Review
Biotechnology & Applied Microbiology
Angelo B. Banares, Grace M. Nisola, Kris Nino G. Valdehuesa, Won-Keun Lee, Wook-Jin Chung
Summary: This review discusses the causes of D-xylonic acid accumulation in metabolically engineered XOP-utilizing microorganisms, and how to address this issue through different engineering and synthetic biology techniques, with a focus on bacterial strains. Additionally, the ability of certain microorganisms to produce and tolerate D-xylonic acid is also examined as an important aspect in developing efficient microbial cell factories.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Ilona Krabicova, Bohumil Dolensky, Michal Rezanka
Summary: Mannosylated structures have been studied in biomedical applications due to their ability to bind with specific biological receptors. The azide-alkyne click reaction is a common method used to link a functional moiety to a structure. In order to maintain its bioactivity, it is necessary to prepare and isolate a high-purity propargylated mannose derivative. Three known methods of preparing propargyl-alpha-mannopyranoside were revisited, and the products were analyzed using NMR spectroscopy. The experiments showed that one-step procedures did not yield pure propargyl-alpha-mannopyranoside, while a three-step procedure produced the desired compound with high purity.
Article
Biotechnology & Applied Microbiology
Xinlei Mao, Baoqi Zhang, Chenxiu Zhao, Jinping Lin, Dongzhi Wei
Summary: The productivity of d-xylonic acid can be improved in Gluconobacter oxydans by overexpressing the mGDH gene, leading to increased tolerance to hydrolysate inhibitors. The recombinant strain G. oxydans/pBBR-R3510-mGDH shows high productivity and tolerance, making it a promising choice for biotechnological production.
MICROBIAL CELL FACTORIES
(2022)
Article
Biochemistry & Molecular Biology
Federico Bonaldo, Fulvio Mattivi, Daniele Catorci, Panagiotis Arapitsas, Graziano Guella
Summary: This passage discusses the behavior of different classes of flavonoids during hydrogen/deuterium exchange processes. Detailed kinetic measurements were reported using H-1-NMR spectra at different temperatures, leading to the proposal of a unifying reaction mechanism. Molecular modeling and QM calculations were also conducted to provide further insights into the proposed mechanism.
Article
Chemistry, Multidisciplinary
Liang Chen, Yiming Huang, Ren Zou, Jiliang Ma, Tingzhen Li, Mingsai Li, Qi Hao, Haibo Xie, Xinwen Peng
Summary: In this study, a TiO2/Ti3C2 photocatalyst was successfully designed for the oxidation of xylose to d-xylonic acid under ambient conditions, achieving a yield of 64.2% with excellent stability. Mechanistic study revealed that electron transfer from TiO2 to Ti3C2 significantly increased the life time of light-induced charge carriers, leading to improved photocatalytic performance.
Article
Chemistry, Physical
Enrico Salvadori, Edoardo Fusco, Mario Chiesa
Summary: In this study, we derived the spatial distribution of single aluminum sites within the ZSM-5 zeolite framework in the nanometer range using the dipolar interaction between paramagnetic metal ions. Our findings were validated using a Monte Carlo approach on a pristine ZSM-5 sample, and the sensitivity of the method allowed us to monitor aluminum redistribution induced by chemical stress in the framework.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Bela Urban, Gabor Szalontai, Mate Papp, Csaba Feher, Attila C. Benyei, Rita Skoda-Foldes
Summary: Numerous organic reactions catalyzed by the ionic liquid product of chlorosulfonation of 1-methylimidazole have been reported recently. Controversial assumptions on the real structure of the catalyst have emerged, but it has now been confirmed to be 1-methylimidazolium chlorosulfate. This structure was verified through X-ray crystallography and NMR spectroscopy, with experiments supporting rapid hydrolysis in the presence of water traces.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Chemistry, Multidisciplinary
Margherita Bazzoni, Rituraj Mishra, Jean-Nicolas Dumez
Summary: Selective NMR experiments are essential for analyzing large molecules and complex mixtures. A novel type of single-scan ultraselective experiments described in this study can significantly improve the sensitivity and broaden the applicability of this powerful class of experiments.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Analytical
Qiao Lin, Chunwang Meng, Jie Liu, Fei Liu, Qinmei Zhou, Juan Liu, Cheng Peng, Liang Xiong
Summary: With the development of NMR spectrometers and probes, 2D qNMR technology has become increasingly accessible for quantitation of complex mixtures. However, the need for a long relaxation recovery time makes it difficult for 2D qNMR to achieve high quantitative accuracy and data acquisition efficiency. By using relaxation optimization and nonuniform sampling, we successfully established an optimized 2D qNMR strategy for accurate quantitation of diester-type C-19-diterpenoid alkaloids.
ANALYTICAL CHEMISTRY
(2023)
Article
Agricultural Engineering
Jian Han, Xia Hua, Xin Zhou, Bin Xu, Huan Wang, Guohong Huang, Yong Xu
Summary: The study demonstrates that diatomite detoxification can effectively achieve commercial production of bio-based chemicals like xylonic acid, reducing costs by recycling bacterial cells. Additionally, a scale-up production of xylonic acid was achieved in a sealed oxygen supply fermenter. Overall, diatomite treatment provides an efficient and practical approach for the production of biochemicals.
