scholarly journals Uncovering a novel molecular mechanism for scavenging sialic acids in bacteria

2020 ◽  
Vol 295 (40) ◽  
pp. 13724-13736 ◽  
Author(s):  
Andrew Bell ◽  
Emmanuele Severi ◽  
Micah Lee ◽  
Serena Monaco ◽  
Dimitrios Latousakis ◽  
...  

The human gut symbiont Ruminococcus gnavus scavenges host-derived N-acetylneuraminic acid (Neu5Ac) from mucins by converting it to 2,7-anhydro-Neu5Ac. We previously showed that 2,7-anhydro-Neu5Ac is transported into R. gnavus ATCC 29149 before being converted back to Neu5Ac for further metabolic processing. However, the molecular mechanism leading to the conversion of 2,7-anhydro-Neu5Ac to Neu5Ac remained elusive. Using 1D and 2D NMR, we elucidated the multistep enzymatic mechanism of the oxidoreductase (RgNanOx) that leads to the reversible conversion of 2,7-anhydro-Neu5Ac to Neu5Ac through formation of a 4-keto-2-deoxy-2,3-dehydro-N-acetylneuraminic acid intermediate and NAD+ regeneration. The crystal structure of RgNanOx in complex with the NAD+ cofactor showed a protein dimer with a Rossman fold. Guided by the RgNanOx structure, we identified catalytic residues by site-directed mutagenesis. Bioinformatics analyses revealed the presence of RgNanOx homologues across Gram-negative and Gram-positive bacterial species and co-occurrence with sialic acid transporters. We showed by electrospray ionization spray MS that the Escherichia coli homologue YjhC displayed activity against 2,7-anhydro-Neu5Ac and that E. coli could catabolize 2,7-anhydro-Neu5Ac. Differential scanning fluorimetry analyses confirmed the binding of YjhC to the substrates 2,7-anhydro-Neu5Ac and Neu5Ac, as well as to co-factors NAD and NADH. Finally, using E. coli mutants and complementation growth assays, we demonstrated that 2,7-anhydro-Neu5Ac catabolism in E. coli depended on YjhC and on the predicted sialic acid transporter YjhB. These results revealed the molecular mechanisms of 2,7-anhydro-Neu5Ac catabolism across bacterial species and a novel sialic acid transport and catabolism pathway in E. coli.

2021 ◽  
Author(s):  
Keisuke Fujiyama ◽  
Naoki Kato ◽  
Suyong Re ◽  
Kiyomi Kinugasa ◽  
Kohei Watanabe ◽  
...  

SummaryMolecular chirality, discovered by Louis Pasteur in the middle of the 19th century1, is found in most primary and secondary metabolites. Particularly, the so-called natural products are rich in chiral centres2. The stereochemistry of natural products is strictly recognized in living organisms, and is thus closely related to their biological functions. The Diels–Alder (DA) reaction, which forms a six-membered ring with up to four chiral centres, is a fundamental practical reaction for C–C bond formation in synthetic chemistry3. Nature has also adopted this reaction to elaborate the complex structures of natural products using enzymes derived from various progenitor proteins4-7. Although enzymes catalysing the DA reaction, Diels–Alderases (DAases), have attracted increasing attention, little is known about the molecular mechanism by which they control the stereochemistry and perform catalysis. Here, we solved the X-ray crystal structures of a pair of decalin synthases, Fsa2 and Phm7, that catalyse intramolecular DA reactions to form enantiomeric decalin scaffolds during biosynthesis of the HIV-1 integrase inhibitor equisetin and its stereochemical opposite, phomasetin8,9. Based on the crystal structures, docking simulations followed by all-atom molecular dynamics simulations provided dynamic binding models demonstrating the folding of linear polyenoyl tetramic acid substrates in the binding pocket of these enzymes, explaining the stereoselectivity in the construction of decalin scaffolds. Site-directed mutagenesis studies verified the binding models and, in combination with density functional theory calculations, clarified how hydrophilic amino acid residues in the Phm7 pocket regulate and catalyse the stereoselective DA reaction. This study highlights the distinct molecular mechanisms of the enzymatic DA reaction and its stereoselectivity experimentally and computationally. We anticipate that clarified molecular mechanism herein provides not only the basic understanding how these important enzymes work but also the guiding principle to create artificial enzymes that produce designer bioactive molecules.


