Article
Biochemistry & Molecular Biology
Marlene Duarte, Victor D. Alves, Marcia Correia, Catarina Caseiro, Luis M. A. Ferreira, Maria Joao Romao, Ana Luisa Carvalho, Shabir Najmudin, Edward A. Bayer, Carlos M. G. A. Fontes, Pedro Bule
Summary: The cellulosome is a complex multi-enzyme structure secreted by anaerobic microorganisms for efficient degradation of lignocellulosic substrates. It consists of catalytic and non-catalytic components that are assembled through protein-protein interactions. The structure of an adaptor scaffoldin-borne ScaH Doc in complex with the Coh from anchoring scaffoldin ScaE was described, revealing a dual-binding mode interaction and identifying key residues for Coh recognition. Rational protein engineering was used to improve the affinity between the two modules, showing the potential for tailored Coh-Doc interactions in bioengineering applications.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biotechnology & Applied Microbiology
Jie Lu, Guodong Wang, Cuiping Yang, Zehao Peng, Lu Yang, Bowen Du, Chuanzhuang Guo, Songsen Sui, Jianbin Wang, Junlin Li, Ruiming Wang, Junqing Wang
Summary: In this study, an efficient recombinant strain of Escherichia coli was constructed for the production of ss-alanine using glucose as the raw material. The yield of ss-alanine was increased by blocking the L-lysine production pathway and improving catalytic efficiency with a two-enzyme method. By combining key enzymes with a cellulosome, the ss-alanine content reached a high level in a 5 L fermenter.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
He Wang, Xiaomin Jiang, Yongchang Qian, Lianghong Yin
Summary: The study successfully displayed beta-galactosidase on the surface of B. subtilis WB600 spores by introducing different pairs of cohesins and dockerins, which led to improved display efficiency.
Article
Green & Sustainable Science & Technology
Fatima Akram, Ikram ul Haq, Amna Aqeel, Zeeshan Ahmed, Fatima Iftikhar Shah
Summary: Human culture has been exploring the potential of using hyperthermophiles and their enzymes as a bio-competitive alternative to fossil-based fuel resources; research has characterized cellulolytic glycoside hydrolases and discussed engineering techniques to enhance the production and stability of thermostable cellulolytic enzymes.
RENEWABLE & SUSTAINABLE ENERGY REVIEWS
(2021)
Review
Agricultural Engineering
Huichuan Zhuang, Po-Heng Lee, Zhuoying Wu, Houde Jing, Jianyu Guan, Xiaojing Tang, Giin-Yu Amy Tan, Shao-Yuan Leu
Summary: Anaerobic digestion (AD) is a promising technology for recovering bioenergy from biodegradable biomass, including cellulose waste. Cellulose has potential in AD but the process is substrate-specific, with cellulolysis bacteria sensitive to enzyme-substrate interactions. The cellulosome, a self-assembled enzyme complex in bacteria, is being gradually studied, but the genomic fingerprints of culture-specific cellulosome in AD are unclear, especially under processing conditions. More research is needed to clarify the factors affecting cellulosome-induced cellulolysis in AD.
BIORESOURCE TECHNOLOGY
(2021)
Article
Microbiology
Fei Yan, Sheng Dong, Ya-Jun Liu, Xingzhe Yao, Chao Chen, Yan Xiao, Edward A. Bayer, Yuval Shoham, Chun You, Qiu Cui, Yingang Feng
Summary: This study clarifies the function and mechanism of substrate specificity of the five putative sugar transporters in Clostridium thermocellum. The results showed that transporter B is the major cellodextrin transporter, while transporter A is the major glucose transporter. The missing ATPase gene of transporter B was identified, and the correlation between transporter B and cellulosome production was revealed. Understanding the mechanism of cellodextrin utilization in C. thermocellum will facilitate the engineering of this strain for industrial applications.
Article
Multidisciplinary Sciences
Je-Kyung Ryu, Celine Bouchoux, Hon Wing Liu, Eugene Kim, Masashi Minamino, Ralph de Groot, Allard J. Katan, Andrea Bonato, Davide Marenduzzo, Davide Michieletto, Frank Uhlmann, Cees Dekker
Summary: This study found that cohesin in yeast exhibits clustering on DNA, displaying biomolecular condensation characteristics, which is dependent on DNA length. They proposed a bridging-induced phase separation model to explain this phenomenon and confirmed this model in live yeast cells through experiments.
