Review
Biotechnology & Applied Microbiology
Tae Seok Moon
Summary: This opinion article discusses the future directions and visions of developing microbial consortia as biomanufacturing hosts to address global problems.
TRENDS IN BIOTECHNOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Nicolas E. Grandel, Kiara Reyes Gamas, Matthew R. Bennett
Summary: Synthetic microbial systems are becoming more complex, but controlling their complexity remains difficult. Recent advances have improved our ability to control the structure of microbial systems, but integrating different parts into a unified system still poses challenges.
TRENDS IN MICROBIOLOGY
(2021)
Article
Chemistry, Inorganic & Nuclear
Liuyan Zhou, Yanling Chen, Yuyu Shen, Jianhua Lin, Jie Fu, Lei Lei, Renguang Ye, Degang Deng, Shiqing Xu
Summary: Down/upconversion Ca14Al10Zn6O35 inorganic phosphors codoped with Ti4+/Eu3+ or Yb3+/Er3+ were prepared and studied for their crystal structure and luminescence properties. The results showed that Ti4+ and Eu3+ ions occupied specific sites in the host lattice and can be used as temperature sensors based on fluorescence intensity ratio (FIR) technology. The phosphors exhibited high relative sensitivity and temperature measurement precision.
INORGANIC CHEMISTRY
(2022)
Review
Nanoscience & Nanotechnology
Tzu-Chieh Tang, Bolin An, Yuanyuan Huang, Sangita Vasikaran, Yanyi Wang, Xiaoyu Jiang, Timothy K. Lu, Chao Zhong
Summary: Synthetic biology utilizes genetic tools to engineer living cells and organisms, similar to machine programming; materials synthetic biology integrates principles from synthetic biology and materials science to redesign living systems into dynamic and responsive materials.
NATURE REVIEWS MATERIALS
(2021)
Article
Biochemical Research Methods
Britta Velten, Jana M. Braunger, Ricard Argelaguet, Damien Arnol, Jakob Wirbel, Danila Bredikhin, Georg Zeller, Oliver Stegle
Summary: MEFISTO is a flexible and versatile toolbox for modeling high-dimensional data with spatial or temporal dependencies, enabling spatio-temporally informed dimensionality reduction, interpolation, and separation of smooth and non-smooth patterns of variation. It can also integrate underlying patterns of variation in multiple related datasets in a data-driven manner.
Article
Multidisciplinary Sciences
Behzad D. Karkaria, Alex J. H. Fedorec, Chris P. Barnes
Summary: In naturally occurring microbial systems, there is a positive relationship between species diversity and community productivity; researchers performed model selection to discover potential amensal interactions that lead to robust stable synthetic microbial consortia.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Silvia Liu, Indira Wu, Yan-Ping Yu, Michael Balamotis, Baoguo Ren, Tuval Ben Yehezkel, Jian-Hua Luo
Summary: LoopSeq is a synthetic long-read sequencing method that generates accurate long-read transcriptome data from short Illumina reads, providing valuable insights into complex transcriptomes and gene expression at the isoform level. When applied to colon cancer samples, LoopSeq showed high accuracy and revealed previously unknown fusion isoforms, demonstrating its potential as a widely accessible approach in transcriptome sequencing.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Le Zhou, Miracle Emenuga, Shreya Kumar, Zachary Lamantia, Marxa Figueiredo, Todd Emrick
Summary: Gene delivery as a therapeutic tool continues to advance, and synthetic polymers show promise as nucleic acid delivery vectors. Recent studies suggest that modifying synthetic cationic polyelectrolytes with additional components and embedding degradable linkages can improve transfection efficiency and biocompatibility.
Article
Biochemistry & Molecular Biology
Donghui Choe, Kangsan Kim, Minjeong Kang, Seung-Goo Lee, Suhyung Cho, Bernhard Palsson, Byung-Kwan Cho
Summary: The study used Term-Seq technology to analyze the 3 '-end of transcripts in Escherichia coli, revealing multiple classes of 3 '-termini and designing novel synthetic metabolic valves for metabolic flux regulation, laying a foundation for 3 '-UTR engineering in synthetic biology applications.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Cell Biology
Maysam Mansouri, Martin Fussenegger
Summary: Cell therapy approaches utilizing engineered mammalian cells for on-demand production of therapeutic agents in the patient's body have advanced beyond proof-of-concept in translational medicine. Customized therapeutic cells can sense user-defined signals, process them, and respond programmably. Various methods of controlling cell behavior, including open-loop and closed-loop systems, are discussed, along with therapeutic applications of engineered cells in early disease diagnosis and treatment. Emerging technologies like digital devices also show potential for future incorporation into cell-based therapies.
