Article
Biochemical Research Methods
Sara Dionisi, Karol Piera, Armin Baumschlager, Mustafa Khammash
Summary: Optogenetic tools are widely used in biological applications, but a light-inducible system for controlling gene expression independently in mammalian cells is still lacking. In this study, a new optogenetic tool based on a previously published system in bacteria was implemented in mammalian cells, offering advantages in protein expression, protein inhibition, and RNA visualization.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Nir Hananya, Xuanjia Ye, Shany Koren, Tom W. Muir, Barbara Imperiali
Summary: Studying dynamic biological processes requires approaches compatible with short lifetimes of biochemical transactions. A genetically encoded system involving a fusion protein and cell-permeable probes allows mapping of protein neighborhoods using visible light. Different labeling pathways are revealed depending on the nature of the exogenous probe employed. This photoproximity labeling system in combination with quantitative proteomics provides snapshots of protein territories with high temporal and spatial resolution, and has broad applications in the biomedical field.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemical Research Methods
Wai Kit David Chee, Jing Wui Yeoh, Viet Linh Dao, Chueh Loo Poh
Summary: This study developed a new thermal control technology that enables the control of cellular behaviors through temperature-inducible/repressible systems. The new technology is compact, reversible, and tunable, expanding the tunability of temperature control. The study also implemented a thermal logic circuitry for regulating cell growth and cell proportions.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemical Research Methods
Giada Forlani, Enoch B. Antwi, Daniel Weis, Mehmet A. Oeztuerk, Bastian A. W. Queck, Dominik Brecht, Barbara Di Ventura
Summary: LEXY is an optogenetic tool that exports proteins from the nucleus. Mutations that improve protein depletion from the nucleus and work under low light conditions also increase system leakiness.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemical Research Methods
Giada Forlani, Enoch B. Antwi, Daniel Weis, Mehmet A. Oeztuerk, Bastian A. W. Queck, Dominik Brecht, Barbara Di Ventura
Summary: The LEXY optogenetic tool with mutated LOV variants showed improved depletion of certain POIs from the nucleus in Drosophila embryos. However, when tested in mammalian cells, these variants led to increased cytoplasmic localization of proteins both after illumination and during dark phases, indicating higher system leakiness.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
William Benman, Erin E. Berlew, Hao Deng, Caitlyn Parker, Ivan A. Kuznetsov, Bomyi Lim, Arndt F. Siekmann, Brian Y. Chow, Lukasz J. Bugaj
Summary: The study introduces single-component optogenetic probes with activation dynamics dependent on both light and temperature. The BcLOV4 photoreceptor was utilized to stimulate signaling in mammalian cells, showing tunable membrane translocation dynamics in response to light and temperature. Quantitative modeling predicted the activation dynamics of BcLOV4 and demonstrated its versatility in generating widely applicable optogenetic tools.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Anna Yudenko, Anastasia Smolentseva, Ivan Maslov, Oleg Semenov, Ivan M. Goncharov, Vera V. Nazarenko, Nina L. Maliar, Valentin Borshchevskiy, Valentin Gordeliy, Alina Remeeva, Ivan Gushchin
Summary: Protein-fragment complementation assays are commonly used to study protein-protein interactions. The development of CagFbFP, a small thermostable FbFP based on a LOV domain-containing protein, provides a split fluorescent reporter that can be used to investigate protein-protein interactions in anaerobic conditions without the need for exogenous fluorophores. This advancement in fluorescent protein technology may lead to further development of LOV and PAS domain-based fluorescent reporters and optogenetic tools.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Immunology
Zara Hannoun, Edmund G. Wee, Alison Crook, Stefano Colloca, Stefania Di Marco, Tomas Hanke
Summary: In this study, novel candidate HIV-1 vaccines were developed through genetic and protein engineering. However, additional nucleotides were unintentionally inserted into the transgene during the preparation process, leading to the termination of manufacturing. Analysis revealed that only a small fraction of the virus dose met the quality acceptance criteria. In vitro experiments suggested that the adenovirus DNA polymerase might have lost accuracy in a specific region.
Article
Nanoscience & Nanotechnology
Daisuke Maemura, The Son Le, Mari Takahashi, Kazuaki Matsumura, Shinya Maenosono
Summary: Bioactuators made of cultured skeletal muscle cells can be driven by electrical or visible light stimuli. However, the low biopermeability of visible light limits its application to thin skeletal muscle films. To overcome this limitation, the study focuses on developing thick skeletal muscle bioactuators that can be driven by near-infrared (NIR) light, which has high permeability in living tissue. By using upconversion nanoparticles (UCNPs) to convert NIR light into blue light, the researchers successfully manipulated the calcium influx of myoblasts through NIR light exposure, showing higher efficiency compared to blue light stimulation.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Cell Biology
Richard J. McDowell, Jessica Rodgers, Nina Milosavljevic, Robert J. Lucas
Summary: Melanopsin in mammals can signal through multiple pathways, with variations in signaling selectivity observed between species.
JOURNAL OF CELL SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Fei Du, Yun-Qi Liu, Ying-Shuang Xu, Zi-Jia Li, Yu-Zhou Wang, Zi-Xu Zhang, Xiao-Man Sun
Summary: Escherichia coli is widely used in prokaryotic expression systems for producing recombinant proteins. By replacing different inducible promoters, the expression level of T7 RNA polymerase can be regulated to optimize the production of recombinant proteins. Engineered strains show higher sensitivity to inducers and lower leakage ability, providing more choices for host selection in protein production.
