-
The Science of the Total Environment Jan 2024Soil microbial necromass is an important contributor to soil organic matter (>50%) and it is largely composed of microbial residues. In soils, fragmented cell wall...
Soil microbial necromass is an important contributor to soil organic matter (>50%) and it is largely composed of microbial residues. In soils, fragmented cell wall residues are mostly found in their polysaccharide forms of fungal chitin and bacterial peptidoglycan. Microbial necromass biomarkers, particularly amino sugars (AS) such as glucosamine (GlcN) and muramic acid (MurA) have been used to trace fungal and bacterial residues in soils, and to distinguish carbon (C) found in microbial residues from non-microbial organic C. Neutral sugars (NS), particularly the hexose/pentose ratio, have also been proposed as tracers of plant polysaccharides in soils. In our study, we extended the range of biomarkers to include AS and NS compounds in the biomass of 120 species belonging to archaea, bacteria, fungi, or plants. GlcN was the most common AS found in all taxa, contributing 42-91% to total AS content, while glucose was the most common NS found, contributing 56-79% to total NS. We identified talosaminuronic acid, found in archaeal pseudopeptidoglycan, as a new potential biomarker specific for Euryarchaeota. We compared the variability of these compounds between the different taxonomic groups using multivariate approaches, such as non-metric multidimensional scaling (NMDS) and partial least squares discriminant analysis (PLS-DA) and statistically evaluated their biomarker potential via indicator species analysis. Both NMDS and PLS-DA showcased the variability in the AS and NS contents between the different taxonomic groups, highlighting their potential as necromass residue biomarkers and allowing their extension from separating bacterial and fungal necromass to separating microbes from plants. Finally, we estimated new conversion factors where fungal GlcN is converted to fungal C by multiplying by 10 and MurA is converted to bacterial C by multiplying by 54. Conversion factors for talosaminuronic acid and galactosamine are also proposed to allow estimation of archaeal or all-microbial necromass residue C, respectively.
Topics: Archaea; Sugars; Carbohydrates; Amino Sugars; Bacteria; Carbon; Fungi; Soil; Biomarkers; Soil Microbiology
PubMed: 37793447
DOI: 10.1016/j.scitotenv.2023.167463 -
Applied and Environmental Microbiology Dec 2020Amino sugars, particularly glucosamine (GlcN) and -acetylglucosamine (GlcNAc), are abundant carbon and nitrogen sources supplied in host secretions and in the diet to...
Amino sugars, particularly glucosamine (GlcN) and -acetylglucosamine (GlcNAc), are abundant carbon and nitrogen sources supplied in host secretions and in the diet to the biofilms colonizing the human oral cavity. Evidence is emerging that these amino sugars provide ecological advantages to beneficial commensals over oral pathogens and pathobionts. Here, we performed transcriptome analysis on and growing in single-species or dual-species cultures with glucose, GlcN, or GlcNAc as the primary carbohydrate source. Compared to glucose, GlcN caused drastic transcriptomic shifts in each species of bacteria when it was cultured alone. Likewise, cocultivation in the presence of GlcN yielded transcriptomic profiles that were dramatically different from the single-species results from GlcN-grown cells. In contrast, GlcNAc elicited only minor changes in the transcriptome of either organism in single- and dual-species cultures. Interestingly, genes involved in pyruvate metabolism were among the most significantly affected by GlcN in both species, and these changes were consistent with measurements of pyruvate in culture supernatants. Differing from what was found in a previous report, growth of alone with GlcN inhibited the expression of multiple operons required for mutacin production. Cocultivation with consistently increased the expression of two manganese transporter operons ( and ) and decreased expression of mutacin genes in Conversely, appeared to be less affected by the presence of but did show increases in genes for biosynthetic processes in the cocultures. In conclusion, amino sugars profoundly alter the interactions between pathogenic and commensal streptococci by reprogramming central metabolism. Carbohydrate metabolism is central to the development of dental caries. A variety of sugars available to dental microorganisms influence the development of caries by affecting the physiology, ecology, and pathogenic potential of tooth biofilms. Using two well-characterized oral bacteria, one pathogen () and one commensal (), in an RNA deep-sequencing analysis, we studied the impact of two abundant amino sugars on bacterial gene expression and interspecies interactions. The results indicated large-scale remodeling of gene expression induced by GlcN in particular, affecting bacterial energy generation, acid production, protein synthesis, and release of antimicrobial molecules. Our study provides novel insights into how amino sugars modify bacterial behavior, information that will be valuable in the design of new technologies to detect and prevent oral infectious diseases.
