Article
Biochemistry & Molecular Biology
Takamitsu Miyafusa, Hideki Watanabe, Shinya Honda
Summary: In this study, an artificial protein AF.2A1 was developed to specifically recognize non-native IgG structures, showing potential applications in quality control of biopharmaceuticals. AF.2A1 was found to recognize an exposed hydrophobic core centered on Trp417, providing molecular rationale for its usage.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Review
Biotechnology & Applied Microbiology
Chao Liu, Jin-Song Gong, Chang Su, Hui Li, Heng Li, Zhi-Ming Rao, Zheng-Hong Xu, Jin-Song Shi
Summary: Pichia pastoris has been recognized as an important platform for heterologous protein production. This article summarizes the process of protein secretion, modification, and transportation in P. pastoris, as well as the roles played by key proteins and their co-expression effects.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Food Science & Technology
Xue Zhang, Chunyue Zhang, Mian Zhou, Quanming Xia, Liqiang Fan, Liming Zhao
Summary: Chitin and its derivatives have diverse applications, and this research achieved increased chitin content in yeast cell walls through gene overexpression and culture condition optimization. This is the first report of chitin production in engineered Pichia pastoris via biosynthetic pathway enhancement.
Article
Biotechnology & Applied Microbiology
Jiao Meng, Shufan Liu, Le Gao, Kai Hong, Shuguang Liu, Xin Wu
Summary: This study elucidated a unique mechanism of P. pastoris for efficient methanol utilization, higher temperature resistance, and high protein synthesis, providing a P. pastoris cell factory for SCP production with environmental, economic, and nutritional benefits. Through adaptive laboratory evolution and metabolic engineering, the engineered strain produced high levels of SCP from methanol in a pilot-scale fed-batch culture, highlighting its potential in sustainable biomanufacturing.
MICROBIAL CELL FACTORIES
(2023)
Article
Biotechnology & Applied Microbiology
Nora Tir, Lina Heistinger, Clemens Gruenwald-Gruber, Leo A. Jakob, Stephan Dickgiesser, Nicolas Rasche, Diethard Mattanovich
Summary: This study successfully employed Pichia pastoris for cost-effective laboratory-scale production of a monoclonal antibody with an unnatural amino acid. By modifying the secretion signal prepeptide and overexpressing lumenal chaperones, as well as knocking out vacuolar targeting for protein degradation, the production yield of the antibody was significantly increased.
MICROBIAL CELL FACTORIES
(2022)
Review
Biochemistry & Molecular Biology
Cristina Bustos, Johan Quezada, Rhonda Veas, Claudia Altamirano, Stephanie Braun-Galleani, Patrick Fickers, Julio Berrios
Summary: Komagataella phaffii has become an important microorganism for recombinant protein production, particularly in industrial settings. Significant progress has been made in improving recombinant protein productivity and reducing production costs. Cell engineering approaches, including metabolic engineering, transcription factor modulation, and manipulation of protein folding and secretion pathways, have shown promising results. However, more research is needed in optimizing cultivation parameters in larger-scale bioreactors.
