Article
Microbiology
Alejandro Arce-Rodriguez, Debbie Pankratz, Matthias Preusse, Pablo I. Nikel, Susanne Haeussler
Summary: In response to the antibiotic crisis, researchers have explored strategies to sensitize bacteria to available antibiotics. By manipulating the redox homeostasis of Pseudomonas aeruginosa, they found that increased NADH levels can lead to both higher antibiotic resistance and enhanced antibiotic killing through the generation of reactive oxygen species (ROS). Their findings also suggest that increased NADH levels can result in low-virulence phenotypes and reduced pathogenicity traits.
Article
Microbiology
Alejandro Arce-Rodriguez, Debbie Pankratz, Matthias Preusse, Pablo Nikel, Susanne Haeussler
Summary: This study artificially manipulated the redox balance of Pseudomonas aeruginosa and found that increasing intracellular NADH concentrations led to higher antibiotic resistance but also increased production of ROS, enhancing antimicrobial killing. This suggests that disrupting cellular redox homeostasis could enhance antibiotic killing by sensitizing pathogens to currently available antibiotics.
Article
Plant Sciences
Qiyu He, Jianfeng Jin, Pengfei Li, Huihui Zhu, Zhanqi Wang, Wei Fan, Jian Li Yang
Summary: The study identified and characterized the SlFDH gene in tomato and found that it plays a role in aluminum tolerance. The expression of SlFDH was induced by aluminum stress but not by other metals. CRISPR/Cas9-generated mutants lacking the SlFDH gene were more sensitive to aluminum stress and formate. The transcription factor SlSTOP1 was found to positively regulate SlFDH expression by directly binding to its promoter.
Article
Microbiology
Justine Turlin, Oscar Puiggene, Stefano Donati, Nicolas T. Wirth, Pablo I. Nikel
Summary: This study investigated the genetic and molecular basis of C1 metabolism in Pseudomonas putida using a systems-level approach. The results identified oxidoreductases encoded by PP_0256 and PP_4596 that were transcriptionally active in the presence of formate and played an important role in C1 tolerance. The study also revealed the detoxification process for methanol and formaldehyde in P. putida. Overall, this research expands our understanding of microbial metabolism and provides a foundation for engineering C1 biomanufacturing.
Article
Microbiology
Michael Agne, Lena Appel, Carola Seelmann, Matthias Boll
Summary: Syntrophic bacteria play a key role in the conversion of biological matter to methane. They can convert fatty acids or alcohols to H-2, formate, and acetate that serve as substrates for methanogenic archaea. The mechanism by which syntrophic bacteria convert unsaturated fatty acids such as crotonate without a partner has remained unresolved. This study provides evidence that during growth with crotonate, the oxidation of 3-hydroxybutyryl-CoA to acetoacetyl-CoA is coupled to the reduction of crotonyl-CoA via formate cycling. This unique energy metabolism, known as enoyl-CoA respiration, generates a proton motive force via a redox-loop.
Review
Biochemical Research Methods
Shawn Kulakowski, Deepanwita Banerjee, Corinne D. Scown, Aindrila Mukhopadhyay
Summary: Microbial bioconversion is an important approach to produce sustainable chemicals and commodities. However, in industrial-scale bioproduction, anaerobic conditions are preferred due to the high cost of oxygen transfer. Anaerobic bioconversion usually has limited substrate utilization, lower product yields, and reduced final product diversity compared to aerobic processes. This study introduces advances in microbial strain engineering, such as redox cofactor engineering, genome-scale metabolic modeling, and functional genomics, to improve bioproduction processes under low oxygen conditions and enable industrial-scale bioproduction systems.
CURRENT OPINION IN BIOTECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Xiu Xing, Yan Liu, Ru-De Lin, Yang Zhang, Zhong-Liu Wu, Xiao-Qi Yu, Kun Li, Na Wang
Summary: In this study, a Zr-based dual-ligand MOFs with pre-installed Rh complex was used for in situ NADH regeneration and immobilization of formic acid dehydrogenase (FDH) to achieve a highly efficient CO2 fixation system. Through detailed investigations, it was shown that the introduction of the photosensitive TCPP ligands increased catalytic active sites and improved photoelectric properties. The electron mediator Rh complex anchored on the MOFs enhanced electron transfer efficiency and facilitated the separation of photogenerated electrons and holes. The optimized photocatalyst, Rh-H2TCPP-UiO-66-NH2, exhibited significantly improved photocatalytic activity for NAD(+) reduction compared to UiO-66-NH2.
