Chemical Synthesis of a Densely Functionalized Aminodisaccharide from Fusobacterium nucleatum ATCC 23726 O-Antigen.

Fusobacterium nucleatum, a colorectal-cancer-associated oncomicrobe, can trigger or accelerate numerous pathologies. We report the first synthesis of a conjugation-ready disaccharide containing six amino groups from F. nucleatum ATCC 23726 O-antigen. Rare 2,3-diamido-d-glucuronic acid amide and 2-acetamido-4-amino-d-fucose were synthesized from d-glucosamine through configuration inversion, nucleophilic substitution, C6 oxidation, and C6 deoxygenation. A judicious choice of protecting groups and reaction conditions enabled the selective installation of N-acetyl, N-propanoyl, N-formyl, and carboxamido groups.

A new member of the flavodoxin superfamily from Fusobacterium nucleatum that functions in heme trafficking and reduction of anaerobilin.

Fusobacterium nucleatum is an opportunistic oral pathogen that is associated with various cancers. To fulfill its essential need for iron, this anaerobe will express heme uptake machinery encoded at a single genetic locus. The heme uptake operon includes HmuW, a class C radical SAM-dependent methyltransferase that degrades heme anaerobically to release Fe2+ and a linear tetrapyrrole called anaerobilin. The last gene in the operon, hmuF encodes a member of the flavodoxin superfamily of proteins. We discovered that HmuF and a paralog, FldH, bind tightly to both FMN and heme. The structure of Fe3+-heme-bound FldH (1.6 Å resolution) reveals a helical cap domain appended to the ⍺/ß core of the flavodoxin fold. The cap creates a hydrophobic binding cleft that positions the heme planar to the si-face of the FMN isoalloxazine ring. The ferric heme iron is hexacoordinated to His134 and a solvent molecule. In contrast to flavodoxins, FldH and HmuF do not stabilize the FMN semiquinone but instead cycle between the FMN oxidized and hydroquinone states. We show that heme-loaded HmuF and heme-loaded FldH traffic heme to HmuW for degradation of the protoporphyrin ring. Both FldH and HmuF then catalyze multiple reductions of anaerobilin through hydride transfer from the FMN hydroquinone. The latter activity eliminates the aromaticity of anaerobilin and the electrophilic methylene group that was installed through HmuW turnover. Hence, HmuF provides a protected path for anaerobic heme catabolism, offering F. nucleatum a competitive advantage in the colonization of anoxic sites of the human body.

Structure of the lipopolysaccharide O-antigens from Fusobacterium nucleatum strains HM-994, HM-995, HM-997.

Fusobacterium nucleatum is an anaerobic bacterium found in the human mouth where it causes periodontitis. It was also found in colorectal cancer tissues and is linked with pregnancy complications, including pre-term and stillbirths. Cell surface structures of the bacterium could be implicated in pathogenesis. Here we report the structure of the lipopolysaccharide O-chain (OPS) of three strains of F. nucleatum HM-994, HM-995, and HM-997, isolated from cancerous tissues: -3-ß-D-ManNAc4Lac-4-ß-D-Glc6OAc-3-ß-D-FucNAc4N- HM-994. -4-α-L-GalNHBuA-3-α-D-QuiNAc4NHBu-3-α-L-Rha-6-α-D-GalN- HM-995. -3-[α-L-GulNAcA-4-]-ß-D-Glc-4-ß-D-ManNAcAN-3-ß-D-FucNAc4N-3- HM-997. where HBu is 3-hydroxybutyryl, ManNAc4Lac is 4-O-(1-carboxyethyl)-2-acetamido-2-deoxy-mannose. All monosaccharides are in the pyranose form. The structures were determined using standard NMR (2D homo- and hetero-nuclear techniques), MS and chemical methods following gtypical LPS isolation and purification methods. In some cases polymeric material was further degraded in order to produce compounds that gave improved NMR spectra that were easier to be fully interpreted. Structure of the OPS from strain HM-994 was identical to the OPS from F. nucleatum strain MJR 7757 B. Structures of the OPS from HM-995 and HM-997 are novel and to our knowledge have not been previously reported and include the often observed 6-deoxy- sugars found in several F. nucleatum strains and butyrate rather than acetate modifications in the HM-995 strain. This structural knowledge adds to the ever increasing variation found in LPS O-antigen structures from F. nucleatum strain from both oral and cancerous origin and suggests that there may be a multitude of different LPS O-antigen structures elaborated by this organism that may present challenges to any serotyping efforts.