Topics: Amino Sugars; Gene Expression; Gene Expression Profiling; Genes, Bacterial; Microbiota; Mouth; Streptococcus gordonii; Streptococcus mutans; Symbiosis
PubMed: 33097515
DOI: 10.1128/AEM.01459-20 -
Molecules (Basel, Switzerland) Aug 2018Bacteria often contain rare deoxy amino sugars which are absent in the host cells. This structural difference can be harnessed for the development of vaccines. Over the... (Review)
Review
Bacteria often contain rare deoxy amino sugars which are absent in the host cells. This structural difference can be harnessed for the development of vaccines. Over the last fifteen years, remarkable progress has been made toward the development of novel and efficient protocols for obtaining the rare sugar building blocks and their stereoselective assembly to construct conjugation ready bacterial glycans. In this review, we discuss the total synthesis of a variety of rare sugar containing bacterial glycoconjugates which are potential vaccine candidates.
Topics: Amino Sugars; Animals; Antigens, Bacterial; Bacteria; Bacterial Infections; Bacterial Vaccines; Glycoconjugates; Glycosylation; Humans; Polysaccharides; Polysaccharides, Bacterial; Serogroup
PubMed: 30103434
DOI: 10.3390/molecules23081997 -
Biochemistry. Biokhimiia Jul 2015Galectins are β-galactoside-binding proteins sharing homology in amino acid sequence of their carbohydrate-recognition domain. Their carbohydrate specificity outside... (Review)
Review
Galectins are β-galactoside-binding proteins sharing homology in amino acid sequence of their carbohydrate-recognition domain. Their carbohydrate specificity outside cells has been studied previously. The main conclusion of these studies was that several levels of glycan ligand recognition exist for galectins: (i) disaccharide Galβ1-4GlcNAc (LN, N-acetyllactosamine) binds stronger than β-galactopyranose; (ii) substitution at O-2 and O-3 of galactose residue as well as core fragments ("right" from GlcNAc) provides significant increase in affinity; (iii) similarly glycosylated proteins can differ significantly in affinity to galectins. Information about the natural cellular receptors of galectins is limited. Until recently, it was impossible to study specificity of cell-bound galectins. A model based on controlled incorporation of a single protein into glycocalyx of cells and subsequent interaction of loaded cells with synthetic glycoprobes measured by flow cytometry made this possible recently. In this review, data about glycan specificity of proto-, chimera-, and tandem-repeat type galectins on the cell surface are systematized, and comparative analysis of the results with data on specificity of galectins in artificial systems was performed. The following conclusions from these studies were made: (i) cellular galectins have practically no ability to bind disaccharide LNn, but display affinity to 3'-substituted oligolactosamines and oligomers LNn; (ii) tandem-repeat type galectins recognize another disaccharide, namely Galβ1-3GlcNAc (Le(c)); (iii) on the cell surface, tandem-repeat type galectins conserve the ability to display high affinity to blood group antigens of ABH system; (iv) in general, when galectins are immersed into glycocalyx, they are more selective regarding glycan interactions. Thus, we conclude that competitive interaction of galectins with cell microenvironment (endogenous cell glycans) is the main factor providing selectivity of galectins in vivo.
