent mechanism of IF1 inhibition. Investigation of mutant IF1 with N-terminal truncations reveals the importance of its interaction with the gamma subunit and the role of the middle long helix in the inhibition of F-1.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Meghna Sobti, Yi C. C. Zeng, James L. L. Walshe, Simon H. J. Brown, Robert Ishmukhametov, Alastair G. G. Stewart
Summary: F1Fo ATP synthase is a crucial enzyme in cellular energy production, functioning as a biological generator. It can catalyze ATP production by generating rotation through proton flow from the F-o motor to the F-1 motor. The enzyme also has the ability to operate in reverse, hydrolyzing ATP and pumping protons. Cryo-EM data of E. coli F1Fo ATP synthase reveal its structural transitions in different rotational and inhibited states, providing insights into the flexible coupling between the F-1 and F-o motors, as well as the regulatory mechanism mediated by the epsilon subunit.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Chui-Fann Wong, Aik-Meng Lau, Amaravadhi Harikishore, Wuan-Geok Saw, Joon Shin, Priya Ragunathan, Shashi Bhushan, So-Fong Cam Ngan, Siu Kwan Sze, Roderick W. Bates, Thomas Dick, Gerhard Gruber
Summary: The mycobacterial F1FO-ATP synthase behaves differently from most bacteria due to the lack of ATP hydrolysis-driven proton translocation. Research on the central stalk subunit e has revealed its role in suppressing the enzyme's ATPase activity, providing insights for developing inhibitors targeting this subunit. By studying mutations at both the N-terminal and C-terminal of subunit epsilon, key residues important for the enzyme's function have been identified, paving the way for potential drug development targeting the F-ATP synthase.
Article
Plant Sciences
Ahmad Farhan Bhatti, Diana Kirilovsky, Herbert van Amerongen, Emilie Wientjes
Summary: The study using FLIM technology in Synechococcus elongatus cells revealed that state transitions occur homogeneously throughout the cell, with PSI enriched in the inner thylakoid, and heterogeneous distribution of PSII quenching and PBS.
Article
Biochemistry & Molecular Biology
Lishu Guo
Summary: This study discovered that mitochondrial ATP synthase inhibitory factor 1 (IF1) regulates the opening of PTP by interacting with the p53-CyPD complex. The presence of IF1 is necessary for the formation of the p53-CyPD complex and its inducing effect on PTP opening.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Plant Sciences
Amit K. Singh, Maria Santos-Merino, Jonathan K. Sakkos, Berkley J. Walker, Daniel C. Ducat
Summary: This study investigates the systemic changes in a model cyanobacterium caused by alterations in carbon availability. The results suggest that Rubisco activity and organization are key variables connected to regulatory pathways involved in metabolic balancing in cyanobacteria.
Article
Microbiology
Rees Rillema, Y. Hoang, Joshua S. MacCready, Anthony G. Vecchiarelli
Summary: Research shows that improper distribution of carboxysomes in cyanobacteria can result in slower cell growth, cell elongation, asymmetric cell division, and elevated levels of cellular Rubisco. Additionally, even wild-type S. elongatus undergoes cell elongation and asymmetric cell division when grown at lower temperatures or switched from high to ambient CO2 conditions. This suggests that the McdAB system plays a crucial role in maintaining the carbon fixation efficiency of Rubisco in cyanobacteria.
Article
Biotechnology & Applied Microbiology
Kristen E. Wendt, Patricia Walker, Annesha Sengupta, Justin Ungerer, Himadri B. Pakrasi
Summary: Natural transformation, a process by which bacteria uptake and incorporate extracellular DNA, plays a significant role in bacterial evolution. Cyanobacteria, serving as important model systems for studying photosynthesis, have not been extensively characterized for natural transformation. By introducing polymorphic alleles, a naturally transformable and fast-growing cyanobacterial strain was created.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Editorial Material
Biochemistry & Molecular Biology
Hector Miranda-Astudillo, Mariel Zarco-Zavala, Jose J. Garcia-Trejo, Diego Gonzalez-Halphen
Summary: The central rotor of F1Fo-ATP synthase can rotate clockwise or counterclockwise, functioning as either ATP synthase or ATP hydrolase. The regulation by inhibitory proteins helps preserve the key function of ATP synthesis. The study highlights the inhibitory role of the epsilon subunit in bacterial F1Fo-ATP synthase.
