Chemoselectivity issues of the asymmetric interaction between cyclohexanone, β-nitrostyrene,and benzoic acid under 5-aryl prolinate's organocatalysis

4-l -menthyloxycarbonyl 5-aryl prolinates were studied as organocatalysts of a novel three-component reaction of cyclohexanone, benzoic acid, and β-nitrostyrene. The presence of ortho-halogen atom in 5-aryl fragment of the catalyst is favored for driving the formation of chiral 7a-hydroxyoctahydro-2H-indol-2-one scaffold. 5-(o-Chlorophenyl) prolinate selectively afforded 3-phenyl-7a-hydroxyoctahydro-2H-indol-2-one with ee 63%, whereas 5-phenyl prolinate led to conjugation of β-nitrostyrene to cyclohexanone (the Michael adduct). Plausible chlorine effect is accounted for the specific interaction of the 5-aryl prolinate enamine intermediate with β-nitrostyrene in the transition state.     

Correlation between the optimal growth pressures of four Shewanella species and the stabilities of their cytochromes c 5

Shewanella species live widely in deep-sea and shallow-water areas, and thus grow piezophilically and piezosensitively. Piezophilic and psychrophilic Shewanella benthica cytochrome c ₅ (SB cytc ₅) was the most stable against guanidine hydrochloride (GdnHCl) and thermal denaturation, followed by less piezophilic but still psychrophilic Shewanella violacea cytochrome c ₅ (SV cytc ₅). These two were followed, as to stability level, by piezosensitive and mesophilic Shewanella amazonensis cytochrome c ₅ (SA cytc ₅), and piezosensitive and psychrophilic Shewanella livingstonensis cytochrome c ₅ (SL cytc ₅). The midpoint GdnHCl concentrations of SB cytc ₅, SV cytc ₅, SL cytc ₅, and SA cytc ₅ correlated with the optimal growth pressures of the species, the correlation coefficient value being 0.93. A similar trend was observed for thermal denaturation. Therefore, the stability of each cytochrome c ₅ is related directly to its host’s optimal growth pressure. Phylogenetic analysis indicated that Lys-37, Ala-41, and Leu-50 conserved in piezosensitive SL cytc ₅ and SA cytc ₅ are ancestors of the corresponding residues in piezophilic SB cytc ₅ and SV cytc ₅, Gln, Thr, and Lys, respectively, which might have been introduced during evolution on adaption to environmental pressure. The monomeric Shewanella cytochromes c ₅ are suitable tools for examining protein stability with regard to the optimal growth pressures of the source species.     

Overexpression of GASA5 increases the sensitivity of Arabidopsis to heat stress

Basal thermotolerance is very important for plant growth and development when plants are subjected to heat stress. However, little is known about the functional mechanism of gibberellins (GAs) in the basal thermotolerance of plants. In the present work, we provide molecular evidence that a member of the gene family encoding the GA-stimulated Arabidopsis (GASA) peptides, namely GASA5, is involved in the regulation of seedling thermotolerance. The GASA5-overexpressing plants displayed a weak thermotolerance, with a faster cotyledon-yellowing rate, lower seedling-survival rate, and slower hypocotyl elongation, in comparison to the wild-type and GASA5 null-mutant (gasa5-1) plants, after heat-stress treatment. The short-hypocotyl phenotype of GASA5-overexpressing plants could be rescued by the exogenous application of salicylic acid (SA), the hormone found to protect plants from heat stress-induced damage. GASA5 expression was inhibited by heat stress but unaffected by the application of exogenous SA. However, expression of the gene encoding the noexpresser of PR genes 1 (NPR1), a key component of the SA-signaling pathway, was downregulated by GASA5 overexpression. Importantly, when different GASA5-genotype plants were treated with heat stress, several genes encoding heat-shock proteins, including HSP101, HSP70B, HSP90.1, HSP17.6-C1, and HSP60, were inhibited by GASA5 overexpression. Meanwhile, hydrogen peroxide was accumulated at high levels in heat stress-treated GASA5-overexpressing plants. These results suggest that the Arabidopsis GASA5 gene acts as a negative regulator in thermotolerance by regulating both SA signaling and heat shock-protein accumulation.     