Topics: Amino Acid Sequence; Amino Sugars; Carbohydrate Sequence; Cell Membrane; Galactosides; Galectins; Humans; Ligands; Molecular Sequence Data; Polysaccharides; Protein Binding; Substrate Specificity
PubMed: 26541999
DOI: 10.1134/S0006297915070056 -
Applied and Environmental Microbiology May 2019-Acetylglucosamine (GlcNAc) and glucosamine (GlcN) enhance the competitiveness of the laboratory strain DL1 of against the caries pathogen Here, we examine how amino...
-Acetylglucosamine (GlcNAc) and glucosamine (GlcN) enhance the competitiveness of the laboratory strain DL1 of against the caries pathogen Here, we examine how amino sugars affect the interaction of five low-passage-number clinical isolates of abundant commensal streptococci with by utilizing a dual-species biofilm model. Compared to that for glucose, growth on GlcN or GlcNAc significantly reduced the viability of in cocultures with most commensals, shifting the proportions of species. Consistent with these results, production of HO was increased in most commensals when growing on amino sugars, and inhibition of by , , or was enhanced by amino sugars on agar plates. All commensals except had higher arginine deiminase activities when grown on GlcN and, in some cases, GlcNAc. In biofilms formed using pooled cell-containing saliva (CCS), the proportions of were drastically diminished when GlcNAc was the primary carbohydrate. Increased production of HO could account in large part for the inhibitory effects of CCS biofilms. Surprisingly, amino sugars appeared to improve mutacin production by on agar plates, suggesting that the commensals have mechanisms to actively subvert antagonism by in cocultures. Collectively, these findings demonstrate that amino sugars can enhance the beneficial properties of low-passage-number commensal oral streptococci and highlight their potential for moderating the cariogenicity of oral biofilms. Dental caries is driven by dysbiosis of oral biofilms in which dominance by acid-producing and acid-tolerant bacteria results in loss of tooth mineral. Our previous work demonstrated the beneficial effects of amino sugars GlcNAc and GlcN in promoting the antagonistic properties of a health-associated oral bacterium, , in competition with the major caries pathogen Here, we investigated 5 low-passage-number clinical isolates of the most common streptococcal species to establish how amino sugars may influence the ecology and virulence of oral biofilms. Using multiple models, including a human saliva-derived microcosm biofilm, experiments showed significant enhancement by at least one amino sugar in the ability of most of these bacteria to suppress the caries pathogen. Therefore, our findings demonstrated the mechanism of action by which amino sugars may affect human oral biofilms to promote health.
Topics: Amino Sugars; Biofilms; Dental Caries; Dental Plaque; Saliva; Streptococcal Infections; Streptococcus gordonii; Streptococcus mutans; Symbiosis
PubMed: 30877119
DOI: 10.1128/AEM.00370-19 -
Molecular Microbiology Apr 2014In Bacillus subtilis separate sets of genes are implicated in the transport and metabolism of the amino sugars, glucosamine and N-acetylglucosamine. The genes for use of...
In Bacillus subtilis separate sets of genes are implicated in the transport and metabolism of the amino sugars, glucosamine and N-acetylglucosamine. The genes for use of N-acetylglucosamine (nagAB and nagP) are found in most firmicutes and are controlled by a GntR family repressor NagR (YvoA). The genes for use of glucosamine (gamAP) are repressed by another GntR family repressor GamR (YbgA). The gamR-gamAP synton is only found in B. subtilis and a few very close relatives. Although NagR and GamR are close phylogenetically, there is no cross regulation between their operons. GlcN6P prevents all binding of GamR to its targets. NagR binds specifically to targets containing the previously identified dre palindrome but its binding is not inhibited by GlcN6P or GlcNAc6P. GamR-like binding sites were also found in some other Bacilli associated with genes for use of chitin, the polymer of N-acetylglucosamine, and with a gene for another GamR homologue (yurK). We show that GamR can bind to two regions in the chi operon of B. licheniformis and that GamR and YurK are capable of heterologous regulation. GamR can repress the B. licheniformis licH-yurK genes and YurK can repress B. subtilis gamA.