Review
Microbiology
Yingjie Pan, Jiao Yang, Jianping Wu, Lirong Yang, Hao Fang
Summary: This article summarizes the most recent advances of Pichia pastoris as an efficient platform for recombinant protein production in the past 5 years, including innovative genetic tools and methodologies for manipulating gene expression systems, novel pathways in metabolic engineering, and the application of high-throughput screening coupled with mathematical models.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Yumei Hu, Hao Li, Jian Min, Yuanyuan Yu, Weidong Liu, Jian-Wen Huang, Lilan Zhang, Yunyun Yang, Longhai Dai, Chun-Chi Chen, Rey-Ting Guo
Summary: Deoxynivalenol (DON) and its acetylated derivatives, such as 3-acetyl-deoxynivalenol (3A-DON) and 15-acetyldeoxynivalenol (15A-DON), are toxic mycotoxins in Fusarium contaminated cereals. A specialized glyoxalase enzyme from Gossypium hirsutum (SPG) can reduce the toxicity of 3A-DON by conducting an isomerization reaction. This study shows that SPG can also recognize and detoxify 15A-DON and DON, possibly using the same mechanism as for 3A-DON. The researchers engineered a variant of SPG with increased catalytic activity towards all three toxins.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biotechnology & Applied Microbiology
Dominic Gaetjen, Florian Tomszak, Johann-Christoph Dettmann, Miriam Droste, Volker Noelle, Marek Wieczorek
Summary: This study successfully established a Pichia pastoris surface display system for antibody selection and expression. By optimizing the combination of genetic elements, high levels of antibody fragment surface display can be achieved.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Immunology
Nicholas J. MacDonald, Kavita Singh, Karine Reiter, Nguyen Vu, Richard Shimp, Apostolos G. Gittis, Beth Chen, Martin Burkhardt, Baoshan Zhang, Zhixiong Wang, Raul Herrera, Mackenzie Moler, Duck-Yeon Lee, Sachy Orr-Gonzalez, Jessica Herrod, Lynn E. Lambert, Kelly M. Rausch, Olga Muratova, David S. Jones, Yimin Wu, Albert J. Jin, David N. Garboczi, Patrick E. Duffy, David L. Narum
Summary: The development of a malaria vaccine that can block transmission of the parasite from mosquitoes to humans is crucial for malaria elimination efforts. The use of Pfs25, a protein on the surface of the parasite, is being investigated as a transmission-blocking vaccine. Two recombinant forms of Pfs25, Pfs25H and Pfs25M, have been studied for their structural and immunological differences.
Article
Biotechnology & Applied Microbiology
Neil C. Dalvie, Andrew M. Biedermann, Sergio A. Rodriguez-Aponte, Christopher A. Naranjo, Harish D. Rao, Meghraj P. Rajurkar, Rakesh R. Lothe, Umesh S. Shaligram, Ryan S. Johnston, Laura E. Crowell, Seraphin Castelino, Mary K. Tracey, Charles A. Whittaker, J. Christopher Love
Summary: Genetically engineered Komagataella phaffii strain was developed to produce RBD protein without methanol induction, increasing production efficiency. This engineered strain enables scalability for manufacturing RBD-based vaccine antigens and other variants for future vaccines.
BIOTECHNOLOGY AND BIOENGINEERING
(2022)
Article
Engineering, Biomedical
Shuo-Fu Yuan, Sierra M. Brooks, Annalee W. Nguyen, Wen-Ling Lin, Trevor G. Johnston, Jennifer A. Maynard, Alshakim Nelson, Hal S. Alper
Summary: Traditional production of industrial and therapeutic proteins by eukaryotic cells typically requires large-scale fermentation capacity, which is not easily portable or reusable for on-demand protein production applications. In this study, a hydrogel-based technique was used to immobilize engineered Pichia pastoris for preservable, on-demand production and secretion of medium- and high-molecular weight proteins. This platform shows potential for establishing a cost-effective bioprocessing strategy for on-demand protein production.
BIOACTIVE MATERIALS
(2021)
Review
Biotechnology & Applied Microbiology
Clara Vida Galrao Correa Carneiro, Luana Assis Serra, Thalyta Fraga Pacheco, Leticia Maria Mallmann Ferreira, Livia Teixeira Duarte Brandao, Mariana Nogueira de Moura Freitas, Debora Trichez, Joao Ricardo Moreira de Almeida
Summary: The development of bio-based processes to replace fossil-based ones has been driven by the need for a more sustainable society. Microorganisms, particularly the methylotrophic yeast Komagataella phaffii, have been used to convert renewable carbon sources into various products, such as chemicals and proteins. This review summarizes the taxonomy and diversity of Komagataella and discusses recent advancements in cell engineering for the production of renewable chemicals and proteins. Strategies for optimizing and developing new fermentative processes using K. phaffii as a cell factory are also presented and discussed.
