Structural Studies on a Mitochondrial Glyoxalase II

Glyoxalase 2 is a β-lactamase fold-containing enzyme that appears to be involved with cellular chemical detoxification. Although the cytoplasmic isozyme has been characterized from several organisms, essentially nothing is known about the mitochondrial proteins. As a first step in understanding the structure and function of mitochondrial glyoxalase 2 enzymes, a mitochondrial isozyme (GLX2-5) from Arabidopsis thaliana was cloned, overexpressed, purified, and characterized using metal analyses, EPR and 1H NMR spectroscopies, and x-ray crystallography. The recombinant enzyme was shown to bind 1.04 ± 0.15 eq of iron and 1.31 ± 0.05 eq of Zn(II) and to exhibit kcat and Km values of 129 ± 10 s-1 and 391 ± 48 μm, respectively, when using S-d-lactoylglutathione as the substrate. EPR spectra revealed that recombinant GLX2-5 contains multiple metal centers, including a predominant Fe(III)Z-n(II) center and an anti-ferromagnetically coupled Fe(III)Fe(II) center. Unlike cytosolic glyoxalase 2 from A. thaliana, GLX2-5 does not appear to specifically bind manganese. 1H NMR spectra revealed the presence of at least eight paramagnetically shifted resonances that arise from protons in close proximity to a Fe(III)Fe(II) center. Five of these resonances arose from solvent-exchangeable protons, and four of these have been assigned to NH protons on metal-bound histidines. A 1.74-Å resolution crystal structure of the enzyme revealed that although GLX2-5 shares a number of structural features with human GLX2, several important differences exist. These data demonstrate that mitochondrial glyoxalase 2 can accommodate a number of different metal centers and that the predominant metal center is Fe(III)Zn(II)

Spectroscopic Studies on Cobalt(II)-Substituted Metallo-β-lactamase ImiS from \u3cem\u3eAeromonas veronii\u3c/em\u3e bv. \u3cem\u3esobria\u3c/em\u3e

In an effort to probe the structure of a group Bb metallo-β-lactamase, Co(II)-substituted ImiS was prepared and characterized by electronic absorption, NMR, and EPR spectroscopies. ImiS containing 1 equiv of Co(II) (Co(II)1-ImiS) was shown to be catalytically active. Electronic absorption studies of Co(II)1-ImiS revealed the presence of two distinct features:  (1) an intense sulfur to Co(II) ligand to metal charge transfer band and (2) less intense, Co(II) ligand field transitions that suggest 4-coordinate Co(II) in Co(II)1-ImiS. 1H NMR studies of Co(II)1-ImiS suggest that one histidine, one aspartic acid, and one cysteine coordinate the metal ion in Co(II)1-ImiS. The addition of a second Co(II) to Co(II)1-ImiS did not result in any additional solvent-exchangeable NMR resonances, strongly suggesting that the second Co(II) does not bind to a site with histidine ligands. EPR studies reveal that the metal ion in Co(II)1-ImiS is 4-coordinate and that the second Co(II) is 5/6 coordinate. Taken together, these data indicate that the catalytic site in ImiS is the consensus Zn2 site, in which Co(II) (and by extrapolation Zn(II)) is 4-coordinate and bound by Cys221, His263, Asp120, and probably one solvent water molecule. These studies also show that the second, inhibitory metal ion does not bind to the consensus Zn1 site and that the metal ion binds at a site significantly removed from the active site. These results give the first structural information on metallo-β-lactamase ImiS and suggest that the second metal binding site in ImiS may be targeted for inhibitors

Quantification of Transcriptome Responses of the Rumen Epithelium to Butyrate Infusion using RNA-seq Technology

Short-chain fatty acids (SCFAs), such as butyrate, produced by gut microorganisms, play a critical role in energy metabolism and physiology of ruminants as well as in human health. In this study, the temporal effect of elevated butyrate concentrations on the transcriptome of the rumen epithelium was quantified via serial biopsy sampling using RNA-seq technology. The mean number of genes transcribed in the rumen epithelial transcriptome was 17,323.63 ± 277.20 (±SD; N = 24) while the core transcriptome consisted of 15,025 genes. Collectively, 80 genes were identified as being significantly impacted by butyrate infusion across all time points sampled. Maximal transcriptional effect of butyrate on the rumen epithelium was observed at the 72-h infusion when the abundance of 58 genes was altered. The initial reaction of the rumen epithelium to elevated exogenous butyrate may represent a stress response as Gene Ontology (GO) terms identified were predominantly related to responses to bacteria and biotic stimuli. An algorithm for the reconstruction of accurate cellular networks (ARACNE) inferred regulatory gene networks with 113,738 direct interactions in the butyrate-epithelium interactome using a combined cutoff of an error tolerance (ɛ = 0.10) and a stringent P-value threshold of mutual information (5.0 × 10−11). Several regulatory networks were controlled by transcription factors, such as CREBBP and TTF2, which were regulated by butyrate. Our findings provide insight into the regulation of butyrate transport and metabolism in the rumen epithelium, which will guide our future efforts in exploiting potential beneficial effect of butyrate in animal well-being and human health

