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1.
Nucleic Acids Res ; 49(8): 4725-4737, 2021 05 07.
Article in English | MEDLINE | ID: mdl-33836064

ABSTRACT

Mammalian cyclic GMP-AMP synthase (cGAS) and its homologue dinucleotide cyclase in Vibrio cholerae (VcDncV) produce cyclic dinucleotides (CDNs) that participate in the defense against viral infection. Recently, scores of new cGAS/DncV-like nucleotidyltransferases (CD-NTases) were discovered, which produce various CDNs and cyclic trinucleotides (CTNs) as second messengers. Here, we present the crystal structures of EcCdnD, a CD-NTase from Enterobacter cloacae that produces cyclic AMP-AMP-GMP, in its apo-form and in complex with ATP, ADP and AMPcPP, an ATP analogue. Despite the similar overall architecture, the protein shows significant structural variations from other CD-NTases. Adjacent to the donor substrate, another nucleotide is bound to the acceptor binding site by a non-productive mode. Isothermal titration calorimetry results also suggest the presence of two ATP binding sites. GTP alone does not bind to EcCdnD, which however binds to pppApG, a possible intermediate. The enzyme is active on ATP or a mixture of ATP and GTP, and the best metal cofactor is Mg2+. The conserved residues Asp69 and Asp71 are essential for catalysis, as indicated by the loss of activity in the mutants. Based on structural analysis and comparison with VcDncV and RNA polymerase, a tentative catalytic pathway for the CTN-producing EcCdnD is proposed.


Subject(s)
Adenosine Triphosphate/chemistry , Enterobacter cloacae/chemistry , Magnesium/chemistry , Nucleotides, Cyclic/chemistry , Nucleotidyltransferases/chemistry , Binding Sites , Calorimetry, Differential Scanning , Catalysis , Crystallography, X-Ray , Enterobacter cloacae/enzymology , Guanosine Triphosphate/chemistry , Ligands , Mutation , Nucleotidyltransferases/chemical synthesis
2.
Biochemistry ; 59(39): 3683-3695, 2020 10 06.
Article in English | MEDLINE | ID: mdl-32930597

ABSTRACT

Proteins are subject to spontaneous rearrangements of their backbones. Most prominently, asparagine and aspartate residues isomerize to their ß-linked isomer, isoaspartate (isoAsp), on time scales ranging from days to centuries. Such modifications are typically considered "molecular wear-and-tear", destroying protein function. However, the observation that some proteins, including the essential bacterial enzyme MurA, harbor stoichiometric amounts of isoAsp suggests that this modification can confer advantageous properties. Here, we demonstrate that nature exploits an isoAsp residue within a hairpin to stabilize MurA. We found that isoAsp formation in MurA is unusually rapid and critically dependent on folding status. Moreover, perturbation of the isoAsp-containing hairpin via site-directed mutagenesis causes aggregation of MurA variants. Structural mass spectrometry revealed that this effect is caused by local protein unfolding in MurA mutants. Our findings demonstrate that MurA evolved to "mature" via a spontaneous post-translational incorporation of a ß-amino acid, which raises the possibility that isoAsp-containing hairpins may serve as a structural motif of biological importance.


Subject(s)
Alkyl and Aryl Transferases/chemistry , Bacterial Proteins/chemistry , Enterobacter cloacae/enzymology , Isoaspartic Acid/chemistry , Enterobacter cloacae/chemistry , Enzyme Stability , Isomerism , Models, Molecular , Protein Aggregates , Protein Conformation , Protein Folding
3.
Microb Cell Fact ; 19(1): 89, 2020 Apr 15.
Article in English | MEDLINE | ID: mdl-32293454

ABSTRACT

BACKGROUND: Biological routes for ethylene glycol production have been developed in recent years by constructing the synthesis pathways in different microorganisms. However, no microorganisms have been reported yet to produce ethylene glycol naturally. RESULTS: Xylonic acid utilizing microorganisms were screened from natural environments, and an Enterobacter cloacae strain was isolated. The major metabolites of this strain were ethylene glycol and glycolic acid. However, the metabolites were switched to 2,3-butanediol, acetoin or acetic acid when this strain was cultured with other carbon sources. The metabolic pathway of ethylene glycol synthesis from xylonic acid in this bacterium was identified. Xylonic acid was converted to 2-dehydro-3-deoxy-D-pentonate catalyzed by D-xylonic acid dehydratase. 2-Dehydro-3-deoxy-D-pentonate was converted to form pyruvate and glycolaldehyde, and this reaction was catalyzed by an aldolase. D-Xylonic acid dehydratase and 2-dehydro-3-deoxy-D-pentonate aldolase were encoded by yjhG and yjhH, respectively. The two genes are part of the same operon and are located adjacent on the chromosome. Besides yjhG and yjhH, this operon contains four other genes. However, individually inactivation of these four genes had no effect on either ethylene glycol or glycolic acid production; both formed from glycolaldehyde. YqhD exhibits ethylene glycol dehydrogenase activity in vitro. However, a low level of ethylene glycol was still synthesized by E. cloacae ΔyqhD. Fermentation parameters for ethylene glycol and glycolic acid production by the E. cloacae strain were optimized, and aerobic cultivation at neutral pH were found to be optimal. In fed batch culture, 34 g/L of ethylene glycol and 13 g/L of glycolic acid were produced in 46 h, with a total conversion ratio of 0.99 mol/mol xylonic acid. CONCLUSIONS: A novel route of xylose biorefinery via xylonic acid as an intermediate has been established.