The structure of the LPS O-chain from five Fusobacterium nucleatum strains CTX47T, CC2_6JVN3, CC2_3FMU1, CC2_1JVN3, HM-996, containing alditol and phosphate in the main chain and development of mouse monoclonal antibodies specific to the O-antigens.

Fusobacterium nucleatum is an anaerobic bacterium found in the human mouth where it causes periodontitis. It was also found in colorectal cancer tissues and is linked with pregnancy complications, including pre-term and stillbirths. Cell surface structures of the bacterium could be implicated in pathogenesis. Here we report four new structures of the lipopolysaccharide O-chain (OPS) from five strains of F. nucleatum CTX47T, CC2_6JVN3, CC2_3FMU1, CC2_1JVN3, HM-996, isolated from cancerous tissues. Three of the four structures have a common sequence of hexose-diaminofucose-hexitol-phosphate in the main chain.

Structure of the lipopolysaccharide O-antigens from Fusobacterium nucleatum strains SB-106CP and HM-992 and immunological comparison to the O-antigen of strain 12230.

Fusobacterium nucleatum is an anaerobic bacterium found in the human mouth where it causes periodontitis. It was also found in colorectal cancer tissues and is linked with pregnancy complications, including pre-term and stillbirths. Cell surface structures of the bacterium could be implicated in pathogenesis. Here we report the structures of the lipopolysaccharide O-chain (OPS) of two strains of F. nucleatum, SB-106CP and HM-992, both isolated from cancerous tissues. These strains elaborate the same sugar chain, differing only by their N-acylation pattern: -6-α-D-GlcNAc-4-ß-D-GlcNHBu3NABuA-3-ß-D-QuiNAc4NABuAc- SB-106CP -6-α-D-GlcNAc-4-ß-D-GlcNHBu3NABuA-3-ß-D-QuiNAc4NAc- HM-992 ABu = (R)-3-amino-butyryl AbuAc = (R)-3-N-acetyl-3-aminobutyryl HBu = (R)-3-hydroxy-butyryl All monosaccharides are in the pyranose form. Previously we published the structure of the OPS from F. nucleatum 12230, a transtracheal isolate, which had similar sugar chain, differing by replacement of GlcNAc with Glc and a different acylation pattern: -6-α-d-Glc-4-ß-d-GlcNHBu3NHBuA-3-ß-d-QuiNAc4NABu- A mouse monoclonal antibody specific for the 12230 O-antigen did not cross react with the LPS of strains SB-106CP and HM-992 confirming the structural differentiation.

Might Cu(II) binding, DNA cleavage and radical production by YadA fragments be involved in the promotion of F. nucleatum related cancers?

In many cases, human microbiota are associated with cancer progression. It was concluded that Fusobacterium nucleatum increases neoplastic changes. This bacterium is naturally present in human dental plaque. However, if it is present in the colon, it becomes a precursor of cancer. Antibiotic treatment of mice infected with F. nucleatum slowed tumor growth, which agrees with the fundamental role of bacteria in tumorigenesis. Remarkably, recent studies indicate that transition metal complexes with fragments of outer membrane proteins are able to promote reactive oxygen species (ROS) formation and are responsible for oxidative stress, which consequently leads to cell damage. Therefore, in this paper, the formation of copper(II) complexes with fragments of adhesin YadA from F. nucleatum is characterized. Moreover, the ability of the complexes to produce ROS has been shown. Importantly, free ligands are efficient DNA-cleaving agents.

Structural analysis of the core oligosaccharides from Fusobacterium nucleatum lipopolysaccharides.

