Article
Biochemistry & Molecular Biology
Rodney Park, Chayanid Ongpipattanakul, Satish K. Nair, Albert A. Bowers, Brian Kuhlman
Summary: Using computational interface design, a substrate recognition domain was installed on a promiscuous enzyme, allowing for directed modification of peptides. The designed enzyme SH3-588 methylates peptides with catalytic efficiencies exceeding the wild-type enzyme by over 1,000-fold. In competition experiments, the designer enzyme preferentially modifies directed substrates over undirected substrates, showing potential for specific post-translational modifications in complex multisubstrate environments.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Fabian Poetz, Joshua Corbo, Yevgen Levdansky, Alexander Spiegelhalter, Doris Lindner, Vera Magg, Svetlana Lebedeva, Jorg Schweiggert, Johanna Schott, Eugene Valkov, Georg Stoecklin
Summary: The study identified RNF219 as an acetylation-regulated cofactor of the CCR4-NOT complex, which inhibits mRNA degradation mediated by the complex through interaction with NOT9. RNF219 attenuates global mRNA turnover in cells with a differential requirement of its RING domain.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Johannes van den Boom, Anja F. Kueck, Bojana Kravic, Helen Mueschenborn, Maike Giesing, Dongqing Pan, Farnusch Kaschani, Markus Kaiser, Andrea Musacchio, Hemmo Meyer
Summary: In this study, it was found that p97 recognizes an internal segment of the PP1 partner I3 and then threads an I3 peptide loop through the channel in p97 to strip I3 off PP1, demonstrating remarkable plasticity in substrate threading by p97.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2021)
Article
Microbiology
Aishwarya Srivastava, Pragya Nagar, Sumit Rathore, Nidhi Adlakha
Summary: This study reveals the crucial role of the linker domain in mediating polysaccharide disintegration during LPMO-mediated biomass fibrillation, suggesting its potential as a candidate for future carbohydrate-active enzyme engineering.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biotechnology & Applied Microbiology
Kaustubh Chandrakant Khaire, Kedar Sharma, Abhijeet Thakur, Vijayanand Suryakant Moholkar, Arun Goyal
Summary: Xylan extracted from sugarcane tops consisted mainly of xylose residues, glucuronic acid residues, and arabinose. It displayed a granular and porous surface structure, suitable for commercial substrate and oligosaccharide production. The xylan showed high specific activity with a recombinant xylanase from Clostridium thermocellum, making it a potential alternative substrate.
JOURNAL OF BIOSCIENCE AND BIOENGINEERING
(2021)
Article
Entomology
Ming-Bo Qu, Shao-Peng Sun, Yuan-Sheng Liu, Xiao-Rui Deng, Jun Yang, Qing Yang
Summary: The insect group II chitinase plays an important role in insect molting and acts synergistically with other chitinases to degrade cuticular chitin efficiently.
Article
Food Science & Technology
Jianli Zhou, Qiuya Gu, Yu Shen, Jean Damascene Harindintwali, Wenhua Yang, Shuliang Zou, Minghai Han, Chao Ma, Xiaobin Yu, Xiaobo Liu
Summary: By fusing a carbohydrate binding module, the affinity, activity, and thermostability of chitosanase Csn75 were enhanced. The specific enzyme activity of the fusion enzymes Csn75-CBM32 and Csn75-2CBM32 increased by 59.18% and 14.29% respectively compared to Csn75. This strategy provides a potential alternative for the bioproduction of desirable COSs for food applications.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Yingxuan Chen, Shudi Zhang, Zhenyu Zhai, Shuo Zhang, Jun Ma, Xiao Liang, Quanshun Li
Summary: This study successfully improved the binding affinity and degradation efficiency of cellulases for poly(ethylene terephthalate) (PET) by constructing fusion proteins, providing a practical and prospective strategy for enhancing the environmental treatment capacity of PET.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Shanshan Li, Kan-Yen Hsieh, Chiao- Kuo, Shih-Chieh Su, Kai-Fa Huang, Kaiming Zhang, Chung- Chang
Summary: Lon protease is able to degrade protein substrates in a processive fashion at each of its six proteolytic active sites, forming a deep groove that encloses the substrate polypeptide chain and allows for continuous cleavage in the C-to-N direction. An acidic residue at the binding groove exit is identified as essential for the proteolytic activity, likely promoting processive proteolysis through carboxyl-carboxylate interactions with cleaved intermediates. These findings reveal a previously unrecognized mechanism for processive substrate degradation by the Lon protease.