Review
Genetics & Heredity
Peter B. Dykstra, Matias Kaplan, Christina D. Smolke
Summary: The versatility of RNA as a substrate for engineering biological systems lies in its ability to sense and interact with various molecules, proteins, and nucleic acids while encoding genetic instructions. Synthetic RNA devices, through integrating sensing, processing, and actuation of signals, have been developed for controlling cell behavior. Recent advances have overcome challenges in expanding analyte sensing range and adding new mechanisms of action, leading to the maturation of synthetic RNA-based devices. These devices find applications in biomedical research and biomanufacturing, and hold promise for novel therapeutics.
NATURE REVIEWS GENETICS
(2022)
Article
Chemistry, Multidisciplinary
Denis Hartmann, Michael J. Booth
Summary: Developing light-controlled 'off' switches for cell-free gene expression is crucial for the future application of DNA nanodevices and synthetic cells. A one-step method for attaching photocages onto antisense oligonucleotides has been developed, allowing for light-induced knockdown of protein synthesis in cell-free systems.
COMMUNICATIONS CHEMISTRY
(2023)
Review
Microbiology
Yue Shi, Tingli Chen, Peter Shaw, Peng-Yuan Wang
Summary: Bacteria form biofilms on material surfaces within hours, which have different properties and applications. The formation of biofilms is influenced by various factors and can be controlled and modified through synthetic biology and materials science approaches. This review summarizes the current research progress and proposes future research directions.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ferhat Alkan, Oscar G. Wilkins, Santiago Hernandez-Perez, Sofia Ramalho, Joana Silva, Jernej Ule, William J. Faller
Summary: Recent studies have identified multiple mechanisms that contribute to the heterogeneity in ribosomal composition, and have developed a new method, called dripARF, to study this phenomenon. This method uses Ribosome Profiling (Ribo-seq) data to detect differential protein incorporation into the ribosome by combining "waste" rRNA fragment data with the known 3D structure of the human ribosome. The results indicate that ribosome heterogeneity can be detected in Ribo-seq data, providing a new tool to study this phenomenon.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Yaara Finkel, Avi Gluck, Aharon Nachshon, Roni Winkler, Tal Fisher, Batsheva Rozman, Orel Mizrahi, Yoav Lubelsky, Binyamin Zuckerman, Boris Slobodin, Yfat Yahalom-Ronen, Hadas Tamir, Igor Ulitsky, Tomer Israely, Nir Paran, Michal Schwartz, Noam Stern-Ginossar
Summary: The study reveals that SARS-CoV-2 infection leads to a global reduction in translation and accelerated degradation of cytosolic cellular mRNAs. It also impairs the translation of transcripts induced in response to infection, probably mediated by inhibition of nuclear mRNA export.
Article
Multidisciplinary Sciences
Mengting Wu, Yi Dong, Qi Zhang, Shengchun Li, Ling Chang, F. Vanessa Loiacono, Stephanie Ruf, Jiang Zhang, Ralph Bock
Summary: This study explores the feasibility of using plastid-mediated RNA interference (PM-RNAi) to control the western flower thrip, a notorious pest. By introducing double-stranded RNA or hairpin RNA into transplastomic tobacco plants, the researchers were able to induce RNAi response in the thrips, leading to efficient suppression of target genes and high insect mortality. This research extends the application of PM-RNAi technology and provides design principles for constructing transplastomic plants expressing double-stranded RNA, offering an effective approach to control tough insect pests in agriculture and horticulture.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Shaobo Wei, Xia Li, Zefu Lu, Hui Zhang, Xiangyuan Ye, Yujie Zhou, Jing Li, Yanyan Yan, Hongcui Pei, Fengying Duan, Danying Wang, Song Chen, Peng Wang, Chao Zhang, Lianguang Shang, Yue Zhou, Peng Yan, Ming Zhao, Jirong Huang, Ralph Bock, Qian Qian, Wenbin Zhou
Summary: In this study, a photosynthesis-related transcription factor, OsDREB1C, was identified and found to regulate various functions such as photosynthetic capacity, nitrogen utilization, and flowering time in rice. Field trials with OsDREB1C-overexpressing rice showed increased yield, shortened growth duration, and improved nitrogen use efficiency.