Article
Biotechnology & Applied Microbiology
Justine Turlin, Beau Dronsella, Alberto De Maria, Steffen N. Lindner, Pablo I. Nikel
Summary: In this study, we used Pseudomonas putida as a platform for synthetic formate assimilation and successfully engineered a strain that can utilize formate as a carbon source. Through laboratory evolution, we achieved significant reduction in doubling times. Our findings expand the landscape of microbial platforms for C1-based biotechnological production.
METABOLIC ENGINEERING
(2022)
Article
Biotechnology & Applied Microbiology
Feronika Heppy Sriherfyna, Minenosuke Matsutani, Kensuke Hirano, Hisashi Koike, Naoya Kataoka, Tetsuo Yamashita, Eiko Nakamaru-Ogiso, Kazunobu Matsushita, Toshiharu Yakushi
Summary: Gluconobacter oxydans oxidizes glucose in the periplasmic space independently of nicotinamide cofactors, but if this oxidation system is eliminated, glucose is oxidized in the cytoplasm. Two types of NADH dehydrogenase in G. oxydans have different substrate specificities, with the auxiliary NDH playing a crucial role in maintaining cell growth in the absence of the periplasmic oxidation system.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Enrique Asin-Garcia, Christos Batianis, Yunsong Li, James D. Fawcett, Ivar de Jong, Vitor A. P. Martins dos Santos
Summary: The inclusion of biosafety strategies in strain engineering pipelines is crucial for safe-by-design bioprocesses. We developed a biocontainment strategy in Pseudomonas putida KT2440 by creating a synthetic dependency on phosphite, which enabled the strain to grow using phosphite as the sole phosphorous source. This strategy not only enhanced biosafety, but also allowed for the cultivation of P. putida under non-sterile conditions, reducing the risk of contamination.
MICROBIAL CELL FACTORIES
(2022)
Article
Cell Biology
Changhao Wu, Chenglong Zheng, Shiyu Chen, Zhiwei He, Hao Hua, Chengyi Sun, Chao Yu
Summary: Pancreatic cancer (PC) is a gastrointestinal tract malignant tumor with a poor prognosis. FOXQ1 has been found to be overexpressed in PC tissues and associated with poor prognosis. FOXQ1 overexpression promotes PC cell proliferation, tumor stemness, invasion, and metastasis, while FOXQ1 silencing shows the reverse effect. Mechanistic studies reveal that FOXQ1 promotes LDHA transcription to enhance aerobic glycolysis, contributing to the progression of PC.
CELL DEATH & DISEASE
(2023)
Article
Chemistry, Physical
Kaiqi Xu, Athanasios Chatzitakis, Paul Hoff Backe, Qiushi Ruan, Junwang Tang, Frode Rise, Magnar Bjoras, Truls Norby
Summary: This study achieved stable and efficient reduction of CO2 to formate in a bio-hybrid PEC cell using a novel cathode and efficient regeneration mechanism, approaching the efficiency of natural photosynthesis.
APPLIED CATALYSIS B-ENVIRONMENTAL
(2021)
Article
Physics, Fluids & Plasmas
Ion Santra, Urna Basu, Sanjib Sabhapandit
Summary: This study investigates four distinct dynamical regimes of active Brownian motion in two dimensions, characterized by the presence of two timescales set by the rotational diffusion constant and the reversal rate. Analytical computation of position distribution and persistence exponents reveals that in regime II, the position distribution orthogonal to the initial orientation can be described using a scaled variable, showing nontrivial scaling behavior with a special scaling function. The exact first-passage time distribution computation demonstrates the emergence of a persistence exponent of 1 due to direction reversal in this regime.
