Biology subjects

Cygler, M.

Publications and source records attributed to Cygler, M..

3 recordsLinked to original sources

bioRxiv2023

The porphyran degradation system of the human gut microbiota is complete, phylogenetically diverse and geographically structured across Asian populations

The human gut microbiota can acquire new catabolic functions by integrating genetic material coming from the environment, for example from food-associated bacteria. The most illustrative example is the acquisition by the human gut microbiota of Asian populations of genes coming from marine bacteria living on the surface of red algae that are incorporated into their diet when eating maki-sushi. To better understand the function and evolution of this set of algal genes corresponding to a polysaccharide utilization locus (PUL) dedicated to the degradation of porphyran, the main polysaccharide of the red algae Porphyra sp., we characterized it biochemically, assessed its genetic diversity and investigated its geographical distribution in large public worldwide datasets. We first demonstrated that both methylated and unmethylated fractions are catabolized without the help of external enzymes. By scanning the genomic data of more than 10,000 cultivated isolates, we then found that the porphyran PUL organization is conserved in 22 different Bacteroides strains coming from at least 8 species, highlighting multiple lateral transfers within the gut microbiota. We then analyzed the metagenomic data of more than 14,000 individuals coming from 32 countries worldwide and showed that the porphyran PUL exists only in East Asia (Japan, China, Korea), but not anywhere else. Finally, we identified three major PUL haplotypes which frequency differ between countries. This geographic structure is likely the reflect of the rate of bacterial horizontal transmission between individuals. BackgroundThe human gut microbiota can acquire new catabolic functions by integrating genetic material coming from the environment, for example from food-associated bacteria. The most illustrative example is the acquisition by the gut microbiota of Asian populations of genes coming from marine bacteria living on the surface of red algae that are incorporated into their diet when eating maki-sushi. To better understand the function and evolution of this set of algal genes corresponding to a polysaccharide utilization locus (PUL) dedicated to the degradation of porphyran, the main polysaccharide of the red algae Porphyra sp., we characterized it biochemically, assessed its genetic diversity and investigated its geographical distribution in large public worldwide datasets. ResultsWe first demonstrated that both methylated and unmethylated fractions of porphyran are catabolized by the porphyran PUL without the help of external enzymes. By scanning the genomic data of more than 10,000 cultivated isolates, we then found that the porphyran PUL organization is conserved in 22 different Bacteroides strains coming from at least 8 species, highlighting multiple lateral transfers within the gut microbiota. We then analyzed the metagenomic data of more than 14,000 individuals coming from 32 countries worldwide and confirmed that the porphyran PUL exists only in East Asia (Japan, China, Korea). We identified three major porphyran PUL haplotypes which frequency differ between countries. ConclusionThe encoded genes of the PUL porphyran can autonomously catabolized all the complex porphyran structure. The PUL is further encoded by a variety of bacterial species, and its genetic diversity is geographically structured, likely reflecting the rate of bacterial horizontal transmission between individuals.

biochemistry↗

bioRxiv2021

Spike protein disulfide disruption as a potential treatment for SARS-CoV-2

The coronaviral pandemic is exerting a tremendously detrimental impact on global health, quality of life and the world economy, emphasizing the need for effective medications for current and future coronaviral outbreaks as a complementary approach to vaccines. The Spike protein, responsible for cell receptor binding and viral internalization, possesses multiple disulfide bonds raising the possibility that disulfide-reducing agents might disrupt Spike function, prevent viral entry and serve as effective drugs against SARS-CoV-2. Here we show the first experimental evidence that reagents capable of reducing disulfide bonds can inhibit viral infection in cell-based assays. Molecular dynamics simulations of the Spike receptor-binding domain (RBD) predict increased domain flexibility when the four disulfide bonds of the domain are reduced. This flexibility is particularly prominent for the surface loop, comprised of residues 456-490, which interacts with the Spike cell receptor ACE2. Consistent with this finding, the addition of exogenous disulfide bond reducing agents affects the RBD secondary structure, lowers its melting temperature from 52 to 36-39{degrees}C and decreases its binding affinity to ACE2 by two orders of magnitude at 37{degrees}C. Finally, the reducing agents dithiothreitol (DTT) and tris(2-carboxyethyl)phosphine (TCEP) inhibit viral replication at high {micro}M - low mM levels with a negligible effect on cell viability at these concentrations. The antiviral effect of monothiol-based reductants N-Acetyl-L-cysteine (NAC) and reduced glutathione (GSH) was not observed due to decreases in cell viability. Our research demonstrates the clear potential for medications that disrupt Spike disulfides as broad-spectrum anticoronaviral agents and as a first-line defense against current and future outbreaks.

microbiology↗

bioRxiv2018

Salmonella effectors SseK1 and SseK3 target death domain proteins in the TNF and TRAIL signaling pathways

Strains of Salmonella utilise two distinct type three secretion systems to deliver effector proteins directly into host cells. The Salmonella effectors SseK1 and SseK3 are arginine glycosyltransferases that modify mammalian death domain containing proteins with N-acetyl glucosamine (GlcNAc) when overexpressed ectopically or as recombinant protein fusions. Here, we combined Arg-GlcNAc glycopeptide immunoprecipitation and mass spectrometry to identify host proteins GlcNAcylated by endogenous levels of SseK1 and SseK3 during Salmonella infection. We observed that SseK1 modified the mammalian signaling protein TRADD, but not FADD as previously reported. Overexpression of SseK1 greatly broadened substrate specificity, while ectopic co-expression of SseK1 and TRADD increased the range of modified arginine residues within the death domain of TRADD. In contrast, endogenous levels of SseK3 resulted in modification of the death domains of receptors of the mammalian TNF superfamily, TNFR1 and TRAILR, at residues Arg376 and Arg293 respectively. Structural studies on SseK3 showed that the enzyme displays a classic GT-A glycosyltransferase fold and binds UDP-GlcNAc in a narrow and deep cleft with the GlcNAc facing the surface. Together our data suggests that Salmonellae carrying sseK1 and sseK3 employ the glycosyltransferase effectors to antagonise different components of death receptor signaling.

microbiology↗