Characterization of quinol-dependent nitric oxide reductase from Geobacillus stearothermophilus: Enzymatic activity and active site structure

Nitric oxide reductase (NOR) catalyzes the reduction of nitric oxide to generate nitrous oxide. We recently reported on the crystal structure of a quinol-dependent NOR (qNOR) from Geobacillus stearothermophilus [Y. Matsumoto, T. Tosha, A.V. Pisliakov, T. Hino, H. Sugimoto, S. Nagano, Y. Sugita and Y. Shiro, Nat. Struct. Mol. Biol. 19 (2012) 238–246], and suggested that a water channel from the cytoplasm, which is not observed in cytochrome c-dependent NOR (cNOR), functions as a pathway transferring catalytic protons. Here, we further investigated the functional and structural properties of qNOR, and compared the findings with those for cNOR. The pH optimum for the enzymatic reaction of qNOR was in the alkaline range, whereas Pseudomonas aeruginosa cNOR showed a higher activity at an acidic pH. The considerably slower reduction rate, and a correlation of the pH dependence for enzymatic activity and the reduction rate suggest that the reduction process is the rate-determining step for the NO reduction by qNOR, while the reduction rate for cNOR was very fast and therefore is unlikely to be the rate-determining step. A close examination of the heme/non-heme iron binuclear center by resonance Raman spectroscopy indicated that qNOR has a more polar environment at the binuclear center compared with cNOR. It is plausible that a water channel enhances the accessibility of the active site to solvent water, creating a more polar environment in qNOR. This structural feature could control certain properties of the active site, such as redox potential, which could explain the different catalytic properties of the two NORs. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.     

Development of a Loop-Mediated Isothermal Amplification Assay for Sensitive and Rapid Detection of the tdh and trh Genes of Vibrio parahaemolyticus and Related Vibrio Species

Thermostable direct hemolysin (TDH) and TDH-related hemolysin (TRH) are the major virulence determinants of Vibrio parahaemolyticus. TRH is further differentiated into TRH1 and TRH2 on the basis of genetic and phenotypic differences. We developed a novel and highly specific loop-mediated isothermal amplification (LAMP) assay for sensitive and rapid detection of the tdh, trh1, and trh2 genes of V. parahaemolyticus. The LAMP assay was designed for both combined and individual detection of the tdh, trh1, and trh2 genes and combined detection of the trh1 and trh2 genes. Our results showed that it gave the same results as DNA probes and conventional PCR assays for 125 strains of V. parahaemolyticus, 3 strains of Grimontia hollisae, and 2 strains of Vibrio mimicus carrying the tdh, trh1, and trh2 genes in various combinations. No LAMP products were detected for any of the 20 bacterial strains lacking the tdh, trh1, and trh2 genes. The sensitivities of the LAMP assay for detection of tdh-, trh1-, and trh2-carrying V. parahaemolyticus strains in spiked shrimp samples were 0.8, 21.3, and 5.0 CFU per LAMP reaction tube, respectively. Starting with DNA extraction from a single colony and from spiked shrimp samples, the LAMP assay required only 27 to 60 min and less than 80 min, respectively. This is the first report of a rapid and specific LAMP assay for detection and differentiation of the tdh, trh1, and trh2 genes of V. parahaemolyticus and related Vibrio species.Vibrio parahaemolyticus, which is widely distributed in estuarine, marine, and coastal environments of tropical and temperate zones, causes seafood-borne gastrointestinal disorders in humans (9). Because most clinical isolates of V. parahaemolyticus produce the thermostable direct hemolysin (TDH), TDH-related hemolysin (TRH), or both (5, 11, 14), these products are considered important virulence markers of V. parahaemolyticus (4, 5, 9, 11, 14). TDH and TRH are encoded by the tdh and trh genes, respectively. Five sequence variants of the tdh gene (tdh1 to tdh5) can be distinguished, which are >97% identical (1, 10). The tdh gene has also been detected in Grimontia (Vibrio) hollisae and some strains of Vibrio mimicus isolated from patients with diarrhea (9). The trh gene shares ca. 68% sequence identity with the tdh gene (5). Although trh gene sequences vary somewhat among strains, the trh variants can be clustered into two subgroups represented by two trh genes (trh1 and trh2), which share 84% sequence identity (5).Although most clinical isolates carry the tdh and trh genes, either alone or in combination, approximately 99% of environmental isolates do not possess either gene (9). These genes are therefore considered important virulence and epidemiological markers (5, 11, 14). Detection of the tdh and trh genes of V. parahaemolyticus using DNA probe methods is time-consuming and laborious. PCR assays, in contrast, although providing rapid detection of both tdh and trh genes (2, 15), require electrophoresis on an agarose gel, which is time-consuming and tedious. A recent real-time PCR assay for detection of the tdh and trh genes (12) is more rapid than conventional PCR assays but requires sophisticated and expensive equipment.A recently developed novel nucleic acid amplification method termed loop-mediated isothermal amplification (LAMP) (13) is a promising candidate for rapid and easy detection of the tdh and trh genes. A LAMP assay allows one-step detection of gene amplification by simple turbidity analysis and requires only a simple incubator, such as a heat block or a water bath providing a constant temperature. LAMP assays are faster, easier to perform, and more specific than conventional PCR assays (6, 7). Further, they synthesize a large amount of DNA and its by-product, an insoluble white precipitate of magnesium pyrophosphate, and the by-product can be detected by simple turbidity analysis. The increase in the turbidity of the reaction mixture due to the production of the white precipitate correlates with the amount of DNA synthesized (6, 7, 13). Thus, LAMP assays do not require expensive equipment and are highly precise (3, 18, 19).Here we describe a rapid and simple LAMP assay for detection of the tdh, trh1, and trh2 genes of V. parahaemolyticus. We also determined the sensitivity of this LAMP assay using spiked shrimp samples.     

