Article
Physics, Fluids & Plasmas
Emma Lathouwers, David A. Sivak
Summary: Researchers are investigating the general design principles for effective energy conversion in microscopic biological systems. Using a model of two strongly coupled stochastic rotary motors, they found that intermediate coupling strength leads to prominent thermodynamic characteristics, such as maximum power and information transfer, as well as equal subsystem entropy production rates.
Article
Biochemistry & Molecular Biology
Francisco Mendoza-Hoffmann, Lingyun Yang, Damiano Buratto, Jorge Brito-Sanchez, Gilberto Garduno-Javier, Emiliano Salinas-Lopez, Cristina Uribe-Alvarez, Raquel Ortega, Oliver Sotelo-Serrano, Miguel angel Cevallos, Leticia Ramirez-Silva, Salvador Uribe-Carvajal, Gerardo Perez-Hernandez, Heliodoro Celis-Sandoval, Jose J. Garcia-Trejo
Summary: In this study, the inhibitory function of the δ subunit in a-proteobacteria was investigated using various methods. It was found that the inhibitory function is mainly present in free-living a-proteobacteria, while it is not important in some symbiotic and parasitic a-proteobacteria.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Review
Microbiology
Francisco Mendoza-Hoffmann, Mariel Zarco-Zavala, Raquel Ortega, Heliodoro Celis-Sandoval, Alfredo Torres-Larios, Jose J. Garcia-Trejo
Summary: This study analyzes the evolution of the F1FO-ATPase inhibitory proteins. Results show that various inhibitory proteins have emerged in bacteria, mitochondria, and chloroplasts to selectively block the activity of F1FO-ATPase. The loss of inhibitory function and ATP-binding site correlates with the evolutionary divergence of different subunits. The zeta subunit has replaced epsilon as the primary inhibitor in free-living bacteria, but its inhibitory function is partially or completely lost in some symbiotic and parasitic bacteria.
Article
Biochemistry & Molecular Biology
David M. Hoi, Sabryna Junker, Lukas Junk, Kristin Schwechel, Katharina Fischel, David Podlesainski, Paige M. E. Hawkins, Lasse van Geelen, Farnusch Kaschani, Julia Leodolter, Francesca Ester Morreale, Stefan Kleine, Somraj Guha, Klaus Rumpel, Volker M. Schmiedel, Harald Weinstabl, Anton Meinhart, Richard J. Payne, Markus Kaiser, Markus Harti, Guido Boehmelt, Uli Kazmaier, Rainer Kalscheuer, Tim Clausen
Summary: By using quantitative proteomics, we found that the antibiotics cyclomarin A and ecumicin can cause proteome imbalances and upregulation of two unannotated stress response factors, ClpC2 and ClpC3. These proteins likely protect the Clp protease from excessive misfolded proteins or the damaging effects of cyclomarin A. By developing a BacPROTAC that degrades both ClpC1 and its caretaker ClpC2, we significantly enhanced the potency of killing pathogenic Mycobacterium tuberculosis.
Article
Virology
Li-Jie Huo, Peng-Yuan Lu, Dian-Xiang Li, Xiu-Zhen Shi
Summary: Short open reading frames (sORFs) are a newly identified family of genes. Two ATP synthase subunits (MjATP5I and MjATP5L) were found to be encoded by sORFs in kuruma shrimp (Marsupenaeus japonicus). These genes are widely expressed in shrimp tissues and are upregulated in hemocytes and intestines in response to WSSV challenge. Further investigation revealed that MjATP5I and MjATP5L facilitate WSSV duplication by regulating ATP production and the expression of antimicrobial peptide genes, and their knockdown improves shrimp survival rates.
Article
Plant Sciences
Akito Machida, Kumiko Kondo, Ken-ichi Wakabayashi, Kan Tanaka, Toru Hisabori
Summary: In this study, the importance of the amino acid at position 252 across cyanobacteria was elucidated by introducing amino acid substitutions in Synechocystis sp. PCC 6803. The results showed that the specific volume of this amino acid is crucial for maintaining cell growth and is related to enzyme complex formation.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Biochemical Research Methods
Parth Garg, Sukriti Sacher, Mrinal, Atul, Prutyay Gautam, Arjun Ray
Summary: This article introduces a method that accurately identifies internal cavities in proteins. The method provides detailed information about the properties of the lining residues and can also calculate conservation scores for the detected residues, allowing for a comprehensive functional characterization of the cavities.