2007 ◽  
Vol 282 (38) ◽  
pp. 27562-27571 ◽  
Author(s):  
Amanda L. Lewis ◽  
Hongzhi Cao ◽  
Silpa K. Patel ◽  
Sandra Diaz ◽  
Wesley Ryan ◽  
...  

Group B Streptococcus (GBS) is a common cause of neonatal sepsis and meningitis. A major GBS virulence determinant is its sialic acid (Sia)-capped capsular polysaccharide. Recently, we discovered the presence and genetic basis of capsular Sia O-acetylation in GBS. We now characterize a GBS Sia O-acetylesterase that modulates the degree of GBS surface O-acetylation. The GBS Sia O-acetylesterase operates cooperatively with the GBS CMP-Sia synthetase, both part of a single polypeptide encoded by the neuA gene. NeuA de-O-acetylation of free 9-O-acetyl-N-acetylneuraminic acid (Neu5,9Ac2) was enhanced by CTP and Mg2+, the substrate and co-factor, respectively, of the N-terminal GBS CMP-Sia synthetase domain. In contrast, the homologous bifunctional NeuA esterase from Escherichia coli K1 did not display cofactor dependence. Further analyses showed that in vitro, GBS NeuA can operate via two alternate enzymatic pathways: de-O-acetylation of Neu5,9Ac2 followed by CMP activation of Neu5Ac or activation of Neu5,9Ac2 followed by de-O-acetylation of CMP-Neu5,9Ac2. Consistent with in vitro esterase assays, genetic deletion of GBS neuA led to accumulation of intracellular O-acetylated Sias, and overexpression of GBS NeuA reduced O-acetylation of Sias on the bacterial surface. Site-directed mutagenesis of conserved asparagine residue 301 abolished esterase activity but preserved CMP-Sia synthetase activity, as evidenced by hyper-O-acetylation of capsular polysaccharide Sias on GBS expressing only the N301A NeuA allele. These studies demonstrate a novel mechanism regulating the extent of capsular Sia O-acetylation in intact bacteria and provide a genetic strategy for manipulating GBS O-acetylation in order to explore the role of this modification in GBS pathogenesis and immunogenicity.


2015 ◽  
Vol 198 (1) ◽  
pp. 7-11 ◽  
Author(s):  
Regine Hengge ◽  
Michael Y. Galperin ◽  
Jean-Marc Ghigo ◽  
Mark Gomelsky ◽  
Jeffrey Green ◽  
...  

In recent years,Escherichia colihas served as one of a few model bacterial species for studying cyclic di-GMP (c-di-GMP) signaling. The widely usedE. coliK-12 laboratory strains possess 29 genes encoding proteins with GGDEF and/or EAL domains, which include 12 diguanylate cyclases (DGC), 13 c-di-GMP-specific phosphodiesterases (PDE), and 4 “degenerate” enzymatically inactive proteins. In addition, six new GGDEF and EAL (GGDEF/EAL) domain-encoding genes, which encode two DGCs and four PDEs, have recently been found in genomic analyses of commensal and pathogenicE. colistrains. As a group of researchers who have been studying the molecular mechanisms and the genomic basis of c-di-GMP signaling inE. coli, we now propose a general and systematicdgcandpdenomenclature for the enzymatically active GGDEF/EAL domain-encoding genes of this model species. This nomenclature is intuitive and easy to memorize, and it can also be applied to additional genes and proteins that might be discovered in various strains ofE. coliin future studies.


2016 ◽  
Vol 198 (20) ◽  
pp. 2803-2809 ◽  
Author(s):  
Ariel Rangel ◽  
Susan M. Steenbergen ◽  
Eric R. Vimr