Article
Biochemistry & Molecular Biology
Alexander Krah, Bas van der Hoeven, Luuk Mestrom, Fabio Tonin, Kirsten C. C. Knobel, Peter J. Bond, Duncan G. G. McMillan
Summary: The study used molecular dynamics simulations to predict the impact of a residue outside the ATP binding site on ATP binding affinity in the B. subtilis epsilon subunit of the ATP synthase. The predictions were confirmed by experimental point mutations, demonstrating how MD can predict changes in substrate binding sites in simple protein structures. This research sheds light on why seemingly identical epsilon subunits in different ATP synthases have significantly different ATP binding affinities.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2021)
Article
Cell Biology
Chiara Galber, Simone Fabbian, Cristina Gatto, Martina Grandi, Stefania Carissimi, Manuel Jesus Acosta, Gianluca Sgarbi, Natascia Tiso, Francesco Argenton, Giancarlo Solaini, Alessandra Baracca, Massimo Bellanda, Valentina Giorgio
Summary: Mitochondrial protein IF1 binds to ATP synthase and inhibits ATP hydrolysis in ischemic tissues. It is overexpressed in tumors and acts as a pro-oncogenic protein. Study found that disruption of ATP5IF1 gene decreases colony formation and tumor mass development in HeLa cells, indicating the role of IF1 in cancer. Lack of IF1 does not affect cell proliferation or mitochondrial respiration, but sensitizes cells to opening of the permeability transition pore (PTP). IF1 binds to ATP synthase OSCP subunit in HeLa cells under oxidative phosphorylation conditions, and this interaction protects cancer cells from PTP-dependent apoptosis under normoxic conditions.
CELL DEATH & DISEASE
(2023)
Article
Chemistry, Physical
Thomas Heitkamp, Michael Boersch
Summary: FoF1-ATP synthases are rotary motor enzymes that catalyze ATP synthesis and hydrolysis. Single-molecule Forster resonance energy transfer has been used to detect their rotation. ABEL trap technology has extended observation time, revealing the fluctuating rates of ATP-dependent catalysis.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Editorial Material
Plant Sciences
Crisanto Gutierrez
Summary: Recent discoveries show that replicative DNA polymerases interact with histone dimers and tetramers, facilitating the transfer of chromatin features during DNA replication. This interaction may explain the transcriptional phenotypic defects observed in Arabidopsis mutants with mutations in genes encoding DNA polymerase subunits.
TRENDS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Jie Zeng, Wei-Nan Kang, Lin Jin, Ahmad Ali Anjum, Guo-Qing Li
Summary: The Vacuolar ATPase subunit F plays a crucial role in the development of Henosepilachna vigintioctopunctata, affecting larval growth, ecdysis, and adult emergence. Knockdown of HvvATPaseF resulted in changes in midgut morphology, reduced levels of biochemical markers, and a decrease in fat body abundance. Additionally, depletion of HvvATPaseF led to alterations in chitin biosynthesis gene expression and cuticle thickness in beetles.
INSECT MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Wakako Takano, Toru Hisabori, Ken-ichi Wakabayashi
Summary: This study established a rapid method for estimating cytosolic ATP levels from ciliary beating frequency in C. reinhardtii, allowing for quick estimation of ATP concentration in live cells. The method permits quantitative and noninvasive assessment of genetic mutations or inhibitors of photosynthesis and respiration, providing a convenient tool for studying ATP production mechanisms in C. reinhardtii or other ciliated organisms.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Plant Sciences
Keisuke Yoshida, Toru Hisabori
Summary: Various proteins in plant chloroplasts are regulated by thiol-based redox processes for light-responsive control. A specific form of phosphofructokinase (PFK), PFK5, is a novel redox-regulated protein that is suppressed upon reduction, while also being activated through oxidization by specific Trx proteins. This redox regulation of PFK5, together with other proteins like FBPase, plays a crucial role in switching light/dark metabolism in chloroplasts.
PLANT AND CELL PHYSIOLOGY
(2021)
Article
Multidisciplinary Sciences
Yuichi Yokochi, Keisuke Yoshida, Florian Hahn, Atsuko Miyagi, Ken-ichi Wakabayashi, Maki Kawai-Yamada, Andreas P. M. Weber, Toru Hisabori
Summary: The redox regulation of enzyme activity through cysteine residues in chloroplasts is crucial for maintaining NADPH homeostasis under different light conditions. A mutation that eliminates a redox switch in chloroplast NADP-malate dehydrogenase results in severe growth retardation in plants under short-day or fluctuating light conditions, highlighting the importance of fine-tuning the activity of key enzymes for efficient photosynthesis.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Kumiko Kondo, Masayuki Izumi, Kosuke Inabe, Keisuke Yoshida, Mari Imashimizu, Toshiharu Suzuki, Toru Hisabori
Summary: This study investigated the role of the beta-hairpin structure in the FoF1 ATP synthase of photosynthetic organisms in ATP synthesis and hydrolysis. By experimenting with genetically modified Synechocystis and proteoliposomes containing the ATP synthase complex, it was found that this structure plays a critical role in ATP synthesis and inhibits ATP hydrolysis.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Nae Fu, Kazunori Sugiura, Kumiko Kondo, Shungo Nakamura, Ken-ichi Wakabayashi, Toru Hisabori
Summary: Reactive oxygen species play a significant role in regulating cellular redox state, and two BRET-based redox sensors, ROBINc and ROBINy, have been developed to address the limitations of fluorescent probes in photosynthetic organisms. These sensors have been successfully used to observe dynamic redox changes in cancer cells and light/dark-dependent redox changes in photosynthetic cyanobacteria. The newly developed sensors are particularly useful for visualizing intracellular phenomena caused by redox changes in cells containing colored pigments as they do not require excitation light.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Plant Sciences
Jun Morishita, Ryutaro Tokutsu, Jun Minagawa, Toru Hisabori, Ken-ichi Wakabayashi
Summary: Researchers isolated seven mutants with positive phototaxis to study the ROS-dependent regulatory mechanism, suggesting that the regulation of phototactic sign is not a single pathway and is influenced by various cellular factors. Interestingly, five mutants showed faster growth rates than the wild type, indicating potential clues for efficient algae cultivation by analyzing mutants with defects in phototactic-sign regulation.