Subject(s)
Enterobacter cloacae/metabolism , Ethylene Glycol/metabolism , Glycolates/metabolism , Xylose/analogs & derivatives , Enterobacter cloacae/chemistry , Ethylene Glycol/chemistry , Glycolates/chemistry , Xylose/chemistry , Xylose/metabolism
4.
Microb Cell Fact ; 17(1): 45, 2018 Mar 19.
Article in English | MEDLINE | ID: mdl-29554914

ABSTRACT

BACKGROUND: In industries lipolytic reactions occur in insensitive conditions such as high temperature thus novel stout esterases with unique properties are attracts to the industrial application. Protein engineering is the tool to obtain desirable characters of enzymes. A novel esterase gene was isolated from South China Sea and subjected to a random mutagenesis and site directed mutagenesis for higher activity and thermo-stability compared to wild type. RESULTS: A novel esterase showed the highest hydrolytic activity against p-nitrophenyl acetate (pNPA, C2) and the optimal activity at 40 °C and pH 8.5. It was a cold-adapted enzyme and retained approximately 40% of its maximum activity at 0 °C. A mutant, with higher activity and thermo-stability was obtained by random mutagenesis. Kinetic analysis indicated that the mutant Val29Ala/Tyr193Cys shown 43.5% decrease in K m , 2.6-fold increase in K cat , and 4.7-fold increase in K cat /K m relative to the wild type. Single mutants V29A and Y193C were constructed and their kinetic parameters were measured. The results showed that the values of K m , K cat , and K cat /K m of V29A were similar to those of the wild type while Y193C showed 52.7% decrease in K m , 2.7-fold increase in K cat , and 5.6-fold increase in K cat /K m compared with the wild type. The 3-D structure and docking analysis revealed that the replacement of Tyr by Cys could enlarge the binding pocket. Moreover Y193C also showed a better thermo-stability for the reason its higher hydrophobicity and retained 67% relative activity after incubation for 3 h at 50 °C. CONCLUSIONS: The superior quality of modified esterase suggested it has great potential application in extreme conditions and the mutational work recommended that important information for the study of esterase structure and function.


Subject(s)
Enterobacter cloacae/chemistry , Esterases/chemistry , Protein Engineering/methods , Cold Temperature
5.
Proteins ; 85(7): 1258-1265, 2017 07.
Article in English | MEDLINE | ID: mdl-28316100

ABSTRACT

Kinetic, thermodynamic, and structural properties of the aminoglycoside N3-acetyltransferase-VIa (AAC-VIa) are determined. Among the aminoglycoside N3-acetyltransferases, AAC-VIa has one of the most limited substrate profiles. Kinetic studies showed that only five aminoglycosides are substrates for this enzyme with a range of fourfold difference in kcat values. Larger differences in KM (∼40-fold) resulted in ∼30-fold variation in kcat /KM . Binding of aminoglycosides to AAC-VIa was enthalpically favored and entropically disfavored with a net result of favorable Gibbs energy (ΔG < 0). A net deprotonation of the enzyme, ligand, or both accompanied the formation of binary and ternary complexes. This is opposite of what was observed with several other aminoglycoside N3-acetyltransferases, where ligand binding causes more protonation. The change in heat capacity (ΔCp) was different in H2 O and D2 O for the binary enzyme-sisomicin complex but remained the same in both solvents for the ternary enzyme-CoASH-sisomicin complex. Unlike, most other aminoglycoside-modifying enzymes, the values of ΔCp were within the expected range of protein-carbohydrate interactions. Solution behavior of AAC-VIa was also different from the more promiscuous aminoglycoside N3-acetyltransferases and showed a monomer-dimer equilibrium as detected by analytical ultracentrifugation (AUC). Binding of ligands shifted the enzyme to monomeric state. Data also showed that polar interactions were the most dominant factor in dimer formation. Overall, thermodynamics of ligand-protein interactions and differences in protein behavior in solution provide few clues on the limited substrate profile of this enzyme despite its >55% sequence similarity to the highly promiscuous aminoglycoside N3-acetyltransferase. Proteins 2017; 85:1258-1265. © 2017 Wiley Periodicals, Inc.


