Article
Chemistry, Multidisciplinary
Tatsushi Yoshikawa, Fumiaki Makino, Tomoko Miyata, Yohei Suzuki, Hideaki Tanaka, Keiichi Namba, Kenji Kano, Keisei Sowa, Yuki Kitazumi, Osamu Shirai
Summary: This study investigates the tungsten-containing formate dehydrogenase from Methylorubrum extroquens AM1 (FoDH1), which has the potential as a biocatalyst. The research reveals the three-dimensional structure, electrode-active sites, and electron transfer pathways of FoDH1 using structural biology and bioelectrochemistry methods.
CHEMICAL COMMUNICATIONS
(2022)
Review
Biochemical Research Methods
Patrick A. Sanford, Benjamin M. Woolston
Summary: Recent metabolic engineering efforts to import C1 catabolic pathways into non-methylotrophic bacteria have led to synthetic strains growing on methanol, but their growth rates and product yields are still inferior to native methylotrophs. Moreover, the development of genetic engineering tools has made native C1 utilizers more tractable, raising the question of whether it is better to use an engineered strain or a native host for the microbial assimilation of C1 substrates.
CURRENT OPINION IN BIOTECHNOLOGY
(2022)
Article
Biochemical Research Methods
Lan-Yu Cui, Jing Yang, Wei-Fan Liang, Song Yang, Chong Zhang, Xin-Hui Xing
Summary: By adding 10 mmol L-1 sodium formate in the mevalonic acid (MEV) accumulating stage (at 72 h), Methylobacterium extorquens AM1 (AM1) achieved a MEV yield of 0.067 gMEV/g methanol, which is the highest reported yield to date. Sodium formate had global effects on metabolic pathways, significantly increasing the ratios of reducing equivalents, enhancing the metabolic rate of pathways demanding reducing cofactors, and redirecting carbon flux to MEV synthesis. Coupling formate to methanol-based production provides a promising way for converting C1 substances to useful chemical products.
BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Jannell V. Bazurto, Dipti D. Nayak, Tomislav Ticak, Milya Davlieva, Jessica A. Lee, Chandler N. Hellenbrand, Leah B. Lambert, Olivia J. Benski, Caleb J. Quates, Jill L. Johnson, Jagdish Suresh Patel, F. Marty Ytreberg, Yousif Shamoo, Christopher J. Marx
Summary: EfgA is a protein that serves as a formaldehyde sensor in methylotrophic bacteria, quickly halting cell growth in response to elevated formaldehyde levels. Its heterologous expression in Escherichia coli enhances formaldehyde resistance, suggesting potential widespread and conserved interaction partners. EfgA represents a unique stress response mechanism in bacteria by directly sensing toxic intracellular metabolites without enzymatic detoxification.
Article
Microbiology
Sebastian Pfeilmeier, Gabriella C. Petti, Miriam Bortfeld-Miller, Benjamin Daniel, Christopher M. Field, Shinichi Sunagawa, Julia A. Vorholt
Summary: This study demonstrates that the maintenance of leaf microbiota homeostasis in Arabidopsis thaliana plants requires the involvement of the NADPH oxidase RBOHD, as its absence leads to enrichment of opportunistic pathogens. The composition of plant microbiota is greatly influenced by the plant immune system, highlighting the importance of both immune system and microbial community in maintaining plant health.
NATURE MICROBIOLOGY
(2021)
Article
Microbiology
Christine M. Vogel, Daniel B. Potthoff, Martin Schafer, Niculo Barandun, Julia A. Vorholt
Summary: Systematic analysis of bacterial isolates from the phyllosphere of Arabidopsis thaliana identified protective strains against the pathogen Pseudomonas syringae pv. tomato DC3000, demonstrating direct bacteria-pathogen interactions. While some strains confer full protection through pattern-triggered immunity, others protect independently of plant immunity receptors. The study highlights the importance of identifying key genes of the microbiota for plant protection.
NATURE MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Lucas Hemmerle, Benjamin A. Maier, Miriam Bortfeld-Miller, Birgitta Ryback, Christoph G. Gabelein, Martin Ackermann, Julia A. Vorholt
Summary: This study empirically tested the concept of dynamic character displacement among interacting bacterial species from leaf-colonizing families using a proteomics approach. The results revealed phenotypic shifts and reduced niche overlap during coexistence, indicating the importance of species differences in promoting stable coexistence. The study also demonstrated the relevance of phenotypic plasticity in mediating character displacement and facilitating species coexistence.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Christoph G. Gabelein, Qian Feng, Edin Sarajlic, Tomaso Zambelli, Orane Guillaume-Gentil, Benoit Kornmann, Julia A. Vorholt
Summary: The study developed a FluidFM-based approach that enables the manipulation of organelles within single live cells. It allows for the extraction, injection, and transplantation of organelles with subcellular spatial resolution. The transferred organelles, such as mitochondria, can fuse with the host cells' organelle network.
Article
Microbiology
Martin Schaefer, Christine M. Vogel, Miriam Bortfeld-Miller, Maximilian Mittelviefhaus, Julia A. Vorholt
Summary: This study investigates bacterial interactions in the phyllosphere microbiota using a synthetic community. The results show that 90% of the interactions in planta were negative and closely related strains had consistent effects on the synthetic community. The changes in the community could be largely explained by binary interactions, but higher-order interactions involving more than two strains were also identified.
NATURE MICROBIOLOGY
(2022)
Article
Biology
Orane Guillaume-Gentil, Christoph G. Gaebelein, Stefanie Schmieder, Vincent Martinez, Tomaso Zambelli, Markus Kuenzler, Julia A. Vorholt
Summary: Guillaume-Gentil et al. present a method that utilizes a modified AFM tip to selectively sample and inject into fungal cells of different morphology. The authors made extensive modifications on their existing system for mammalian cells to overcome challenges encountered when working on single fungal cells. They demonstrate the effectiveness of fluidic force microscopy in injecting solutions and extracting cytoplasmic fluid from individual fungal cells, providing new opportunities for manipulating and analyzing fungi.