Article
Multidisciplinary Sciences
Yuichi Yokochi, Yuka Fukushi, Ken-ichi Wakabayashi, Keisuke Yoshida, Toru Hisabori
Summary: Thioredoxin and its related proteins play crucial roles in chloroplasts, regulating and coordinating the redox state of various photosynthesis-related proteins to adapt to the constantly changing light environment.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Yuma Asahina, Kazuma Sakamoto, Toru Hisabori, Ken-ichi Wakabayashi
Summary: This study found that TR1 functions as a pathway for scavenging ROS in Chlamydomonas reinhardtii. Knocking out TR1 reduced tolerance to high-light and ROS stresses, as well as affected the regulation of phototactic orientation.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Plant Sciences
Kazuha Fukui, Keisuke Yoshida, Yuichi Yokochi, Takatoshi Sekiguchi, Ken-ichi Wakabayashi, Toru Hisabori, Shoko Mihara
Summary: This study investigates the Trx-mediated regulation of phosphoribulokinase (PRK) in cyanobacteria and Arabidopsis. The results show that the redox status of the C-terminal Cys pair is crucial for activity regulation and complex dissociation/formation in both organisms.
PLANT AND CELL PHYSIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Yuka Fukushi, Yuichi Yokochi, Ken-ichi Wakabayashi, Keisuke Yoshida, Toru Hisabori
Summary: Thioredoxin (Trx) plays a crucial role in regulating enzyme activities in chloroplasts through reducing disulfide bonds. Some stromal proteins have slow response to changes in redox condition caused by light/dark changes, while ATP synthase gamma subunit on the thylakoid membrane shows high sensitivity. The difference in redox kinetics may be determined by the localization of each protein in the chloroplast.
Article
Chemistry, Multidisciplinary
Yasuto Todokoro, Su-Jin Kang, Toshiharu Suzuki, Takahisa Ikegami, Masatsune Kainosho, Masasuke Yoshida, Toshimichi Fujiwara, Hideo Akutsu
Summary: Proton translocation through the Fo component of F-type ATP synthase is facilitated by the rotation of the c-subunit ring. The study determined the chemical conformation of essential acidic residues in the c-ring and elucidated a unique proton translocation mechanism. These findings provide insights into ATP synthesis.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Takatoshi Sekiguchi, Keisuke Yoshida, Ken-Ichi Wakabayashi, Toru Hisabori
Summary: This study demonstrates that the redox regulation of CFoCF1 in ATP synthesis under light conditions is influenced by the oxidation of CF1-γ subunit and physiological oxidants in the chloroplast. The generation status of Delta mu H+ controls the redox regulation of CFoCF1 to prevent energetic disadvantages in plants.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Machi Toriu, Momoka Horie, Yuka Kumaki, Taku Yoneyama, Shin Kore-eda, Susumu Mitsuyama, Keisuke Yoshida, Toru Hisabori, Yoshitaka Nishiyama
Summary: Through studying the sensitivity of chloroplast-localized EF-Tu protein in Arabidopsis to oxidative stress, it was found that nucleotide-free cpEF-Tu can be oxidized by oxidative agents, leading to a decrease in translational activity. Addition of thioredoxin f1 can reduce the oxidized cpEF-Tu and reactivate its translational activity, indicating that the oxidation-reduction dependent mechanism plays a reversible regulatory role in chloroplast translation.
BIOCHEMICAL JOURNAL
(2023)
Review
Plant Sciences
Keisuke Yoshida, Toru Hisabori
Summary: Thiol/disulfide-based redox regulation is a common post-translational protein modification in plant chloroplasts, tightly associated with the light-induced activation of photosynthetic enzymes. The thioredoxin-mediated pathway has long been recognized as the fundamental machinery of chloroplast redox regulation, but recent studies have revealed the presence of multiple Trx isoforms and Trx-like proteins, as well as potential redox regulation targets among chloroplast enzymes. The discovery of novel redox-regulated processes and functional diversity in the Trx family proteins has shed new light on the molecular basis and physiological importance of this redox regulation system in chloroplasts.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Shungo Nakamura, Nae Fu, Kumiko Kondo, Ken-Ichi Wakabayashi, Toru Hisabori, Kazunori Sugiura
Summary: The development of a luminescent pH sensor Luphin, by fusing Nanoluc with a pH-sensitive GFP variant protein, allows for real-time pH measurement in plants and observation of photosynthetic processes.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)