Transcription of a zebrafish gene of the hairy-Enhancer of split family delineates the midbrain anlage in the neural plate

her5 encodes a basic helix-loop-helix (bHLH) protein with all features characteristic of the Drosophila hairy-E(spl) family. her5 is expressed in a band of cells within the neural anlage from about 90% epiboly on to at least 36 h postfertilization (hpf). After completion of brain morphogenesis, her5-expressing cells are located in the caudal region of the midbrain, at the boundary with the rhombencephalon. Labelling of cells within the her5 expression domain in the neural plate by injection of fluorescein-dextran allows their labelled progeny to be localized in the 36-hpf-old embryo using an anti-fluorescein antibody. This shows that the her5 expression domain corresponds to the midbrain primordium, including both the tectum and the tegmentum, in the neural plate. A possible function for her5 in regionalization of the brain and/or control of the midbrain-hindbrain boundary is discussed.     

Stereochemistry of the reaction catalyzed by mevaldate reductase

3RS-[5-D₁]Mevalonate was prepared by the reduction of RS-mevaldate with [4R-4-D₁]NADH and mevaldate reductase and was resolved enzymically into the 3R- and 3S-isomers. Spectropolarimetric measurements gave nearly mirror-image optical rotatory dispersion curves with a minimum and maximum at 240 nm and a negative and positive Cotton effect, λ₀ being at 227 nm, for the 3R- and 3S-lactone, respectively. Since the H-atoms at C-5 of mevalonolactone form a virtual ABX₂ system in nmr, the chemical shifts of the equatorial and axial H-atoms being at δ 4.33 and 4.58, respectively, it was possible to show by nmr that the two [5-D₁]-lactones were diastereoisomers, both having the 5R absolute configuration. This conclusion was confirmed by the finding that speciments of 3-methyl[5-D₁]pent-2-eno-5-lactone made by the dehydration of 3S-[5-D₁]mevalonolactone and of 3RS-[5-D₁]mevalonolactone had identical optical activities and of the same sign. The implications of the observations and a correlation between the stereochemistry of the reactions catalyzed by mevaldate reductase and 3-hydroxy-3-methylglutaryl-CoA reductase are discussed.     

Study of the Individual Cytochrome b5 and Cytochrome b5 Reductase Domains of Ncb5or Reveals a Unique Heme Pocket and a Possible Role of the CS Domain

NADH cytochrome b₅ oxidoreductase (Ncb5or) is found in animals and contains three domains similar to cytochrome b₅ (b₅), CHORD-SGT1 (CS), and cytochrome b₅ reductase (b₅R). Ncb5or has an important function, as suggested by the diabetes and lipoatrophy phenotypes in Ncb5or null mice. To elucidate the structural and functional properties of human Ncb5or, we generated its individual b₅ and b₅R domains (Ncb5or-b₅ and Ncb5or-b₅R, respectively) and compared them with human microsomal b₅ (Cyb5A) and b₅R (Cyb5R3). A 1.25 Å x-ray crystal structure of Ncb5or-b₅ reveals nearly orthogonal planes of the imidazolyl rings of heme-ligating residues His⁸⁹ and His¹¹², consistent with a highly anisotropic low spin EPR spectrum. Ncb5or is the first member of the cytochrome b₅ family shown to have such a heme environment. Like other b₅ family members, Ncb5or-b₅ has two helix-loop-helix motifs surrounding heme. However, Ncb5or-b₅ differs from Cyb5A with respect to location of the second heme ligand (His¹¹²) and of polypeptide conformation in its vicinity. Electron transfer from Ncb5or-b₅R to Ncb5or-b₅ is much less efficient than from Cyb5R3 to Cyb5A, possibly as a consequence of weaker electrostatic interactions. The CS linkage probably obviates the need for strong interactions between b₅ and b₅R domains in Ncb5or. Studies with a construct combining the Ncb5or CS and b₅R domains suggest that the CS domain facilitates docking of the b₅ and b₅R domains. Trp¹¹⁴ is an invariant surface residue in all known Ncb5or orthologs but appears not to contribute to electron transfer from the b₅R domain to the b₅ domain.     

Recombination in the Vicinity of Insertions of Transposon Tn 5 in MYXOCOCCUS XANTHUS

To test genetic recombination in the vicinity of insertions of the transposon Tn5, crosses were performed by transduction between M. xanthus strains carrying different insertions of Tn5. One member of each pair carried resistance to kanamycin (Tn5-Km); the other carried resistance to tetracycline (Tn5-Tc). The distance between each pair of Tn5 insertions was also measured by restriction mapping. The physical distance corresponding to each recombination frequency was calculated from the transductional linkage and compared with distance on the restriction map. A good correspondence between the two measures of distance was obtained for a pair of Tn5 insertions near the cglB locus and for another pair near the mgl locus. Correspondence between the two measurements of distance, the observed allelic behavior of Tn5-Km and Tn5 -Tc at the same locus and the finding of the same frequencies of recombinants in reciprocal crosses implied that recombination in the vicinity of Tn 5 was normal.     