ABSTRACTThe sialic acids (N-acylneuraminates) are a group of nine-carbon keto-sugars existing mainly as terminal residues on animal glycoprotein and glycolipid carbohydrate chains. Bacterial commensals and pathogens exploit host sialic acids for nutrition, adhesion, or antirecognition, whereN-acetyl- orN-glycolylneuraminic acids are the two predominant chemical forms of sialic acids. Each form may be modified by acetyl esters at carbon position 4, 7, 8, or 9 and by a variety of less-common modifications. Modified sialic acids produce challenges for colonizing bacteria, because the chemical alterations toN-acetylneuraminic acid (Neu5Ac) confer increased resistance to sialidase and aldolase activities essential for the catabolism of host sialic acids. Bacteria withO-acetyl sialate esterase(s) utilize acetylated sialic acids for growth, thereby gaining a presumed metabolic advantage over competitors lacking this activity. Here, we demonstrate the esterase activity ofEscherichia coliNanS after purifying it as a C-terminal HaloTag fusion. Using a similar approach, we show thatE. colistrain O157:H7 Stx prophage or prophage remnants invariably include paralogs ofnanSoften located downstream of the Shiga-like toxin genes. These paralogs may include sequences encoding N- or C-terminal domains of unknown function where the NanS domains can act as sialateO-acetyl esterases, as shown by complementation of anE. colistrain K-12nanSmutant and the unimpaired growth of anE. coliO157nanSmutant onO-acetylated sialic acid. We further demonstrate thatnanShomologs inStreptococcusspp. also encode active esterase, demonstrating an unexpected diversity of bacterial sialateO-acetyl esterase.IMPORTANCEThe sialic acids are a family of over 40 naturally occurring 9-carbon keto-sugars that function in a variety of host-bacterium interactions. These sugars occur primarily as terminal carbohydrate residues on host glycoproteins and glycolipids. Available evidence indicates that diverse bacterial species use host sialic acids for adhesion or as sources of carbon and nitrogen. Our results show that the catabolism of the diacetylated form of host sialic acid requires a specialized esterase, NanS. Our results further show thatnanShomologs exist in bacteria other thanEscherichia coli, as well as part of toxigenicE. coliprophage. The unexpected diversity of these enzymes suggests new avenues for investigating host-bacterium interactions. Therefore, these original results extend our previous studies ofnanSto include mucosal pathogens, prophage, and prophage remnants. This expansion of thenanSsuperfamily suggests important, although as-yet-unknown, functions in host-microbe interactions.


2009 ◽  
Vol 191 (22) ◽  
pp. 7134-7139 ◽  
Author(s):  
Susan M. Steenbergen ◽  
Jamie L. Jirik ◽  
Eric R. Vimr

ABSTRACT The nanATEK-yhcH, yjhATS, and yjhBC operons in Escherichia coli are coregulated by environmental N-acetylneuraminic acid, the most prevalent sialic acid in nature. Here we show that YjhS (NanS) is a probable 9-O-acetyl N-acetylneuraminic acid esterase required for E. coli to grow on this alternative sialic acid, which is commonly found in mammalian host mucosal sites.


Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 980-980
Author(s):  
Soracha E Ward ◽  
Jamie M O'Sullivan ◽  
Sonia Aguila Martinez ◽  
Clive Drakeford ◽  
Thomas Anthony Jude McKinnon ◽  
...  