MICROBIAL CELL FACTORIES
(2021)
Article
Chemistry, Medicinal
Nikolas T. Martin, Mathieu J. F. Crupi, Zaid Taha, Joanna Poutou, Jack T. Whelan, Sydney Vallati, Julia Petryk, Ricardo Marius, Bradley Austin, Taha Azad, Mason Boulanger, Tamara Burgess, Ilson Sanders, Camille Victoor, Bryan C. Dickinson, Jean-Simon Diallo, Carolina S. Ilkow, John C. Bell
Summary: Combining cytokines with oncolytic viruses can effectively treat cancer, but dose-limiting toxicities have been a challenge. Researchers developed an inducible expression system for oncolytic poxviruses to regulate the expression of a beneficial transgene. This treatment approach offers a triple anti-tumour effect through the virus, transgene, and inducer.
Review
Chemistry, Multidisciplinary
Willem J. de Grip, Srividya Ganapathy
Summary: This review discusses the origin and development of the rhodopsin family, including its animal and microbial branches. The animal branch belongs to the superfamily of G protein-coupled receptors and is essential for light-dependent animal sensory physiology. The microbial branch mainly functions as light-driven ion pumps or channels, and contains subspecies with sensory activity and enzyme-sustaining capabilities.
FRONTIERS IN CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Zhuo Li, Parminder Kaur, Chen-Yu Lo, Neil Chopra, Jamie Smith, Hong Wang, Yang Gao
Summary: By using high-resolution structural analysis and real-time observation, this study reveals the mechanism of Twinkle protein self-loading onto DNA and the role of disease-related mutations. The non-catalytic N-terminal domain of Twinkle is highlighted, and its relationship with helicase activity and stability of Twinkle hexamer is determined.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Nathan Tague, Virgile Andreani, Yunfan Fan, Winston Timp, Mary J. Dunlop
Summary: A pooled library approach is used to generate and screen various split protein constructs, providing a streamlined method for achieving inducible post-translational control of a protein of interest.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Veronika Perz, Armin Baumschlager, Klaus Bleymaier, Sabine Zitzenbacher, Altijana Hromic, Georg Steinkellner, Andris Pairitsch, Andrzej Lyskowski, Karl Gruber, Carsten Sinkel, Ulf Kueper, Doris Ribitsch, Georg M. Guebitz
BIOTECHNOLOGY AND BIOENGINEERING
(2016)
Article
Biochemistry & Molecular Biology
J. K. B. Cahn, A. Baumschlager, S. Brinkmann-Chen, F. H. Arnold
PROTEIN ENGINEERING DESIGN & SELECTION
(2016)
Article
Engineering, Environmental
Veronika Perz, Altijana Hromic, Armin Baumschlager, Georg Steinkellner, Tea Paykov-Keller, Karl Gruber, Klaus Bleymaier, Sabine Zitzenbacher, Armin Zankel, Claudia Mayrhofer, Carsten Sinkel, Ulf Kueper, Katharina Schlegel, Doris Ribitsch, Georg M. Guebitz
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2016)
Article
Biochemical Research Methods
Jackson K. B. Cahn, Caroline A. Werlang, Armin Baumschlager, Sabine Brinkrnann-Chen, Stephen L. Mayo, Frances H. Arnold
ACS SYNTHETIC BIOLOGY
(2017)
Article
Multidisciplinary Sciences
Thomas Vogl, Thomas Kickenweiz, Julia Pitzer, Lukas Sturmberger, Astrid Weninger, Bradley W. Biggs, Eva-Maria Kohler, Armin Baumschlager, Jasmin Elgin Fischer, Patrick Hyden, Marlies Wagner, Martina Baumann, Nicole Borth, Martina Geier, Parayil Kumaran Ajikumar, Anton Glieder
NATURE COMMUNICATIONS
(2018)
Article
Multidisciplinary Sciences
Stephanie K. Aoki, Gabriele Lillacci, Ankit Gupta, Armin Baumschlager, David Schweingruber, Mustafa Khammash
Article
Multidisciplinary Sciences
Armin Baumschlager, Marc Rullan, Mustafa Khammash
NATURE COMMUNICATIONS
(2020)
Correction
Multidisciplinary Sciences
Thomas Vogl, Thomas Kickenweiz, Julia Pitzer, Lukas Sturmberger, Astrid Weninger, Bradley W. Biggs, Eva-Maria Koehler, Armin Baumschlager, Jasmin Elgin Fischer, Patrick Hyden, Marlies Wagner, Martina Baumann, Nicole Borth, Martina Geier, Parayil Kumaran Ajikumar, Anton Glieder
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Edoardo Romano, Armin Baumschlager, Emir Bora Akmeric, Navaneethan Palanisamy, Moustafa Houmani, Gregor Schmidt, Mehmet Ali ozturk, Leonard Ernst, Mustafa Khammash, Barbara Di Ventura
Summary: This study modified the sensing capability of AraC from L-arabinose to blue light, creating a new light-inducible gene expression system BLADE, which enables spatial and temporal control of gene expression in microorganisms. Additionally, BLADE can be used to externally steer bacterial growth and provides a convenient tool for optogenetic experiments.
NATURE CHEMICAL BIOLOGY
(2021)
Review
Materials Science, Biomaterials
Armin Baumschlager, Mustafa Khammash
Summary: Light has become an established tool in biology for visualizing, investigating, and steering biological systems. This review discusses the unique features of light in biology, its progression in control mechanisms, and focuses on the application of transcriptional light regulators in synthetic biology.