Article
Multidisciplinary Sciences
Maren Nattermann, Sebastian Wenk, Pascal Pfister, Hai He, Seung Hwan Lee, Witold Szymanski, Nils Guntermann, Fayin Zhu, Lennart Nickel, Charlotte Wallner, Jan Zarzycki, Nicole Paczia, Nina Gaissert, Giancarlo Francio, Walter Leitner, Ramon Gonzalez, Tobias J. Erb
Summary: Researchers developed a two-enzyme route to activate formate into formyl phosphate and reduce it to formaldehyde, providing a potential tool for synthetic formate assimilation.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Pavlos Stephanos Bekiaris, Steffen Klamt
Summary: The study presents a computational framework to analyze the impact of redox cofactor swaps on the thermodynamic potential of a metabolic network. It suggests that the specificity of NAD(P)H reactions is influenced by the metabolic network structure, enabling thermodynamic driving forces close to the theoretical optimum.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Tobias Vornholt, Fadri Christoffel, Michela M. Pellizzoni, Sven Panke, Thomas R. Ward, Markus Jeschek
Summary: Artificial metalloenzymes (ArMs) could play a crucial role in transitioning toward a sustainable economy, but methods for rapidly discovering active ArM variants are needed. A reaction-independent, automation-compatible platform based on biotin-streptavidin technology was introduced to engineer ArMs in Escherichia coli, resulting in up to 15-fold activity enhancements. Smart screening strategies and machine learning models were proposed to accurately predict ArM activity, which has significant implications for future ArM development.
Article
Chemistry, Multidisciplinary
Yeying Zhang, Li Chen, Jake A. Wilson, Jerry Cui, Hannah Roodhouse, Chase Kayrouz, Tiffany M. Pham, Kou-San Ju
Summary: This study reports the complete biosynthetic pathway for valinophos, a phosphonopeptide natural product, expanding our understanding of these natural products and revealing new enzymatic transformations and intermediates. The discovery of genes for DHPPA biosynthesis suggests the existence of unknown bioactive compounds originating from this core pathway.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Multidisciplinary Sciences
Carol S. Henger, Dyan J. Straughan, Charles C. Y. Xu, Batya R. Nightingale, Heidi E. Kretser, Mary K. Burnham-Curtis, Denise McAloose, Tracie A. Seimon
Summary: All species of big cats are protected under international regulations due to population declines caused by poaching and illegal trade in their products. A rapid qPCR test has been developed to identify and differentiate DNA from six big cat species in wildlife products, with high efficiency, sensitivity, and specificity. This test can be used as a screening method to combat illegal trade in big cats, benefiting their conservation efforts globally.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Enrico Orsi, Nico J. Claassens, Pablo Nikel, Steffen N. Lindner
Summary: Synthetic biology has revolutionized the ability to redesign microbial metabolic networks by combining metabolic pathway-modularization with growth-coupled selection schemes. This powerful tool enables deep rewiring of cell factories' biochemistry for rational bioproduction.
NATURE COMMUNICATIONS
(2021)
Article
Infectious Diseases
Alec Truswell, Rebecca Abraham, Mark O'Dea, Zheng Zhou Lee, Terence Lee, Tanya Laird, John Blinco, Shai Kaplan, John Turnidge, Darren J. Trott, David Jordan, Sam Abraham
Summary: The robotic platform RASP showed superior throughput and data resolution in high-throughput AMR surveillance compared to an experienced human technician, achieving consistent MICs and demonstrating potential in identifying diversity in fecal samples.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2021)
Article
Infectious Diseases
Meng-Ke Zhang, Meng-Yao Zhang, Shuo-Bo Liu, Ying-Ying Yang, Ya-Jun Zhai, Dan-Dan He, Hua Wu, Yu-Shan Pan, Jian-Hua Liu, Li Yuan, Gong-Zheng Hu
Summary: This study revealed that the double deletion of cpxR and tolC significantly increases the susceptibility of S. Typhimurium to colistin. The molecular mechanisms underlying this phenomenon were elucidated through transcriptomic analysis.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2021)
Article
Multidisciplinary Sciences
Olivia Dwijayanti Wiguna, Diana Elizabeth Waturangi, Yogiara
Summary: This study found that DW-EC bacteriophage isolated from Indonesian traditional food has inhibitory and destructive effects on the biofilms of pathogenic E. coli, and its activity is significantly higher than that against B. cereus. This indicates that DW-EC bacteriophage has the potential to be used as an anti-biofilm candidate for polystyrene and stainless steel equipment in the food industry.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Bhishem Thakur, Kanika Arora, Archit Gupta, Purnananda Guptasarma
Summary: Researchers investigated whether the nucleoid-associated histone-like protein (HU) could act as a glue in biofilms, finding evidence through various experiments to support this hypothesis.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Biotechnology & Applied Microbiology
Dongdong Zhao, Ju Li, Siwei Li, Xiuqing Xin, Muzi Hu, Marcus A. Price, Susan J. Rosser, Changhao Bi, Xueli Zhang
Summary: This study presents new glycosylase base editors (GBEs) that can induce C-to-A and C-to-G transversions in bacteria and mammalian cells, respectively. The GBEs can serve as a complement to existing adenine and cytidine base editors (ABE and CBE) and have the potential to target G/C disease-causing mutations.