Abstract Introduction Although the biological mechanisms underpinning VWF clearance remain poorly understood, accumulating data has shown that increased clearance is a common pathophysiology in type 1 VWD patients. Moreover, enhanced clearance has been implicated in the etiology of types 2 and 3 VWD. Previous studies have shown that loss of terminal sialic acid from VWF glycans results in enhanced clearance. Furthermore, ST3Gal-IV knockout mice exhibit reduced plasma VWF levels due to rapid in vivo clearance. Initial studies suggested that clearance of hyposialylated VWF was mediated via the asialoglycoprotein receptor (ASGPR). However, we recently reported a novel role for the Macrophage Galactose Lectin (MGL) in regulating clearance of VWF (Ward et al, Blood 2018). In this study, we sought to elucidate the molecular mechanisms through which MGL interacts with human VWF. Methods Recombinant VWF variants, truncated A1A2A3 and isolated A1, A2 and A3 domains were expressed in HEK293T cells. Human plasma derived (pdVWF) was purified from commercial VWF concentrates as before. VWF glycoforms were generated by digestion with exoglycosidases. VWF-MGL interaction was assessed using plate binding ELISA assays. In vivo clearance of VWF variants was assessed in both Asgr1+/+VWF-/-and Asgr1-/-VWF-/-mice in the presence/absence of anti-MGL blocking antibodies. Results Previous studies have shown 80% of total sialic acid on VWF is expressed on N glycans in α2-6 linkage. In contrast, the other 20% of VWF sialylation is α2-3 linked on O linked glycans. Removal O linked sialylation (with α2-3 neuraminidase) was sufficient to increase VWF clearance in VWF-/- and Asgr1-/-VWF-/-mice (half life = 9.0 ± 1 mins and 8.3 ± 2mins). Interestingly, in vivo clearance of α2-3 Neu VWF in VWF-/-andAsgr1-/-VWF-/-mice was almost as rapid as that of asialo-VWF (digested with α2-3,6,8,9 neuraminidase). Critically, the increased clearance of α2-3 Neu VWF in VWF-/- is attenuated in the presence of MGL blocking antibodies (120mins residual α2-3 Neu VWF is 10.6% ±2% , compared to 10.2% ±1% for that of pdVWF). Plate-binding studies confirmed that α2-3 Neu VWF and α2-3,6,8,9 Neu VWF demonstrated enhanced binding to MGL compared to pdVWF (155% and 134% versus 100%; p =0.017 and 0.006). In keeping with in vivo clearance data, removal of α2-6 linked sialic acid from N glycans did not further promote binding to MGL. Finally, although PNGase removal of VWF N glycans did not affect MGL binding, treatment with O glycosidase significantly attenuated binding (p<0.0001). All together, these data demonstrate that O-linked sialylation plays a critical role in protecting VWF from MGL mediated clearance. The mature VWF monomer contains 10 O linked glycans, with eight clustered around the A1 domain. To further investigate the role of these glycans in regulating MGL interaction, site directed mutagenesis was used to generate VWF molecules lacking either O-linked cluster 1 (T1248, T1255, T1256, T1263) or O-linked cluster 2 (T1468, T1477, S1486, T1487) respectively. Binding of Δcluster 1 VWF to MGL was similar to that of wild-type VWF. In contrast, binding of the Δcluster 2 VWF variant to MGL was markedly reduced (84 % vs 40%; p=0.0027). O linked glycan structures are known to play important roles in maintaining glycoprotein conformation. To further define the mechanism through which these O glycan structures influence MGL mediated clearance, binding of a truncated A1A2A3 fragment and isolated recombinant A1, A2 and A3 domains were examined. Interestingly, MGL-binding to full length rVWF and A1A2A3 were both significantly increased in the presence of ristocetin. Interestingly, no binding of isolated A2 or A3 domains to MGL was observed, while A1 domain binding to MGL was seen both in the presence and absence of ristocetin. Conclusions In conclusion, these findings define a novel role for O linked sialylation in protecting VWF from MGL mediated clearance. Our data further demonstrate that the cluster of O linked glycans located at the C-terminal end of the A1 domain play a specific role in regulating VWF clearance via MGL, and that conformation of A1A2A3 may be important in determining accessibility of these glycans for the clearance receptor. Further studies will be required to determine whether abnormalities in these O-glycan determinants may be important in the pathophysiology of VWD, particularly in patients with type 1C VWD who lack VWF gene coding mutations. Disclosures O'Donnell: Bayer: Research Funding, Speakers Bureau; Novo Nordisk: Research Funding, Speakers Bureau; Leo Pharma: Speakers Bureau; Octapharma: Speakers Bureau; CSL Behring: Consultancy; Daiichi Sankyo: Consultancy; Pfizer: Consultancy, Research Funding; Baxter: Research Funding, Speakers Bureau; Shire: Research Funding, Speakers Bureau.


2013 ◽  
Vol 60 (4) ◽  
Author(s):  
Anna Timoszyk ◽  
Lidia Latanowicz

Biological membranes are complex systems which have attracted scientific interest for a long time and for various reasons. The sialic acid-liposome interactions at the molecular level depend on their hydro-lipophilic characteristics. The aim of the present study was to investigate the changes of conformation of the phospholipid (1,2-Diacyl-sn-glycero-3-phosphocholine) and sialic acid (2,8-(N-acetylneuraminic acid)) molecules and the type of interactions induced by the sialic acid molecules on membrane-like systems (liposomes) by 2D NMR (TOCSY, HETCOR, ROESY). The nature of the interaction of sialic acid with the model membrane depends on the structure of the phospholipid headgroups and the hydration of membrane. In ROESY spectra was observed the absence of dipole-dipole couplings within the choline head, between headgroups and glycerol, and between glycerol and fatty acid chains. It indicates an increase of the membrane dynamics in the presence of sialic acid. Moreover, the conformation of sialic acid molecule is changed in the presence of liposomes, which depends on stereochemistry of the chemical groups of the carbon atoms C7 and C8, and oxygen O8. The observed differences between the ROESY spectra of free and liposome bound sialic acid may be a consequence of a changed orientation of the pyranose ring from trans to gauche in the presence of liposomes. The sialic acid penetrate into the phospholipid bilayer to a sufficient depth to allow the dipole interaction. The present result that the correlation signal was found only between the methyl protons from the acetyl group of sialic acid and the methylene tail of phospholipid molecule in the ROESY spectrum indicates that the opposite end of the sialic acid molecule stays in the aqueous phase without interacting with membrane molecules.


