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Journal of Bacteriology Sep 2023The L-arabinose inducible pBAD vectors are commonly used to turn on and off the expression of specific genes in bacteria. The utilization of certain carbohydrates can...
The L-arabinose inducible pBAD vectors are commonly used to turn on and off the expression of specific genes in bacteria. The utilization of certain carbohydrates can influence bacterial growth, virulence factor production, and biofilm formation. , the causative agent of seafood-associated gastroenteritis, can grow in media with L-arabinose as the sole carbon source. However, the effects of L-arabinose on physiology have not been investigated. In this study, we show that the growth rate, biofilm formation capacity, capsular polysaccharide production, motility, and c-di-GMP production of are negatively affected by L-arabinose. RNA-seq data revealed significant changes in the expression levels of 752 genes, accounting for approximately 15.6% of genes in the presence of L-arabinose. The affected genes included those associated with L-arabinose utilization, major virulence genes, known key biofilm-related genes, and numerous regulatory genes. In the majority of type III secretion system, two genes were upregulated in the presence of L-arabinose, whereas in those of type VI secretion system, two genes were downregulated. Ten putative c-di-GMP metabolism-associated genes were also significantly differentially expressed, which may account for the reduced c-di-GMP levels in the presence of L-arabinose. Most importantly, almost 40 putative regulators were significantly differentially expressed due to the induction by L-arabinose, indicating that the utilization of L-arabinose is strictly regulated by regulatory networks in . The findings increase the understanding of how L-arabinose affects the physiology of . Researchers should use caution when considering the use of L-arabinose inducible pBAD vectors in . IMPORTANCE The data in this study show that L-arabinose negatively affects the growth rate, biofilm formation, capsular polysaccharide production, motility, and c-di-GMP production of . The data also clarify the gene expression profiles of the bacterium in the presence of L-arabinose. Significantly differentially expressed genes in response to L-arabinose were involved in multiple cellular pathways, including L-arabinose utilization, virulence factor production, biofilm formation, motility, adaptation, and regulation. The collective findings indicate the significant impact of L-arabinose on the physiology of . There may be similar effects on other species of bacteria. Necessary controls should be established when pBAD vectors must be used for ectopic gene expression.
Topics: Bacterial Proteins; Vibrio parahaemolyticus; Arabinose; Biofilms; Cyclic GMP; Virulence Factors; Gene Expression; Gene Expression Regulation, Bacterial
PubMed: 37655915
DOI: 10.1128/jb.00100-23 -
Biochemical and Biophysical Research... Dec 2022Rare sugar was defined as a sugar that occurs in very small quantities in nature. Among them, l-ribose and d-tagatose were of high added value and useful as...
Rare sugar was defined as a sugar that occurs in very small quantities in nature. Among them, l-ribose and d-tagatose were of high added value and useful as pharmaceutical intermediate for anti-HBV drugs or low calorie sweetener in food industry. Bio-production of the two rare sugar from biomass waste has not been investigated. Hence, development of a feasible and efficient co-production method was of practical usage. However, lack of suitable biocatalyst has become a bottleneck. By sequence alignment and analysis, a C-terminal α-helix from l-arabinose isomerase (L-AI) family was selected as a tool for protein engineering. This α-helix was ligated to C-terminal of Lactobacillus fermentum L-AI (LFAI) and significantly enhanced its thermostability and robustness for both l-arabinose and galactose catalysis. The mutant LFAI-C4 enzyme was immobilized by alginate and antimicrobial peptide poly-l-lysine, and was used to convert pretreated corncob acid hydrolysate (PCAH) into l-ribulose and d-tagatose in the presence of boric acid. In addition, we identified and immobilized a novel thermostable mannose-6-phosphate isomerase from Bacillus subtilis (BsMPI-2) which was efficient in catalyzing retaining l-ribulose into l-ribose and showing no activity on d-tagatose. The dual immobilized enzymes (LFAI-C4 and BsMPI-2) system co-produced 191.9 g/L l-ribose and 80.1 g/L d-tagatose, respectively. Showing a total yield of 46.6% from l-arabinose to l-ribose, which was the highest among reported. The dual immobilized enzymes system preserved 82% activity after 40 batches reaction, showing excellent potentials for industrial use. This study presents a promising alternative for rare sugar production from low-value raw material and showed satisfied conversion rate, product concentration, and operation stability.
Topics: Sugars; Ribose; Arabinose; Enzymes, Immobilized
PubMed: 36410270
DOI: 10.1016/j.bbrc.2022.11.024 -
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 -
Microbiological Research Feb 2021In this study the intraspecies diversity of Fructilactobacillus (F.) sanfranciscensis (formerly Lactobacillus sanfranciscensis) was characterized by comparative genomics...