Review
Genetics & Heredity
Junjie Tan, Joachim Forner, Daniel Karcher, Ralph Bock
Summary: Genome editing has revolutionized biological research, with CRISPR/Cas-based editing being the preferred technology due to its simplicity and flexibility. Fusion of Cas nucleases with large protein domains allows for combination of DNA recognition properties with new enzymatic activities. Base editors and prime editors, produced by fusion with nucleoside deaminase or reverse transcriptase domains, induce site-specific alterations of a few nucleotides without generating double-strand breaks. Protein-only genome editing reagents based on transcription activator-like effectors have expanded base editing to chloroplast and mitochondrial genomes. This review summarizes current base editing methods for nuclear and organellar genomes, highlighting advances in precision, specificity, and efficiency, as well as discussing limitations and future challenges. In addition, applications in agricultural biotechnology and gene therapy are briefly overviewed.
TRENDS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Omar Sandoval-Ibanez, David Rolo, Rabea Ghandour, Alexander P. Hertle, Tegan Armarego-Marriott, Arun Sampathkumar, Reimo Zoschke, Ralph Bock
Summary: The DEIP1 protein interacts with the PetA and PetB subunits and plays an essential role in the assembly of the Cytb6f complex. This finding provides insights into the assembly pathway of a crucial complex in photosynthesis.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Leonie Steinhorst, Gefeng He, Lena K. Moore, Stefanie Schultke, Ina Schmitz-Thom, Yibo Cao, Kenji Hashimoto, Zaida Andres, Katrin Piepenburg, Paula Ragel, Smrutisanjita Behera, Bader O. Almutairi, Oliver Batistic, Thomas Wyganowski, Philipp Koster, Kai H. Edel, Chunxia Zhang, Melanie Krebs, Caifu Jiang, Yan Guo, Francisco J. Quintero, Ralph Bock, Jorg Kudla
Summary: Excessive Na+ in soils inhibits plant growth. This study found that Na+ stress triggers primary calcium signals in a specific cell group within the root differentiation zone of Arabidopsis, forming a sodium-sensing niche. The amplitude and speed of these calcium signals increase with rising Na+ concentrations, providing quantitative information about the stress intensity. The researchers also identified a Ca2+-sensing mechanism that measures the stress intensity and activates appropriate salt detoxification responses.
DEVELOPMENTAL CELL
(2022)
Article
Biochemistry & Molecular Biology
F. Vanessa Loiacono, Dirk Walther, Stefanie Seeger, Wolfram Thiele, Ines Gerlach, Daniel Karcher, Mark Aurel Schoettler, Reimo Zoschke, Ralph Bock
Summary: RNA editing is an important process in converting cytidines to uridines in plant organellar transcripts. This study investigates the evolution and recognition of a recently gained editing site, demonstrating that changes in RNA recognition motifs allow an ancient PPR protein, QED1, to specifically target this site. The study also finds that the target specificity of PPR proteins depends on the RNA:protein ratio and the low expression levels of PPR proteins are necessary to ensure editing site selection specificity.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Plant Sciences
Mengting Wu, Qi Zhang, Yi Dong, Zican Wang, Wenqin Zhan, Zebin Ke, Shengchun Li, Lin He, Stephanie Ruf, Ralph Bock, Jiang Zhang
Summary: Spider mites take up plastid RNA upon feeding. Transplastomic plants expressing dsRNA targeted against spider mite beta-Actin mRNA showed high levels of resistance to spider mites and induced a more robust RNAi response compared to nuclear transgenic plants expressing dsRNA. This study demonstrates the potential of PM-RNAi as an efficient pest control measure for spider mites.
Article
Plant Sciences
Andre Vidal-Meireles, Soujanya Kuntam, Eszter Szeles, David Toth, Juliane Neupert, Ralph Bock, Szilvia Z. Toth
Summary: The lifetime of PSBO in green algae is strongly influenced by light intensity and carbon availability. It is crucial for the stability of photosystem II and loss of PSBO leads to significant changes in cell morphology and cell cycle.