Invasion assay of Listeria monocytogenes using Vero and Caco-2 cells

The invasion ability of Listeria monocytogenes into cultured cells has been used to evaluate its pathogenicity. In this study, invasive ability was investigated using Vero and Caco-2 cell lines. The form of invasion showed no morphological differences between both cell lines inoculated with L. monocytogenes L89-H2 or L96-23C1 strains when double fluorescence stained with rhodamine and FITC or with Giemsa staining. Recovery count and recovery rate of L. monocytogenes from Vero cells was related to the number of inoculated bacteria (2 x 10(5) to 2 x 10(7)/ml) in a bell-shape pattern, though the relationship was unclear in Caco-2 cells. Recovery rate of L. monocytogenes was higher in Vero cells than Caco-2 cells at a multiplicity of infection (MOI) 10, though the rates in both cells showed different stable stages over a considerably wide range of MOI. The recovery rate of all five L. monocytogenes strains from listeriosis patients was 15% at MOI 10 from infected Vero cells, while meat-derived strains showed variable rates regardless of the serovar. These results suggest that the Vero cell line is suitable for an invasion assay and that a recovery rate of 15% may be the critical limit for the expression of pathogenicity in the host.     

Fusion of Doppel to octapeptide repeat and N-terminal half of hydrophobic region of prion protein confers resistance to serum deprivation

Our previous studies have shown an essential role played by the octapeptide repeat region (OR) and the N-terminal half of hydrophobic region (HR) in the anti-apoptotic activity of prion protein (PrP). As PrP-like protein Doppel (Dpl), which structurally resembles an N-terminally truncated PrP, did not show any anti-apoptotic activity, we examined apoptosis of HpL3-4 cells expressing Dpl fused to various lengths of the N-terminal region of PrP to investigate whether the PrP/Dpl fusion proteins retain anti-apoptotic function. HpL3-4 cells expressing Dpl fused to PrP(1-124) with the OR and N-terminal half of HR of PrP showed anti-apoptotic function, whereas Dpl fused to PrP(1-95) with OR did not rescue cells from apoptotic cell death induced by serum deprivation. These results indicate that the OR and N-terminal half of HR of PrP retains anti-apoptotic activity similar to full-length PrP.     

Compatible invasion of a phylogenetically distant host embryo by a hymenopteran parasitoid embryo

Embryonic invasion into the tissue of genetically different organisms has been known only in mother-embryo interactions of viviparous organisms. Hence, embryonic invasions have been thought to occur only within the same or closely related species. For endoparasitic Hymenoptera, which are oviposited in their host egg but complete their development in the later stages, entry into the host embryo is essential. To date, the entry of these parasitoids is known to be accomplished by either egg deposition directly into the embryo or by the newly hatched larva boring into the embryo. However, Copidosoma floridanum is a polyembryonic parasitoid whose development is characterized by a prolonged embryonic stage, and which lacks a larval form during its host embryogenesis. We have analyzed the behavior and fate of C. floridanum embryos co-cultured with their host embryo in vitro. Here, we show that the morula-stage embryo of C. floridanum actively invades the host embryo. Histological analyses have demonstrated that C. floridanum embryonic invasion is associated with adherent junction to host cells rather than causing an obvious wound on the host cells. These findings provide a novel case of embryonic invasion into a phylogenetically distant host embryo, ensuring cellular compatibility with host tissues.     