Determination of three different pools of reduced one-carbon-substituted folates: I. A study of the fundamental chemical reactions

The reduced one-carbon-substituted derivatives of folic acid can be grouped in three pools according to their response to acid treatment. Pool 1 is made up of N⁵,N¹⁰-methylene-tetrahydrofolic acid and unsubstituted dihydro- and tetrahydrofolic acid which at pH 1.0 and subsequent exposure to air cleave to p-aminobenzoylglutamic acid. Pool 2 is made up by the acid-stable N⁵-methyl-tetrahydrofolic acid, and pool 3 includes N⁵,N¹⁰-methenyl-tetrahydrofolic acid, N¹⁰-formyltetrahydrofolic acid, N⁵-formyltetrahydrofolic acid, and N⁵-formiminotetrahydrofolic acid, all of which convert to the stable N⁵,N¹⁰-methenyl-tetrahydro form when acid treated. Conditions are described to selectively cleave the C⁹-N¹⁰ bond of the folates of pool 1, pools 1 + 2, and pools 1 + 2 + 3. The cleaved pools are quantitated as the Bratton-Marshall azo dyes of p-aminobenzoylglutamate. The uncleaved pools are converted to Bratton-Marshall-negative products. Pool 1 is determined by converting pool 2 to 4a-hydroxy-5-methyltetrahydrofolic acid and pool 3 to N¹⁰-formylfolic acid, both Bratton-Marshall negative, by 10% hydrogen peroxide oxidation at pH 6.0. Pools 1 + 2 are cleaved with 0.015% hydrogen peroxide and 0.1% potassium permanganate at pH 9.0 which convert the N⁵-methyltetrahydrofolic acid to the acid-cleavable N⁵-methyl-dihydrofolic acid. Pool 3 oxidizes to the Bratton-Marshall-negative N¹⁰-formylfolic acid. Pools 1 + 2 + 3 are cleaved by first reducing pool 3 to N⁵-methyltetrahydrofolic acid with sodium borohydride followed by oxidation at pH 9.0 to its acid-labile dihydro form. Determination of the poly-γ-glutamyl chain length of each pool is possible by chromatographing the azo-p-aminobenzoylpolyglutamates with authentic synthetic markers.     

Interactions between membrane-bound cellulose synthases involved in the synthesis of the secondary cell wall

It has not yet been reported how the secondary CESA (cellulose synthase) proteins are organized in the rosette structure. A membrane-based yeast two-hybrid (MbYTH) approach was used to analyze the interactions between the CESA proteins involved in secondary cell wall synthesis of Arabidopsis and the findings were confirmed in planta by bimolecular fluorescence complementation (BiFC) assay. Results indicated that although all CESA proteins can interact with each other, only CESA4 is able to form homodimers. A model is proposed for the secondary rosette structure. The RING-motif proved not to be essential for the interaction between the CESA proteins.

Structured summary

MINT-6951243: PIP2-1 (uniprotkb:P43286) physically interacts (MI:0218) with PIP2-1 (uniprotkb:P43286) by bimolecular fluorescence complementation (MI:0809)MINT-6950816: CESA4 (uniprotkb:Q84JA6) physically interacts (MI:0218) withCESA4 (uniprotkb:Q84JA6) by membrane bound complementation assay (MI:0230)MINT-6951056, MINT-6951071, MINT-6951088, MINT-6951103: CESA7 (uniprotkb:Q9SWW6) physically interacts (MI:0218) with CESA4 (uniprotkb:Q84JA6) by bimolecular fluorescence complementation (MI:0809)MINT-6950949, MINT-6950990: CESA4 (uniprotkb:Q84JA6) physically interacts (MI:0218) with CESA8 (uniprotkb:Q8LPK5) by membrane bound complementation assay (MI:0230)MINT-6950909, MINT-6951030: CESA4 (uniprotkb:Q8LPK5) physically interacts (MI:0218) with CESA7 (uniprotkb:Q9SWW6) by membrane bound complementation assay (MI:0230)MINT-6951042: CESA4 (uniprotkb:Q84JA6) physically interacts (MI:0218) with CESA4 (uniprotkb:Q84JA6) by bimolecular fluorescence complementation (MI:0809)MINT-6951004, MINT-6951016: CESA8 (uniprotkb:Q8LPK5) physically interacts (MI:0218) with CESA7 (uniprotkb:Q9SWW6) by membrane bound complementation assay (MI:0230)MINT-6951217, MINT-6951230: CESA4 (uniprotkb:Q84JA6) physically interacts (MI:0218) with CESA8 (uniprotkb:Q8LPK5) by bimolecular fluorescence complementation (MI:0809)MINT-6951120, MINT-6951140, MINT-6951156, MINT-6951170, MINT-6951185: CESA8 (uniprotkb:Q8LPK5) physically interacts (MI:0218) withCESA7 (uniprotkb:Q9SWW6) by bimolecular fluorescence complementation (MI:0809)MINT-6951199: CESA8 (uniprotkb:Q8LPK5) physically interacts (MI:0218) withCESA8 (uniprotkb:Q8LPK5) by bimolecular fluorescence complementation (MI:0809)     