FERMENTATION-BASEL
(2022)
Article
Multidisciplinary Sciences
Neil C. Dalvie, Sergio A. Rodriguez-Aponte, Brittany L. Hartwell, Lisa H. Tostanoski, Andrew M. Biedermann, Laura E. Crowell, Kawaljit Kaur, Ozan S. Kumru, Lauren Carter, Jingyou Yu, Aiquan Chang, Katherine McMahan, Thomas Courant, Celia Lebas, Ashley A. Lemnios, Kristen A. Rodrigues, Murillo Silva, Ryan S. Johnston, Christopher A. Naranjo, Mary Kate Tracey, Joseph R. Brady, Charles A. Whittaker, Dongsoo Yun, Natalie Brunette, Jing Yang Wang, Carl Walkey, Brooke Fiala, Swagata Kar, Maciel Porto, Megan Lok, Hanne Andersen, Mark G. Lewis, Kerry R. Love, Danielle L. Camp, Judith Maxwell Silverman, Harry Kleanthous, Sangeeta B. Joshi, David B. Volkin, Patrice M. Dubois, Nicolas Collin, Neil P. King, Dan H. Barouch, Darrell J. Irvine, J. Christopher Love
Summary: Subunit vaccines based on recombinant proteins are crucial tools for controlling COVID-19 due to their low manufacturing cost, scalability, and proven safety and efficacy. Engineered RBD variants exhibit high manufacturability and immunogenicity, showing enhanced immune responses after a single dose and cross-reactivity to new variants of concern.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biotechnology & Applied Microbiology
Xihao Liao, Lu Li, Aysha Jameel, Xin-Hui Xing, Chong Zhang
Summary: A CRISPR-based toolbox for gene editing and transcriptional regulation in P. pastoris was developed, allowing efficient and flexible gene expression control. This toolkit will accelerate the application of P. pastoris in metabolic engineering and synthetic biology by providing a simple and multifunctional system for genetic engineering.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Mattia Deluigi, Lena Morstein, Matthias Schuster, Christoph Klenk, Lisa Merklinger, Riley R. Cridge, Lazarus A. de Zhang, Alexander Klipp, Santiago Vacca, Tasneem M. Vaid, Peer R. E. Mittl, Pascal Egloff, Stefanie A. Eberle, Oliver Zerbe, David K. Chalmers, Daniel J. Scott, Andreas Pluckthun
Summary: This study reports the X-ray structure of the alpha(1B)-adrenergic G protein-coupled receptor bound to an inverse agonist and identifies key determinants of subtype-selective ligand binding. This finding is important for the design of aminergic drugs with fewer side-effects.
NATURE COMMUNICATIONS
(2022)
Article
Medicine, Research & Experimental
Sofia S. Guimaraes Koch, Robin Thorpe, Nana Kawasaki, Marie-Paule Lefranc, Sarel Malan, Andrew C. R. Martin, Gilles Mignot, Andreas Pluckthun, Menico Rizzi, Stephanie Shubat, Karin Weisser, Raffaella Balocco
Summary: Appropriate nomenclature is crucial for pharmaceutical substances and their development. The WHO INN Programme has revised the naming system for antibody-based drugs and introduced new stems to address the challenge of distinguishing names.
Article
Medicine, Research & Experimental
Rachael Fay, Imre Toro, Anna-Lena Schinke, Branko Simic, Jonas Schaefer, Birgit Dreier, Andreas Plueckthun, Jason P. Holland
Summary: Designed ankyrin repeat proteins (DARPins) modified with enzymatic methods and Zr-89-radiolabeled can serve as a new class of protein-based radiotracers for PET, exhibiting high specificity and affinity in HER2/neu-positive tumors.
