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FEMS Microbiology Letters Jun 2017Pseudomonas aeruginosa is a versatile opportunistic pathogen capable of infecting a broad range of hosts, in addition to thriving in a broad range of environmental... (Review)
Review
Pseudomonas aeruginosa is a versatile opportunistic pathogen capable of infecting a broad range of hosts, in addition to thriving in a broad range of environmental conditions outside of hosts. With this versatility comes the need to tightly regulate its genome to optimise its gene expression and behaviour to the prevailing conditions. Two-component systems (TCSs) comprising sensor kinases and response regulators play a major role in this regulation. This minireview discusses the growing number of TCSs that have been implicated in the virulence of P. aeruginosa, with a special focus on the emerging theme of multikinase networks, which are networks comprising multiple sensor kinases working together, sensing and integrating multiple signals to decide upon the best response. The networks covered in depth regulate processes such as the switch between acute and chronic virulence (GacS network), the Cup fimbriae (Roc network and Rcs/Pvr network), the aminoarabinose modification of lipopolysaccharide (a network involving the PhoQP and PmrBA TCSs), twitching motility and virulence (a network formed from the Chp chemosensory pathway and the FimS/AlgR TCS), and biofilm formation (Wsp chemosensory pathway). In addition, we highlight the important interfaces between these systems and secondary messenger signals such as cAMP and c-di-GMP.
Topics: Arabinose; Bacterial Proteins; Cyclic AMP; Cyclic GMP; Fimbriae, Bacterial; Gene Expression Regulation, Bacterial; Genes, Bacterial; Lipopolysaccharides; Pseudomonas aeruginosa; Virulence Factors
PubMed: 28510688
DOI: 10.1093/femsle/fnx104 -
Biochemistry Oct 2023Covalent modification of lipid A with 4-deoxy-4-amino-l-arabinose (Ara4N) mediates resistance to cationic antimicrobial peptides and polymyxin antibiotics in...
Covalent modification of lipid A with 4-deoxy-4-amino-l-arabinose (Ara4N) mediates resistance to cationic antimicrobial peptides and polymyxin antibiotics in Gram-negative bacteria. The proteins required for Ara4N biosynthesis are encoded in the and loci, with ArnT ultimately transferring the amino sugar from undecaprenyl-phospho-4-deoxy-4-amino-l-arabinose (C55P-Ara4N) to lipid A. However, Ara4N is N-formylated prior to its transfer to undecaprenyl-phosphate by ArnC, requiring a deformylase activity downstream in the pathway to generate the final C55P-Ara4N donor. Here, we show that deletion of the gene in an mutant that constitutively expresses the operon leads to accumulation of the formylated ArnC product undecaprenyl-phospho-4-deoxy-4-formamido-l-arabinose (C55P-Ara4FN), suggesting that ArnD is the downstream deformylase. Purification of ArnD (stArnD) shows that it is membrane-associated. We present the crystal structure of stArnD revealing a NodB homology domain structure characteristic of the metal-dependent carbohydrate esterase family 4 (CE4). However, ArnD displays several distinct features: a 44 amino acid insertion, a C-terminal extension in the NodB fold, and sequence divergence in the five motifs that define the CE4 family, suggesting that ArnD represents a new family of carbohydrate esterases. The insertion is responsible for membrane association as its deletion results in a soluble ArnD variant. The active site retains a metal coordination H-H-D triad, and in the presence of Co or Mn, purified stArnD efficiently deformylates C55P-Ara4FN confirming its role in Ara4N biosynthesis. Mutations D9N and H233Y completely inactivate stArnD implicating these two residues in a metal-assisted acid-base catalytic mechanism.
Topics: Polymyxins; Lipid A; Arabinose; Amino Sugars; Anti-Bacterial Agents; Escherichia coli; Carbohydrates; Bacterial Proteins
PubMed: 37782650
DOI: 10.1021/acs.biochem.3c00293 -
Biochemical and Biophysical Research... May 2022l-Arabinose 1-dehydrogenase (AraDH) catalyzes the NAD(P)-dependent oxidation of l-arabinose to L-arabinono-1,4-lactone in the non-phosphorylative l-arabinose pathway,...