Subject(s)
Acetyltransferases/chemistry , Anti-Bacterial Agents/chemistry , Bacterial Proteins/chemistry , Enterobacter cloacae/chemistry , Protons , Sisomicin/chemistry , Acetyltransferases/genetics , Acetyltransferases/metabolism , Amino Acid Motifs , Anti-Bacterial Agents/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Binding Sites , Cloning, Molecular , Deuterium Oxide/chemistry , Enterobacter cloacae/enzymology , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Gentamicins/chemistry , Gentamicins/metabolism , Kanamycin/chemistry , Kanamycin/metabolism , Kinetics , Ligands , Models, Molecular , Protein Binding , Protein Interaction Domains and Motifs , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Sisomicin/metabolism , Structural Homology, Protein , Substrate Specificity , Thermodynamics , Tobramycin/chemistry , Tobramycin/metabolism , Water/chemistry
6.
Article in English | MEDLINE | ID: mdl-28971872

ABSTRACT

Sulbactam is one of four ß-lactamase inhibitors in current clinical use to counteract drug resistance caused by degradation of ß-lactam antibiotics by these bacterial enzymes. As a ß-lactam itself, sulbactam is susceptible to degradation by ß-lactamases. I investigated the Michaelis-Menten kinetics of sulbactam hydrolysis by 14 ß-lactamases, representing clinically widespread groups within all four Ambler classes, i.e., CTX-M-15, KPC-2, SHV-5, and TEM-1 for class A; IMP-1, NDM-1, and VIM-1 for class B; Acinetobacter baumannii ADC-7, Pseudomonas aeruginosa AmpC, and Enterobacter cloacae P99 for class C; and OXA-10, OXA-23, OXA-24, and OXA-48 for class D. All of the ß-lactamases were able to hydrolyze sulbactam, although they varied widely in their kinetic constants for the reaction, even within each class. I also investigated the inactivation kinetics of the inhibition of these enzymes by sulbactam. The class A ß-lactamases varied widely in their susceptibility to inhibition, the class C and D enzymes were very weakly inhibited, and the class B enzymes were essentially or completely unaffected. In addition, we measured the sulbactam turnover number, the sulbactam/enzyme molar ratio required for complete inhibition of each enzyme. Class C enzymes had the lowest turnover numbers, class A enzymes varied widely, and class D enzymes had very high turnover numbers. These results are valuable for understanding which ß-lactamases ought to be well inhibited by sulbactam. Moreover, since sulbactam has intrinsic antibacterial activity against Acinetobacter species pathogens, these results contribute to understanding ß-lactamase-mediated sulbactam resistance in Acinetobacter, especially due to the action of the widespread class D enzymes.


Subject(s)
Acinetobacter baumannii/chemistry , Enterobacter cloacae/chemistry , Pseudomonas aeruginosa/chemistry , Sulbactam/metabolism , beta-Lactamase Inhibitors/metabolism , beta-Lactamases/metabolism , Acinetobacter baumannii/enzymology , Acinetobacter baumannii/genetics , Enterobacter cloacae/enzymology , Enterobacter cloacae/genetics , Gene Expression , Hydrolysis , Kinetics , Pseudomonas aeruginosa/enzymology , Pseudomonas aeruginosa/genetics , Species Specificity , Sulbactam/pharmacology , beta-Lactamase Inhibitors/pharmacology , beta-Lactamases/classification , beta-Lactamases/genetics , beta-Lactamases/isolation & purification
7.
Antimicrob Agents Chemother ; 60(1): 356-60, 2016 01.
Article in English | MEDLINE | ID: mdl-26525789

ABSTRACT

New Delhi metallo-ß-lactamase-1 (NDM-1) is expressed by various members of Enterobacteriaceae as a defense mechanism to hydrolyze ß-lactam antibiotics. Despite various studies showing the significance of active-site residues in the catalytic mechanism, there is a paucity of reports addressing the role of non-active-site residues in the structure and function of NDM-1. In this study, we investigated the significance of non-active-site residue Trp-93 in the structure and function of NDM-1. We cloned blaNDM-1 from an Enterobacter cloacae clinical strain (EC-15) and introduced the mutation of Trp-93 to Ala (yielding the Trp93Ala mutant) by PCR-based site-directed mutagenesis. Proteins were expressed and purified to homogeneity by affinity chromatography. The MICs of the Trp93Ala mutant were reduced 4- to 8-fold for ampicillin, cefotaxime, ceftazidime, cefoxitin, imipenem, and meropenem. The poor hydrolytic activity of the Trp93Ala mutant was also reflected by its reduced catalytic efficiency. The overall catalytic efficiency of the Trp93Ala mutant was reduced by 40 to 55% (the Km was reduced, while the kcat was similar to that of wild-type NDM-1 [wtNDM-1]). Heat-induced denaturation showed that the ΔGD (o) and Tm of Trp93Ala mutant were reduced by 1.8 kcal/mol and 4.8°C, respectively. Far-UV circular dichroism (CD) analysis showed that the α-helical content of the Trp93Ala mutant was reduced by 2.9%. The decrease in stability and catalytic efficiency of the Trp93Ala mutant was due to the loss of two hydrogen bonds with Ser-63 and Val-73 and hydrophobic interactions with Leu-65, Val-73, Gln-123, and Asp-124. The study provided insight into the role of non-active-site amino acid residues in the hydrolytic mechanism of NDM-1.


