Analysis of <Emphasis Type="Italic">Escherichia coli</Emphasis> nicotinate mononucleotide adenylyltransferase mutants <Emphasis Type="Italic">in vivo</Emphasis> and <Emphasis Type="Italic">in vitro</Emphasis>

Background  

Adenylation of nicotinate mononucleotide to nicotinate adenine dinucleotide is the penultimate step in NAD⁺ synthesis. In Escherichia coli, the enzyme nicotinate mononucleotide adenylyltransferase is encoded by the nadD gene. We have earlier made an initial characterization in vivo of two mutant enzymes, NadD72 and NadD74. Strains with either mutation have decreased intracellular levels of NAD⁺, especially for one of the alleles, nadD72.     

Biochemical characterization of the maltokinase from <Emphasis Type="Italic">Mycobacterium bovis</Emphasis> BCG

Background  

Maltose-1-phosphate was detected in Mycobacterium bovis BCG extracts in the 1960's but a maltose-1-phosphate synthetase (maltokinase, Mak) was only much later purified from Actinoplanes missouriensis, allowing the identification of the mak gene. Recently, this metabolite was proposed to be the intermediate in a pathway linking trehalose with the synthesis of glycogen in M. smegmatis. Although the M. tuberculosis H37Rv mak gene (Rv0127) was considered essential for growth, no mycobacterial Mak has, to date, been characterized.     

The yeast <Emphasis Type="Italic">ISN1</Emphasis> (<Emphasis Type="Italic">YOR155c</Emphasis>) gene encodes a new type of IMP-specific 5'-nucleotidase

Background  

The purine salvage enzyme inosine 5'-monophosphate (IMP)-specific 5'-nucleotidase catalyzes degradation of IMP to inosine. Although this enzymatic activity has been purified and characterized in Saccharomyces cerevisiae, the gene encoding IMP 5'-nucleotidase had not been identified.     

Thermochemical study on ternary complex of dysprosium <Emphasis Type="Italic">m</Emphasis>-nitrobenzoic acid with <Emphasis Type="Italic">o</Emphasis>-phenanthroline

A ternary binuclear complex of dysprosium chloride hexahydrate with m-nitrobenzoic acid and 1,10-phenanthroline, [Dy(m-NBA)₃phen]₂·4H₂O (m-NBA: m-nitrobenzoate; phen: 1,10-phenanthroline) was synthesized. The dissolution enthalpies of [2phen·H₂O(s)], [6m-HNBA(s)], [2DyCl₃·6H₂O(s)], and [Dy(m-NBA)₃phen]₂·4H₂O(s) in the calorimetric solvent (V_DMSO:V_MeOH = 3:2) were determined by the solution–reaction isoperibol calorimeter at 298.15 K to be \Updelta_\texts H_\textm^q \Updelta_{\text{s}} H_{\text{m}}^{\theta } [2phen·H₂O(s), 298.15 K] = 21.7367 ± 0.3150 kJ·mol⁻¹, \Updelta_\texts H_\textm^q \Updelta_{\text{s}} H_{\text{m}}^{\theta } [6m-HNBA(s), 298.15 K] = 15.3635 ± 0.2235 kJ·mol⁻¹, \Updelta_\texts H_\textm^q \Updelta_{\text{s}} H_{\text{m}}^{\theta } [2DyCl₃·6H₂O(s), 298.15 K] = −203.5331 ± 0.2200 kJ·mol⁻¹, and \Updelta_\texts H_\textm^q \Updelta_{\text{s}} H_{\text{m}}^{\theta } [[Dy(m-NBA)₃phen]₂·4H₂O(s), 298.15 K] = 53.5965 ± 0.2367 kJ·mol⁻¹, respectively. The enthalpy change of the reaction was determined to be \Updelta_\textr H_\textm^q = 3 6 9. 4 9 ±0. 5 6   \textkJ·\textmol ^{- 1} . \Updelta_{\text{r}} H_{\text{m}}^{\theta } = 3 6 9. 4 9 \pm 0. 5 6 \;{\text{kJ}}\cdot {\text{mol}}^{ - 1} . According to the above results and the relevant data in the literature, through Hess’ law, the standard molar enthalpy of formation of [Dy(m-NBA)₃phen]₂·4H₂O(s) was estimated to be \Updelta_\textf H_\textm^q \Updelta_{\text{f}} H_{\text{m}}^{\theta } [[Dy(m-NBA)₃phen]₂·4H₂O(s), 298.15 K] = −5525 ± 6 kJ·mol⁻¹.     