Mechanistic Studies on the Mononuclear Zn\u3csup\u3eII\u3c/sup\u3e-Containing Metallo-β-lactamase ImiS from \u3cem\u3eAeromonas sobria\u3c/em\u3e

In an effort to understand the reaction mechanism of a B2 metallo-β-lactamase, steady-state and pre-steady-state kinetic and rapid freeze quench electron paramagnetic resonance (EPR) studies were conducted on ImiS and its reaction with imipenem and meropenem. pH dependence studies revealed no inflection points in the pH range of 5.0−8.5, while proton inventories demonstrated at least 1 rate-limiting proton transfer. Site-directed mutagenesis studies revealed that Lys224 plays a catalytic role in ImiS, while the side chain of Asn233 does not play a role in binding or catalysis. Stopped-flow fluorescence studies on ImiS, which monitor changes in tryptophan fluorescence on the enzyme, and its reaction with imipenem and meropenem revealed biphasic fluorescence time courses with a rate of fluorescence loss of 160 s-1 and a slower rate of fluorescence regain of 98 s-1. Stopped-flow UV−vis studies, which monitor the concentration of substrate, revealed a rapid loss in absorbance during catalysis with a rate of 97 s-1. These results suggest that the rate-limiting step in the reaction catalyzed by ImiS is C−N bond cleavage. Rapid freeze quench EPR studies on CoII-substituted ImiS demonstrated the appearance of a rhombic signal after 10 ms that is assigned to a reaction intermediate that has a five-coordinate metal center. A distinct product (EP) complex was also observed and began to appear in 18−19 ms. When these results are taken together, they allow for a reaction mechanism to be offered for the B2 metallo-β-lactamases and demonstrate that the mono- and dinuclear ZnII-containing enzymes share a common rate-limiting step, which is C−N bond cleavage

Sequential Binding of Cobalt(II) to Metallo-β-lactamase CcrA

In an effort to probe Co(II) binding to metallo-β-lactamase CcrA, EPR, EXAFS, and 1H NMR studies were conducted on CcrA containing 1 equiv (1-Co(II)-CcrA) and 2 equiv (Co(II)Co(II)-CcrA) of Co(II). The EPR spectra of 1-Co(II)-CcrA and Co(II)Co(II)-CcrA are distinct and indicate 5/6-coordinate Co(II) ions. The EPR spectra also reveal the absence of significant spin-exchange coupling between the Co(II) ions in Co(II)Co(II)-CcrA. EXAFS spectra of 1-Co(II)-CcrA suggest 5/6-coordinate Co(II) with two or more histidine ligands. EXAFS spectra of Co(II)Co(II)-CcrA also indicate 5/6 ligands at a similar average distance to 1-Co(II)-CcrA, including an average of about two histidines per Co(II). 1H NMR spectra for 1-Co(II)-CcrA revealed seven paramagnetically shifted resonances, three of which were solvent-exchangeable, while the NMR spectra for Co(II)Co(II)-CcrA showed at least 16 shifted resonances, including an additional solvent-exchangeable resonance and a resonance at 208 ppm. The data indicate sequential binding of Co(II) to CcrA and that the first Co(II) binds to the consensus Zn1 site in the enzyme

Nano-Scale Strain-Induced Giant Pseudo-Magnetic Fields and Charging Effects in CVD-Grown Graphene on Copper

Scanning tunneling microscopic and spectroscopic (STM/STS) studies of graphene grown by chemical vapor deposition (CVD) on copper reveal that the monolayer carbon structures remaining on copper are strongly strained and rippled, with different regions exhibiting different lattice structures and local electronic density of states (LDOS). The large and non-uniform strain induces pseudo-magnetic field up to ∼ 50 Tesla, as manifested by the integer and fractional pseudo-magnetic field quantum Hall effects (IQHE and FQHE) in the LDOS of graphene. Additionally, ridges appear along the boundaries of different lattice structures, which exhibit excess charging effects. For graphene transferred from copper to SiO_2 substrates after the CVD growth, the average strain and the corresponding charging effects and pseudo-magnetic fields become much reduced. These findings suggest the feasibility of strain-engineering of graphene-based nano-electronics