l-Arabinose 1-dehydrogenase (AraDH) catalyzes the NAD(P)-dependent oxidation of l-arabinose to L-arabinono-1,4-lactone in the non-phosphorylative l-arabinose pathway, and is classified into glucose-fructose oxidoreductase and short-chain dehydrogenase/reductase (SDR). We herein report the crystal structure of a SDR-type AraDH (from Herbaspirillum huttiense) for the first time. The interactions between Asp49 and the 2'- and 3'-hydroxyl groups of NAD were consistent with strict specificity for NAD. In a binding model for the substrate, Ser155 and Tyr168, highly conserved in the SDR superfamily, interacted with the C1 and/or C2 hydroxyl(s) of l-arabinose, whereas interactions between Asp107, Arg109, and Gln206 and the C2 and/or C3 hydroxyl(s) were unique to AraDH. Trp200 significantly contributed to the selectivities of the C4 hydroxyl and C6 methyl of substrates.
Topics: Arabinose; NAD; Oxidoreductases; Short Chain Dehydrogenase-Reductases; Substrate Specificity
PubMed: 35279441
DOI: 10.1016/j.bbrc.2022.03.028 -
World Journal of Microbiology &... Sep 2022The first hyperthermophilic L-arabinose/D-galactose 1-dehydrogenase (TmAraDH) from Thermotoga maritima was heterologously purified from Escherichia coli. It belongs to...
The first hyperthermophilic L-arabinose/D-galactose 1-dehydrogenase (TmAraDH) from Thermotoga maritima was heterologously purified from Escherichia coli. It belongs to the Gfo/Idh/MocA protein family, prefers NAD/NADP as a cofactor. The purified TmAraDH exhibited maximum activity toward L-arabinose at 75 °C and pH 8.0, and retained 63.7% of its activity after 24 h at 60 °C, and over 60% of its activity after holding a pH ranging from 7.0 to 9.0 for 1 h. Among all tested substrates, TmAraDH exclusively catalyzed the NAD(P)-dependent oxidation of L-arabinose, D-galactose and D-fucose. The catalytic efficiency (k/K) towards L-arabinose and D-galactose was 123.85, 179.26 min mM for NAD, and 56.06, 18.19 min mM for NADP, respectively. TmAraDH exhibited complete oxidative conversion in 12 h at 70 °C to D-galactonate with 5 mM D-galactose. Modelling provides structural insights into the cofactor and substrate recognition specificity. Our results suggest that TmAraDH have great potential for the conversion of L-arabinose and D-galactose to L-arabonate and D-galactonate.
Topics: Arabinose; Escherichia coli; Fucose; Galactose; Galactose Dehydrogenases; NAD; NADP; Thermotoga maritima
PubMed: 36109417
DOI: 10.1007/s11274-022-03406-1 -
International Journal of Biological... Dec 2022In the current study, the effects of fermentation manners on the structure and immunomodulatory activity of polysaccharide in longan wine or vinegar were investigated....
In the current study, the effects of fermentation manners on the structure and immunomodulatory activity of polysaccharide in longan wine or vinegar were investigated. Compared to longan polysaccharide (CP1), polysaccharide in longan wine (CP2) or vinegar (CP3 and CP4) had smaller molecular weights, and was consisted of more mannose, arabinose, rhamnose, galactose and less glucose. After purification, the major fraction (P1-P4) was obtained from CP1-CP4, respectively. The structures and immunoregulatory activities of P1-P4 were characterized. Fermentation and purification were favorable to increase the immunoregulatory activities of P2-P4, which were contributed to their different structural features. The structure-activity relationship analysis indicated that molecular weight, mannose, rhamnose, glucuronic acid, glucose and arabinose were significantly associated with the cytokines secretion. Compared with other polysaccharides, P3 displayed better immunomodulatory activity due to its lower molecular weight, lower contents of rhamnose and glucose, and higher levels of mannose and arabinose by activating MAPK and PI3K/Akt signaling pathways.