Fusobacterium nucleatum is a gram-negative bacterium, part of the normal human microflora. It is associated with various health complications, including periodontitis and colorectal cancer. Its surface is covered with lipopolysaccharide, which interacts with the immune system and can be involved in various processes in health and disease conditions. Here we present the results of structural analysis of core oligosaccharides from the lipopolysaccharides of several strains of F. nucleatum. Pure compounds were isolated using mild acid hydrolysis or alkaline deacylation of the lipopolysaccharides and analyzed by NMR spectroscopy, mass-spectrometry and chemical methods. All cores analyzed had a common octasaccharide region, including five heptose residues and a non-phosphorylated 3-deoxy-d-manno-oct-2-ulosonic acid residue. The common region is substituted with different additional components specific for each strain. By structure type the F. nucleatum core is similar to that produced by Aeromonas.

Heat-Killed Fusobacterium nucleatum Triggers Varying Heme-Related Inflammatory and Stress Responses Depending on Primary Human Respiratory Epithelial Cell Type.

Fusobacterium nucleatum (Fn) is generally an opportunistic oral pathogen that adheres to mammalian mucosal sites, triggering a host inflammatory response. In general, Fn is normally found within the human oral cavity; however, it was previously reported that Fn is a risk factor for certain respiratory diseases. Surprisingly, this was never fully elucidated. Here, we investigated the virulence potential of heat-killed Fn on primary human tracheal, bronchial, and alveolar epithelial cells. In this study, we measured the secretion of inflammatory- (IL-8 and IL-6), stress- (total heme and hydrogen peroxide), and cell death-related (caspase-1 and caspase-3) signals. We established that the inflammatory response mechanism varies in each epithelial cell type: (1) along tracheal cells, possible Fn adherence would trigger increased heme secretion and regulated inflammatory response; (2) along bronchial cells, potential Fn adherence would simultaneously initiate an increase in secreted H2O2 and inflammatory response (ascribable to decreased secreted heme amounts); and (3) along alveolar cells, putative Fn adherence would instigate the increased secretion of inflammatory responses attributable to a decrease in secreted heme levels. Moreover, regardless of the epithelial cell-specific inflammatory mechanism, we believe these are putative, not harmful. Taken together, we propose that any potential Fn-driven inflammation along the respiratory tract would be initiated by differing epithelial cell-specific inflammatory mechanisms that are collectively dependent on secreted heme.

Protocol of proceedings with Fusobacterium nucleatum and optimization of ABTS method for detection of reactive oxygen species.

Aim: Characterization of the ability of Fusobacterium nucleatum DSM 15643 and DSM 20482 strains in the presence of Cu2+ and H2O2 to reactive oxygen species generation. Method: Spectrophotometric ABTS (2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) method was used. Results: Determination of: MIC for Cu2+, H2O2 and ABTS; survivability of F. nucleatum under atmospheric oxygen exposure; the level and rate constants of free radicals production by the bacteria. Conclusion:F. nucleatum in the presence of Cu2+ and H2O2 is able to generate free radicals. Reactive oxygen species are produced mainly outside the bacterial cell, which suggests that outer membrane proteins may be involved in oxidative process.

Immune induction identified by TMT proteomics analysis in Fusobacterium nucleatum autoinducer-2 treated macrophages.

Background: The immune-inducing effect of the quorum sensing (QS) molecule autoinducer-2 (AI-2) on macrophages has not been previously comprehensively studied.Methods: We performed proteomic analysis on macrophages cocultured with purified Fusobacterium nucleatum (F. nucleatum) AI-2 and performed western blot analysis to verify the differential protein expression. We further used the Gene Expression Profiling Interactive Analysis and Tumor Immune Estimation Resource databases to analyze the expression of differentially expressed proteins in microbial-associated digestive tract tumors.Results: Based on proteomic analysis, we identified 46 upregulated proteins and 11 downregulated proteins. The upregulated proteins were mostly inflammatory factors such as tumor necrosis factor ligand superfamily member 9 (TNFSF9). These proteins have a range of biological functions associated with the regulation of inflammatory responses, apoptosis and tumorigenesis. TNFSF9 is highly expressed in pancreatic adenocarcinoma (PAAD) tissues and is associated with M1 polarization of macrophages.Conclusions: Our data indicated that F. nucleatum AI-2 induced inflammatory responses and activated multiple signaling pathways in macrophages. TNFSF9 is the most significantly differentially expressed protein induced by F. nucleatum AI-2 and is involved in regulating immune cell infiltration in PAAD. Thus, AI-2 may become a new focus for studying the relationship between bacteria and cancer.