Article
Multidisciplinary Sciences
Runyu Zhao, Annesha Sengupta, Albern X. X. Tan, Ryan Whelan, Taylor Pinkerton, Javier Menasalvas, Thomas Eng, Aindrila Mukhopadhyay, Young-Shin Jun, Himadri B. Pakrasi, Yinjie J. Tang
Summary: In this study, the challenge of growth interference in multispecies microbial co-cultures was addressed by encapsulating engineered strains in calcium-alginate hydrogel beads. This allowed the cyanobacterial culture to produce high sucrose concentrations, enabling the production of indigoidine and beta-carotene in the heterotroph. The results showed a significant increase in the yields of indigoidine and beta-carotene compared to the traditional co-culture system.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Daniel C. Volke, Roman A. Martino, Ekaterina Kozaeva, Andrea M. Smania, Pablo I. Nikel
Summary: The authors developed an enhanced cytidine base editor for efficient genome editing of Gram-negative bacteria. With optimized CRISPR/Cas technologies and streamlined guide RNA processing, they achieved single-nucleotide resolution manipulations and multiplex base editing with high efficiency. The toolset was successfully applied to construct and deconstruct complex phenotypes in Pseudomonas putida, demonstrating its versatility.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Jana Fees, Jonas J. Christ, Sabine Willbold, Lars M. Blank
Summary: A biotechnological process using Saccharomyces cerevisiae to upgrade phosphate-containing wastewater into pure sodium polyphosphate was developed in this study. The quality of polyphosphate was independent of the composition of the wash water and can be reused in various applications, contributing to the sustainable utilization of phosphate and reducing the need for phosphate rock.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Patrick Bongartz, Tobias Karmainski, Moritz Meyer, John Linkhorst, Till Tiso, Lars M. Blank, Matthias Wessling
Summary: Bioreactors play a crucial role in the production of biopharmaceuticals, biomaterials, and sustainable substitutes for chemicals. However, the traditional aeration technique used in bioreactors has limitations such as shear stress, foaming, and sterility concerns. This study presents a membrane stirrer (MemStir) that combines simulations and experiments, providing efficient bubble-free aeration. The MemStir demonstrated excellent performance in a foam-free recombinant production process, delivering high oxygen transfer rates and demonstrating its potential for various applications including animal cell cultivation.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Review
Gastroenterology & Hepatology
Josefin Soppert, Elisa Fabiana Brandt, Nicole Maria Heussen, Emona Barzakova, Lars Mathias Blank, Lars Kuepfer, Mathias Walter Hornef, Jonel Trebicka, Joachim Jankowski, Marie -Luise Berres, Heidi Noels
Summary: This study provides evidence that blood endotoxin levels are associated with gut permeability and disease stage in patients with NAFLD. Blood endotoxin levels can serve as a diagnostic biomarker for NAFLD and can be used for staging during disease progression.
CLINICAL GASTROENTEROLOGY AND HEPATOLOGY
(2023)
Review
Agriculture, Multidisciplinary
Shangkun Qiu, Lars M. Blank
Summary: Plant natural products are valuable resources for novel chemical structures, but their extraction often leads to high prices, fluctuation in quantity and quality, and negative environmental impact. Synthetic biology allows for large-scale production of these natural products using yeasts as hosts. This article focuses on the recent advancements in metabolic engineering of Saccharomyces cerevisiae and Yarrowia lipolytica for the synthesis of ginsenoside triterpenoids, discussing synthetic biology, bioprocess strategies, and current challenges. Future directions in metabolic and process engineering for sustainable ginsenoside production are also summarized.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Biochemical Research Methods
Matti Froning, Carolin Gruetering, Lars M. M. Blank, Heiko Hayen
Summary: The double bond position of medium chain length methyl ketones derived from Pseudomonas taiwanensis VLB120 were determined using gas chromatography-electron ionization-mass spectrometry. The use of DMDS derivatization enabled the identification of isobaric fragment ions for different possible double bond positions, which could be differentiated using high-resolution MS.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2023)
Correction
Biochemical Research Methods
Hao Guo, Huiyan Wang, Tongtong Chen, Liwei Guo, Lars M. Blank, Birgitta E. Ebert, Yi-Xin Huo
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biochemical Research Methods
Dairio Neves, Ulf W. Liebal, Salome C. Nies, Tobias B. Alter, Christian Pitzler, Lars M. Blank, Birgitta E. Ebert
Summary: By characterizing libraries of synthetic and sigma;(70)-dependent promoters, researchers compared the expression of promoters in both Escherichia coli TOP10 and Pseudomonas taiwanensis VLB120. They quantitatively described the strength of the promoters, expanded the genetic toolbox of P. taiwanensis VLB120, and evaluated its potential as a chassis for biotechnology applications.
