Biology subjects

Volk, R.

Publications and source records attributed to Volk, R..

3 recordsLinked to original sources

bioRxiv2023

RNA binding proteins and glycoRNAs form domains on the cell surface for cell penetrating peptide entry

The composition and organization of the cell surface determine how cells interact with their environment. Traditionally, glycosylated transmembrane proteins were thought to be the major constituents of the external surface of the plasma membrane. Here, we provide evidence that a group of RNA binding proteins (RBPs) are present on the surface of living cells. These cell surface RBPs (csRBPs) precisely organize into well-defined nanoclusters that are enriched for multiple RBPs, glycoRNAs, and their clustering can be disrupted by extracellular RNase addition. These glycoRNA-csRBP clusters further serve as sites of cell surface interaction for the cell penetrating peptide TAT. Removal of RNA from the cell surface, or loss of RNA binding activity by TAT, causes defects in TAT cell internalization. Together, we provide evidence of an expanded view of the cell surface by positioning glycoRNA-csRBP clusters as a regulator of communication between cells and the extracellular environment.

cell biology↗

bioRxiv2022

The global anaerobic metabolism regulator fnr is necessary for the degradation of food dyes and drugs by Escherichia coli

The microbiome is an underappreciated contributor to intestinal drug metabolism with broad implications for drug efficacy and toxicity. While considerable progress has been made towards identifying the gut bacterial genes and enzymes involved, the role of environmental factors in shaping their activity remains poorly understood. Here, we focus on the gut bacterial reduction of azo bonds (R-N=N-R), found in diverse chemicals in both food and drugs. Surprisingly, the canonical azoR gene in Escherichia coli was dispensable for azo bond reduction. Instead, azo reductase activity was controlled by the fumarate and nitrate reduction (fnr) regulator, consistent with a requirement for the anoxic conditions found within the gastrointestinal tract. Paired transcriptomic and proteomic analysis of the fnr regulon revealed that in addition to altering the expression of multiple reductases, FNR is necessary for the metabolism of L-Cysteine to hydrogen sulfide, enabling the degradation of azo bonds. Taken together, these results show how gut bacteria sense and respond to their intestinal environment to enable the metabolism of chemical motifs found in both dietary and pharmaceutical compounds. IMPORTANCEThis work has broad relevance due to the ubiquity of dyes containing azo bonds in food and drugs. We report that azo dyes can be degraded by human gut bacteria through both enzymatic and non-enzymatic mechanisms, even from a single gut bacterial species. Furthermore, we revealed that environmental factors, oxygen and cysteine, control the ability of E. coli to degrade azo dyes due to their impacts on bacterial transcription and metabolism. These results open up new opportunities to manipulate the azoreductase activity of the gut microbiome through the manipulation of host diet, suggest that azoreductase potential may be altered in patients suffering from gastrointestinal disease, and highlight the importance of studying bacterial enzymes for drug metabolism in their natural cellular and ecological context.

microbiology↗

bioRxiv2022

MFGE8 links absorption of dietary fatty acids with catabolism of enterocyte lipid stores through HNF4 γ- dependent transcription of CES enzymes

Enterocytes modulate the extent of postprandial lipemia, a potent risk factor for developing atherosclerotic disease, by storing dietary fats in cytoplasmic lipid droplets (cLDs). We have previously demonstrated that the integrin ligand MFGE8 links absorption of dietary fats with activation of triglyceride (TG) hydrolases that catabolize cLDs for chylomicron production. The hydrolase(s) responsible for mobilization of TG from diet-derived cLDs is unknown though recent evidence indicates that this process is independent of the canonical pathway of TG hydrolysis mediated by ATGL. Here we identify CES1D as the key hydrolase downstream of the MFGE8-v{beta}5 integrin pathway that regulates catabolism of diet-drive cLDs. Mfge8 KO enterocytes have reduced CES1D transcript and protein levels and reduced protein levels of the transcription factor HNF4{gamma}. Mice KO for Ces1d or Hnf4{gamma} have decreased enterocyte TG hydrolase activity coupled with retention of TG in cLDs. Mechanistically, MFGE8-dependent fatty acid uptake through CD36 leads to stabilization of HNF4{gamma} protein levels; HNF4{gamma} then increases Ces1d transcription. Our work identifies a regulatory network by which MFGE8 and v{beta}5 regulate the severity of postprandial lipemia by linking dietary fat absorption with protein stabilization of a transcription factor that increases expression of enterocyte TG hydrolases that catabolize diet-derived cLDs.

physiology↗