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  • Journal Article

  • Sterols from cholesterol synthesis control distinct gene regulatory pathways

    • Authors : Skubic, Cene (2023)

  • Sterol intermediates of cholesterol synthesis are largely dedicated to cholesterol. Here we assess how they influence downstream gene regulatory pathways by developing knockouts (KOs) for consecutive enzymes of cholesterol synthesis. Depletion of CYP51, DHCR24 and SC5D resulted in accumulation of specific sterols. The overlap of deregulated genes was only 9% in terms of steroid metabolism and proliferation control, with majority of pathways changed i...
  • Journal article

  • RNA-catalyzed RNA Ligation within Prebiotically Plausible Model Protocells

    • Authors : DasGupta, Saurja (2023)

  • Demonstrating RNA catalysis within prebiotically relevant models of primordial cells (protocells) remains a challenge in Origins of life research. Fatty acid vesicles encapsulating genomic and catalytic RNAs (ribozymes) are attractive models for protocells; however, RNA catalysis has largely been incompatible with fatty acid vesicles due to their instability in the presence of Mg2+ at concentrations required for ribozyme function. Here, we report a r...
  • Journal article

  • Increasing proteome depth while maintaining quantitative precision in short gradient data-independent acquisition proteomics

    • Authors : Doellinger, Joerg (2023)

  • The combination of short liquid chromatography (LC) gradients and data independent acquisition (DIA) by mass spectrometry (MS) has proven its huge potential for high-throughput proteomics. This methodology benefits from the speed of the latest generation of mass spectrometers, which enable short MS cycle times needed to provide sufficient sampling of sharp LC peaks. However, the optimization of isolation window schemes resulting in a certain num...
  • Journal Article

  • Structural and biochemical characterisation of the N-Carbamoyl-β-Alanine Amidohydrolase from Rhizobium radiobacter MDC 8606

    • Authors : Paloyan, Ani  (2023)

  • N-Carbamoyl-β-Alanine Amidohydrolase (CβAA) constitute one of the most important groups of 26 industrially relevant enzymes used in production of optically pure amino acids and derivatives. In 27 this study, a N-carbamoyl-β-alanine amidohydrolase encoding gene from Rhizobium radiobacter 28 MDC 8606 was cloned and overexpressed in Escherichia coli. The purified recombinant enzyme 29 (RrCβAA) showed a specific activity of 14 U/mg using N-carbamoyl- β-a...
  • Journal article

  • Coenzyme A binding sites induce proximal acylation across protein families

    • Authors : Carrico, Chris (2023)

  • Lysine Nɛ-acylations, such as acetylation or succinylation, are post-translational modifications that regulate protein function. In mitochondria, lysine acylation is predominantly non-enzymatic, and only a specific subset of the proteome is acylated. Coenzyme A (CoA) can act as an acyl group carrier via a thioester bond, but what controls the acylation of mitochondrial lysines remains poorly understood. Using published datasets, here we found that pr...
  • Journal article

  • Non-specific recognition of histone modifications by H3K9bhb antibody

    • Authors : Tsusaka, Takeshi  (2023)

  • Ketone bodies are short chain fatty acids produced in the liver during periods of limited glucose availability that provide an alternative source of energy for the brain, heart, and skeletal muscle. Beyond this classical metabolic role, β-hydroxybutyrate (BHB), is gaining recognition as a pleiotropic signaling molecule. Lysine β-hydroxybutyrylation (Kbhb) is a newly discovered post-translational modification in which BHB is covalently attached to lysine ε-amino groups....
  • Journal Article

  • PROTEOMICS OF HYPOTHERMIC ADAPTATION REVEALS THAT RBM3 ENHANCES MITOCHONDRIAL METABOLISM AND MUSCLE STEM-CELL DIFFERENTIATION

    • Authors : Dey, Paulami  (2023)

  • Adaptation to hypothermic stress is important for skeletal muscle cells, but a 17 comprehensive knowledge of molecular mediators is lacking. We show that adaptation to 18 mild hypothermia (320C) improves the ability of skeletal muscle myoblasts to differentiate 19 into myotubes in vitro. We performed proteomic analysis of mouse myoblasts exposed to 20 mild hypothermia for various time points and identified dynamic changes in 21 mitochondrial metabolism a...
  • Journal article

  • A Comparison of Quantitative Mass Spectrometric Methods for Drug Target Identification by Thermal Proteome Profiling

    • Authors : George, Amy L. (2023)

  • Thermal proteome profiling (TPP) provides a powerful approach to studying proteome-wide interactions of small therapeutic molecules and their target and off-target proteins, complementing phenotypic-based drug screens. Detecting differences in thermal stability due to target engagement requires high quantitative accuracy and consistent detection. Isobaric tandem mass tags (TMT) are used to multiplex samples and increase quantification precision in TPP analysis by data-dependent acqui...