Ion-dependent mobility effects of the Fusobacterium nucleatum glycine riboswitch aptamer II via site-directed spin-labeling (SDSL) electron paramagnetic resonance (EPR).

Site-directed spin-labeling (SDSL) with continuous wave electron paramagnetic resonance (cw-EPR) spectroscopy was utilized to probe site-specific changes in backbone dynamics that accompany folding of the isolated 84 nucleotide aptamer II domain of the Fusobacterium nucleatum (FN) glycine riboswitch. Spin-labels were incorporated using splinted ligation strategies. Results show differential dynamics for spin-labels incorporated into the backbone at a base-paired and loop region. Additionally, the addition of a biologically relevant concentration of 5 mM  Mg2+, to an RNA solution with 100 mM K+, folds and compacts the structure, inferred by a reduction in spin-label mobility. Furthermore, when controlling for ionic strength, Mg2+ added to the RNA induces more folding/less flexibility at the two sites than RNA with K+ alone. Addition of glycine does not alter the dynamics of this singlet aptamer II, indicating that the full length riboswitch construct may be needed for glycine binding and induced conformational changes. This work adds to our growing understanding of how splinted-ligation SDSL can be utilized to interrogate differential dynamics in large dynamic RNAs, providing insights into how RNA folding and structure is differentially stabilized by monovalent versus divalent cations.

Structure of F1-ATPase from the obligate anaerobe Fusobacterium nucleatum.

The crystal structure of the F1-catalytic domain of the adenosine triphosphate (ATP) synthase has been determined from the pathogenic anaerobic bacterium Fusobacterium nucleatum. The enzyme can hydrolyse ATP but is partially inhibited. The structure is similar to those of the F1-ATPases from Caldalkalibacillus thermarum, which is more strongly inhibited in ATP hydrolysis, and in Mycobacterium smegmatis, which has a very low ATP hydrolytic activity. The ßE-subunits in all three enzymes are in the conventional 'open' state, and in the case of C. thermarum and M. smegmatis, they are occupied by an ADP and phosphate (or sulfate), but in F. nucleatum, the occupancy by ADP appears to be partial. It is likely that the hydrolytic activity of the F. nucleatum enzyme is regulated by the concentration of ADP, as in mitochondria.

Structural insight into the high reduction potentials observed for Fusobacterium nucleatum flavodoxin.

Flavodoxins are small flavin mononucleotide (FMN)-containing proteins that mediate a variety of electron transfer processes. The primary sequence of flavodoxin from Fusobacterium nucleatum, a pathogenic oral bacterium, is marked with a number of distinct features including a glycine to lysine (K13) substitution in the highly conserved phosphate-binding loop (T/S-X-T-G-X-T), variation in the aromatic residues that sandwich the FMN cofactor, and a more even distribution of acidic and basic residues. The Eox/sq (oxidized/semiquinone; -43 mV) and Esq/hq (semiquinone/hydroquinone; -256 mV) are the highest recorded reduction potentials of known long-chain flavodoxins. These more electropositive values are a consequence of the apoprotein binding to the FMN hydroquinone anion with ~70-fold greater affinity compared to the oxidized form of the cofactor. Inspection of the FnFld crystal structure revealed the absence of a hydrogen bond between the protein and the oxidized FMN N5 atom, which likely accounts for the more electropositive Eox/sq . The more electropositive Esq/hq is likely attributed to only one negatively charged group positioned within 12 Å of the FMN N1. We show that natural substitutions of highly conserved residues partially account for these more electropositive reduction potentials.

De novo synthesis of novel bacterial monosaccharide fusaminic acid.