NATURE BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Dongdong Zhao, Ju Li, Siwei Li, Xiuqing Xin, Muzi Hu, Marcus A. Price, Susan J. Rosser, Changhao Bi, Xueli Zhang
Summary: The study introduces novel glycosylase base editors (GBEs) that can induce C-to-A and C-to-G transversions in Escherichia coli and mammalian cells, respectively. The new editors exhibit high editing specificity and efficiency, making them potential tools for targeting G/C disease-causing mutations.
NATURE BIOTECHNOLOGY
(2021)
Article
Physics, Multidisciplinary
Gaspard Junot, Thierry Darnige, Anke Lindner, Vincent A. Martinez, Jochen Arlt, Angela Dawson, Wilson C. K. Poon, Harold Auradou, Eric Clement
Summary: This article investigates the movement and biofilm formation of motile bacteria on surfaces. Using a novel tracking technique, the researchers observed surface residence and escape behaviors. A motility model was proposed to explain the findings and provide new insights into surface trapping efficiency.
PHYSICAL REVIEW LETTERS
(2022)
Article
Multidisciplinary Sciences
Nicola Pellicciotta, Matteo Paoluzzi, Dario Buonomo, Giacomo Frangipane, Luca Angelani, Roberto Di Leonardo
Summary: By modulating bacterial motility with light, researchers have found a way to control the transport direction and speed of microscopic particles by adjusting the active pressure gradients. This discovery provides new insights into the potential use of active pressure for controlled transport of microscopic objects.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Helena Massana-Cid, Claudio Maggi, Giacomo Frangipane, Roberto Di Leonardo
Summary: Optical feedback can be used to confine and gather bacteria, forming dense high-activity regions. This method is general and scalable, making it versatile for microengineering applications and studying non-equilibrium phenomena in active systems.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Clemens Mayer, Christopher Dulson, Eswar Reddem, Andy-Mark W. H. Thunnissen, Gerard Roelfes
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2019)
Article
Biochemistry & Molecular Biology
Clemens Mayer
Article
Chemistry, Multidisciplinary
Rudy Rubini, Ilya Ivanov, Clemens Mayer
CHEMISTRY-A EUROPEAN JOURNAL
(2019)
Article
Chemistry, Physical
Marina Simona Robescu, Rudy Rubini, Elisa Beneventi, Michele Tavanti, Chiara Lonigro, Francesca Zito, Francesco Filippini, Laura Cendron, Elisabetta Bergantino
Article
Chemistry, Multidisciplinary
Kim C. Liu, Konstantin Roeder, Clemens Mayer, Santosh Adhikari, David J. Wales, Shankar Balasubramanian
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2020)
Review
Biochemistry & Molecular Biology
Jelle A. Fok, Clemens Mayer
Article
Chemistry, Physical
Jim Ottele, Andreas S. Hussain, Clemens Mayer, Sijbren Otto
Article
Biochemistry & Molecular Biology
Antonija Marjanovic, Henriette J. Rozeboom, Meintje S. de Vries, Clemens Mayer, Marleen Otzen, Hein J. Wijma, Dick B. Janssen
Summary: Caprolactamase is the first enzyme in the caprolactam degradation pathway of Pseudomonas jessenii. It is composed of two subunits (CapA and CapB) and exhibits sequence-related to other ATP-dependent enzymes involved in lactam hydrolysis. The enzyme requires ATP for activity and is sensitive to the presence of bicarbonate in the assay buffer. Additionally, mutations in the ATP-binding site of CapA and metal binding site of CapB significantly affect the enzyme's function and stability, providing insights into possible mechanisms for ATP-dependent lactam hydrolysis.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2021)
Article
Chemistry, Multidisciplinary
Titia Rixt Oppewal, Ivar D. Jansen, Johan Hekelaar, Clemens Mayer
Summary: Macrocyclic peptides (MPs) are a privileged class of compounds used for discovering therapeutics and chemical probes. Researchers have developed an efficient two-step strategy to synthesize MPs with asymmetric cyclization units by modifying a unique cysteine residue and an N-terminal amine.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Rudy Rubini, Suzanne C. Jansen, Houdijn Beekhuis, Henriette J. Rozeboom, Clemens Mayer
Summary: In this study, we developed an in vivo selection strategy by utilizing recoded organisms addicted to non-canonical amino acids (ncAAs) to evolve biocatalysts that can provide building blocks from synthetic precursors. By performing serial passaging, we were able to obtain improved variants with higher catalytic efficiencies. This strategy requires minimal human intervention and no specialized equipment, making it a versatile tool for the in vivo directed evolution of diverse biocatalysts.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Biochemistry & Molecular Biology
Andreea Stan, Clemens Mayer
Summary: The ribosome is the core element of the translational apparatus and has exceptional accuracy and efficiency in synthesizing long polymers with defined sequences and diverse compositions. Repurposing ribosomes for the assembly of nonproteinogenic (bio)polymers has significant implications for fundamental science, bioengineering, and synthetic biology. In this review, we discuss tethered ribosomes, which have inseparable large and small subunits that can be evolved for novel functions. We introduce design and optimization strategies for creating orthogonal and tethered ribosomes, and highlight studies where engineered ribosomes enabled the evolution of new functions. Finally, we discuss future prospects and challenges for ribosomal synthesis of tailor-made (bio)polymers.