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H-NS represses fliD transcription for lateral flagellar filament cap in Vibrio parahaemolyticus.
Arch Microbiol
January 2025
Department of Critical Care Medicine, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, 637000, PR China.
Vibrio parahaemolyticus propels itself through liquids using a polar flagellum and efficiently swarms across surfaces or viscous environments with the aid of lateral flagella. H-NS plays a negative role in the swarming motility of V. parahaemolyticus by directly repressing the transcription of the lateral flagellin gene lafA.
View Article and Find Full Text PDFChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning.
Nat Commun
January 2025
Laboratory of Systems Biology and Genetics, Institute of Bio-engineering and Global Health Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
Gene regulation is inherently multiscale, but scale-adaptive machine learning methods that fully exploit this property in single-nucleus accessibility data are still lacking. Here, we develop ChromatinHD, a pair of scale-adaptive models that uses the raw accessibility data, without peak-calling or windows, to link regions to gene expression and determine differentially accessible chromatin. We show how ChromatinHD consistently outperforms existing peak and window-based approaches and find that this is due to a large number of uniquely captured, functional accessibility changes within and outside of putative cis-regulatory regions.
View Article and Find Full Text PDFPromoter Analysis and Dissection Using Reporter Genes, Comparative Genomics, and Gel Shift Assays in Phytophthora.
Methods Mol Biol
December 2024
Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA.
Transcriptional regulation allows cells to execute developmental programs, maintain homeostasis, and respond to intra- and extracellular signals. Central to these processes are promoters, which in eukaryotes are sequences upstream of genes that bind transcription factors (TFs) and which recruit RNA polymerase to initiate mRNA synthesis. Valuable tools for studying promoters include reporter genes, which can be used to indicate when and where genes are activated.
View Article and Find Full Text PDFPositive regulation of a LuxR family protein, MilO, in mildiomycin biosynthesis.
Appl Environ Microbiol
December 2024
State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
Mildiomycin is a representative peptidyl nucleoside antibiotic and was first isolated from , which has been used as an important biological agent to control powdery mildew in plants. Despite its importance, the biosynthetic pathways and regulatory mechanisms remain to be fully elucidated. In this study, we identified MilO as a positive pathway-specific regulator of mildiomycin biosynthesis in the heterologous host .
View Article and Find Full Text PDFThe exometabolome as a hidden driver of bacterial virulence and pathogenesis.
Trends Microbiol
December 2024
Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France. Electronic address:
Article Synopsis
- The understanding of metabolism is shifting from just powering cells and creating building blocks to recognizing its role in regulating gene expression and coordinating cellular activities.
- Many bacterial pathogens can quickly adapt to various environments, including hostile conditions inside a host, thanks to their flexible metabolism.
- This review emphasizes the largely overlooked impact of bacterial 'exometabolomes'—substances released by bacteria—on disease development, drug resistance, and immune system interactions, revealing new insights into how bacteria interact with their hosts.
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