Review
Agricultural Engineering
Aarjoo Sharma, Sanjeev Balda, Neena Capalash, Prince Sharma
Summary: Lignocellulosic biomass is a rich renewable resource that can be efficiently and cost-effectively transformed by constructing multifunctional enzymes. Researchers have explored various strategies for domain tailoring and extracellular secretion, as well as attempted to connect different catalytic activities in a single host.
BIORESOURCE TECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Ryota Takaki, Atreya Dey, Guang Shi, D. Thirumalai
Summary: The study combines modeling and simulations to predict the force-dependent velocity and step-size distribution of condensin in loop extrusion. The results suggest that a large conformational change in condensin is necessary for extruding chromosome loops, providing an allosteric basis for chromosome packaging in the restricted nuclear volume.
NATURE COMMUNICATIONS
(2021)
Editorial Material
Genetics & Heredity
Kyle P. Eagen
Summary: Two new studies demonstrate the involvement of BET proteins, particularly BRD4, in both loop extrusion and compartmentalization processes, where BRD4 facilitates one while surprisingly inhibiting the other.
Article
Multidisciplinary Sciences
Indra A. Shaltiel, Sumanjit Datta, Lea Lecomte, Markus Hassler, Marc Kschonsak, Sol Bravo, Catherine Stober, Jenny Ormanns, Sebastian Eustermann, Christian H. Haering
Summary: This study reveals the molecular mechanism underlying the activity of the active condensin complex in shaping chromosome structure by extruding DNA loops. The study shows that the condensin complex entraps the bases of a DNA loop in two separate chambers, with a power-stroke movement feeding DNA into the SMC-kleisin ring and the second chamber holding on upstream of the same DNA double helix.
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.
Editorial Material
Biochemistry & Molecular Biology
Davide Michieletto, Wendy A. Bickmore
Summary: In a recent study published in Science, Gabriele et al. utilized super-resolution imaging and computational modeling to quantify the dynamics of a topologically associating domain (TAD) in live cells. This research revealed that TADs spend most of their lifespan in a partially extruded state and that CTCF-CTCF loops are infrequent.
Article
Multidisciplinary Sciences
Alfredo Quijano-Rubio, Hsien-Wei Yeh, Jooyoung Park, Hansol Lee, Robert A. Langan, Scott E. Boyken, Marc J. Lajoie, Longxing Cao, Cameron M. Chow, Marcos C. Miranda, Jimin Wi, Hyo Jeong Hong, Lance Stewart, Byung-Ha Oh, David Baker
Summary: Protein switches have been repurposed for biosensor development by inverting the flow of information, creating modular molecular devices with a closed dark state and an open luminescent state. These sensors, based on thermodynamic coupling, require only one target binding domain for direct readout in solution, allowing for the detection of various molecules clinically, including the SARS-CoV-2 spike protein with high sensitivity and a 50-fold higher luminescence signal than background level. The modularity and sensitivity of this platform enable rapid sensor construction for a wide range of analytes, demonstrating the power of de novo protein design in creating multi-state protein systems with new functions.