PLANT CELL AND ENVIRONMENT
(2023)
Article
Multidisciplinary Sciences
Matthijs P. Hoelscher, Joachim Forner, Silvia Calderone, Carolin Kraemer, Zachary Taylor, F. Vanessa Loiacono, Shreya Agrawal, Daniel Karcher, Fabio Moratti, Xenia Kroop, Ralph Bock
Summary: This study explores the potential of using chloroplasts in plants to synthesize antimicrobial peptides (AMPs). By utilizing inducible expression and fusions to the cleavable carrier protein SUMO, the cytotoxic effects of AMPs are alleviated and plants with wildtype-like phenotypes are obtained. Furthermore, purified AMP fusion proteins display antimicrobial activity independently of proteolytic removal of the carrier protein.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Rabea Ghandour, Yang Gao, Josephin Laskowski, Rouhollah Barahimipour, Stephanie Ruf, Ralph Bock, Reimo Zoschke
Summary: In plant biotechnology, the expression of transgenes in chloroplasts is common practice. However, the potential unintended effects on native chloroplast genes are often overlooked. This study examined the expression of the chloroplast genome in transplastomic tobacco plants and found that transgene insertion can lead to overexpression of downstream genes and interfere with the transcription and translation of nearby genes. The study suggests strategies to minimize unintended consequences of transgene expression on native chloroplast genes.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Plant Sciences
Deserah D. Strand, Daniel Karcher, Stephanie Ruf, Anne Schadach, Mark A. Schoettler, Omar Sandoval-Ibanez, David Hall, David M. Kramer, Ralph Bock
Summary: Understanding the regulation of photosynthetic light harvesting and electron transfer is crucial to improving the electron transport chain for downstream metabolism. ATP synthase, a central regulator of the chain, is thermodynamically and post-translationally regulated, with proposed phosphorylation sites. This study focused on the N-terminal serines on the catalytic subunit beta in tobacco, previously suggested to be important for dark inactivation of ATP synthase. The findings show that phosphorylation may not play a clear role in dark inactivation, but loss of N-terminal phosphorylation affects ATP synthase accumulation during assembly.
Article
Plant Sciences
Rudan Geng, Xiaoqing Pang, Xia Li, Shanshan Shi, Boris Hedtke, Bernhard Grimm, Ralph Bock, Jirong Huang, Wenbin Zhou
Summary: This study investigates the role of chloroplast-localized gene PCD8 in tetrapyrrole biosynthesis (TBS) and reveals its interaction with ClpC1 and several TBS enzymes. The findings uncover the function of PCD8 and provide a new perspective for understanding the molecular regulation of TBS in plants.
Review
Plant Sciences
Hang Su, Andre van Eerde, Espen Rimstad, Ralph Bock, Norica Branza-Nichita, Igor A. Yakovlev, Jihong Liu Clarke
Summary: Plants are valuable sources of food, feed, herbal medicines, and raw materials for industry. They can also serve as green factories for producing biopharmaceuticals and vaccines. Plant-based production platforms offer advantages such as scalability, cost-effectiveness, and safety. Recent developments include plant-made vaccines for COVID-19 and Ebola, as well as clinical trials for plant-made influenza vaccines.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Julia Smirnova, Justus Loerke, Gunnar Kleinau, Andrea Schmidt, Joerg Buerger, Etienne H. Meyer, Thorsten Mielke, Patrick Scheerer, Ralph Bock, Christian M. T. Spahn, Reimo Zoschke
Summary: Translation in plant cells occurs in three compartments, and this study focuses on the structure of the 80S ribosomes in the cytosol. By using cryo-electron microscopy, the researchers solved the structure of translating tobacco ribosomes and gained insights into the molecular underpinnings of cytosolic translation in plants.
Article
Plant Sciences
Joachim Forner, Dennis Kleinschmidt, Etienne H. Meyer, Axel Fischer, Robert Morbitzer, Thomas Lahaye, Mark A. Schoettler, Ralph Bock
Summary: This study presents a method for targeted mutagenesis of plant mitochondrial DNA using transcription activator-like effector nuclease (TALEN) gene-drive mutagenesis (GDM). The method combines TALEN-induced site-specific DNA cleavage with selection for mutations that confer resistance to the TALEN cut, resulting in genetically stable plants with edited mitochondrial genomes.