Topics: Fermentation; Mannose; Arabinose; Rhamnose; Acetic Acid; Phosphatidylinositol 3-Kinases; Polysaccharides; Glucose
PubMed: 36170929
DOI: 10.1016/j.ijbiomac.2022.09.195 -
Applied Microbiology and Biotechnology Jul 2020Currently, due to the special functions and potential application values, rare sugars become the hot topic in carbohydrate fields. L-Ribulose, an isomer of L-ribose, is... (Review)
Review
Currently, due to the special functions and potential application values, rare sugars become the hot topic in carbohydrate fields. L-Ribulose, an isomer of L-ribose, is an expensive rare ketopentose. As an important precursor for other rare sugars and L-nucleoside analogue synthesis, L-ribulose attracts more and more attention in recent days. Compared with complicated chemical synthesis, the bioconversion method becomes a good alternative approach to L-ribulose production. Generally, the bioconversion of L-ribulose was linked with ribitol, L-arabinose, L-ribose, L-xylulose, and L-arabitol. Herein, an overview of recent advances in the metabolic pathway, chemical synthesis, bioproduction of L-ribulose, and the potential application of L-ribulose is reviewed in detail in this paper. KEY POINTS: 1. L-Ribulose is a rare sugar and the key precursor for L-ribose production. 2. L-Ribulose is the starting material for L-nucleoside derivative synthesis. 3. Chemical synthesis, bioproduction, and applications of L-ribulose are reviewed.
Topics: Arabinose; Bacteria; Bacterial Proteins; Biocatalysis; Biotransformation; Metabolic Networks and Pathways; Pentoses; Ribitol; Ribose; Sugar Alcohols; Xylulose
PubMed: 32372201
DOI: 10.1007/s00253-020-10637-5 -
Biotechnology Journal Jan 2019Extending the host substrate range of industrially relevant microbes, such as Saccharomyces cerevisiae, has been a highly-active area of research since the conception of... (Review)
Review
Extending the host substrate range of industrially relevant microbes, such as Saccharomyces cerevisiae, has been a highly-active area of research since the conception of metabolic engineering. Yet, rational strategies that enable non-native substrate utilization in this yeast without the need for combinatorial and/or evolutionary techniques are underdeveloped. Herein, this review focuses on pentose metabolism in S. cerevisiae as a case study to highlight the challenges in this field. In the last three decades, work has focused on expressing exogenous pentose metabolizing enzymes as well as endogenous enzymes for effective pentose assimilation, growth, and biofuel production. The engineering strategies that are employed for pentose assimilation in this yeast are reviewed, and compared with metabolism and regulation of native sugar, galactose. In the case of galactose metabolism, multiple signals regulate and aid growth in the presence of the sugar. However, for pentoses that are non-native, it is unclear if similar growth and regulatory signals are activated. Such a comparative analysis aids in identifying missing links in xylose and arabinose utilization. While research on pentose metabolism have mostly concentrated on pathway level optimization, recent transcriptomics analyses highlight the need to consider more global regulatory, structural, and signaling components.
Topics: Arabinose; Galactose; Metabolic Engineering; Pentoses; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Systems Biology
PubMed: 30171750
DOI: 10.1002/biot.201800364 -
Molecules (Basel, Switzerland) Nov 2022It has been reported that polysaccharides in wine can interact with tannins and other wine components and modify the sensory properties of the wine. Unfortunately, the...
It has been reported that polysaccharides in wine can interact with tannins and other wine components and modify the sensory properties of the wine. Unfortunately, the contribution of polysaccharides to wine quality is poorly understood, mainly due to their complicated structure and varied composition. In addition, the composition and molecular structure of polysaccharides in different wines can vary greatly. In this study, the polysaccharides were isolated from pinot noir wine, then separated into high-molecular-weight (PNWP-H) and low-molecular-weight (PNWP-L) fractions using membrane-based ultrafiltration. Each polysaccharide fraction was further studied using size exclusion chromatography, UV-Vis, FT-IR, matrix-assisted laser desorption/ionization-high-resolution mass spectrometry, and gas chromatography-mass spectrometry (GC-MS). The results showed that PNWP-L and PNWP-H had different chemical properties and compositions. The FT-IR analysis showed that PNWPs were acidic polysaccharides with α- and β-type glycosidic linkages. PNWP-L and PNWP-H had different α- and β-type glycosidic linkage structures. FT-IR showed stronger antisymmetric and symmetric stretching vibrations of carboxylate anions of uronic acids in PNWP-L, suggesting more uronic acid in PNWP-L. The size exclusion chromatography results showed that over 72% of the PNWP-H fraction had molecular sizes from 25 kDa to 670 kDa. Only a small percentage of smaller molecular polysaccharides was found in the PNWP-H fraction. In comparison, all of the polysaccharides in the PNWP-L fraction were below 25 KDa, with a majority distributed approximately 6 kDa (95.1%). GC-MS sugar composition analysis showed that PNWP-L was mainly composed of galacturonic acid, rhamnose, galactose, and arabinose, while PNWP-H was mainly composed of mannose, arabinose, and galactose. The molecular size distribution and sugar composition analysis suggested that the PNWP-L primarily consisted of rhamnogalacturonans and polysaccharides rich in arabinose and galactose (PRAG). In comparison, PNWP-H were mostly mannoproteins and polysaccharides rich in arabinose and galactose (PRAG). Further research is needed to understand the impacts of these fractions on wine organoleptic properties.