Article
Multidisciplinary Sciences
Yang Xu, Han Han, Ian Cooney, Yuxuan Guo, Noah G. Moran, Nathan R. Zuniga, John C. Price, Christopher P. Hill, Peter S. Shen
Summary: The structures of human p97 in complex with its p47 adaptor are reported. One structure is six-fold symmetric without substrate, while the other structure adopts a helical conformation with substrate running through the pore. These findings support a hand-over-hand mechanism of p97 for ATP hydrolysis.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Hao Li, Shuangshuang Shu, Miaomiao Zhou, Ying Chen, An Xiao, Yuanyuan Ma, Fengxin Zhu, Zheng Hu, Jing Nie
Summary: In this study, researchers found that Numb, an adaptor protein, increases the protein abundance of DEPTOR by inhibiting the ubiquitination mediated by SCF beta-TrCP2, leading to increased autophagy flux. Numb disrupts the interaction between beta-TrCP2 and SKP1 by directly binding with SKP1. In a mouse model of renal fibrosis, Numb expression was significantly increased and depletion of Numb reduced DEPTOR abundance and attenuated autophagy in fibrotic lesions. These findings indicate that Numb plays an important role in regulating autophagy.
CELL DEATH AND DIFFERENTIATION
(2022)
Article
Biochemistry & Molecular Biology
Konstantin E. Komolov, Sarah M. Sulon, Anshul Bhardwaj, Sin C. van Keulen, Nguyen Minh Duc, Daniela K. Laurinavichyute, Hua Jane Lou, Benjamin E. Turk, Ka Young Chung, Ron O. Dror, Jeffrey L. Benovic
Summary: In this study, the complex of CaM with GRK5 was analyzed structurally, computationally, and biochemically to reveal how CaM modulates GRK5 response to calcium, leading to activation and localization effects for selective substrate targeting by GRK5.
Article
Cell Biology
Fabienne Mauxion, Jerome Basquin, Sevim Ozgur, Marion Rame, Jana Albrecht, Ingmar Schaefer, Bertrand Seraphin, Elena Conti
Summary: The CCR4-NOT complex is an important mRNA deadenylase involved in constitutive and regulated mRNA decay pathways in the cytoplasm. While the structure and function of most modules in this complex are known, the N-terminal module remains unclear. However, recent studies using structural approaches have revealed the high-resolution architecture of the human N-terminal module, composed of CNOT1, CNOT10, and CNOT11. Further analysis showed that GGNBP2, a protein involved in tumor suppression and spermatogenesis, interacts with the conserved antenna domain of CNOT11. These findings highlight the N-terminal module as a crucial protein-protein interaction platform.
Article
Biotechnology & Applied Microbiology
Lijuan Gao, Yaru Su, Wenxia Song, Weican Zhang, Qingsheng Qi, Xuemei Lu
Summary: This study identified the gene locus chu_0922 as crucial for the degradation of crystalline cellulose in C. hutchinsonii. The gene is essential for the expression of cellulose-binding proteins and the cell surface localization of a key protein involved in crystalline cellulose utilization. The findings provide insights into the complex cellulose degradation system of C. hutchinsonii.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Vasty Osei-Amponsa, Kylie J. Walters
Summary: The ubiquitin-proteasome system (UPS) plays a critical role in protein quality control and regulation of protein lifespans. This article provides an overview of UPS, focusing on its receptors and deubiquitinating enzymes (DUBs). The importance of dynamics and the presence of functional domains in substrate receptors for binding and processing ubiquitin chains are highlighted. The UPS offers therapeutic opportunities, including the use of proteasome inhibitors and the development of PROTACs for degrading disease-associated proteins. The therapeutic potential of proteasome receptors, such as hRpn13, is discussed.