In this study the intraspecies diversity of Fructilactobacillus (F.) sanfranciscensis (formerly Lactobacillus sanfranciscensis) was characterized by comparative genomics supported by physiological data. Twenty-four strains of F. sanfranciscensis were analyzed and sorted into six different genomic clusters. The core genome comprised only 43,14 % of the pan genome, i.e. 0.87 Mbp of 2.04 Mbp. The main annotated genomic differences reside in maltose, fructose and sucrose as well as nucleotide metabolism, use of electron acceptors, and exopolysacchride formation. Furthermore, all strains are well equipped to cope with oxidative stress via NADH oxidase and a distinct thiol metabolism. Only ten of 24 genomes contain two maltose phosphorylase genes (mapA and mapB). In F. sanfranciscensis TMW 1.897 only mapA was found. All strains except those from genomic cluster 2 contained the mannitol dehydrogenase and should therefore be able to use fructose as external electron acceptor. Moreover, six strains were able to grow on fructose as sole carbon source, as they contained a functional fructokinase gene. No growth was observed on pentoses, i.e. xylose, arabinose or ribose, as sole carbon source. This can be referred to the absence of ribose pyranase rbsD in all genomes, and absence of or mutations in numerous other genes, which are essential for arabinose and xylose metabolism. Seven strains were able to produce exopolysaccharides (EPS) from sucrose. In addition, the strains containing levS were able to grow on sucrose as sole carbon source. Strains of one cluster exhibit auxotrophies for purine nucleotides. The physiological and genomic analyses suggest that the biodiversity of F. sanfranciscensis is larger than anticipated. Consequently, "original" habitats and lifestyles of F. sanfranciscensis may vary but can generally be referred to an adaptation to sugary (maltose/sucrose/fructose-rich) and aerobic environments as found in plants and insects. It can dominate sourdoughs as a result of reductive evolution and cooperation with fructose-delivering, acetate-tolerant yeasts.
Topics: Bacterial Proteins; Biodiversity; Bread; Genome Size; Genome, Bacterial; Lactobacillaceae; Multienzyme Complexes; NADH, NADPH Oxidoreductases; Phylogeny; Sucrose; Triticum; Xylose
PubMed: 33129664
DOI: 10.1016/j.micres.2020.126625 -
Nutrients Jan 2022Non-alcoholic fatty liver disease (NAFLD) has become the most prevalent liver disease worldwide and is impacted by an unhealthy diet with excessive calories, although...
Non-alcoholic fatty liver disease (NAFLD) has become the most prevalent liver disease worldwide and is impacted by an unhealthy diet with excessive calories, although the role of sugars in NAFLD etiology remains largely unexplored. Rare sugars are natural sugars with alternative monomers and glycosidic bonds, which have attracted attention as sugar replacers due to developments in enzyme engineering and hence an increased availability. We studied the impact of (rare) sugars on energy production, liver cell physiology and gene expression in human intestinal colorectal adenocarcinoma (Caco-2) cells, hepatoma G2 (HepG2) liver cells and a coculture model with these cells. Fat accumulation was investigated in the presence of an oleic/palmitic acid mixture. Glucose, fructose and galactose, but not mannose, l-arabinose, xylose and ribose enhanced hepatic fat accumulation in a HepG2 monoculture. In the coculture model, there was a non-significant trend ( = 0.08) towards higher (20-55% increased) median fat accumulation with maltose, kojibiose and nigerose. In this coculture model, cellular energy production was increased by glucose, maltose, kojibiose and nigerose, but not by trehalose. Furthermore, glucose, fructose and l-arabinose affected gene expression in a sugar-specific way in coculture HepG2 cells. These findings indicate that sugars provide structure-specific effects on cellular energy production, hepatic fat accumulation and gene expression, suggesting a health potential for trehalose and l-arabinose, as well as a differential impact of sugars beyond the distinction of conventional and rare sugars.
Topics: Caco-2 Cells; Carcinoma, Hepatocellular; Coculture Techniques; Humans; Liver Neoplasms; Sugars
PubMed: 35276968
DOI: 10.3390/nu14030611 -
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 -
Foods (Basel, Switzerland) Jan 2022L-arabinose is a bio-active compound derived from the side-streams of plant food processing. L-arabinose lowers glycemic and insulinemic responses when added to simple...
L-arabinose is a bio-active compound derived from the side-streams of plant food processing. L-arabinose lowers glycemic and insulinemic responses when added to simple water-based sugary liquids. However, the effect in more complex foods, including fat and starch, is inconsistent. This study assessed the effect of fat or starch in a sugary drink on the efficacy of L-arabinose. Twenty-three healthy volunteers (12 female/11 male; aged 24 ± 3 years; BMI 23 ± 3 kg/m) participated in a randomised cross-over trial with six drinks: control: 50 g sucrose in water; fat: control + 22 g oil; starch: control + 50 g starch; and all three with and without the addition of 5 g L-arabinose. The addition of L-arabinose to the control drink lowered glucose and insulin peaks by 15% and 52%; for the fat drink by 8% and 45%; and for the starch drink by 7% and 29%. For all three drinks, adding L-arabinose increased glucagon-like peptide 1 (GLP-1) responses and lowered Glucose-dependent insulinotropic polypeptide (GIP) responses. Despite adding large quantities of starch and fat to sugary drinks, L-arabinose significantly lowered postprandial glycemic and insulinemic responses in healthy subjects. These findings suggest that L-arabinose can be functional in more complex foods; however, the factors affecting its efficacy in solid food matrices need to be studied in more detail.
PubMed: 35053889
DOI: 10.3390/foods11020157 -
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