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Nature Chemical Biology Jul 2021The L-arabinose-responsive AraC and its cognate P promoter underlie one of the most often used chemically inducible prokaryotic gene expression systems in microbiology...
The L-arabinose-responsive AraC and its cognate P promoter underlie one of the most often used chemically inducible prokaryotic gene expression systems in microbiology and synthetic biology. Here, we change the sensing capability of AraC from L-arabinose to blue light, making its dimerization and the resulting P activation light-inducible. We engineer an entire family of blue light-inducible AraC dimers in Escherichia coli (BLADE) to control gene expression in space and time. We show that BLADE can be used with pre-existing L-arabinose-responsive plasmids and strains, enabling optogenetic experiments without the need to clone. Furthermore, we apply BLADE to control, with light, the catabolism of L-arabinose, thus externally steering bacterial growth with a simple transformation step. Our work establishes BLADE as a highly practical and effective optogenetic tool with plug-and-play functionality-features that we hope will accelerate the broader adoption of optogenetics and the realization of its vast potential in microbiology, synthetic biology and biotechnology.
Topics: AraC Transcription Factor; Arabinose; Escherichia coli; Escherichia coli Proteins; Genetic Engineering; Light
PubMed: 33903769
DOI: 10.1038/s41589-021-00787-6 -
Carbohydrate Polymers Mar 2021Two novel arabinose- and galactose-rich pectic polysaccharides, AELP-B5 (M, 4.25 × 10 g/mol) and B6 (M, 1.56 × 10 g/mol), were rapidly obtained from the leaves of...
Two novel arabinose- and galactose-rich pectic polysaccharides, AELP-B5 (M, 4.25 × 10 g/mol) and B6 (M, 1.56 × 10 g/mol), were rapidly obtained from the leaves of Aralia elata (Miq.) Seem. with anion resin and sequenced ultrafiltration membrane columns. The structural backbone and branched chains of AELP-B5 and B6 were preliminarily elucidated by mild acid hydrolysis with HILIC-ESI-MS/MS. The planar structures and spatial configurations were further identified using UPLC-QDa and GC-MS for compositions, Smith degradation and methylation analysis, FT-IR, NMR (H/C, DEPT, HSQC, HMBC, COSY, NOESY and TOCSY) and SEC-MALLS-RID. (1) AELP-B5 possessed →GalA→ as smooth regions (HG) and a repeating disaccharide moiety of →GalA→Rha→ as hairy regions (RG-I) with a 1:5 molar ratio, whereas AELP-B6 had a distinguishing 1:1 molar ratio between the HG and RG-I; (2) complex side chains were constituted of T-α-Araf, 1,3-α-Araf, 1,5-α-Araf, T-β-Galp, 1,3-β-Galp, 1,4-β-Galp, 1,6-β-Galp, 1,3,4-β-Galp and 1,3,4,6-β-Galp connected at C-4 of the rhamnosyl units in RG-I of AELP-B5 and B6; and (3) both possessed highly branched and compact coil conformations. The CCK-8 assay illustrated that AELP-B6 possessed higher cytotoxicity against HepG2 and HT-29 than that of AELP-B5. Surface plasmon resonance showed the binding affinity of AELP-B6 to galectin-3 (6.488 × 10 M) was about 10 times stronger than that of AELP-B5 (4.588 × 10 M). The above findings provide a molecular structure and bioactivity basis for future potential applications of AELP in the food and medical industries.
Topics: Antineoplastic Agents, Phytogenic; Arabinose; Aralia; Blood Proteins; Carbohydrate Sequence; Cell Survival; Dose-Response Relationship, Drug; Galactose; Galectins; HT29 Cells; HeLa Cells; Hep G2 Cells; Humans; Hydrolysis; Pectins; Plant Extracts; Plant Leaves; Polysaccharides; Protein Binding; Structure-Activity Relationship
PubMed: 33436169
DOI: 10.1016/j.carbpol.2020.117326 -
ELife Dec 2016Reward perception guides all aspects of animal behavior. However, the relationship between the perceived value of a reward, the latent value of a reward, and the...
Reward perception guides all aspects of animal behavior. However, the relationship between the perceived value of a reward, the latent value of a reward, and the behavioral response remains unclear. Here we report that, given a choice between two sweet and chemically similar sugars-L- and D-arabinose- prefers D- over L- arabinose, but forms long-term memories of L-arabinose more reliably. Behavioral assays indicate that L-arabinose-generated memories require sugar receptor Gr43a, and calcium imaging and electrophysiological recordings indicate that L- and D-arabinose differentially activate Gr43a-expressing neurons. We posit that the immediate valence of a reward is not always predictive of the long-term reinforcement value of that reward, and that a subset of sugar-sensing neurons may generate distinct representations of similar sugars, allowing for rapid assessment of the salient features of various sugar rewards and generation of reward-specific behaviors. However, how sensory neurons communicate information about L-arabinose quality and concentration-features relevant for long-term memory-remains unknown.