DNA biosensors for the detection of aflatoxin producing <Emphasis Type="Italic">Aspergillus flavus</Emphasis> and <Emphasis Type="Italic">A. parasiticus</Emphasis>

Abstract  In this work, we report on the development of a DNA-based piezoelectric biosensor specific for the detection of an amplicon of the aflD gene of Aspergillus flavus and A. parasiticus. Expression of this gene is consistently correlated with a strain’s ability to produce aflatoxins that are considered very potent liver carcinogens in various animal species and humans. The DNA biosensor has been characterized with synthetic oligonucleotides and amplicons. Moreover, it has been applied to the analysis of real samples consisting of amplicons of DNA extracted from flours and feed contaminated with A. flavus and A. parasiticus. Graphical Abstract        

Volatile profiling reveals intracellular metabolic changes in <Emphasis Type="Italic">Aspergillus parasiticus</Emphasis>: <Emphasis Type="Italic">veA</Emphasis> regulates branched chain amino acid and ethanol metabolism

Background  

Filamentous fungi in the genus Aspergillus produce a variety of natural products, including aflatoxin, the most potent naturally occurring carcinogen known. Aflatoxin biosynthesis, one of the most highly characterized secondary metabolic pathways, offers a model system to study secondary metabolism in eukaryotes. To control or customize biosynthesis of natural products we must understand how secondary metabolism integrates into the overall cellular metabolic network. By applying a metabolomics approach we analyzed volatile compounds synthesized by Aspergillus parasiticus in an attempt to define the association of secondary metabolism with other metabolic and cellular processes.     

4<Emphasis Type="Italic">p</Emphasis><Superscript>2</Superscript> resonances in photoionization from 4<Emphasis Type="Italic">s</Emphasis>4<Emphasis Type="Italic">p</Emphasis> levels in neutral zinc

In neutral zinc the 4p ² configuration lies above the 3d ¹⁰4s ionization limit and its levels become perturbers in the continuum. Lines have been identified in the Zn I spectrum for the multiplet, whereas no lines have been found for transitions to 4p ^{2 1} D or ¹ S. In this paper, cross sections for photoionization from 4s4p levels are reported that reveal the positions and widths of the 4p ² resonances. Calculations were performed using the multiconfiguration Hartree-Fock (MCHF) and B-spline R-matrix (BSR) method. Results from Breit–Pauli calculations that ignore the background continua are also presented. Included in the latter are energies for the levels and transition data (transition energies, line strengths, f-values, and A-rates) for all E1 transitions between these levels. Transition energies and the agreement in the length and velocity values, particularly for allowed transitions, indicate the accuracy of the computational model. Line widths are compared with other estimates. Contribution to the Serafin Fraga Memorial Issue.     

Functional redundancy between <Emphasis Type="Italic">trans</Emphasis>-Golgi network SNARE family members in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

Background

Vesicle fusion is an essential process for maintaining the structure and function of the endomembrane system. Fusion is mediated by t-SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) fusion proteins on the target membrane and v-SNAREs on the vesicle membrane; v-and t-SNAREs interact with each other, driving vesicle fusion with the target membrane. The Arabidopsis thaliana trans-Golgi network resident SNAREs SYP41 and VTI12, along with YKT61/62, have been shown to function in vesicle fusion in vitro, consistent with immunoprecipitation results showing their interaction in Arabidopsis cell extracts. Conflicting published results have indicated that SYP4 family members are either functionally redundant or have distinct and essential functions; the reason for this discrepancy is unclear.

Results

Here we used a proteoliposome fusion assay to demonstrate that SYP42 and SYP43 can substitute for SYP41 in driving lipid mixing, providing support for functional overlap between family members. Previous reports have also suggested that VTI11 and VTI12 SNAREs show partial overlap in function, despite having mostly distinct localizations and binding partners. We show that VTI11 can substitute for VTI12 in in vitro lipid mixing reactions, providing molecular support for the genetic evidence for partial functional redundancy in vivo.

Conclusions

Our data provide biochemical evidence for functional overlap in membrane fusion between members of the SYP4 or VTI1 SNARE groups, supporting previous genetic data suggesting redundancy.

     

Molecular characterization of <Emphasis Type="Italic">tlyA</Emphasis> gene product,Rv1694 of <Emphasis Type="Italic">Mycobacterium tuberculosis</Emphasis>: A non-conventional hemolysin and a ribosomal RNA methyl transferase

Background  

Mycobacterium tuberculosis is a virulent bacillus causing tuberculosis, a disease responsible for million deaths each year worldwide. In order to understand its mechanism of pathogenesis in humans and to help control tuberculosis, functions of numerous Mycobacterium tuberculosis genes are being characterized. In this study we report the dual functionality of tlyA gene product of Mycobacterium tuberculosis annotated as Rv1694, a 268 amino acid long basic protein.     

