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Revealing novel protein interaction partners of glyphosate in Escherichia coli.
Environ Int
December 2024
Department of Molecular Toxicology, Helmholtz-Centre for Environmental Research GmbH (UFZ), Leipzig, Germany.
Despite all debates about its safe use, glyphosate remains the most widely applied active ingredient in herbicide products, with renewed approval in the European Union until 2033. Non-target organisms are commonly exposed to glyphosate as a matter of its mode of application, with its broader environmental and biological impacts remaining under investigation. Glyphosate displays structural similarity to phosphoenolpyruvate (PEP), thereby competitively inhibiting the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), crucial for the synthesis of aromatic amino acids in plants, fungi, bacteria, and archaea.
View Article and Find Full Text PDFOptimized extraction, identification and characterization of the mosquitocidal surface layer protein from a local bacterial isolate Lysinibacillus sphaericus Q001.
Protein Expr Purif
March 2025
School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan; Biological Sciences, University of Southampton, SO17 1BJ, UK.
Surface layer (S-layer) is an extracellular proteinous layer consisting of two-dimensional lattice. It is typically present on archaea and also found on some bacteria. S-layer proteins from some bacteria are reported to be toxic to mosquito larvae.
View Article and Find Full Text PDFDiscovery of antibiotics in the archaeome using deep learning.
bioRxiv
November 2024
Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
Antimicrobial resistance (AMR) is one of the greatest threats facing humanity, making the need for new antibiotics more critical than ever. While most antibiotics have traditionally been derived from bacteria and fungi, archaea-a distinct and underexplored domain of life-offer a largely untapped reservoir for antibiotic discovery. In this study, we leveraged deep learning to systematically explore the archaeome, uncovering promising new candidates for combating AMR.
View Article and Find Full Text PDFStructure and identification of the native PLP synthase complex from lysate.
mBio
January 2025
Department of Microbiology, Immunology & Molecular Genetics, University of California Los Angeles, Los Angeles, California, USA.
Many protein-protein interactions behave differently in biochemically purified forms as compared to their states. As such, determining native protein structures may elucidate structural states previously unknown for even well-characterized proteins. Here, we apply the bottom-up structural proteomics method, , toward a model methanogenic archaeon.
View Article and Find Full Text PDFGenome-resolved metaproteogenomic and nanosolid characterization of an inactive vent chimney densely colonized by enigmatic DPANN archaea.
ISME J
January 2024
Department of Earth and Planetary Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
Recent successes in the cultivation of DPANN archaea with their hosts have demonstrated an episymbiotic lifestyle, whereas the lifestyle of DPANN archaea in natural habitats is largely unknown. A free-living lifestyle is speculated in oxygen-deprived fluids circulated through rock media, where apparent hosts of DPANN archaea are lacking. Alternatively, DPANN archaea may be detached from their hosts and/or rock surfaces.
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