Design and Synthesis of De Novo Peptide for Manganese Binding

The de novo peptide with 63-residues (MHB) has been synthesized biochemically and used for the binding of manganese (II) ions. In designed peptide, the leucine of the peptide dA1 (prototype) was replaced by His27 and Asp41 for binding the manganese (II) ions. The different chromatography studies and mass determination showed that new peptide folds into a monomeric, highly helical with a active site structure similar to the native Mn–SOD in an aqueous solution. Electron paramagnetic resonance (EPR) study suggested that the peptide binds single manganese (II) ion per molecule loosely with K _D value of about 36 μM. The circular dichroism (CD) studies demonstrated that the helical contents of the peptide did not change significantly even after binding the metal ions. The SOD activity study of the Mn–peptide complex showed that the IC₅₀ values is 8.08 μM.     

1.25 A resolution crystal structures of human haemoglobin in the oxy, deoxy and carbonmonoxy forms

The most recent refinement of the crystallographic structure of oxyhaemoglobin (oxyHb) was completed in 1983, and differences between this real-space refined model and later R state models have been interpreted as evidence of crystallisation artefacts, or numerous sub-states. We have refined models of deoxy, oxy and carbonmonoxy Hb to 1.25 A resolution each, and compare them with other Hb structures. It is shown that the older structures reflect the software used in refinement, and many differences with newer structures are unlikely to be physiologically relevant. The improved accuracy of our models clarifies the disagreement between NMR and X-ray studies of oxyHb, the NMR experiments suggesting a hydrogen bond to exist between the distal histidine and oxygen ligand of both the alpha and beta-subunits. The high-resolution crystal structure also reveals a hydrogen bond in both subunit types, but with subtly different geometry which may explain the very different behaviour when this residue is mutated to glycine in alpha or beta globin. We also propose a new set of relatively fixed residues to act as a frame of reference; this set contains a similar number of atoms to the well-known "BGH" frame yet shows a much smaller rmsd value between R and T state models of HbA.     

Molecular structure and function of bacterial nitric oxide reductase

The crystal structure of the membrane-integrated nitric oxide reductase cNOR from Pseudomonas aeruginosa was determined. The smaller NorC subunit of cNOR is comprised of 1 trans-membrane helix and a hydrophilic domain, where the heme c is located, while the larger NorB subunit consists of 12 trans-membrane helices, which contain heme b and the catalytically active binuclear center (heme b(3) and non-heme Fe(B)). The roles of the 5 well-conserved glutamates in NOR are discussed, based on the recently solved structure. Glu211 and Glu280 appear to play an important role in the catalytic reduction of NO at the binuclear center by functioning as a terminal proton donor, while Glu215 probably contributes to the electro-negative environment of the catalytic center. Glu135, a ligand for Ca(2+) sandwiched between two heme propionates from heme b and b(3), and the nearby Glu138 appears to function as a structural factor in maintaining a protein conformation that is suitable for electron-coupled proton transfer from the periplasmic region to the active site. On the basis of these observations, the possible molecular mechanism for the reduction of NO by cNOR is discussed. This article is part of a Special Issue entitled: Respiratory Oxidases.     

Structure and function of bacterial nitric oxide reductases: Nitric oxide reductase, anaerobic enzymes

The crystal structures of bacterial nitric oxide reductases (NOR) from Pseudomonas aeruginosa and Geobacillus stearothermophilus were reported. The structural characteristics of these enzymes, especially at the catalytic site and on the pathway that catalytic protons are delivered, are compared, and the corresponding regions of aerobic and micro-aerobic cytochrome oxidases, O(2) reducing enzymes, which are evolutionarily related to NOR are discussed. On the basis of these structural comparisons, a mechanism for the reduction of NO to produce N(2)O by NOR, and the possible molecular evolution of the proton pumping ability of the respiratory enzymes is discussed. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).