Localization of the ultraviolet-sensor Opn5m and its effect on myopia-related gene expression in the late-embryonic chick eye

Recent studies show that exposure to ultraviolet (UV) light suppresses ocular elongation, which causes myopia development. However, the specific mechanisms of this process have not been elucidated. A UV-sensor, Opsin 5 (Opn5) mRNA was shown to be present in extraretinal tissues. To test the possibility that UV-signals mediated by Opn5 would have a direct effect on the outer connective tissues of the eye, we first examined the expression patterns of a mammalian type Opn5 (Opn5m) in the late-embryonic chicken eye. Quantitative PCR showed Opn5m mRNA expression in the cornea and sclera. The anti-Opn5m antibody stained a small subset of cells in the corneal stroma and fibrous sclera. We next assessed the effect of UV-A (375 nm) irradiation on the chicken fibroblast cell line DF-1 overexpressing chicken Opn5m. UV-A irradiation for 30 min significantly increased the expression of Early growth response 1 (Egr1), known as an immediate early responsive gene, and of Matrix metalloproteinase 2 (Mmp2) in the presence of retinal chromophore 11-cis-retinal. In contrast, expression of Transforming growth factor beta 2 and Tissue inhibitor of metalloproteinase 2 was not significantly altered. These results indicate that UV-A absorption by Opn5m can upregulate the expression levels of Egr1 and Mmp2 in non-neuronal, fibroblasts. Taken together with the presence of Opn5m in the cornea and sclera, it is suggested that UV-A signaling mediated by Opn5 in the extraretinal ocular tissues could influence directly the outer connective tissues of the chicken late-embryonic eye.     

On the Modularity of the Intrinsic Flexibility of the μ Opioid Receptor: A Computational Study

The µ opioid receptor (µOR), the principal target to control pain, belongs to the G protein-coupled receptors (GPCRs) family, one of the most highlighted protein families due to their importance as therapeutic targets. The conformational flexibility of GPCRs is one of their essential characteristics as they take part in ligand recognition and subsequent activation or inactivation mechanisms. It is assessed that the intrinsic mechanical properties of the µOR, more specifically its particular flexibility behavior, would facilitate the accomplishment of specific biological functions, at least in their first steps, even in the absence of a ligand or any chemical species usually present in its biological environment. The study of the mechanical properties of the µOR would thus bring some indications regarding the highly efficient ability of the µOR to transduce cellular message. We therefore investigate the intrinsic flexibility of the µOR in its apo-form using all-atom Molecular Dynamics simulations at the sub-microsecond time scale. We particularly consider the µOR embedded in a simplified membrane model without specific ions, particular lipids, such as cholesterol moieties, or any other chemical species that could affect the flexibility of the µOR. Our analyses highlighted an important local effect due to the various bendability of the helices resulting in a diversity of shape and volume sizes adopted by the µOR binding site. Such property explains why the µOR can interact with ligands presenting highly diverse structural geometry. By investigating the topology of the µOR binding site, a conformational global effect is depicted: the correlation between the motional modes of the extra- and intracellular parts of µOR on one hand, along with a clear rigidity of the central µOR domain on the other hand. Our results show how the modularity of the µOR flexibility is related to its pre-ability to activate and to present a basal activity.     