COMMUNICATIONS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Wanze Chen, Orane Guillaume-Gentil, Pernille Yde Rainer, Christoph G. Gaebelein, Wouter Saelens, Vincent Gardeux, Amanda Klaeger, Riccardo Dainese, Magda Zachara, Tomaso Zambelli, Julia A. Vorholt, Bart Deplancke
Summary: Live-seq is a novel single-cell transcriptomic profiling approach that preserves cell viability during RNA extraction, allowing for the correlation analysis between a cell's ground-state transcriptome and its downstream molecular or phenotypic behavior. It accurately stratifies diverse cell types and states without major cellular perturbations, and can be used to map a cell's trajectory and evaluate gene effects on cell phenotypes.
Article
Ecology
Birgitta Ryback, Miriam Bortfeld-Miller, Julia A. Vorholt
Summary: Auxotrophs are organisms that cannot synthesize all the essential metabolites and rely on others for their survival. In a study of bacteria isolated from Arabidopsis thaliana leaves, it was found that about half of the strains require biotin, niacin, pantothenate, and/or thiamine. These auxotrophic strains were able to store coenzymes and grow exponentially for a few generations without vitamin supplementation, with biotin showing the highest storage capacity. Co-culture experiments showed that auxotrophic strains had higher species richness when provided with external vitamins. The results suggest that auxotrophs can benefit from metabolic by-products beyond vitamins.
Article
Multidisciplinary Sciences
Philipp Keller, Michael A. Reiter, Patrick Kiefer, Thomas Gassler, Lucas Hemmerle, Philipp Christen, Elad Noor, Julia A. Vorholt
Summary: This study reports the conversion of Escherichia coli into a synthetic methylotroph that can assimilate methanol via the ribulose monophosphate cycle. The methylotrophic E. coli strain optimizes methanol oxidation by upregulating an improved methanol dehydrogenase, increasing ribulose monophosphate cycle activity, channeling carbon flux through the Entner-Doudoroff pathway, and downregulating tricarboxylic acid cycle enzymes. This research lays the foundation for the efficient utilization of methanol as a carbon and energy resource.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Christoph G. Gaebelein, Michael A. Reiter, Chantal Ernst, Gabriel H. Giger, Julia A. Vorholt
Summary: Studying endosymbiosis is crucial for understanding cellular evolution and engineering. By injecting different bacteria into mammalian cells, we tested their potential for endosymbiosis and found that limiting the uptake of specific nutrients can slow down the intracellular growth of the endosymbiont.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Martin Schafer, Alan R. Pacheco, Rahel Kunzler, Miriam Bortfeld-Miller, Christopher M. Field, Evangelia Vayena, Vassily Hatzimanikatis, Julia A. Vorholt
Summary: Resource allocation affects the structure of microbiomes, including those associated with living hosts. Understanding the degree to which this dependency determines interspecies interactions may advance efforts to control host-microbiome relationships. We combined synthetic community experiments with computational models to predict interaction outcomes between plant-associated bacteria. The models recapitulated outcomes observed in planta with >89% accuracy, highlighting the role of carbon utilization and the contributions of niche partitioning and cross-feeding in the assembly of leaf microbiomes.
Article
Multidisciplinary Sciences
Julien Massoni, Miriam Bortfeld-Miller, Alex Widmer, Julia A. Vorholt
Summary: The study revealed that at least 25% of phyllosphere bacteria reach plants from the soil, with a majority belonging to the Burkholderiaceae family. These findings support future investigations on the routes used by soil microbes to reach leaves and flowers, as well as the ubiquitous environmental filtering of Burkholderiaceae across plant species and environments.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Jethro L. Hemmann, Manuel R. Bruehwiler, Miriam Bortfeld-Miller, Julia A. Vorholt
Summary: Through high-resolution liquid chromatography-mass spectrometry, it was found that nine bacterial strains contained MYFR, with two strains resembling MYFR in M. extorquens and six strains containing modified MYFR. Gene deletions identified orf5, orfY, and orf17 as essential for MYFR biosynthesis, with Orf5 (now MyfB) playing a key role in glutamate addition. The study sheds light on the structural and functional features of MYFR biosynthesis in various bacterial strains.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Microbiology
Viktoriya Shyp, Badri Nath Dubey, Raphael Bohm, Johannes Hartl, Jutta Nesper, Julia A. Vorholt, Sebastian Hiller, Tilman Schirmer, Urs Jenal
Summary: This study demonstrates that the small signaling molecules (p)ppGpp and c-di-GMP reciprocally regulate the growth of Caulobacter crescentus by converging on the small-molecule-binding protein SmbA. (p)ppGpp promotes growth on glucose, while c-di-GMP inhibits glucose consumption, with SmbA playing a role in this metabolic switch and quenching redox stress associated with growth on glucose. The identification of SmbA as a central regulatory hub for these two global second messengers suggests potential for future studies on specific crosstalk between small-molecule-based regulatory networks.
NATURE MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
Christoph G. Gaebelein, Michael A. Reiter, Chantal Ernst, Gabriel H. Giger, Julia A. Vorholt
Summary: Researchers tested the potential of artificial endosymbiosis in mammalian cells, and found that the growth rate of E. coli within the cell can be slowed down by limiting the uptake of aromatic amino acids, prolonging the survival of the endosymbiont-host pair.
ACS SYNTHETIC BIOLOGY
(2022)