Topics: Animals; Arabinose; Drosophila Proteins; Drosophila melanogaster; Feeding Behavior; Perception; Receptors, Cell Surface; Reward; Sensory Receptor Cells
PubMed: 28005005
DOI: 10.7554/eLife.22283 -
Journal of Bioscience and Bioengineering Nov 2019Rhizobium sp. RM and RS are Vigna radiata root nodule isolates with the ability to solubilize tricalcium phosphate and rock phosphate under 50 mM Tris-Cl buffering...
Rhizobium sp. RM and RS are Vigna radiata root nodule isolates with the ability to solubilize tricalcium phosphate and rock phosphate under 50 mM Tris-Cl buffering conditions. Rhizobium sp. RM and RS were unique as they could produce two different organic acids, gluconic acid and oxalic acid using glucose and arabinose, respectively, which are two of the most prominent sugars present in the rhizospheric soil. However, P solubilization in these isolates was repressed in the presence of succinate resembling the phenomenon of catabolite repression. RM and RS produced 24 mM and 20 mM gluconic acid in presence of glucose which was repressed to 10 mM and 8 mM, respectively, in glucose + succinate conditions. Similarly, RM and RS produced 28 mM and 23 mM oxalic acid in arabinose containing media which was repressed to 9 mM and 8 mM, respectively, in the presence of arabinose + succinate. Results of enzyme activities indicated 66% repression of quinoprotein glucose dehydrogenase in glucose + succinate compared to glucose grown cells and 84% repression of glyoxylate oxidase in arabinose + succinate compared to arabinose grown cells. This is perhaps the first report on mechanism of P solubilization in rhizobia through utilization of two different sugars, glucose and arabinose and its repression by succinate. Succinate-mediated catabolite repression of arabinose is the unique aspect of this study.
Topics: Arabinose; Catabolite Repression; Gluconates; Glucose; Oxidoreductases; Phosphates; Rhizobium; Succinic Acid
PubMed: 31147219
DOI: 10.1016/j.jbiosc.2019.04.020 -
Journal of Bioscience and Bioengineering Apr 2022Arabinan in plant cell wall constitutes a major source of arabinose and arabino-oligosaccharides in nature. Exo-α-l-1,5-arabinanases release arabinose or...
Arabinan in plant cell wall constitutes a major source of arabinose and arabino-oligosaccharides in nature. Exo-α-l-1,5-arabinanases release arabinose or arabino-oligosaccharides from arabinan in an exo-acting manner and therefore contribute to arabinan degradation. In this study, an exo-α-l-1,5-arabinanase belonging to GH93 family was identified from the thermophilic filamentous fungus Rasamsonia emersonii. The corresponding encoding gene (Reabn93) was cloned from the R. emersonii genome and heterologously expressed in Pichia pastoris. The purified recombinant ReAbn93 exhibited the maximum activity at 70 °C and retained 70% of its activity after incubation at 70 °C for 3 h ReAbn93 had an acidic pH optimum (pH 4.0) but remained stable over a broad pH range (pH 3-9). The specific activity of ReAbn93 toward linear arabinan under optimal conditions was 466.08 U mg. Similar to the few other reported GH93 members, ReAbn93 degrades linear arabinan or arabino-oligosaccharides in an exo-acting manner with arabinobiose as the only hydrolytic product. Of note, ReAbn93 possessed remarkably better thermostability and higher specific activity compared to the only reported thermophilic counterpart in GH93, and therefore holds potential in relevant biotechnological applications.
Topics: Arabinose; Eurotiales; Fungal Proteins; Glycoside Hydrolases; Substrate Specificity
PubMed: 35031213
DOI: 10.1016/j.jbiosc.2021.12.010 -
Analytical Chemistry Sep 2022Most interesting problems in chemistry, biology, and pharmacy involve mixtures. However, analysis of such mixtures by NMR remains a challenge, often requiring the...
Most interesting problems in chemistry, biology, and pharmacy involve mixtures. However, analysis of such mixtures by NMR remains a challenge, often requiring the mixture components to be physically separated before analysis. A variety of methods have been proposed that exploit species-specific properties such as diffusion and relaxation to distinguish between the signals of different components in a mixture without the need for laborious separation. However, these methods can struggle to distinguish between components when signals overlap. Here, we exploit the relaxation properties of selected nuclei to distinguish between different components of a mixture while using pure shift methods to increase spectral resolution by up to an order of magnitude, greatly reducing signal overlap. The advantages of the new method are demonstrated in a mixture of d-xylose and l-arabinose, distinguishing unambiguously between the five major species present.
Topics: Arabinose; Diffusion; Magnetic Resonance Spectroscopy; Xylose
PubMed: 36069721
DOI: 10.1021/acs.analchem.2c02411 -
Bioconjugate Chemistry Nov 2018The development of stimuli-responsive nanocontainers is an issue of utmost importance for many applications such as targeted drug delivery, regulation of the cell and...