TRENDS IN BIOCHEMICAL SCIENCES
(2022)
Article
Microbiology
Indrani Mukhopadhya, Sarah Morais, Jenny Laverde-Gomez, Paul O. Sheridan, Alan W. Walker, William Kelly, Athol V. Klieve, Diane Ouwerkerk, Sylvia H. Duncan, Petra Louis, Nicole Koropatkin, Darrell Cockburn, Ryan Kibler, Philip J. Cooper, Carlos Sandoval, Emmanuelle Crost, Nathalie Juge, Edward A. Bayer, Harry J. Flint
ENVIRONMENTAL MICROBIOLOGY
(2018)
Article
Biochemistry & Molecular Biology
Albert Galera-Prat, Sarah Morais, Yael Vazana, Edward A. Bayer, Mariano Carrion-Vazquez
JOURNAL OF BIOLOGICAL CHEMISTRY
(2018)
Article
Chemistry, Physical
Haim Yuval Aviram, Menahem Pirchi, Yoav Barak, Inbal Riven, Gilad Haran
JOURNAL OF CHEMICAL PHYSICS
(2018)
Article
Multidisciplinary Sciences
Haim Yuval Aviram, Menahem Pirchi, Hisham Mazal, Yoav Barak, Inbal Riven, Gilad Haran
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2018)
Article
Microbiology
Lior Artzi, Tali Dadosh, Elad Milrot, Sarah Morais, Smadar Levin-Zaidman, Ely Morag, Edward A. Bayer
Article
Biotechnology & Applied Microbiology
Johanna Stern, Sarah Morais, Yonit Ben-David, Rachel Salama, Melina Shamshoum, Raphael Lamed, Yuval Shoham, Edward A. Bayer, Itzhak Mizrahi
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2018)
Article
Chemistry, Physical
Raisa Kantaev, Inbal Riven, Adi Goldenzweig, Yoav Barak, Orly Dym, Yoav Peleg, Shira Albeck, Sarel J. Fleishman, Gilad Haran
JOURNAL OF PHYSICAL CHEMISTRY B
(2018)
Review
Biochemistry & Molecular Biology
Sarah Morais, Itzhak Mizrahi
TRENDS IN MICROBIOLOGY
(2019)
Article
Biotechnology & Applied Microbiology
Amaranta Kahn, Sarah Morais, Anastasia P. Galanopoulou, Daehwan Chung, Nicholas S. Sarai, Neal Hengge, Dimitris G. Hatzinikolaou, Michael E. Himmel, Yannick J. Bomble, Edward A. Bayer
BIOTECHNOLOGY FOR BIOFUELS
(2019)
Article
Multidisciplinary Sciences
Hisham Mazal, Marija Iljina, Yoav Barak, Nadav Elad, Rina Rosenzweig, Pierre Goloubinoff, Inbal Riven, Gilad Haran
NATURE COMMUNICATIONS
(2019)
Article
Chemistry, Physical
Arina Dalaloyan, Andrea Martorana, Yoav Barak, Diana Gataulin, Eitan Reuveny, Andrew Howe, Michael Elbaum, Shira Albeck, Tamar Unger, Veronica Frydman, Elwy H. Abdelkader, Gottfried Otting, Daniella Goldfarb
Article
Environmental Sciences
Michal Pardo, Fanfan Xu, Michal Shemesh, Xinghua Qiu, Yoav Barak, Tong Zhu, Yinon Rudich
SCIENCE OF THE TOTAL ENVIRONMENT
(2019)
Article
Multidisciplinary Sciences
Angeliki Giannoulis, Akiva Feintuch, Yoav Barak, Hisham Mazal, Shira Albeck, Tamar Unger, Feng Yang, Xun-Cheng Su, Daniella Goldfarb
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biotechnology & Applied Microbiology
Yonit Ben-David, Sarah Morais, Edward A. Bayer, Itzhak Mizrahi
MICROBIAL BIOTECHNOLOGY
(2020)
Article
Biology
Meltem Tatli, Sarah Morais, Omar E. Tovar-Herrera, Yannick J. Bomble, Edward A. Bayer, Ohad Medalia, Itzhak Mizrahi
Summary: Microbes live and operate at micron and nanoscales, and studying them at these resolutions is crucial for understanding their ecology. The cellulose degradation process reveals how microbes build and utilize cellulosomal machinery at nanometer scales. Bacterial cells form "cellulosome capsules" driven by catalytic product-dependent dynamics, increasing the hydrolysis rate. Biosynthesis of this energy-intensive machinery and cell growth are decoupled at the single-cell level, suggesting a division-of-labor strategy through phenotypic heterogeneity. This study highlights the importance of intrapopulation interactions in understanding rates of fiber degradation.