Article
Biochemical Research Methods
Parth Garg, Sukriti Sacher, Mrinal, Atul, Prutyay Gautam, Arjun Ray
Summary: The article introduces a new method called CICLOP that accurately identifies the structure and characteristics of protein internal cavities, as well as provides functional characterization. This method fills the gap of computational tools for accurate characterization of protein internal cavities.
Review
Chemistry, Medicinal
Milan Urban, Veronika Slachtova, Lucie Brulikova
Summary: Mycobacterial energy metabolism, particularly the oxidative phosphorylation pathway, has become increasingly important as a molecular target for the development of new anti-TB drugs. Small organic molecules targeting this pathway have shown promising activity against latent and resistant TB strains, with FDA-approved inhibitors confirming the value of targeting mycobacterial energy metabolism.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Agriculture, Multidisciplinary
Xue Yao, Yunpeng Duan, Zhongyuan Deng, Wenli Zhao, Jizhen Wei, Xianchun Li, Shiheng An
Summary: This study confirms the involvement of Helicoverpa armigera ATP synthase subunit a (HaATPs-a) in Cry1Ac resistance and demonstrates the downregulation of HaATPs-a expression in response to Cry1Ac. The interaction between HaATPs-a and Cry1Ac is verified, and purified HaATPs-a is shown to enhance Cry1Ac toxicity to H. armigera larvae.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Takahiro Kosugi, Tatsuya Iida, Mikio Tanabe, Ryota Iino, Nobuyasu Koga
Summary: Allostery allows for the coordinated function of protein complexes by facilitating cooperative interaction between subunits. This study presents an approach to artificially create allosteric sites in protein complexes. By restoring the lost functions of pseudo-active sites, it is possible to generate allosteric sites within certain protein complexes. Computational design was used to restore ATP-binding ability in the pseudo-active site of the B subunit of V-1-ATPase. Single-molecule experiments with X-ray crystallography analysis demonstrated that binding of ATP to the designed allosteric site enhances the activity of V-1 and allows for modulation of rotation rate through ATP's binding affinity. This approach holds promise for programmable allosteric control of protein complex functions.
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
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
Biochemistry & Molecular Biology
Owen D. Jarman, Olivier Biner, Judy Hirst
Summary: The regulation of ATP synthase in Paracoccus denitrificans involves the epsilon and zeta subunits as well as Mg-ADP inhibition, as shown through studies on mutants lacking the epsilon-CTD and the zeta subunit. Activation of ATP hydrolysis was not substantial in these mutants, indicating the importance of other inhibitory mechanisms in controlling the enzyme.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2021)
Article
Biotechnology & Applied Microbiology
Yucheng Lu, Qingyun Liu, Zhiqi Huang, Xiuli Chen, Chunling Yang, Yueling Zhang, Yongzhen Zhao, Fan Wang
Summary: Researchers identified candidate genes affecting the growth rate of Penaeus vannamei through a high throughput method, and confirmed the correlation between these genes and shrimp growth in various lineages.
Article
Plant Sciences
Yoshihisa Hirakawa, Ken-ichiro Ishida
Article
Evolutionary Biology
Shigekatsu Suzuki, Ken-Ichiro Ishida, Yoshihisa Hirakawa
GENOME BIOLOGY AND EVOLUTION