Topics: Amino Sugars; Bacillus subtilis; Bacterial Proteins; Binding Sites; Chitin; DNA, Bacterial; Gene Expression Regulation, Bacterial; Genes, Bacterial; Glucosamine; Operon; Phylogeny; Promoter Regions, Genetic; Repressor Proteins
PubMed: 24673833
DOI: 10.1111/mmi.12544 -
Scientific Reports Sep 2016The nitrogen-metabolic phosphotransferase system, PTS(Ntr), consists of the enzymes I(Ntr), NPr and IIA(Ntr) that are encoded by ptsP, ptsO, and ptsN, respectively. Due...
The nitrogen-metabolic phosphotransferase system, PTS(Ntr), consists of the enzymes I(Ntr), NPr and IIA(Ntr) that are encoded by ptsP, ptsO, and ptsN, respectively. Due to the proximity of ptsO and ptsN to rpoN, the PTS(Ntr) system has been postulated to be closely related with nitrogen metabolism. To define the correlation between PTS(Ntr) and nitrogen metabolism, we performed ligand fishing with EIIA(Ntr) as a bait and revealed that D-glucosamine-6-phosphate synthase (GlmS) directly interacted with EIIA(Ntr). GlmS, which converts D-fructose-6-phosphate (Fru6P) into D-glucosamine-6-phosphate (GlcN6P), is a key enzyme producing amino sugars through glutamine hydrolysis. Amino sugar is an essential structural building block for bacterial peptidoglycan and LPS. We further verified that EIIA(Ntr) inhibited GlmS activity by direct interaction in a phosphorylation-state-dependent manner. EIIA(Ntr) was dephosphorylated in response to excessive nitrogen sources and was rapidly degraded by Lon protease upon amino sugar depletion. The regulation of GlmS activity by EIIA(Ntr) and the modulation of glmS translation by RapZ suggest that the genes comprising the rpoN operon play a key role in maintaining amino sugar homeostasis in response to nitrogen availability and the amino sugar concentration in the bacterial cytoplasm.
Topics: Amino Sugars; Bacterial Proteins; Cytoplasm; Fructosephosphates; Glucosamine; Glucose-6-Phosphate; Homeostasis; Nitrogen; Phosphoenolpyruvate Sugar Phosphotransferase System; Phosphorylation; Salmonella typhimurium
PubMed: 27628932
DOI: 10.1038/srep33055 -
Proceedings of the National Academy of... Feb 2019Glycan-lectin recognition is assumed to elicit its broad range of (patho)physiological functions via a combination of specific contact formation with generation of...
Glycan-lectin recognition is assumed to elicit its broad range of (patho)physiological functions via a combination of specific contact formation with generation of complexes of distinct signal-triggering topology on biomembranes. Faced with the challenge to understand why evolution has led to three particular modes of modular architecture for adhesion/growth-regulatory galectins in vertebrates, here we introduce protein engineering to enable design switches. The impact of changes is measured in assays on cell growth and on bridging fully synthetic nanovesicles (glycodendrimersomes) with a chemically programmable surface. Using the example of homodimeric galectin-1 and monomeric galectin-3, the mutual design conversion caused qualitative differences, i.e., from bridging effector to antagonist/from antagonist to growth inhibitor and vice versa. In addition to attaining proof-of-principle evidence for the hypothesis that chimera-type galectin-3 design makes functional antagonism possible, we underscore the value of versatile surface programming with a derivative of the pan-galectin ligand lactose. Aggregation assays with ,'-diacetyllactosamine establishing a parasite-like surface signature revealed marked selectivity among the family of galectins and bridging potency of homodimers. These findings provide fundamental insights into design-functionality relationships of galectins. Moreover, our strategy generates the tools to identify biofunctional lattice formation on biomembranes and galectin-reagents with therapeutic potential.