Subject(s)
Alanine/chemistry , Anti-Bacterial Agents/chemistry , Enterobacter cloacae/chemistry , Tryptophan/chemistry , beta-Lactamases/chemistry , beta-Lactams/chemistry , Alanine/metabolism , Biocatalysis , Cloning, Molecular , Enterobacter cloacae/enzymology , Enzyme Stability , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Hydrogen Bonding , Hydrolysis , Hydrophobic and Hydrophilic Interactions , Kinetics , Models, Molecular , Mutation , Protein Structure, Secondary , Protein Structure, Tertiary , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Structure-Activity Relationship , Thermodynamics , Tryptophan/metabolism , beta-Lactamases/genetics , beta-Lactamases/metabolism
8.
Biochemistry ; 54(21): 3370-80, 2015 Jun 02.
Article in English | MEDLINE | ID: mdl-25938261

ABSTRACT

OXA-163 and OXA-48 are closely related class D ß-lactamases that exhibit different substrate profiles. OXA-163 hydrolyzes oxyimino-cephalosporins, particularly ceftazidime, while OXA-48 prefers carbapenem substrates. OXA-163 differs from OXA-48 by one substitution (S212D) in the active-site ß5 strand and a four-amino acid deletion (214-RIEP-217) in the loop connecting the ß5 and ß6 strands. Although the structure of OXA-48 has been determined, the structure of OXA-163 is unknown. To further understand the basis for their different substrate specificities, we performed enzyme kinetic analysis, inhibition assays, X-ray crystallography, and molecular modeling. The results confirm the carbapenemase nature of OXA-48 and the ability of OXA-163 to hydrolyze the oxyimino-cephalosporin ceftazidime. The crystal structure of OXA-163 determined at 1.72 Å resolution reveals an expanded active site compared to that of OXA-48, which allows the bulky substrate ceftazidime to be accommodated. The structural differences with OXA-48, which cannot hydrolyze ceftazidime, provide a rationale for the change in substrate specificity between the enzymes. OXA-163 also crystallized under another condition that included iodide. The crystal structure determined at 2.87 Å resolution revealed iodide in the active site accompanied by several significant conformational changes, including a distortion of the ß5 strand, decarboxylation of Lys73, and distortion of the substrate-binding site. Further studies showed that both OXA-163 and OXA-48 are inhibited in the presence of iodide. In addition, OXA-10, which is not a member of the OXA-48-like family, is also inhibited by iodide. These findings provide a molecular basis for the hydrolysis of ceftazidime by OXA-163 and, more broadly, show how minor sequence changes can profoundly alter the active-site configuration and thereby affect the substrate profile of an enzyme.


Subject(s)
Enterobacter cloacae/enzymology , Enzyme Inhibitors/pharmacology , Iodides/pharmacology , Klebsiella pneumoniae/enzymology , beta-Lactamases/chemistry , Anti-Bacterial Agents/metabolism , Carbapenems/metabolism , Catalytic Domain , Ceftazidime/metabolism , Cephalosporins/metabolism , Enterobacter cloacae/chemistry , Enterobacteriaceae Infections/microbiology , Humans , Klebsiella Infections/microbiology , Klebsiella pneumoniae/chemistry , Molecular Docking Simulation , Protein Conformation
9.
Wei Sheng Wu Xue Bao ; 55(4): 467-75, 2015 Apr 04.
Article in Zh | MEDLINE | ID: mdl-26211321

ABSTRACT

OBJECTIVE: To characterize a neutral invertase from Enterobacter cloacae GX-3. METHODS: By searching GenBank database, we found the genes encoding invertase from the same genus Enterobacter. These sequences were aligned and analyzed. Then, a gene encoding neutral invertase was amplified by PCR. The recombinant plasmid pQE-Einv was constructed. We purified the expressed protein Einv with nickel-nitrilotriacetic acid chromatography. At last, the characterics of the recombinant protein Einv were studied in detail. RESULTS: A gene encoding neutral invertase was discovered and cloned from E. cloacae GX-3. The recombinant enzyme Einv was characterized. Einv had an optimum pH of 6.5 and an optimum temperature of 40 degrees C. The results of sodium dodecyl sulfate polyacrylamide gel electropheresis (SDS-PAGE) and gel permeation chromatography ( GPC) showed that Einv was a homo-dimer protein. Einv retained 80% activity at sucrose concentrations up to 1170 mmol/L. But, Einv had no transglycosylation activity at high sucrose concentration. It could hydrolyze raffinose, 1-kestose, nystose, fructofuranosylnystose and stachyose. CONCLUSION: It is first reported that an invertase from Enterobacter cloacae is a beta-fructofuranosidase at neutral pH range. It only has hydrolysis activity without tranglycosylation activity. These characteristics indicate that the neutral invertase Einv has important applications in food industry.