The development of stimuli-responsive nanocontainers is an issue of utmost importance for many applications such as targeted drug delivery, regulation of the cell and tissue behavior, making bacteria have useful functions and here converting light. The present work shows a new contribution to the design of polyelectrolyte (PE) containers based on surface modified mesoporous titania particles with deposited Ag nanoparticles to achieve chemical light upconversion via biofilms. The PE shell allows slowing down the kinetics of a release of loaded l-arabinose and switching the bacteria luminescence in a certain time. The hybrid TiO/Ag/PE containers activated at 980 nm (IR) illumination demonstrate 10 times faster release of l-arabinose as opposed to non-activated containers. Fast IR-released l-arabinose switch bacteria fluorescence which we monitor at 510 nm. The approach described herein can be used in many applications where the target and delayed switching and light upconversion are required.
Topics: Arabinose; Biofilms; Drug Carriers; Escherichia coli; Fluorescence; Humans; Luminescence; Metal Nanoparticles; Nanostructures; Polyelectrolytes; Silver; Titanium
PubMed: 30350577
DOI: 10.1021/acs.bioconjchem.8b00648 -
Genetics Jul 2015Invasion of the intestinal epithelium is a critical step in Salmonella enterica infection and requires functions encoded in the gene cluster known as Salmonella...
Invasion of the intestinal epithelium is a critical step in Salmonella enterica infection and requires functions encoded in the gene cluster known as Salmonella Pathogenicity Island 1 (SPI-1). Expression of SPI-1 genes is repressed by L-arabinose, and not by other pentoses. Transport of L-arabinose is necessary to repress SPI-1; however, repression is independent of L-arabinose metabolism and of the L-arabinose-responsive regulator AraC. SPI-1 repression by L-arabinose is exerted at a single target, HilD, and the mechanism appears to be post-translational. As a consequence of SPI-1 repression, l-arabinose reduces translocation of SPI-1 effectors to epithelial cells and decreases Salmonella invasion in vitro. These observations reveal a hitherto unknown role of L-arabinose in gene expression control and raise the possibility that Salmonella may use L-arabinose as an environmental signal.
Topics: AraC Transcription Factor; Arabinose; Gene Expression Regulation, Bacterial; Genomic Islands; Salmonella enterica; Virulence
PubMed: 25991823
DOI: 10.1534/genetics.115.178103 -
Molecular Nutrition & Food Research Aug 2023Notopterygium incisum is a traditional Chinese medicine that is commonly used to treat rheumatoid arthritis. Polysaccharides from N. incisum can be one of its main...
SCOPE
Notopterygium incisum is a traditional Chinese medicine that is commonly used to treat rheumatoid arthritis. Polysaccharides from N. incisum can be one of its main active components. However, there have been little investigations on N. incisum polysaccharides.
METHODS AND RESULTS
A novel polysaccharide named NIP is extracted from N. incisum with a molecular weight of 2.34 × 10 Da. NIP, composed of arabinose, galactose, glucose, and galacturonic acid, is linked by methyl esterified 1,4-linked α-galacturonic acid, 1,6-linked β-galactose, 1,5-linked α-arabinose, and 1,4,6-linked β- glucose. In vitro, NIP can inhibit the NO production of LPS-stimulated RAW264.7 cells. In vivo, NIP relieves toe redness and swelling of AIA rats, reduces the release of inflammatory factors in the serum, and inhibits the activation of NF-κB and JAK/STAT3 signaling pathways. In addition, NIP can effectively decrease oxidative stress, reverse intestinal flora imbalance, and promote butyric acid-producing bacteria's proliferation to exert anti-RA activity.
CONCLUSION
NIP may be recommended as a functional food that can alleviate the damage of rheumatoid arthritis.
Topics: Rats; Animals; Arabinose; Galactose; Arthritis, Rheumatoid; Apiaceae; Polysaccharides
PubMed: 37143438
DOI: 10.1002/mnfr.202200713 -
FEBS Letters Jan 2018Trichoderma reesei is used to produce saccharifying enzyme cocktails for biofuels. There is limited understanding of the transcription factors (TFs) that regulate genes...
Trichoderma reesei is used to produce saccharifying enzyme cocktails for biofuels. There is limited understanding of the transcription factors (TFs) that regulate genes involved in release and catabolism of l-arabinose and d-galactose, as the main TF XYR1 is only partially involved. Here, the T. reesei ortholog of ARA1 from Pyricularia oryzae that regulates l-arabinose releasing and catabolic genes was deleted and characterized by growth profiling and transcriptomics along with a xyr1 mutant and xyr1/ara1 double mutant. Our results show that in addition to the l-arabinose-related role, T. reesei ARA1 is essential for expression of d-galactose releasing and catabolic genes, while XYR1 is not involved in this process.
Topics: Arabinose; Fungal Proteins; Galactose; Gene Expression Regulation, Fungal; Genes, Fungal; Magnaporthe; Mutation; Trichoderma
PubMed: 29215697
DOI: 10.1002/1873-3468.12932