Fusobacterium nucleatum is an oral bacteria related to various types of diseases. As Gram-negative bacteria, lipopolysaccharide (LPS) of Fusobacterium nucleatum could be a potential virulence factor. Recently, the structure of O-antigen in LPS of Fusobacterium nucleatum strain 25586 was elucidated to contain a trisaccharide repeating unit -(4-ß-Nonp5Am-4-α-L-6dAltpNAc3PCho-3-ß-D-QuipNAc)-. The nonulosonic acid characterized as 5-acetamidino-3,5,9-trideoxy-L-glycero-L-gluco-non-2-ulosonic acid (named as fusaminic acid), and 2-acetamido-2,6-dideoxy-L-altrose are the novel monosaccharides isolated. Herein we report the de novo synthesis of 5-N-acetyl fusaminic acid and the thioglycoside derivative in order to further investigate the biological significance of nonulosonic acids for bacterial pathogenesis.

Effects of sub-minimal inhibitory concentrations of antibiotics on the morphology and surface hydrophobicity of periodontopathic anaerobes.

It has been reported that sub-minimal inhibitory concentrations (sub-MICs) of antibiotics are capable of altering bacterial surface properties and phenotype. In this study, the effects of sub-MICs of certain antibiotics on surface hydrophobicity, cell morphology, and protein profile were ascertained using Fusobacterium nucleatum, Porphyromonas gingivalis and Treponema denticola strains, which are pathogenic bacterial species in periodontal diseases. The MICs of antibiotics were determined by culturing bacteria in media supplemented with serially diluted antibiotic solutions, and sub-MIC of antibiotics was used. The effect of sub-MIC of antibiotics on cell morphology was determined by scanning electron microscopy. Microscopic observation of F. nucleatum and P. gingivalis grown at a sub-MIC of amoxicillin revealed cell enlargement. T. denticola grown at a sub-MIC of doxycycline also showed cell elongation. The relative surface hydrophobicity determined by measuring the ability of the bacteria to absorb n-hexadecane revealed an increase in surface hydrophobicity of F. nucleatum grown at sub-MIC of penicillin and amoxicillin, but a decrease with metronidazole; whereas increased hydrophobicity was observed in T. denticola grown at sub-MIC of doxycycline, metronidazole and tetracycline. The surface hydrophobicity of P. gingivalis increased only when grown in sub-MIC of metronidazole. The protein expression profile of the treated bacteria differed from their respective controls. These results confirmed that sub-MIC concentrations of antibiotics can affect the phenotype, surface properties and morphology of periodontal pathogenic anaerobic bacteria.

Copper(II) complexes with Fusobacterium nucleatum adhesin FadA: Coordination pattern, physicochemical properties and reactivity.

Fusobacterium nucleatum is an anaerobic, Gram-negative bacteria linked to colon cancer. It is interesting to determine how metal ions interact with bacterial adhesin proteins. To this end, the coordination of ATDAAS-NH2 and MKKFL-NH2 fragments of Fusobacterium adhesin A (FadA) to copper(II) ions was studied by potentiometry, spectroscopic techniques (UV-Vis, CD, EPR and NMR) and the density functional theory (DFT) methods. At pH 6.8 (colon physiological pH), the metal ion in the first peptide (ATDAAS-NH2) is coordinated by one oxygen and three nitrogen donors while in the second one (MKKFL-NH2) - by sulfur and three nitrogen atoms. Both complexes form two five- and one six-membered stable chelate rings. Moreover, reactivity studies confirmed the production of reactive oxygen species such as hydroxyl radical, superoxide anion radical and singlet oxygen. Generation of reactive oxygen species (ROS) was observed during gel electrophoresis and spectroscopic assays with reporting molecules like NDMA (N,N-dimethyl-p-nitrosoaniline) and NBT (Nitrotetrazolium Blue Chloride). All reactions were conducted in the presence of hydrogen peroxide as endogenous oxidant.

Litsea japonica Leaf Extract Suppresses Proinflammatory Cytokine Production in Periodontal Ligament Fibroblasts Stimulated with Oral Pathogenic Bacteria or Interleukin-1ß.