Subject(s)
Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Enterobacter cloacae/enzymology , beta-Fructofuranosidase/chemistry , beta-Fructofuranosidase/genetics , Bacterial Proteins/isolation & purification , Bacterial Proteins/metabolism , Enterobacter cloacae/chemistry , Enterobacter cloacae/genetics , Enzyme Stability , Hydrogen-Ion Concentration , Kinetics , Molecular Weight , Substrate Specificity , Temperature , beta-Fructofuranosidase/isolation & purification , beta-Fructofuranosidase/metabolism
10.
J AOAC Int ; 95(1): 216-21, 2012.
Article in English | MEDLINE | ID: mdl-22468362

ABSTRACT

To eliminate the interference caused by Pseudomonas aeruginosa in the isolation of Salmonella, a rabbit polyclonal antibody against P. aeruginosa was prepared by inoculating four New Zealand rabbits with the pathogen. The antiserum was purified using saturated ammonium sulfate and added into Rappaport-Vassiliadis medium with soya (RVS) broth and Muller-Kauffmann tetrathionate novobiocin broth (MKTTn broth) to evaluate whether it could inhibit the growth of P. aeruginosa. Observations by scanning electron microscopy demonstrated that P. aeruginosa was attacked and destroyed by the antibody when incubated for 10 min at 37 degrees C. The activity of the antibody was also effective against 11 other strains of P. aeruginosa. Twenty-six strains of Salmonella were mixed with P. aeruginosa in RVS and MKTTn broth at 37 degrees C for 12 h, respectively, and the cultures were plated on Salmonella chromogenic medium (SCM; Oxoid, Basingstoke, UK). Only Salmonella grew on SCM; five colonies were randomly selected for identification by VITEK 2 (bioMérieux, Lyon, France). Additionally, when mixed with two strains of Enterobacter cloacae (ATCC 700323 and YG001), the prepared antibody did not affect the growth of E. cloacae. The results demonstrated that the microbicidal activity of the antibody did not affect the tested Salmonella sp. or E. cloacae strains. Therefore, the antibody generated could be used to increase the accuracy of Salmonella isolation.


Subject(s)
Antibodies, Bacterial/chemistry , Bacteria/isolation & purification , Animal Feed/microbiology , Animals , Anti-Bacterial Agents/chemistry , Antibodies, Bacterial/isolation & purification , Cattle , Colony Count, Microbial , Cross Reactions , Culture Media , Enterobacter cloacae/chemistry , Enterobacter cloacae/isolation & purification , False Positive Reactions , Fishes , Novobiocin/chemistry , Pseudomonas aeruginosa/chemistry , Pseudomonas aeruginosa/isolation & purification , Rabbits , Salmonella/chemistry , Salmonella/isolation & purification , Sheep
11.
Carbohydr Res ; 519: 108612, 2022 Sep.
Article in English | MEDLINE | ID: mdl-35779303

ABSTRACT

The O-polysaccharide (OPS) was isolated by mild acid degradation of the lipopolysaccharide of Enterobacter cloacae G2559 and studied by sugar analysis along with 1D and 2D 1H and 13C NMR spectroscopy. The following structure of the branched pentasaccharide repeating unit was established. The O-antigen gene cluster of Enterobacter cloacae G2559 was sequenced. The gene functions were tentatively assigned by comparison with sequences in the available databases and found to be in full agreement with the O-antigen structure.


Subject(s)
Enterobacter cloacae , O Antigens , Carbohydrate Sequence , Enterobacter cloacae/chemistry , Lipopolysaccharides/chemistry , Multigene Family , O Antigens/chemistry
12.
Chembiochem ; 12(5): 738-49, 2011 Mar 21.
Article in English | MEDLINE | ID: mdl-21374779

ABSTRACT

We have conducted a site-specific saturation mutagenesis study of H181 and H184 of flavoprotein pentaerythritol tetranitrate reductase (PETN reductase) to probe the role of these residues in substrate binding and catalysis with a variety of α,ß-unsaturated alkenes. Single mutations at these residues were sufficient to dramatically increase the enantiopurity of products formed by reduction of 2-phenyl-1-nitropropene. In addition, many mutants exhibited a switch in reactivity to predominantly catalyse nitro reduction, as opposed to CC reduction. These mutants showed an enhancement in a minor side reaction and formed 2-phenylpropanal oxime from 2-phenyl-1-nitropropene. The multiple binding conformations of hydroxy substituted nitro-olefins in PETN reductase were examined by using both structural and catalytic techniques. These compounds were found to bind in both active and inhibitory complexes; this highlights the plasticity of the active site and the ability of the H181/H184 couple to coordinate with multiple functional groups. These properties demonstrate the potential to use PETN reductase as a scaffold in the development of industrially useful biocatalysts.


