Marine bacteria for the production of asparaginase
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB44382 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Macroalgae contribute substantially to primary production in coastal ecosystems. Their biomass, mainly consisting of polysaccharides, is cycled into the environment by marine heterotrophic bacteria (MHB), using largely uncharacterized mechanisms. In Zobellia galactanivorans, we discovered and characterized the complete catabolic pathway for carrageenans, major cell wall polysaccharides of red macroalgae, providing a model system for carrageenan utilization by MHB. We further demonstrate that carrageenan catabolism relies on a multifaceted carrageenan-induced regulon, including a non-canonical polysaccharide utilization locus (PUL) and several distal genes. The genetic structure of the carrageenan utilization system is well conserved in marine Bacteroidetes, but modified in other MHB phyla. The core system is completed by additional functions which can be assumed by non-orthologous genes in different species. This complex genetic structure is due to multiple evolutionary events including gene duplications and horizontal gene transfers. These results allow for an extension on the definition of bacterial PUL-mediated polysaccharide digestion.
2017-12-06 | GSE101142 | GEO
Project description:Bacterial extracellular vesicles (BEVs) are spherical membranous structures released by bacterial cells that act as a transport and delivery mechanism for various biological compounds. Experimental investigation of BEVs in marine bacteria, largely limited to a number of laboratory model systems, have suggested putative roles in their ecophysiology. Yet the functional potential of BEVs in their ecological context has never been explored directly in the marine environment. Here we report the results of the first large-scale oceanographic survey of marine BEVs carried out across surface waters of the South Pacific Ocean. The presence of marine BEVs was consistently observed across a range of biogeochemical conditions, with an overall abundance comparable to that of bacterial communities (ca. 108 BEVs L-1). The protein cargoes of marine BEVs differed significantly between environmental conditions, being enriched in carbohydrate transporters and hydrolytic enzymes under phytoplankton bloom conditions, and enriched in different iron uptake proteins in nutrient-limited waters, indicating key extracellular functions they perform in marine bacterial communities. Our observations highlight the importance of marine BEVs and their potential functions across oceanic scales, with implications for our general understanding of key processes in marine microbial ecology.
2026-09-07 | PXD062682 | Pride
Project description:Isolation of newly marine bacteria for l-asparaginase enzymatic activity
| PRJNA670955 | ENA
Project description:Spider dragline silk protein, major ampullate spidroin (MaSp) are mainly composed of multiple types of MaSp, such as MaSp1 and MaSp2. MaSp has a conserved primary structure comprising three domains: a repetitive central domain and nonrepetitive N-terminal and C-terminal domains. The MaSp repetitive domains are arranged in alternating blocks of polyalanine (crystalline) and glycine-rich (amorphous) sequences, which are responsible for the high tensile strength and high elasticity, respectively, of spider silk fibers. Recombinant spidroins have been successfully expressed in various hosts such as bacteria, yeasts, insects, plants, and animals. However, it is still a great challenge to produce spidroins on a large scale with a sustainable production process. In this study, we develop an economical and sustainable marine photosynthetic microbial cell factory using Rhodovulum sulfidophilum, which is a marine purple nonsulfur bacterium that is capable of producing the hydrophobic repetitive sequence of MaSp1 (1-mer, 2-mer, 3-mer and 6-mer from Nephila clavipes) using small amount of organic substance under photoheterotrophic or photoautotrophic growth conditions.
2021-06-16 | PXD019821 | JPOST Repository
Project description:To identify genes affected by L-asparaginase, we treated with L-asparaginase 1U/ml. After 2 days, RNA was extracted, and then expression analysis was performed using agilent microarray.
2017-01-31 | GSE94289 | GEO
Project description:Abstract: To investigate the effect of l-asparaginase on acute lymphoblastic leukemia (ALL), we used cDNA microarrays to obtain a genome-wide view of gene expression both at baseline and after in vitro exposure to l-asparaginase in cell lines and pediatric ALL samples. In 16 cell lines, a baseline gene expression pattern distinguished l-asparaginase sensitivity from resistance. However, for 28 pediatric ALL samples, no consistent baseline expression pattern was associated with sensitivity to l-asparaginase. In particular, baseline expression of asparagine synthetase (ASNS) was not predictive of response to l-asparaginase. After exposure to l-asparaginase, 5 cell lines and 10 clinical samples exhibited very similar changes in the expression of a large number of genes. However, the gene expression changes occurred more slowly in the clinical samples. These changes included a consistent increase in expression of tRNA synthetases and solute transporters and activating transcription factor and CCAAT/enhancer binding protein family members, a response similar to that observed with amino acid starvation. There was also a consistent decrease in many genes associated with proliferation. Taken together, the changes seem to reflect a consistent coordinated response to asparagine starvation in both cell lines and clinical samples. Importantly, in the clinical samples, increased expression of ASNS after l-asparaginase exposure was not associated with in vitro resistance to l-asparaginase, indicating that ASNS-independent mechanisms of in vitro l-asparaginase resistance are common in ALL. These results suggest that targeting particular genes involved in the response to amino acid starvation in ALL cells may provide a novel way to overcome l-asparaginase resistance. This SuperSeries is composed of the SubSeries listed below.