MOLECULAR PHARMACEUTICS
(2022)
Article
Multidisciplinary Sciences
Chao Qi, Pia Lavriha, Ved Mehta, Basavraj Khanppnavar, Inayathulla Mohammed, Yong Li, Michalis Lazaratos, Jonas V. Schaefer, Birgit Dreier, Andreas Pluckthun, Ana-Nicoleta Bondar, Carmen W. Dessauer, Volodymyr M. Korkhov
Summary: Adenylyl cyclase 9 (AC9) is an enzyme that converts ATP to cAMP, activated weakly by forskolin and fully by G protein G alpha s subunit, and autoinhibited by AC9 C-terminus. Cryo-EM structures of AC9 in different states show that conformational changes in the region surrounding the forskolin binding site are essential for AC9 activation, with an artificial activator DARPin C4 partially activating AC9 by binding at a site overlapping with G alpha s binding site.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Erich Michel, Stefano Cucuzza, Peer R. E. Mittl, Oliver Zerbe, Andreas Plueckthun
Summary: The study aims to improve the stability of proteins for applications in therapeutics, diagnostics, and basic research. By designing a novel N-cap protein, the stability of proteins was successfully enhanced, addressing the issue of partial unfolding and making the proteins more resistant to proteolysis and aggregation.
Article
Multidisciplinary Sciences
Jie Shi, Kristine Hauschulte, Ivan Mikicic, Srijana Maharjan, Valerie Arz, Tina Strauch, Jan B. Heidelberger, Jonas Schaefer, Birgit Dreier, Andreas Plueckthun, Petra Beli, Helle D. Ulrich, Hans-Peter Wollscheid
Summary: The study investigates the role of actin and associated molecules in the nucleus, focusing on the actin-based motor myosin VI in protecting stalled replication forks. The actin cytoskeleton is important for cellular structure and plasticity, but the abundance and function of filamentous actin in the nucleus are still debated.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Christoph Klenk, Maria Scrivens, Anina Niederer, Shuying Shi, Loretta Mueller, Elaine Gersz, Maurice Zauderer, Ernest S. Smith, Ralf Strohner, Andreas Pluckthun
Summary: The authors developed a method to alter the biophysical and functional properties of G protein-coupled receptors through directed evolution in mammalian cells. They evolved neurotensin receptor 1 for high stability and expression and demonstrated that receptors with complex molecular architectures and large ligands can also be evolved. Importantly, their approach allows for the evolution of functional receptor properties in the presence of the mammalian signaling environment, resulting in receptor variants with increased allosteric coupling.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Marine Blanc, Clara Lettl, Jeremy Guerin, Anais Vieille, Sven Furler, Sylvie Briand-Schumacher, Birgit Dreier, Celia Berge, Andreas Pluckthun, Sandrine Vadon-Le Goff, Remi Fronzes, Patricia Rousselle, Wolfgang Fischer, Laurent Terradot
Summary: The study focuses on Helicobacter pylori, a bacterial pathogen that injects the oncoprotein CagA into gastric cells using a type IV secretion system (cagT4SS). The research shows that CagI, a protein present on the surface of the bacterium, is crucial for the formation of the pilus that facilitates CagA delivery. DARPins targeting CagI are identified as potent inhibitors of the cagT4SS, which is a major risk factor for gastric cancer development.
Article
Biology
Rajib Schubert, Taegeun Bae, Branko Simic, Sheena N. Smith, Seong-Ho Park, Gabriela Nagy-Davidescu, Viviana Gradinaru, Andreas Pluckthun, Junho K. Hur
Summary: Tissue clearing combined with deep imaging is a powerful tool for expanding classical histological techniques. However, imaging highly melanin-rich tissues remains challenging. To address this, researchers developed a CRISPR-based gene editing method called CRISPR-Clear, which can be incorporated into existing tissue-clearing workflows. The method was successfully applied to melanoma tumors, allowing detailed characterization through staining and imaging techniques.