Subject(s)
Enterobacter cloacae/enzymology , Mutagenesis, Site-Directed , Oxidoreductases/genetics , Oxidoreductases/metabolism , Shewanella/enzymology , Aldehydes/metabolism , Alkenes/metabolism , Crystallography, X-Ray , Enterobacter cloacae/chemistry , Enterobacter cloacae/genetics , Models, Molecular , Oxidoreductases/chemistry , Oximes/metabolism , Phenols/metabolism , Protein Binding , Shewanella/chemistry , Shewanella/genetics , Stereoisomerism , Substrate Specificity
13.
Carbohydr Res ; 510: 108440, 2021 Dec.
Article in English | MEDLINE | ID: mdl-34619615

ABSTRACT

The O-polysaccharide (OPS) was isolated by mild acid degradation of the lipopolysaccharide of Enterobacter cloacae G3422 and studied by chemical methods, including sugar analyses, Smith degradation, and solvolysis with anhydrous trifluoroacetic acid, along with 1H and 13C NMR spectroscopy. The following structure of the branched tetrasaccharide repeating unit was established: The O-antigen gene cluster of Enterobacter cloacae G3422 was sequenced. The gene functions were tentatively assigned by comparison with sequences in the available databases and found to be in a good agreement with the O-antigen structure.


Subject(s)
Enterobacter cloacae/chemistry , O Antigens/chemistry , O Antigens/genetics , Carbohydrate Conformation , Carbohydrate Sequence , Magnetic Resonance Spectroscopy , Multigene Family
14.
Microbiol Spectr ; 9(1): e0066121, 2021 09 03.
Article in English | MEDLINE | ID: mdl-34378957

ABSTRACT

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is commonly used by clinical microbiology laboratories to identify pathogens, despite some limitations of the technique. The Enterobacter cloacae complex (ECC) taxonomy has recently been expanded, leading to uncertain identification of some species within the ECC when commercial MALDI-TOF MS is used. This technique is especially unsuited in the case of E. hormaechei, the main species responsible for infections and one of the most prone, within the ECC, to acquire antibiotic resistance. Hence, rapid and reliable identification at the species level could improve patient management. Here, we evaluated the performance of the Bruker Microflex MALDI-TOF MS instrument to identify ECC isolates using two databases and algorithms in comparison to the hsp60 gene sequencing reference method: the Bruker database included in the MALDI Biotyper software and an extensive online database coupled to an original Mass Spectrometric Identification (MSI) algorithm. Among a panel of 94 ECC isolates tested in triplicate, the online database coupled to MSI software allowed the highest rate of identification at the species level (92%) compared to the MALDI Biotyper database (25%), especially for the species E. hormaechei (97% versus 20%). We show that by creating a database of MALDI-TOF reference spectral profiles with a high number of representatives associated with the performant MSI software, we were able to substantially improve the identification of the E. cloacae complex members, with only 8% of isolates misidentified at the species level. This online database is available through a free online MSI application (https://msi.happy-dev.fr/). IMPORTANCE Creation of a database of MALDI-TOF reference spectral profiles with a high number of representatives associated with the performant MSI software enables substantial improvement in identification of E. cloacae complex members. Moreover, this online database is available through a free online MSI application (https://msi.happy-dev.fr/).


Subject(s)
Bacterial Typing Techniques/methods , Enterobacter cloacae/isolation & purification , Enterobacteriaceae Infections/microbiology , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Algorithms , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Databases, Factual , Enterobacter cloacae/chemistry , Enterobacter cloacae/genetics , Enterobacter cloacae/metabolism , Humans
15.
Int J Biol Macromol ; 183: 861-869, 2021 Jul 31.
Article in English | MEDLINE | ID: mdl-33940061

ABSTRACT

We previously obtained and characterized a novel sulfated derivative of the exopolysaccharides from Enterobacter cloacae Z0206 (SEPS). This study aimed at investigating the effects and mechanism of SEPS against dextran sulfate sodium (DSS) induced intestinal injury. The results showed that SEPS increased the proliferation and survival of intestinal epithelial cells during DSS stimulation. Furthermore, SEPS maintained the barrier function and inflammatory response via JAK2 and MAPK signaling to protect against DSS-induced intestinal injury. Mechanistically, SEPS elevated the DNA methylation in the promoter region to negatively regulate the JAK2 and MAPKs expression. Thus, the current study shows the potential effects and mechanism of SEPS on DSS-induced intestinal epithelial cell injury.