ACS SYNTHETIC BIOLOGY
(2023)
Editorial Material
Biotechnology & Applied Microbiology
Lars M. Blank
MICROBIAL BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Mariam Dianat, Ute Muenchberg, Lars M. Blank, Erik Freier, Birgitta E. Ebert
Summary: In this study, we demonstrate the detection and monitoring of triterpenoids in living yeast cells using coherent anti-Stokes Raman scattering (CARS) and second-harmonic-generation (SHG) microscopy techniques. This method provides new insights into the dynamics of triterpenoid production and storage inside cells, which is crucial for rationalizing microbial engineering.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Review
Microbiology
Alessandro Satta, Lygie Esquirol, Birgitta E. Ebert
Summary: Cyanobacteria are photosynthetic microorganisms that can use solar energy to convert CO2 and H2O into O-2 and energy-rich organic compounds for sustainable production of bio-products. This review provides an overview of the most well-known, newest, and most promising cyanobacterial strains for bioproduction. It also explores the latest innovative strategies and synthetic biology tools used for metabolic pathway engineering to increase the production of value-added compounds.
Article
Biochemical Research Methods
Anna Lipphardt, Tobias Karmainski, Lars M. Blank, Heiko Hayen, Till Tiso
Summary: A novel biosurfactant synthesized by the marine bacterium Alcanivorax borkumensis has been discovered, which enhances the bacterium's attachment to oil droplets and facilitates the uptake of hydrocarbons. A method combining HPLC with HRMS has been developed to separate and identify the biosurfactant, and charged-aerosol detection (CAD) enables absolute quantification without authentic standards. The biosurfactant production by A. borkumensis using different carbon sources has been investigated, and various congeners with different chain lengths and degrees of unsaturation have been identified. Hexadecane was found to result in a higher titer of biosurfactant compared to pyruvate. The analytical method presented allows for the identification, characterization, and quantification of complex and varying glycolipids.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Niki Baccile, Alexandre Poirier, Javier Perez, Petra Pernot, Daniel Hermida-Merino, Patrick Le Griel, Christian C. Blesken, Conrad Mu''ller, Lars M. Blank, Till Tiso
Summary: The structure-property relationship of rhamnolipids, a type of microbial biosurfactants, is investigated using cryo-TEM and SAXS. The self-assembly behavior of different rhamnolipids and a rhamnose-free fatty acid in water at various pH values is studied. Micellar structures are found for RhaC10 and RhaRhaC10C10, while RhaC10C10 undergoes a micelle-to-vesicle transition at pH 6.5. The hydrophobic core radius, hydrophilic shell thickness, aggregation number, and surface area per rhamnolipid are estimated using modeling and SAXS data fitting. The packing parameter model explains the observed micellar morphology but fails to explain the lamellar phase of protonated RhaRhaC10C10 at acidic pH.
Article
Biotechnology & Applied Microbiology
Dario Neves, Daniel Meinen, Tobias B. B. Alter, Lars M. M. Blank, Birgitta E. E. Ebert
Summary: As a main precursor, acetyl-CoA leads to the production of even-chain products. Extending the acyl-CoA portfolio of a cell factory is important for producing relevant odd-chain alcohols, acids, ketones, and polyketides. Incorporating propionyl-CoA into the metabolic network can facilitate the bioproduction of odd-chain molecules. The evaluation and optimization of propionyl-CoA production pathways in Pseudomonas taiwanensis VLB120 highlight the potential of Pseudomonas to produce propionyl-CoA derived, odd-chain products.
MICROBIAL BIOTECHNOLOGY
(2023)