COMMUNICATIONS BIOLOGY
(2023)
Article
Radiology, Nuclear Medicine & Medical Imaging
Ruben D. Houvast, Nada Badr, Taryn March, Lysanne D. A. N. de Muynck, Vincent Q. Sier, Timo Schomann, Shadhvi Bhairosingh, Victor M. Baart, Judith A. H. M. Peeters, Gerard J. P. van Westen, Andreas Plueckthun, Jacobus Burggraaf, Peter J. K. Kuppen, Alexander L. Vahrmeijer, Cornelis F. M. Sier
Summary: This study evaluated the preclinical potential of EpCAM-binding DARPins for NIRF and PA imaging of cancer, demonstrating clear tumor delineation in vivo.
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING
(2023)
Article
Biochemistry & Molecular Biology
Sarah Klinnert, Corinne D. Schenkel, Patrick C. Freitag, Huldrych F. Guenthard, Andreas Plueckthun, Karin J. Metzner
Summary: This study uses gene therapy to target and eliminate cells infected with HIV-1 by activating latent virus and killing the cells. This targeted gene therapy approach has the potential to effectively and safely eliminate infected cells.
Article
Immunology
Liridona Maliqi, Nikolas Friedrich, Matthias Glogl, Stefan Schmutz, Daniel Schmidt, Peter Rusert, Merle Schanz, Maryam Zaheri, Chloe Pasin, Cyrille Niklaus, Caio Foulkes, Thomas Reinberg, Birgit Dreier, Irene Abela, David Peterhoff, Alexandra Hauser, Roger D. Kouyos, Huldrych F. Guenthard, Marit J. van Gils, Rogier W. Sanders, Ralf Wagner, Andreas Plueckthun, Alexandra Trkola
Summary: Understanding the balance between epitope shielding and accessibility on HIV-1 envelope trimers is crucial for selecting immunogens for bnAb-based vaccines. This study introduces a strategy using synthetic DARPin libraries to investigate the antigenic properties of Env immunogens. The in vitro screening tool, DANA, can provide relevant information of antigenic features of Env immunogens. The findings demonstrate that stronger trimer stabilization leads to the selection of highly mutated DARPins, mirroring observations made for bnAbs. By mimicking immunization regimens, DANA can be used to select immunogen combinations that favor trimer-reactive binders.
Article
Biochemistry & Molecular Biology
Melanie Gut, Birgit Dreier, Sven Furler, Jens Sobek, Andreas Pluckthun, Jason P. Holland
Summary: Late-stage prostate cancer often becomes resistant to standard chemotherapy and transforms into a hormone-resistant, drug-resistant, and incurable disease. Developing non-invasive tools to detect biochemical changes that indicate drug efficacy and identify drug resistance could have significant implications in managing individual patients' treatment plans. In this study, new Designed Ankyrin Repeat Proteins (DARPins) with high affinity for prostate-specific antigen (PSA) were selected using ribosome display and in vitro screening tools. These PSAbinding DARPins showed nanomolar affinity for PSA and could be radiolabeled for potential use in imaging-based monitoring of androgen receptor (AR)-targeted therapies.
RSC CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Christian Baumann, Wan-Chin Chiang, Renato Valsecchi, Simon Jurt, Mattia Deluigi, Matthias Schuster, Karl Johan Rosengren, Andreas Pluckthun, Oliver Zerbe
Summary: This study investigates the rapid side-chain dynamics of an alpha(1B)-adrenergic receptor using methyl relaxation. The results show that the overall side-chain dynamics of the receptor are similar in the presence of different ligands. However, the allosteric ligand increases the flexibility of certain key residues, suggesting differences in the mechanisms for receptor activation. These findings demonstrate the feasibility of studying receptor-wide side-chain dynamics in GPCRs to gain functional insights.
Meeting Abstract
Biotechnology & Applied Microbiology
Sebastian Schellhorn, Dominik Bruecher, Natascha A. Wolff, Katrin Schroeer, Erwan Sallard, Kemal Mese, Wenli Zhang, Eric Ehrke-Schulz, Frank Thevenod, Andreas Plueckthun, Anja Ehrhardt