Subject(s)
Colitis/drug therapy , DNA Methylation , Enterobacter cloacae/chemistry , Janus Kinase 2/genetics , Polysaccharides, Bacterial/administration & dosage , Animals , Cell Proliferation/drug effects , Cell Survival/drug effects , Colitis/chemically induced , Colitis/genetics , Dextran Sulfate , Disease Models, Animal , Epigenesis, Genetic/drug effects , Epithelial Cells/chemistry , Epithelial Cells/cytology , Epithelial Cells/drug effects , Intestines/chemistry , Intestines/cytology , Intestines/drug effects , MAP Kinase Signaling System/drug effects , Mice , Mice, Inbred C57BL , Polysaccharides, Bacterial/chemistry , Polysaccharides, Bacterial/pharmacology , Protective Agents
16.
Proteomics ; 10(20): 3631-43, 2010 Oct.
Article in English | MEDLINE | ID: mdl-20845332

ABSTRACT

Currently, most MS-based proteomic studies of bacteria and archea match experimental data to known amino acid sequences from the target organism. Top-down studies use a protein's molecular weight along with data gathered from MS/MS experiments to identify proteins by database matching. For Erwinia herbicola and Enterobacter cloacae, studied here, the necessary protein sequences are not available in protein sequence repositories. We apply top-down protein fragmentation, but match the experimental data with homologous proteins from related organisms with sequenced genomes, demonstrating considerable shared protein sequence between closely related bacteria. Using this homology-based approach, we are not only able to identify representative proteins, but are also able to place the two target bacteria in their correct phylogeny. Furthermore, we show that the unexpected mass delta between the experimental precursor and matched protein sequence can often be localized and characterized using accurate-mass precursor and fragment ion measurements. Finally, we demonstrate that proteins identified by top-down workflows provide strong experimental evidence for correct, missing, and misannotated bacterial protein sequences, not only in the analyzed organism, but also for homologous proteins in closely related species.


Subject(s)
Bacterial Proteins , Proteomics , Sequence Analysis, Protein , Tandem Mass Spectrometry , Amino Acid Sequence , Bacterial Proteins/analysis , Bacterial Proteins/classification , Bacterial Proteins/genetics , Chromatography, Liquid/instrumentation , Chromatography, Liquid/methods , Databases, Protein , Enterobacter cloacae/chemistry , Enterobacter cloacae/genetics , Erwinia/chemistry , Erwinia/genetics , Molecular Sequence Data , Phylogeny , Proteomics/instrumentation , Proteomics/methods , Sequence Analysis, Protein/instrumentation , Sequence Analysis, Protein/methods , Tandem Mass Spectrometry/instrumentation , Tandem Mass Spectrometry/methods
17.
Carbohydr Polym ; 237: 116147, 2020 Jun 01.
Article in English | MEDLINE | ID: mdl-32241420

ABSTRACT

The present study aimed to unveil potential protective mechanisms of SEPS-4, a novel sulfated derivative of exopolysaccharide produced by Enterobacter cloacae Z0206, against H2O2-induced oxidative damage in murine macrophages based on proteomic approaches. SEPS-4 pre-treatment was found to be capable of alleviating H2O2-induced reduction of RAW264.7 cell viability. Two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry were used to evaluate proteins with significant expression alterations in H2O2-challenged RAW264.7 cells following pre-incubation with SEPS-4. Here 12 up-regulated proteins and 12 down-regulated proteins were successfully identified. Bio-informatic analysis was applied for further mechanistic studies. GO annotation and KEGG pathway enrichment analyses demonstrated that differentially expressed proteins were mainly clustered in stress-related biological processes, including metabolic process, stimulus to response, cell growth and death. Peroxiredoxin-2 and Eef1g were core modules of protein-protein interaction network. Collectively, our data indicated that SEPS-4 may exert protective effects against H2O2-induced oxidative damage via the regulation of these functional proteins and related biological processes.


Subject(s)
Enterobacter cloacae/chemistry , Oxidative Stress/drug effects , Polysaccharides/pharmacology , Sulfates/pharmacology , Animals , Cell Survival/drug effects , Hydrogen Peroxide/pharmacology , Mice , Protein Interaction Maps , Proteomics , RAW 264.7 Cells
18.
J Mass Spectrom ; 54(1): 7-18, 2019 Jan.
Article in English | MEDLINE | ID: mdl-30324699

ABSTRACT

In this work, the extraction, structural analysis, and identification as well as antimicrobial, anti-adhesive, and antibiofilm activities of lipopeptides produced by Enterobacter cloacae C3 strain were studied. A combination of chromatographic and spectroscopic techniques offers opportunities for a better characterization of the biosurfactant structure. Thin layer chromatography (TLC) and HPLC for amino acid composition determination are used. Efficient spectroscopic techniques have been utilized for investigations on the biochemical structure of biosurfactants, such as Fourier transform infrared (FT-IR) spectroscopy and mass spectrometry analysis. This is the first work describing the production of different isoforms belonging to kurstakin and surfactin families by E cloacae strain. Three kurstakin homologues differing by the fatty acid chain length from C10 to C12 were detected. The spectrum of lipopeptides belonging to surfactin family contains various isoforms differing by the fatty acid chain length as well as the amino acids at positions four and seven. Lipopeptide C3 extract exhibited important antibacterial activity against Gram-positive and Gram-negative bacteria, antifungal activity, and interesting anti-adhesive and disruptive properties against biofilm formation by human pathogenic bacterial strains: Salmonella typhimurium, Klebsiella pneumoniae, Staphylococcus aureus, Bacillus cereus, and Candida albicans.