Topics: Amino Sugars; Binding Sites; Blood Proteins; Cell Adhesion; Cell Proliferation; Galectin 1; Galectin 3; Galectins; Glycoconjugates; Humans; Lactose; Ligands; Nanoparticles; Polysaccharides
PubMed: 30718416
DOI: 10.1073/pnas.1813515116 -
Scientific Reports Sep 2022Soil organic matter (SOM) is of vital importance to soil health, and also plays a crucial role in the quality of the crops such as tobacco. However, the link between...
Soil organic matter (SOM) is of vital importance to soil health, and also plays a crucial role in the quality of the crops such as tobacco. However, the link between tobacco quality and SOM chemical compositions is still not well understood. To fill the information gap, we analyzed the quality of tobacco leaves and the corresponding SOM molecular compositions by electrospray ionization (ESI) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), that were collected from six different sites in Bijie, Guizhou Province, China. The tobacco quality variedin six sites based on their chemical compositions. SOM compounds had a remarked impact on the quality of tobacco leaves and a distinct difference in SOM composition between low-quality and high-quality tobacco leaves was observed as well. Specifically, 105 common molecular formulas were detected in three SOM compounds of high-quality tobacco, which were more than those in low-quality samples. Although amino sugar, proteins, lipids, tannins, and carbohydrates had a collective influence on the chemical composition of tobacco leaves, the effect contributed by amino sugar and tannins was more prominent. In summary, fully understanding the association between tobacco chemical composition and SOM compounds can provide new insight into the regulation of tobacco quality and the sustainable development of agriculture.
Topics: Agriculture; Amino Sugars; Organic Chemicals; Soil; Tannins; Nicotiana
PubMed: 36097148
DOI: 10.1038/s41598-022-19428-6 -
Biochemistry Nov 2010Everninomicin is a highly modified octasaccharide that belongs to the orthosomycin family of antibiotics and possesses potent Gram-positive antibiotic activity,...
Everninomicin is a highly modified octasaccharide that belongs to the orthosomycin family of antibiotics and possesses potent Gram-positive antibiotic activity, including broad-spectrum efficacy against multidrug resistant enterococci and Staphylococcus aureus. Among its distinctive structural features is a nitro sugar, l-evernitrose, analogues of which decorate a variety of natural products. Recently, we identified a nitrososynthase enzyme encoded by orf36 from Micromonospora carbonacea var. africana that mediates the flavin-dependent double oxidation of synthetically generated thymidine diphosphate (TDP)-l-epi-vancosamine to the corresponding nitroso sugar. Herein, we utilize a five-enzyme in vitro pathway both to verify that ORF36 catalyzes oxidation of biogenic TDP-l-epi-vancosamine and to determine whether ORF36 exhibits catalytic competence for any of its biosynthetic progenitors, which are candidate substrates for nitrososynthases in vivo. Progenitors solely undergo single-oxidation reactions and terminate in the hydroxylamine oxidation state. Performing the in vitro reactions in the presence of (18)O(2) establishes that molecular oxygen, rather than oxygen from water, is incorporated into ORF36-generated intermediates and products and identifies an off-pathway product that correlates with the oxidation product of a progenitor substrate. The 3.15 Å resolution X-ray crystal structure of ORF36 reveals a tetrameric enzyme that shares a fold with acyl-CoA dehydrogenases and class D flavin-containing monooxygenases, including the nitrososynthase KijD3. However, ORF36 and KijD3 have unusually open active sites in comparison to these related enzymes. Taken together, these studies map substrate determinants and allow the proposal of a minimal monooxygenase mechanism for amino sugar oxidation by ORF36.
Topics: Amino Sugars; Aminoglycosides; Anti-Bacterial Agents; Crystallography, X-Ray; Metabolic Networks and Pathways; Micromonospora; Mixed Function Oxygenases; Oxidation-Reduction
PubMed: 20866105
DOI: 10.1021/bi101336u