(2016)
Article
Plant Sciences
Shigekatsu Suzuki, Yoshihisa Hirakawa, Rumiko Kofuji, Mamoru Sugita, Ken-ichiro Ishida
JOURNAL OF PLANT RESEARCH
(2016)
Article
Marine & Freshwater Biology
Yoshihisa Hirakawa, Takuro Nakayama, Nadine Keilert, Ken-ichiro Ishida
PHYCOLOGICAL RESEARCH
(2017)
Article
Multidisciplinary Sciences
Javier del Campo, Erick R. James, Yoshihisa Hirakawa, Rebecca Fiorito, Martin Kolisko, Nicholas A. T. Irwin, Varsha Mathur, Vittorio Boscaro, Elisabeth Hehenberger, Anna Karnkowska, Rudolf H. Scheffrahn, Patrick J. Keeling
SCIENTIFIC REPORTS
(2017)
Article
Multidisciplinary Sciences
Shigekatsu Suzuki, Rikiya Endoh, Ri-ichiroh Manabe, Moriya Ohkuma, Yoshihisa Hirakawa
SCIENTIFIC REPORTS
(2018)
Article
Ecology
Yuichiro Kashiyama, Akiko Yokoyama, Takashi Shiratori, Sebastian Hess, Fabrice Not, Charles Bachy, Andres Gutierrez-Rodriguez, Jun Kawahara, Toshinobu Suzaki, Masami Nakazawa, Takahiro Ishikawa, Moe Maruyama, Mengyun Wang, Man Chen, Yingchun Gong, Kensuke Seto, Maiko Kagami, Yoko Hamamoto, Daiske Honda, Takahiro Umetani, Akira Shihongi, Motoki Kayama, Toshiki Matsuda, Junya Taira, Akinori Yabuki, Masashi Tsuchiya, Yoshihisa Hirakawa, Akane Kawaguchi, Mami Nomura, Atsushi Nakamura, Noriaki Namba, Mitsufumi Matsumoto, Tsuyoshi Tanaka, Tomoko Yoshino, Rina Higuchi, Akihiro Yamamoto, Tadanobu Maruyama, Aika Yamaguchi, Akihiro Uzuka, Shinya Miyagishima, Goro Tanifuji, Masanobu Kawachi, Yusuke Kinoshita, Hitoshi Tamiaki
Article
Parasitology
Hirokazu Sakarnoto, Yoshihisa Hirakawa, Ken-ichiro Ishida, Patrick J. Keeling, Kiyoshi Kita, Motomichi Matsuzaki
PARASITOLOGY INTERNATIONAL
(2019)
Article
Biochemistry & Molecular Biology
Yoshihisa Hirakawa, Arisa Watanabe
Article
Biochemical Research Methods
Drahomira Faktorova, R. Ellen R. Nisbet, Jose A. Fernandez Robledo, Elena Casacuberta, Lisa Sudek, Andrew E. Allen, Manuel Ares, Cristina Areste, Cecilia Balestreri, Adrian C. Barbrook, Patrick Beardslee, Sara Bender, David S. Booth, Francois-Yves Bouget, Chris Bowler, Susana A. Breglia, Colin Brownlee, Gertraud Burger, Heriberto Cerutti, Rachele Cesaroni, Miguel A. Chiurillo, Thomas Clemente, Duncan B. Coles, Jackie L. Collier, Elizabeth C. Cooney, Kathryn Coyne, Roberto Docampo, Christopher L. Dupont, Virginia Edgcomb, Elin Einarsson, Pia A. Elustondo, Fernan Federici, Veronica Freire-Beneitez, Nastasia J. Freyria, Kodai Fukuda, Paulo A. Garcia, Peter R. Girguis, Fatma Gomaa, Sebastian G. Gornik, Jian Guo, Vladimir Hampl, Yutaka Hanawa, Esteban R. Haro-Contreras, Elisabeth Hehenberger, Andrea Highfield, Yoshihisa Hirakawa, Amanda Hopes, Christopher J. Howe, Ian Hu, Jorge Ibanez, Nicholas A. T. Irwin, Yuu Ishii, Natalia Ewa Janowicz, Adam C. Jones, Ambar Kachale, Konomi Fujimura-Kamada, Binnypreet Kaur, Jonathan Z. Kaye, Eleanna Kazana, Patrick J. Keeling, Nicole King, Lawrence A. Klobutcher, Noelia Lander, Imen Lassadi, Zhuhong Li, Senjie Lin, Jean-Claude Lozano, Fulei Luan, Shinichiro Maruyama, Tamara Matute, Cristina Miceli, Jun Minagawa, Mark Moosburner, Sebastian R. Najle, Deepak Nanjappa, Isabel C. Nimmo, Luke Noble, Anna M. G. Novak Vanclova, Mariusz Nowacki, Isaac Nunez, Arnab Pain, Angela Piersanti, Sandra Pucciarelli, Jan Pyrih, Joshua S. Rest, Mariana Rius, Deborah Robertson, Albane Ruaud, Inaki Ruiz-Trillo, Monika A. Sigg, Pamela A. Silver, Claudio H. Slamovits, G. Jason Smith, Brittany N. Sprecher, Rowena Stern, Estienne C. Swart, Anastasios D. Tsaousis, Lev Tsypin, Aaron Turkewitz, Jernej Turnsek, Matus Valach, Valerie Verge, Peter von Dassow, Tobias von der Haar, Ross F. Waller, Lu Wang, Xiaoxue Wen, Glen Wheeler, April Woods, Huan Zhang, Thomas Mock, Alexandra Z. Worden, Julius Lukes