Periodontal disease, a chronic disease caused by bacterial infection, eventually progresses to severe inflammation and bone loss. Regulating excessive inflammation of inflamed periodontal tissues is critical in treating periodontal diseases. The periodontal ligament (PDL) is primarily a connective tissue attachment between the root and alveolar bone. PDL fibroblasts (PDLFs) produce pro-inflammatory cytokines in response to bacterial infection, which could further adversely affect the tissue and cause bone loss. In this study, we determined the ability of Litsea japonica leaf extract (LJLE) to inhibit pro-inflammatory cytokine production in PDLFs in response to various stimulants. First, we found that LJLE treatment reduced lipopolysaccharide (LPS)-induced pro-inflammatory cytokine (interleukin-6 and interleukin-8) mRNA and protein expression in PDLFs without cytotoxicity. Next, we observed the anti-inflammatory effect of LJLE in PDLFs after infection with various oral bacteria, including Fusobacterium nucleatum, Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia. These anti-inflammatory effects of LJLE were dose-dependent, and the extract was effective following both pretreatment and posttreatment. Moreover, we found that LJLE suppressed the effect of interleukin-1 beta-induced pro-inflammatory cytokine production in PDLFs. Taken together, these results indicate that LJLE has anti-inflammatory activity that could be exploited to prevent and treat human periodontitis by controlling inflammation.

Structure of the LPS O-chain from Fusobacterium nucleatum strain ATCC 23726 containing a novel 5,7-diamino-3,5,7,9-tetradeoxy-l-gluco-non-2-ulosonic acid presumably having the d-glycero-l-gluco configuration.

Fusobacterium nucleatum is an anaerobic bacterium found in the human mouth where it causes periodontitis. It was also found in colorectal cancer tissues and is linked with pregnancy complications, including pre-term and still births. Cell surface structures of the bacterium could be implicated in pathogenesis. Here we report the following structure of the lipopolysaccharide O-chain of a spontaneous streptomycin resistant (SmR) mutant of F. nucleatum strain ATCC 23726: -4-ß-Non5Am7Ac-4-ß-d-GlcNAcyl3NFoAN-3-ß-d-FucNAc4N- where GlcNAcyl3NFoAN indicates 2,3-diamino-2,3-dideoxyglucuronic acid amide with Fo at N-3 being formyl and Acyl at N-2 being propanoyl (∼70%) or butanoyl (∼30%); Non5Am7Ac indicates 7-acetamido-5-acetimidoylamino-3,5,7,9-tetradeoxy-l-gluco-non-2-ulosonic acid presumably having the d-glycero-l-gluco configuration. To our knowledge, no l-gluco isomer of higher sugars of this class as well as no N-propanoyl or N-butanoyl group have so far been found in bacterial polysaccharides.

Structure of the LPS O-chain from Fusobacterium nucleatum strain MJR 7757 B.

Fusobacterium nucleatum is an anaerobic bacterium found in the human mouth where it causes periodontitis. It was also found in colorectal cancer tissues and is linked with pregnancy complications, including pre-term and still births. Cell surface structures of the bacterium could be implicated in pathogenesis. Here we report the following structure of the lipopolysaccharide O-chain of F. nucleatum strain MJR 7757 B:where Lac is (R)-1-carboxyethyl (lactic acid residue); all monosaccharides are in the pyranose form. ManNAc4Lac, analogue of N-acetylmuramic acid, is found for the first time in natural sources.

Crowding Shifts the FMN Recognition Mechanism of Riboswitch Aptamer from Conformational Selection to Induced Fit.

In bacteria, the binding between the riboswitch aptamer domain and ligand is regulated by environmental cues, such as low Mg2+ in macrophages during pathogenesis to ensure spatiotemporal expression of virulence genes. Binding was investigated between the flavin mononucleotide (FMN) riboswitch aptamer and its anionic ligand in the presence of molecular crowding agent without Mg2+ ion, which mimics pathogenic conditions. Structural, kinetic, and thermodynamic analyses under the crowding revealed more dynamic conformational rearrangements of the FMN riboswitch aptamer compared to dilute Mg2+ -containing solution. It is hypothesized that under crowding conditions FMN binds through an induced fit mechanism in contrast to the conformational selection mechanism previously demonstrated in dilute Mg2+ solution. Since these two mechanisms involve different conformational intermediates and rate constants, these findings have practical significance in areas such as drug design and RNA engineering.