1999 ◽  
Vol 343 (2) ◽  
pp. 397-402 ◽  
Author(s):  
Daniel M. STOUGHTON ◽  
Gerardo ZAPATA ◽  
Robert PICONE ◽  
Willie F. VANN

Escherichia coli K1 CMP-sialic acid synthetase catalyses the synthesis of CMP-sialic acid from CTP and sialic acid. The active site of the 418 amino acid E. coli enzyme was localized to its N-terminal half. The bacterial CMP-sialic acid synthetase enzymes have a conserved motif, IAIIPARXXSKGLXXKN, at their N-termini. Several basic residues have been identified at or near the active site of the E. coli enzyme by chemical modification and site-directed mutagenesis. Only one of the lysines in the N-terminal motif, Lys-21, appears to be essential for activity. Mutation of Lys-21 in the N-terminal motif results in an inactive enzyme. Furthermore, Arg-12 of the N-terminal motif appears to be an active-site residue, based on the following evidence. Substituting Arg-12 with glycine or alanine resulted in inactive enzymes, indicating that this residue is required for enzymic activity. The Arg-12 → Lys mutant was partially active, demonstrating that a positive charge is required at this site. Steady-state kinetic analysis reveals changes in kcat, Km and Ks for CTP, which implicates Arg-12 in catalysis and substrate binding.


2019 ◽  
Author(s):  
Smriti Pandey ◽  
Chandra M Gravel ◽  
Oliver M Stockert ◽  
Clara D Wang ◽  
Courtney L Hegner ◽  
...  

The FinO-domain-protein ProQ is an RNA-binding protein that has been known to play a role in osmoregulation in proteobacteria. Recently, ProQ has been shown to act as a global RNA-binding protein in Salmonella and E. coli, binding to dozens of small RNAs (sRNAs) and messenger RNAs (mRNAs) to regulate mRNA-expression levels through interactions with both 5′ and 3′ untranslated regions (UTRs). Despite excitement around ProQ as a novel global RNA-binding protein interacting with many sRNAs and mRNAs, and its potential to serve as a matchmaking RNA chaperone, significant gaps remain in our understanding of the molecular mechanisms ProQ uses to interact with RNA. In order to apply the tools of molecular genetics to this question, we have adapted a bacterial three-hybrid (B3H) assay to detect ProQ's interactions with target RNAs. Using domain truncations, site-directed mutagenesis and an unbiased forward genetic screen, we have identified a group of highly conserved residues on ProQ's NTD as the primary face for in vivo recognition of two RNAs, and propose that the NTD structure serves as an electrostatic scaffold to recognize the shape of an A-form RNA duplex.


Blood ◽  
2007 ◽  
Vol 110 (7) ◽  
pp. 2685-2695 ◽  
Author(s):  
Balázs Csóka ◽  
Zoltán H. Németh ◽  
László Virág ◽  
Pál Gergely ◽  
S. Joseph Leibovich ◽  
...  

We recently showed that A2A adenosine receptor activation by endogenous adenosine contributes to interleukin-10 (IL-10) production in polymicrobial sepsis. Here we investigated the molecular mechanisms underpinning this interaction between adenosine receptor signaling and infection by exposing macrophages to Escherichia coli. We demonstrated using receptor knockout mice that A2A receptor activation is critically required for the stimulatory effect of adenosine on IL-10 production by E coli–challenged macrophages, whereas A2B receptors have a minor role. The stimulatory effect of adenosine on E coli–induced IL-10 production did not require toll-like receptor 4 (TLR4) or MyD88, but was blocked by p38 inhibition. Using shRNA we demonstrated that TRAF6 impairs the potentiating effect of adenosine. Measuring IL-10 mRNA abundance and transfection with an IL-10 promoter-luciferase construct indicated that E coli and adenosine synergistically activate IL-10 transcription. Sequential deletion analysis and site-directed mutagenesis of the IL-10 promoter revealed that a region harboring C/EBP binding elements was responsible for the stimulatory effect of adenosine on E coli–induced IL-10 promoter activity. Adenosine augmented E coli–induced nuclear accumulation and DNA binding of C/EBPβ. C/EBPβ-deficient macrophages failed to produce IL-10 in response to adenosine and E coli. Our results suggest that the A2A receptor–C/EBPβ axis is critical for IL-10 production after bacterial infection.


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