Subject(s)
Enterobacter cloacae/chemistry , Lipopeptides/chemistry , Lipopeptides/isolation & purification , Peptides, Cyclic/chemistry , Peptides, Cyclic/isolation & purification , Anti-Bacterial Agents/chemistry , Anti-Bacterial Agents/isolation & purification , Chromatography/methods , Protein Isoforms , Spectrophotometry/methods
19.
Food Environ Virol ; 11(3): 238-246, 2019 09.
Article in English | MEDLINE | ID: mdl-30915682

ABSTRACT

Human noroviruses (hNoV) are the primary cause of foodborne disease in the USA. Most studies on inactivation kinetics of hNoV and its surrogates are performed in monoculture, while the microbial ecosystem effect on virus inactivation remains limited. This study investigated the persistence of hNoV surrogates, murine norovirus (MNV) and Tulane virus (TuV), along with Aichi virus (AiV) under thermal and chemical inactivation in association with Gram-negative (Enterobacter cloacae) bacteria. Thermal inactivation of viruses in co-culture with E. cloacae revealed no protective effects of bacteria. At 56 °C, AiV with and without bacteria was completely inactivated by 10 min with decimal reduction values (D-values) of 41 and 43 s, respectively. Similar results were also observed for TuV. Conversely, MNV with bacteria was completely inactivated by 10 min while MNV alone remained stable up to 30 min at 56 °C. Both MNV and TuV were slightly more stable than AiV at 63 °C with TuV detection up to 2 min without bacteria. For chemical inactivation on stainless steel surfaces, viruses alone and in association with bacteria were treated with 1000 ppm sodium hypochlorite. Virus association with bacteria had no significant effect (p > 0.05) on virus resistance to bleach inactivation compared to virus alone. Specifically, exposure to 1000 ppm bleach for 5 min resulted in an average of 3.86, 2.14, and 0.94 log10 PFU/ml reductions for TuV, MNV, and AiV without bacteria, respectively. Reductions in TuV, MNV, and AiV were 3.50, 1.88, and 0.61 log10 PFU/ml when associated with E. cloacae, respectively.


Subject(s)
Enterobacter cloacae/drug effects , Kobuvirus/drug effects , Norovirus/drug effects , Sodium Hypochlorite/pharmacology , Coculture Techniques , Enterobacter cloacae/chemistry , Enterobacter cloacae/growth & development , Hot Temperature , Kobuvirus/chemistry , Kobuvirus/growth & development , Norovirus/chemistry , Norovirus/growth & development , Virus Inactivation/drug effects
20.
Int J Biol Macromol ; 122: 58-63, 2019 Feb 01.
Article in English | MEDLINE | ID: mdl-30336239

ABSTRACT

In the present study, a polysaccharide (ECP) from Enterobacter cloacae dose and time-dependently inhibited cell growth of human osteosarcoma U-2 OS cells via induction of apoptosis. ECP treatment was selectively toxic to U-2 OS cells whereas had no cytotoxic effect on normal human osteoblast cell line NHOst. ECP-induced apoptotic cell death was associated with collapse of mitochondrial membrane, cytochrome c release into the cytosol, activation of caspase-9 and-3, degradation of poly (ADP-ribose) polymerase (PARP), elevated the ratio of Bax/Bcl-2 protein and overexpression of p53, suggesting the involvement of the activation of p53 and mitochondrial intrinsic pathway in ECP-induced apoptosis. Likewise, ECP oral administration significantly inhibited the U-2 OS cancer growth in xenograft tumor model. All these first evidence indicated that ECP was a potential antitumor supplement for the treatment of human osteosarcoma.


Subject(s)
Apoptosis/drug effects , Enterobacter cloacae/chemistry , Mitochondria/drug effects , Osteosarcoma/pathology , Polysaccharides, Bacterial/pharmacology , Tumor Suppressor Protein p53/metabolism , Animals , Caspases/metabolism , Cell Line, Tumor , Cell Proliferation/drug effects , Cytochromes c/metabolism , Cytosol/drug effects , Cytosol/metabolism , Gene Expression Regulation, Neoplastic/drug effects , Humans , Male , Mice , Mitochondria/pathology , Mitochondrial Membranes/drug effects , Proto-Oncogene Proteins c-bcl-2/metabolism , Tumor Burden/drug effects , Xenograft Model Antitumor Assays , bcl-2-Associated X Protein/metabolism
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