2006-03-08 | GSE4397 | GEO
Project description:Resistance to asparaginase, an antileukemic enzyme that depletes asparagine, is a common clinical problem. Using a genome-wide CRISPR/Cas9 screen, we found a synthetic lethal interaction between Wnt pathway activation and asparaginase in acute leukemias resistant to this enzyme. Wnt pathway activation induced asparaginase sensitivity in distinct treatment-resistant subtypes of acute leukemia, but not in normal hematopoietic progenitors. Sensitization to asparaginase was mediated by Wnt-dependent stabilization of proteins (Wnt/STOP), which inhibits GSK3-dependent protein ubiquitination and proteasomal degradation, a catabolic source of asparagine. Inhibiting the alpha isoform of GSK3 phenocopied this effect, and pharmacologic GSK3 inhibition profoundly sensitized drug-resistant leukemias to asparaginase. Our findings provide a molecular rationale for activation of Wnt/STOP signaling to improve the therapeutic index of asparaginase. To gain further insights into mechanisms of cytotoxicity of this combination, we applied unbiased mass spectrometry proteomics to CCRF-CEM cells, a human T-cell acute lymphoblastic leukemia cell line, treated with vehicle, asparaginase alone, the GSK3 inhibitor BRD0705 (which phenocopies Wnt/STOP pathway activation), or the combination of asparaginase and BRD0705.
2019-03-29 | PXD013061 | Pride
Project description:<p>Refinements of multidrug regimens, and particularly the addition of L-asparaginase, resulted in an immediate gain in survival for pediatric acute lymphoblastic leukemia patients. Yet L-asparaginase has substantial side effects which may require dose reductions or delays in subsequent doses. There are at least 3 possible sources of L-asparagine to consider when balancing blood levels with asparaginase dosing, the diet, cell synthesis and bacterial synthesis. To date, there is one precedent in which blood L-asparagine levels are reduced in parallel with a reduction in consumed levels, in mice. We build on that approach in experiments aimed at testing whether a long-term dietary restriction of L-asparagine (Asn) can impact blood levels and possibly enhance L-asparaginase efficacy. In our experiment, 2 groups of mice received food pellets either with 4% or 0% Asn. Blood and fecal metabolites and fecal bacteria were sampled over 72 days. After this accommodation period, all mice continued their diet and received a single injection of pegylated E. coli recombinant L-asparaginase (P-ASP). Samples for bacteria and metabolites were collected 4 and 5 days later, respectively. Neither diet had adverse effects on the general health of the mice nor did diet alone change blood Asn levels. Both diets led to changes in gut bacteria. P-ASP depleted blood Asn in mice consuming either diet. Bacteria identified in fecal pellets revealed that the microbiomes of mice in the 2 cages were different (cage effect) and remained different. Metagenomic analyses of day 72 stool indicated there were no diet-dependent differences in bacterial asparaginase and asparagine synthetase. Further research should confirm these results, as well as include approaches to determine the source of Asn in the blood while ingesting diets with no/low or high amounts of Asn</p>
2026-01-25 | MTBLS13764 | MetaboLights
Project description:Sulfated fucans are key component of brown algal cell walls. These polysaccharides are particularly complex and structurally diverse, with multiple modifications (e.g. branches, sulfation, acetylation). A few bacterial enzymes involved in their biodegradation have been characterized but the catabolism of sulfated fucans remains largely uncharted. In Mariniflexile fucanivorans SW5, we discovered and studied a large Polysaccharide Utilization locus (PUL) specific for sulfated fucans. More than 20 enzymes have been characterized providing a model system for sulfated fucans utilization by marine heterotrophic bacteria. We further studied the transcriptomic responses of M. fucanivorans SW5 to sulfated fucan utilization demonstrating that this large PUL is indeed induced by sulfated fucans. Other gene clusters distantly localized in the genome are also strongly induced revealing a complex regulon. Notably genes involved into sulfite reduction are upregulated suggesting an adaptation to the abundance of sulfate ions released during the biodegradation of sulfated fucans.
2026-09-10 | GSE209534 | GEO