Topics: Galactose; Spectroscopy, Fourier Transform Infrared; Wine; Polysaccharides; Tannins; Arabinose
PubMed: 36500422
DOI: 10.3390/molecules27238330 -
Applied Microbiology and Biotechnology Nov 2018Xylan has a main chain consisting of β-1,4-linked xylose residues with diverse substituents. Endoxylanases cleave the xylan chain at cleavage sites determined by the... (Review)
Review
Xylan has a main chain consisting of β-1,4-linked xylose residues with diverse substituents. Endoxylanases cleave the xylan chain at cleavage sites determined by the substitution pattern and thus give different oligosaccharide product patterns. Most known endoxylanases belong to glycoside hydrolase (GH) families 10 and 11. These enzymes work well on unsubstituted xylan but accept substituents in certain subsites. The GH11 enzymes are more restricted by substituents, but on the other hand, they are normally more active than the GH10 enzymes on insoluble substrates, because of their smaller size. GH5 endoxylanases accept arabinose substituents in several subsites and require it in the - 1 subsite. This specificity makes the GH5 endoxylanases very useful for degradation of highly arabinose-substituted xylans and for the selective production of arabinoxylooligosaccharides, without formation of unsubstituted xylooligosaccharides. The GH30 endoxylanases have a related type of specificity in that they require a uronic acid substituent in the - 2 subsite, which makes them very useful for the production of uronic acid substituted oligosaccharides. The ability of dietary xylooligosaccharides to function as prebiotics in humans is governed by their substitution patterns. Endoxylanases are thus excellent tools to tailor prebiotic oligosaccharides to stimulate various types of intestinal bacteria and to cause fermentation in different parts of the gastrointestinal tract. Continuously increasing knowledge on the function of the gut microbiota and discoveries of novel endoxylanases increase the possibilities to achieve health-promoting effects.
Topics: Arabinose; Endo-1,4-beta Xylanases; Gastrointestinal Microbiome; Gastrointestinal Tract; Glucuronates; Humans; Oligosaccharides; Prebiotics; Substrate Specificity; Uronic Acids; Xylans
PubMed: 30196329
DOI: 10.1007/s00253-018-9343-4 -
Bioprocess and Biosystems Engineering Feb 2021The deconstruction of banana peel for carbohydrate recovery was performed by sequential treatment (acid, alkaline, and enzymatic). The pretreatment with citric acid...
The deconstruction of banana peel for carbohydrate recovery was performed by sequential treatment (acid, alkaline, and enzymatic). The pretreatment with citric acid promoted the extraction of pectin, resulting in a yield of 8%. In addition, xylose and XOS, 348.5 and 17.3 mg/g xylan, respectively, were also quantified in acidic liquor as a result of partial depolymerization of hemicellulose. The spent solid was pretreated with alkaline solution (NaOH or KOH) for delignification and release of residual carbohydrates from the hemicellulose. The yields of xylose and arabinose (225.2 and 174.0 mg/g hemicellulose) were approximately 40% higher in the pretreatment with KOH, while pretreatment with NaOH promoted higher delignification (67%), XOS yield (32.6 mg/g xylan), and preservation of cellulosic fraction. Finally, the spent alkaline solid, rich in cellulose (76%), was treated enzymatically to release glucose, reaching the final concentration of 28.2 g/L. The mass balance showed that through sequential treatment, 9.9 g of xylose, 0.5 g of XOS, and 8.2 g of glucose were obtained from 100 g of raw banana peels, representing 65.8% and 46.5% conversion of hemicellulose and cellulose, respectively. The study of the fractionation of carbohydrates in banana peel proved to be a useful tool for valorization, mainly of the hemicellulose fraction for the production of XOS and xylose with high value applications in the food industry.
Topics: Arabinose; Fruit; Hydrolysis; Hydroxides; Musa; Pectins; Polysaccharides; Potassium Compounds; Sodium Hydroxide; Xylose
PubMed: 32948889
DOI: 10.1007/s00449-020-02442-1