Correction
Biochemical Research Methods
Drahomira Faktorova, R. Ellen R. Nisbet, Jose A. Robledo, Elena Casacuberta, Lisa Sudek, Andrew E. Allen, Manuel Ares, Cristina Areste, Cecilia Balestreri, Adrian C. Barbrook, Patrick Beardslee, Sara Bender, David S. Booth, Francois-Yves Bouget, Chris Bowler, Susana A. Breglia, Colin Brownlee, Gertraud Burger, Heriberto Cerutti, Rachele Cesaroni, Miguel A. Chiurillo, Thomas Clemente, Duncan B. Coles, Jackie L. Collier, Elizabeth C. Cooney, Kathryn Coyne, Roberto Docampo, Christopher L. Dupont, Virginia Edgcomb, Elin Einarsson, Pia A. Elustondo, Fernan Federici, Veronica Freire-Beneitez, Nastasia J. Freyria, Kodai Fukuda, Paulo A. Garcia, Peter R. Girguis, Fatma Gomaa, Sebastian G. Gornik, Jian Guo, Vladimir Hampl, Yutaka Hanawa, Esteban R. Haro-Contreras, Elisabeth Hehenberger, Andrea Highfield, Yoshihisa Hirakawa, Amanda Hopes, Christopher J. Howe, Ian Hu, Jorge Ibanez, Nicholas A. T. Irwin, Yuu Ishii, Natalia Ewa Janowicz, Adam C. Jones, Ambar Kachale, Konomi Fujimura-Kamada, Binnypreet Kaur, Jonathan Z. Kaye, Eleanna Kazana, Patrick J. Keeling, Nicole King, Lawrence A. Klobutcher, Noelia Lander, Imen Lassadi, Zhuhong Li, Senjie Lin, Jean-Claude Lozano, Fulei Luan, Shinichiro Maruyama, Tamara Matute, Cristina Miceli, Jun Minagawa, Mark Moosburner, Sebastian R. Najle, Deepak Nanjappa, Isabel C. Nimmo, Luke Noble, Anna M. G. Vanclova, Mariusz Nowacki, Isaac Nunez, Arnab Pain, Angela Piersanti, Sandra Pucciarelli, Jan Pyrih, Joshua S. Rest, Mariana Rius, Deborah Robertson, Albane Ruaud, Inaki Ruiz-Trillo, Monika A. Sigg, Pamela A. Silver, Claudio H. Slamovits, G. Smith, Brittany N. Sprecher, Rowena Stern, Estienne C. Swart, Anastasios D. Tsaousis, Lev Tsypin, Aaron Turkewitz, Jernej Turnsek, Matus Valach, Valerie Verge, Peter von Dassow, Tobias von der Haar, Ross F. Waller, Lu Wang, Xiaoxue Wen, Glen Wheeler, April Woods, Huan Zhang, Thomas Mock, Alexandra Z. Worden, Julius Lukes
Article
Microbiology
Ryo Harada, Yoshihisa Hirakawa, Akinori Yabuki, Yuichiro Kashiyama, Moe Maruyama, Ryo Onuma, Petr Soukal, Shinya Miyagishima, Vladimir Hampl, Goro Tanifuji, Yuji Inagaki
Article
Biotechnology & Applied Microbiology
Kodai Fukuda, Elizabeth C. Cooney, Nicholas A. T. Irwin, Patrick J. Keeling, Yoshihisa Hirakawa
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2020)
Article
Biology
Yoshihisa Hirakawa, Miki Senda, Kodai Fukuda, Hong Yang Yu, Masaki Ishida, Masafumi Taira, Kazushi Kinbara, Toshiya Senda
Summary: COG4337 proteins are a novel metal-independent variant of iota-class carbonic anhydrases, which accelerate CO2 hydration and are localized in organelles for CO2 metabolism. They share structural features with iota-class CAs but exhibit activity without reliance on metals.
Article
Biochemistry & Molecular Biology
Yoshihisa Hirakawa, Yutaka Hanawa, Kohei Yoneda, Iwane Suzuki
Summary: This study reports the discovery of a gene encoding a fusion protein of beta-CA and iota-CA in a haptophyte species. The C-terminal iota-CA region of the fusion protein catalyzes CO2 hydration, while the N-terminal beta-CA region loses its enzymatic activity. This finding suggests an intermediate stage in which mitochondrial beta-CA is replaced by plastid-localized iota-CA in haptophyte species.