BIORESOURCE TECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Jingwen Li, Jingfei Chen, Yefei Wang, Lishan Yao
Summary: The hydrogen bond cooperativity in the beta-sheet of GB3 protein is investigated using a NMR hydrogen/deuterium exchange method. It is found that weakening one hydrogen bond perturbs other neighboring hydrogen bonds, with three being cooperative and one being anticooperative. This hydrogen bond cooperativity plays a significant role in the stability and conformational coupling of the beta-sheet.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Ya-Ting Chen, Bin Li, Xia-Yan Li, Jia-Liang Chen, Chao-Yu Cui, Kaifeng Hu, Xun-Cheng Su
Summary: A robust method using 1D F-19 NMR has been established to identify and quantify amino acids close to physiological conditions, showing great potential in metabolomics and biochemical analysis. Each F-19-derivatized amino acid has a characteristic chemical-shift profile that can be readily identified in mixtures or biofluids, such as fetal bovine serum and cell lysates.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Sergei S. Arzumanov, Anton A. Gabrienko, Dieter Freude, Juergen Haase, Alexander G. Stepanov
Summary: This article investigates the kinetics of H/D hydrogen exchange reactions using H-1 MAS NMR. The results show that the loading of Zn species can change the reaction mechanism from indirect exchange to direct exchange.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Multidisciplinary Sciences
Moritz Becker, Yen-Tse Cheng, Achim Voigt, Ajmal Chenakkara, Mengjia He, Soeren Lehmkuhl, Mazin Jouda, Jan G. Korvink
Summary: The rapid development of drugs requires high-throughput screening technology. NMR can benefit from parallel detection, but technical obstacles hinder its progress. In this study, we propose a method to rapidly calibrate parallel detectors by using a separate shim system for each detector and utilizing deep learning to handle overlapping non-orthogonal shim fields. Additionally, we report the smallest NMR stripline detectors to date, based on an origami technique, which facilitates further increasing the number of detection sites within the magnet bore.
SCIENTIFIC REPORTS
(2023)
Article
Chemistry, Applied
Cristian A. Fuentes, Mecit Halil Oztop, Macarena Rojas-Rioseco, Martin Bravo, Aylin Ozguer Goksu, Marena Manley, Rosario del P. Castillo
Summary: This study analyzed commercial brown sugars and sugar beet extracts using H-1 NMR spectroscopy and found that this preprocessing strategy could effectively differentiate sugars from different sources. By applying a segmented analysis via MCR-ALS, the selectivity of H-1 NMR spectroscopy for sugar source differentiation was improved.
Article
Multidisciplinary Sciences
Laszlo Mozsik, Mirthe Hoekzema, Niels A. W. de Kok, Roel A. L. Bovenberg, Yvonne Nygard, Arnold J. M. Driessen
Summary: Filamentous fungi are rich sources of bioactive compounds, but many biosynthetic gene clusters are transcriptionally silent under lab conditions. A CRISPRa tool was developed to activate these clusters, demonstrating potential for identifying novel compounds like antimicrobials. This technology offers a rapid and convenient method for activating silent fungal biosynthetic gene clusters.
SCIENTIFIC REPORTS
(2021)
Article
Biotechnology & Applied Microbiology
Joosu Kuivanen, Matti Kannisto, Dominik Mojzita, Heiko Rischer, Mervi Toivari, Jussi Jantti
Summary: In this study, the metabolism of Saccharomyces cerevisiae was engineered for improved anthranilate production. The highest anthranilate titer of 567.9 mg l(-1) was achieved in SCD medium, which is the highest reported with an eukaryotic microorganism. Furthermore, by expressing anthranilic acid methyltransferase 1 from Medicago truncatula, the anthranilate biosynthetic pathway was extended to enable production of grape flavor compound methyl anthranilate in S. cerevisiae at 414 mg l(-1).
MICROBIAL CELL FACTORIES
(2021)
Article
Plant Sciences
Yagut Allahverdiyeva, Eva-Mari Aro, Bert van Bavel, Carlos Escudero, Christiane Funk, Jarna Heinonen, Lars Herfindal, Peter Lindblad, Sari Makinen, Merja Penttila, Kaarina Sivonen, Matilde Skogen Chauton, Hanne Skomedal, Jorunn Skjermo
Summary: NordAqua is a Nordic Center of Excellence focused on promoting Blue Bioeconomy and reforming the use of natural resources sustainably. Their key research includes improving photosynthesis, developing novel photosynthetic cell factories, promoting diversity of Nordic cyanobacteria and algae, and improving bio-based wastewater purification technologies.
PHYSIOLOGIA PLANTARUM
(2021)
Article
Biotechnology & Applied Microbiology
Anna Ylinen, Hannu Maaheimo, Adina Anghelescu-Hakala, Merja Penttila, Laura Salusjarvi, Mervi Toivari
Summary: In this study, PDLA and P(LA-3HB) were successfully produced and characterized in yeast for the first time. The engineered enzymes resulted in accumulation of 3.6% P(LA-3HB) and 0.73% PDLA, showing the potential of yeast for producing 2-hydroxy acid containing PHAs.
JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY
(2021)
Article
Plant Sciences
Konstantinos Vavitsas, Amit Kugler, Alessandro Satta, Dimitris G. Hatzinikolaou, Peter Lindblad, David P. Fewer, Pia Lindberg, Mervi Toivari, Karin Stensjo
Summary: The use of photosynthetic microbes in synthetic biology for sustainable production has garnered increasing attention. While there have been advancements in research and resources for microalgae, genetic engineering tools for these organisms still lag behind. The review provides an overview of commonly used photosynthetic microbes, outlines techniques and tools available, and emphasizes the importance of CRISPR technology in advancing the field.
PHYSIOLOGIA PLANTARUM
(2021)
Article
Biotechnology & Applied Microbiology
Anna Ylinen, Jorg C. de Ruijter, Paula Jouhten, Merja Penttila
Summary: This study demonstrated the production of poly(hydroxybutyrate) (PHB) in yeast Saccharomyces cerevisiae using cellobiose as a sole carbon source. Utilizing different cellobiose utilization routes led to increased PHB production and accumulation percentage, offering a promising solution for sustainable polymer production using microbial cells.
MICROBIAL CELL FACTORIES
(2022)
Article
Biochemical Research Methods
Maryam Sabzevari, Sandor Szedmak, Merja Penttila, Paula Jouhten, Juho Rousu
Summary: This paper presents an AI approach using multi-agent reinforcement learning to guide the strain optimization of engineered microbial cells. The method learns from experiments to improve production by tuning metabolic enzyme levels. The results show that multi-agent reinforcement learning holds promise for guiding strain optimization and achieving industrially attractive production levels.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Natalia Kakko, Anssi Rantasalo, Tino Koponen, Virve Vidgren, Matti Kannisto, Natalia Maiorova, Heli Nygren, Dominik Mojzita, Merja Penttila, Paula Jouhten
Summary: We achieved inducible synthetic resource-use control overSaccharomyces cerevisiae by expressing a bacterial ClpXP proteasome from an inducible promoter. This control method efficiently repressed cell growth, improved product yields, and did not compromise biomass accumulation. The study provides a new approach to tackle uncertainties in strain optimization and address strain stability and low productivity challenges.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Robert Pylkkanen, Daniel Werner, Ajit Bishoyi, Dominik Weil, Ernesto Scoppola, Wolfgang Wagermaier, Adil Safeer, Salima Bahri, Marc Baldus, Arja Paananen, Merja Penttila, Geza R. Szilvay, Pezhman Mohammadi
Summary: We demonstrate that Fomes fomentarius is a unique material with exceptional mechanical properties due to its structural design. It consists of three distinct layers with different microstructures and adhesive properties, resulting in its high strength and toughness.
Article
Agriculture, Multidisciplinary
Markus Laurel, Dominik Mojzita, Tuulikki Seppanen-Laakso, Kirsi-Marja Oksman-Caldentey, Heiko Rischer
Summary: Raspberry ketone has gained attention as a flavor agent and health supplement. The fusion of certain enzymes allows for efficient production of raspberry ketone in plants and yeast. This study successfully expressed key pathway genes for raspberry ketone formation in N. benthamiana, achieving high production levels.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Biotechnology & Applied Microbiology
Anna Ylinen, Laura Salusjarvi, Mervi Toivari, Merja Penttila
Summary: In this study, a precise synthetic biology method was used to adjust the composition of polymers by controlling gene expression. The results demonstrate the ability to tune polymer properties by adjusting the monomer content.
METABOLIC ENGINEERING COMMUNICATIONS
(2022)
Correction
Chemistry, Multidisciplinary
Robert Pylkkanen, Pezhman Mohammadi, Ville Liljestrom, Wojciech Plazinski, Gregory Beaune, Jaakko V. I. Timonen, Merja Penttila
Article
Chemistry, Multidisciplinary
Robert Pylkkanen, Pezhman Mohammadi, Ville Liljestrom, Wojciech Plazinski, Gregory Beaune, Jaakko V. Timonen, Merja Penttila
Summary: This study provides the first evidence of supramolecular complexation of beta-1,3-glucans and explains their formation of intricate hierarchical architectures at multiple length scales. The findings expand our understanding of beta-1,3-glucan molecular organization and offer a new approach for the synthesis of materials for diverse medical and industrial applications.
Article
Biotechnology & Applied Microbiology
Nicolas Huber, Edgar Alberto Alcala-Orozco, Thomas Rexer, Udo Reichl, Steffen Klamt
Summary: Cell-free production systems are commonly used for synthesizing industrial chemicals and biopharmaceuticals. This study presents a model-based optimization framework for cell-free enzyme cascades, taking into account parameter uncertainties. The approach was exemplified using the synthesis of GDP-fucose, resulting in significant improvements in the process.
METABOLIC ENGINEERING
(2024)