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Employing ancestral sequence reconstruction and consensus sequence analysis, the thermostability of a novel d-carbamoylase derived from (HyuC) was engineered through greedy-oriented iterative combinatorial mutagenesis. A mutant S202P/E208D/R277L (M4Th3) was obtained with significantly elevated thermostability. M4Th3 has a half-life of 36.5 h at 40 °C, about 28.5 times of 1.3 h of its parent M4. For the reaction at 40 °C, M4Th3 can catalyze 10 mM -carbamoyl-d-tryptophan to produce d-tryptophan with a conversion ratio of 96.4% after 12 h, which is significantly higher than 64.1% of M4. MD simulation reveals that new hydrogen bonds emerging from E208D on the surface can increase the hydrophobicity of the protein, leading to improved stability. More importantly, R277L could contribute to enhanced interface stability of homodimeric M4. This study provides a thermostable d-carbamoylase for the "hydantoinase process", which has potential in the industrial synthesis of optically pure natural and non-natural amino acids.
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http://dx.doi.org/10.1021/acs.jafc.2c07781 | DOI Listing |
mBio
September 2025
School of Biological Sciences, University of Auckland, Auckland, New Zealand.
The rotation of the bacterial flagellum is powered by the MotAB stator complex, which converts ion flux into torque. Despite its central role in flagellar function, the evolutionary origin and structural diversity of this system remain poorly understood. Here, we present the first comprehensive phylogenetic and structural characterization of MotAB and its closest non-flagellar homologs.
View Article and Find Full Text PDFGenome Biol
September 2025
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China.
Background: Centromeres are crucial for precise chromosome segregation and maintaining genome stability during cell division. However, their evolutionary dynamics, particularly in polyploid organisms with complex genomic architectures, remain largely enigmatic. Allopolyploid wheat, with its well-defined hierarchical ploidy series and recent polyploidization history, serves as an excellent model to explore centromere evolution.
View Article and Find Full Text PDFNat Genet
September 2025
Department of Statistics, University of California, Berkeley, CA, USA.
The Ancestral Recombination Graph (ARG), which describes the genealogical history of a sample of genomes, is a vital tool in population genomics and biomedical research. Recent advancements have substantially increased ARG reconstruction scalability, but they rely on approximations that can reduce accuracy, especially under model misspecification. Moreover, they reconstruct only a single ARG topology and cannot quantify the considerable uncertainty associated with ARG inferences.
View Article and Find Full Text PDFEvol Med Public Health
July 2025
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.
Background And Objectives: Copper is an essential micronutrient and a widely used antimicrobial, yet its widespread application may accelerate microbial resistance. We investigated how long-term copper (II) sulfate (CuSO₄) exposure drives genetic and phenotypic changes in , focusing on survival, resistance mechanisms, and antibiotic cross-resistance.
Methodology: Fifty populations were evolved for 55 days under progressively increasing CuSO₄ concentrations.
Genetics
September 2025
Institute of Ecology and Evolution, School of Biological Sciences, The University of Edinburgh, Edinburgh, EH9 3FL, United Kingdom.
Recent advances in methods to infer and analyse ancestral recombination graphs (ARGs) are providing powerful new insights in evolutionary biology and beyond. Existing inference approaches tend to be designed for use with fully-phased datasets, and some rely on model assumptions about demography and recombination rate. Here I describe a simple model-free approach for genealogical inference along the genome from unphased genotype data called Sequential Tree Inference by Collecting Compatible Sites (sticcs).
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