Protein-protein interactions in the systems of cytochromes P450 3A4 and 3A5

Molecular interactions between protein partners of the monooxygenase system involved in drug biotransformation (cytochromes P450 3A4, 3A5 and cytochrome b ₅) have been investigated. Human cytochromes P450 3A4 and 3A5 (CYP3A4 and CYP3A5) form complexes with various forms of cytochrome b ₅, including microsomal (b ₅ mc) and mitochondrial (b ₅ om) forms of this protein, as well as two chimeric constructs (b ₅(om-mc),(b ₅(mc-om). Interestingly, significant differences were observed only during interactions with b ₅ om. Electroanalytical characteristics of electrodes with immobilized hemoproteins have been determined for CYP3A4, CYP3A5, b ₅ mc, b ₅ om, b ₅ mc(om-mc), and b ₅ mc(mc-om). The electrochemical analysis revealed that these proteins are characterized by close reduction potentials ranged from ?0.435 V to ?0.350 V (vs. Ag/AgCl). Cytochrome b ₅ mc stimulated the electrocatalytic activity of CYP3A4.     

Methylation of the DFNA5 increases risk of lymph node metastasis in human breast cancer

The pathogenesis of breast cancer involves multiple genetic and epigenetic events. In this study, we report an epigenetic alteration of DFNA5 in human breast cancer. DFNA5 gene was silenced in breast cancer cell lines that were methylated in the DFNA5 promoter, and restored by treatment with the demethylating agent, 5-aza-dC, and gene knock-down of DFNA5 increased cellular invasiveness in vitro. The mRNA expression of DFNA5 in breast cancer tissues was down-regulated as compared to normal tissues. Moreover, the DFNA5 promoter was found to be methylated in primary tumor tissues with high frequency (53%, 18/34). Quantitative methylation-specific PCR of DFNA5 clearly discriminated primary breast cancer tissues from normal breast tissues (15.3%, 2/13). Moreover, methylation status of DFNA5 was correlated with lymph node metastasis in breast cancer patients. Our data implicate DFNA5 promoter methylation as a novel molecular biomarker in human breast cancer.     

Improvement and application of a promoter-probe vector bearing the PHO5 gene as the indicator marker in Saccharomyces cerevisiae

A promoter-probe plasmid vector, pVC701, in Saccharomyces cerevisiae having the repressible acid phosphatase (rAPase; EC 3.1.3.2) gene, PHO5, of S. cerevisiae as the selection marker (Hwang et al., Appl. Microbiol. Biotechnol., 28, 155–159, 1988) was improved by inserting multiple cloning sites in the 5′ non-transcribed region of PHO5 and by replacing a 93-bp sequence containing three ATG sequences out of the frame but directly flanked by the translation initiation codon ATG with a 5′-CACC-3′ sequence. The resulting YCp type plasmid, pVC727, is replicable in both S. cerevisiae and Escherichia coli hosts. The function of the vector was confirmed by inserting a DNA fragment bearing a promoter region of the GAP gene encoding glyceraldehyde-3-phosphate dehydrogenase of S. cerevisiae at the cloning site. Using the vector, we could analyse the cis-acting upstream regulatory region of the HIS5 gene of S. cerevisiae and also isolate Gcd⁻ (general control derepressed) mutants occurring in the trans-acting loci of the general amino acid control.     

Proofreading exonuclease on a tether: the complex between the E. coli DNA polymerase III subunits α, ε, θ and β reveals a highly flexible arrangement of the proofreading domain

A complex of the three (αεθ) core subunits and the β₂ sliding clamp is responsible for DNA synthesis by Pol III, the Escherichia coli chromosomal DNA replicase. The 1.7 Å crystal structure of a complex between the PHP domain of α (polymerase) and the C-terminal segment of ε (proofreading exonuclease) subunits shows that ε is attached to α at a site far from the polymerase active site. Both α and ε contain clamp-binding motifs (CBMs) that interact simultaneously with β₂ in the polymerization mode of DNA replication by Pol III. Strengthening of both CBMs enables isolation of stable αεθ:β₂ complexes. Nuclear magnetic resonance experiments with reconstituted αεθ:β₂ demonstrate retention of high mobility of a segment of 22 residues in the linker that connects the exonuclease domain of ε with its α-binding segment. In spite of this, small-angle X-ray scattering data show that the isolated complex with strengthened CBMs has a compact, but still flexible, structure. Photo-crosslinking with p-benzoyl-L-phenylalanine incorporated at different sites in the α-PHP domain confirm the conformational variability of the tether. Structural models of the αεθ:β₂ replicase complex with primer-template DNA combine all available structural data.