Review
Dermatology
Jean Krutmann, Tamara Schikowski, Akimichi Morita, Mark Berneburg
Summary: The skin, as a barrier organ, is an ideal model for studying environmentally-induced aging. This review explains how exposure to specific exposomal factors can lead to extrinsic skin aging, involving interactions between these factors and genetic modifications, ultimately causing macromolecular damage and changes in fibroblasts in the dermal compartment of the skin.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2021)
Article
Microbiology
Katherine M. M. Collins, Nicola J. J. Evans, James H. H. Torpey, Jonathon M. M. Harris, Bethany A. A. Haynes, Amy H. H. Camp, Rivka L. L. Isaacson
Summary: Bacteria utilize different sigma factors to regulate gene expression in different stages of their life cycles. AlphaFold has successfully provided plausible full-length models for most sigma factors, overcoming the challenge of experimentally obtaining their complete structures. This study discusses the current understanding of the structures and functions of sigma factors in the model organism Bacillus subtilis, and presents an X-ray crystal structure of a region of B. subtilis SigE, a critical sigma factor involved in the developmental process of spore formation.
Article
Multidisciplinary Sciences
Yang Yang, Chang Liu, Wei Zhou, Wei Shi, Ming Chen, Baoyue Zhang, David G. Schatz, Yangbo Hu, Bin Liu
Summary: The MerR family of transcriptional regulators, such as EcmrR, activate promoters with a suboptimal structure for recognition by RNA polymerase holoenzyme. Structural insights into the EcmrR-dependent transcription process elucidate the mechanisms enabling optimal promoter recognition and transition from initiation to elongation.
NATURE COMMUNICATIONS
(2021)
Article
Parasitology
Francisco Macias, Raquel Afonso-Lehmann, Patricia E. Carreira, M. Carmen Thomas
Summary: This study identified TBP and SNAP50 as part of the DNA-protein complex formed by the Pr77 promoter sequence and nuclear proteins of Trypanosoma cruzi. TBP establishes direct and specific contact with the Pr77 sequence, while SNAP50's direct binding to the Pr77 sequence is weak and may be mediated by protein-protein interactions.
PARASITES & VECTORS
(2021)
Article
Biochemistry & Molecular Biology
Wenting Liu, Bo-Chen Zhu, Liu-Yi Liu, Xiao-Yu Xia, Zong-Wan Mao
Summary: This study elucidates the pathways of G4 transitions driven by a platinum(II) compound Pt-phen. The formation of complexes differs under physiological conditions compared to low potassium ion conditions. The results demonstrate the crucial role of Pt-phen binding sites in the G4 transition process.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cell Biology
Jimin Park, Harris H. Wang
Summary: The study investigates the relationship between sequence diversity and functional differences of primary sigma(70) factors in different bacteria, revealing significant fitness deficits across sigma(70) orthologs. This analysis provides insights to improve understanding of the evolution and engineering potential of this global regulator.
Review
Microbiology
James Chen, Hande Boyaci, Elizabeth A. Campbell
Summary: This review examines universal pathways and diverse regulatory mechanisms in transcription initiation in evolutionarily divergent bacteria, as well as the mechanisms by which antimicrobials inhibit transcription initiation. The study highlights the simplicity of mechanistic studies in transcription initiation in bacteria and the importance of bacteria in human health.
NATURE REVIEWS MICROBIOLOGY
(2021)
Review
Biotechnology & Applied Microbiology
Xiaoyan Ma, Lianjie Ma, Yi-Xin Huo
Summary: This review discusses recent engineering strategies targeting the transcription machinery, aiming to reprogram the resource allocation pattern from growth to production. By rearranging the gene regulatory network, a production-oriented phenotype can be constructed, fully harnessing the potential of microbial cell factories.
TRENDS IN BIOTECHNOLOGY
(2022)
Article
Engineering, Civil
Carlos A. Moreira, Gabriel B. Barbat, Miguel Cervera, Michele Chiumenti
Summary: In this study, the performance of the mixed 3-field displacement/deviatoric-strain/pressure finite element method is examined for nonlinear thermo-mechanical structural applications. The proposed method shows improved solution accuracy and numerical stability in incompressible conditions.
ENGINEERING STRUCTURES
(2022)
Article
Chemistry, Physical
Qiman Liu, Yunhu Hu, Xiaoyan Zhang, Fengwu Wang, Longjiu Cheng
Summary: This study investigates the geometric structures, stabilities, and electronic properties of BenPt clusters using a method combining genetic algorithm and density function theory. The results show that the Be4Pt and Be10Pt clusters are two very stable 8e/20e superatoms in this series.
Article
Materials Science, Multidisciplinary
Kaiyang Yin, Bo Cao, Juraj Todt, Florian Gutmann, Hasan Furkan Tuncay, Antonina Roth, Frank Fischer, Nadira Gruebel, Aron Pfaff, Georg C. Ganzenmueller, Jozef Keckes, Stefan Hiermaier, Christoph Eberl
Summary: The size effect on the mechanical properties of Ti-6Al-4V submillimeter structures manufactured by selective laser melting was systematically investigated. X-ray microtomography scans, texture analysis, and mechanical characterization were performed on the additively manufactured microbeams. The results showed that the porosities decreased linearly, while the mechanical properties and texture increased with increasing diameter from 250 to 500 μm.