Article
Biochemistry & Molecular Biology
Chao Chen, Kuan Qi, Fang Chi, Xiaojin Song, Yingang Feng, Qiu Cui, Ya-Jun Liu
Summary: This study investigates the inhibitory effects of different non-cellulose components of lignocellulose on the saccharification process mediated by cellulosome. It reveals that lignin and arabinoxylan have inhibitory effects, while xylan and xylooligosaccharides have minimal effects. The timely removal of dissolved xylan is found to be crucial for efficient saccharification.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biochemistry & Molecular Biology
Andrew Hettle, Alexander Fillo, Kento Abe, Patricia Massel, Benjamin Pluvinage, David N. Langelaan, Steven P. Smith, Alisdair B. Boraston
JOURNAL OF BIOLOGICAL CHEMISTRY
(2017)
Article
Multidisciplinary Sciences
Julie M. Grondin, Da Duan, Alyssa C. Kirlin, Kento T. Abe, Seth Chitayat, Holly L. Spencer, Craig Spencer, Alisha Campigotto, Scott Houliston, Cheryl H. Arrowsmith, John S. Allingham, Alisdair B. Boraston, Steven P. Smith
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Biochemistry & Molecular Biology
Corey A. Stevens, Joanna Semrau, Dragos Chiriac, Morgan Litschko, Robert L. Campbell, David N. Langelaan, Steven P. Smith, Peter L. Davies, John S. Allingham
Article
Multidisciplinary Sciences
Pedro Bule, Victor D. Alves, Vered Israeli-Ruimy, Ana L. Carvalho, Luis M. A. Ferreira, Steven P. Smith, Harry J. Gilbert, Shabir Najmudin, Edward A. Bayer, Carlos M. G. A. Fontes
SCIENTIFIC REPORTS
(2017)
Article
Multidisciplinary Sciences
Shuaiqi Guo, Corey A. Stevens, Tyler D. R. Vance, Luuk L. C. Olijve, Laurie A. Graham, Robert L. Campbell, Saeed R. Yazdi, Carlos Escobedo, Maya Bar-Dolev, Victor Yashunsky, Ido Braslavsky, David N. Langelaan, Steven P. Smith, John S. Allingham, Ilja K. Voets, Peter L. Davies
Article
Biochemistry & Molecular Biology
Pedro Bule, Kate Cameron, Jose A. M. Prates, Luis M. A. Ferreira, Steven P. Smith, Harry J. Gilbert, Edward A. Bayer, Shabir Najmudin, Carlos M. G. A. Fontes, Victor D. Alves
JOURNAL OF BIOLOGICAL CHEMISTRY
(2018)
Article
Biochemistry & Molecular Biology
Bryce Nelson, Jarrett Adams, Andreas Kuglstatter, Zhijian Li, Seth F. Harris, Yang Liu, Sandya Bohini, Han Ma, Klaus Klumpp, Junjun Gao, Sachdev S. Sidhu
JOURNAL OF MOLECULAR BIOLOGY
(2018)
Article
Medicine, Research & Experimental
Zvezdan Pavlovic, Jarrett J. Adams, Levi L. Blazer, Amandeep K. Gakhal, Nick Jarvik, Zachary Steinhart, Melanie Robitaille, Keith Mascall, James Pan, Stephane Angers, Jason Moffat, Sachdev S. Sidhu
Article
Medicine, Research & Experimental
Minyoung Park, Xiaobai Xu, Weixian Min, Seiji N. Sugiman-Marangos, Greg L. Beilhartz, Jarret J. Adams, Sachdev S. Sidhu, Eyal Grunebaum, Roman A. Melnyk
MOLECULAR PHARMACEUTICS
(2018)
Article
Oncology
Daniel Newsted, Sunandan Banerjee, Kathleen Watt, Sarah Nersesian, Peter Truesdell, Levi L. Blazer, Lia Cardarelli, Jarrett J. Adams, Sachdev S. Sidhu, Andrew W. Craig
Article
Biology
Yuyong Tao, Monika Mis, Levi Blazer, Mart Ustav, Zachary Steinhart, Rony Chidiac, Elli Kubarakos, Siobhan O'Brien, Xiaomei Wang, Nick Jarvik, Nish Patel, Jarrett Adams, Jason Moffat, Stephane Angers, Sachdev S. Sidhu
Article
Medicine, Research & Experimental
Eugenio Gallo, Abdellali Kelil, Peter E. Bayliss, Ajitha Jeganathan, Olga Egorova, Lynda Ploder, Jarret A. Adams, Patricia Giblin, Sachdev S. Sidhu
Article
Medicine, Research & Experimental
Leonie Enderle, Karim H. Shalaby, Maryna Gorelik, Alexander Weiss, Levi L. Blazer, Marcin Paduch, Lia Cardarelli, Anthony Kossiakoff, Jarrett J. Adams, Sachdev S. Sidhu
Summary: Researchers developed a novel Double Antigen T cell Engager (DATE) format for guiding T cells to specific features of solid cancer cells. They further improved double-DATE to target two tumor antigens simultaneously, enhancing selectivity in immune redirection.
Article
Biochemistry & Molecular Biology
Steven P. Smith, Edward A. Bayer, Mirjam Czjzek
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2017)
Article
Biophysics
Brigid S. Conroy, Emma R. Weiss, Steven P. Smith, David N. Langelaan
BIOMOLECULAR NMR ASSIGNMENTS
(2017)
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)