JOURNAL OF MATERIALS SCIENCE & TECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Zhe Sun, Alexander Yakhnin, Peter C. FitzGerald, Carl E. McIntosh, Mikhail Kashlev
Summary: The study reveals that a large number of E. coli sigma70-dependent pauses, clustered at a 10-20-bp distance from promoters, are regulated by Gre cleavage factors constituting a mechanism for rapid response to changing environmental cues. Transcription factors encoding genes are enriched in these pauses, implying that sigma (70) and Gre proteins regulate transcription in response to changing environmental cues. Transcription by bacterial RNA polymerase is interrupted by pausing events that play diverse regulatory roles.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Raul Fernandez-Lopez, Raul Ruiz, Irene del Campo, Lorena Gonzalez-Montes, D. Roeland Boer, Fernando de la Cruz, Gabriel Moncalian
Summary: Some transcription factors prefer binding to DNA motifs with direct or inverted sequence repeats based on structural constraints. Most prokaryotic regulators form symmetric oligomers that require operators with a dyad structure. Breaking the internal symmetry is necessary for binding to direct repeats, a property mostly seen in a few regulators from the AraC family. The KorA family of transcriptional repressors, involved in plasmid propagation and stability, includes members that form symmetric dimers and recognize inverted repeats. Our structural analyses reveal that ArdK, a member of this family, can form a symmetric dimer similar to KorA, but it binds to direct sequence repeats as a non-symmetric dimer by rotating one of the helix-turn-helix domains by 180 degrees. We also confirmed ArdK's affinity for an inverted repeat, which surprisingly is also recognized by a non-symmetrical dimer. Our findings suggest that structural flexibility at different positions in the dimerization interface restricts transcription factors to bind to DNA sequences with one of these two alternative DNA topologies.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Han Gao, Xing Fan, Qi-Chun Wu, Chuan Chen, Fei Xiao, Kun Wu
Summary: This study characterized the promoter of SHP in a teleost fish and found that zinc reduces hepatic lipid deposition by activating the FXR/SHP pathway.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Gunhyoung Lim, Seungha Hwang, Kilwon Yu, Jin Young Kang, Changwon Kang, Sungchul Hohng
Summary: In this single-molecule study, researchers discovered that actively transcribing RNA polymerase can act as an efficient sensor for DNA double-strand breaks (DSBs), resulting in the formation of R-loops. The efficiency of R-loop formation is influenced by DNA end structures and can interfere with transcription and prevent subsequent rounds of transcription. These findings provide valuable insights into the initiation of DSB repair on transcription templates across different organisms.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Jakub W. Kaminski, Laura Vera, Dennis P. Stegmann, Jonatan Vering, Deniz Eris, Kate M. L. Smith, Chia Ying Huang, Nathalie Meier, Julia Steuber, Meitian Wang, Guenter Fritz, Justyna A. Wojdyla, May E. Sharpe
Summary: Fragment-based drug discovery has been proven to be an effective and efficient method for identifying new chemical scaffolds. X-ray crystallography can be used to validate and develop identified fragments, and recent technological advancements have enabled the development of dedicated platforms for FBDD using X-ray crystallography.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Bill Pedrini, Aaron D. Finke, May Marsh, Pierangelo Luporini, Adriana Vallesi, Claudio Alimenti
Summary: The crystal structures of two pheromones Er-1 and Er-13 from the ciliate Euplotes raikovi support the cooperative model of pheromone/receptor binding, with molecules arranged into linear chains in an alternate opposite orientation. These structures provide new insights into the mechanisms underlying the different behavior of autocrine and heterologous pheromone/receptor complexes.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
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
Biochemical Research Methods
Chia Ying Huang, Sylvain Aumonier, Sylvain Engilberge, Deniz Eris, Kate Mary Louise Smith, Filip Leonarski, Justyna Aleksandra Wojdyla, John H. Beale, Dominik Buntschu, Anuschka Pauluhn, May Elizabeth Sharpe, Alexander Metz, Vincent Olieric, Meitian Wang
Summary: Continuous developments in cryogenic X-ray crystallography have provided us with most of our understanding of 3D protein structures. However, the use of cryogenic temperatures may result in fictitious structures, limiting our knowledge of protein dynamics. In this study, a room-temperature X-ray crystallographic method was developed to capture structural snapshots under physiological conditions, revealing surprising binding discrepancies and capturing multiple binding poses and their interactions with DMSO. This opens up new prospects for structure determination and interpretation at physiological temperatures.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
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
Instruments & Instrumentation
Kate Mary Louise Smith, Ezequiel Panepucci, Jakub Wojciech Kaminski, Sylvain Aumonier, Chia-Yiang Huang, Deniz Eris, Dominik Buntschu, Nathalie Meier, Wayne Glettig, Katherine Evelyn McAuley, Meitian Wang, May Elizabeth Sharpe, Justyna Aleksandra Wojdyla
Summary: Recent advances in automation have enabled the development of unattended data collection services in several synchrotron facilities globally. This paper focuses on the Swiss Light Source, where the implementation of new high-throughput sample changers and the commissioning of the Fast Fragment and Compound Screening pipeline provided an opportunity for automated data acquisition. The paper discusses the upgrades in the DA+ microservice software stack, the automatic loop-centering service, and the deployment of the Smart Digital User (SDU) software for unattended data collection. The SDU software plays a crucial role in communication between services, ensuring sample and device safety, sample centering, alignment with grid-based X-ray diffraction, and ultimately, data collection.
JOURNAL OF SYNCHROTRON RADIATION
(2023)
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
Sebastien Campagne, Daniel Jutzi, Florian Malard, Maja Matoga, Ksenija Romane, Miki Feldmuller, Martino Colombo, Marc-David Ruepp, Frederic H-T. Allain
Summary: This study discovers that RBM39 can regulate its own expression level by selecting the 3'-splice site of a poison exon, and identifies the mechanism and regulatory elements involved in RNA selection. These findings provide a solid basis for designing alternative anti-cancer therapies.
NATURE COMMUNICATIONS
(2023)
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)