<Emphasis Type="Italic">CrMAPK3</Emphasis> regulates the expression of iron-deficiency-responsive genes in <Emphasis Type="Italic">Chlamydomonas reinhardtii</Emphasis>

Background

Under iron-deficient conditions, Chlamydomonas exhibits high affinity for iron absorption. Nevertheless, the response, transmission, and regulation of downstream gene expression in algae cells have not to be investigated. Considering that the MAPK pathway is essential for abiotic stress responses, we determined whether this pathway is involved in iron deficiency signal transduction in Chlamydomonas.

Results

Arabidopsis MAPK gene sequences were used as entry data to search for homologous genes in Chlamydomonas reinhardtii genome database to investigate the functions of mitogen-activated protein kinase (MAPK) gene family in C. reinhardtii under iron-free conditions. Results revealed 16 C. reinhardtii MAPK genes labeled CrMAPK2–CrMAPK17 with TXY conserved domains and low homology to MAPK in yeast, Arabidopsis, and humans. The expression levels of these genes were then analyzed through qRT-PCR and exposure to high salt (150 mM NaCl), low nitrogen, or iron-free conditions. The expression levels of these genes were also subjected to adverse stress conditions. The mRNA levels of CrMAPK2, CrMAPK3, CrMAPK4, CrMAPK5, CrMAPK6, CrMAPK8, CrMAPK9, and CrMAPK11 were remarkably upregulated under iron-deficient stress. The increase in CrMAPK3 expression was 43-fold greater than that in the control. An RNA interference vector was constructed and transformed into C. reinhardtii 2A38, an algal strain with an exogenous FOX1:ARS chimeric gene, to silence CrMAPK3. After this gene was silenced, the mRNA levels and ARS activities of FOX1:ARS chimeric gene and endogenous CrFOX1 were decreased. The mRNA levels of iron-responsive genes, such as CrNRAMP2, CrATX1, CrFTR1, and CrFEA1, were also remarkably reduced.

Conclusion

CrMAPK3 regulates the expression of iron-deficiency-responsive genes in C. reinhardtii.

     

Interactions between co-expressed <Emphasis Type="Italic">Arabidopsis</Emphasis> sucrose transporters in the split-ubiquitin system

Background  

The Arabidopsis genome contains nine sucrose transporter paralogs falling into three clades: SUT1-like, SUT2 and SUT4. The carriers differ in their kinetic properties. Many transport proteins are known to exist as oligomers. The yeast-based split ubiquitin system can be used to analyze the ability of membrane proteins to interact.     

High Level Expression of an Acid-Stable Phytase from <Emphasis Type="Italic">Citrobacter freundii</Emphasis> in <Emphasis Type="Italic">Pichia pastoris</Emphasis>

To obtain a high level expression of phytase with favorable characteristics, a codon-optimized phytase gene from Citrobacter freundii was synthesized and transferred into Pichia pastoris. Small-scale expression experiments and activity assays were used to screen positive colonies. After purified by Ni²⁺–NTA agarose affinity column, the characterizations of the recombinant phytase were determined. The recombinant phytase (r-phyC) had two distinct pH optima at 2.5 and 4.5 and an optimal temperature at 50 °C. It retained more than 80% activity after being incubated under various buffer (pH 1.5–8.0) at 37 °C for 1 h. The specific activity, Km, and Vmax values of r-phyC for sodium phytate were 2,072 ± 18 U mg⁻¹, 0.52 ± 0.04 mM, and 2,380 ± 84 U mg⁻¹ min⁻¹, respectively. The enzyme activity was significantly improved by 1 mM of K⁺, Ca²⁺, and Mg²⁺. These characteristics contribute to its potential application in feed industry.     

A new ten-membered lactone from <Emphasis Type="Italic">Tubercularia</Emphasis> sp<Emphasis Type="Italic">.</Emphasis> TF5, an endophytic fungus of <Emphasis Type="Italic">Taxus mairei</Emphasis>

One new ten-membered lactone (1) named (Z)-4,6,9-trihydroxy-10-nonyl-3,4,5,6,9,10-hexahydrooxecin-2-one along with 5-methoxycarbonylmellein (2) and cytochalasin D (3) were isolated from the culture of the endophytic fungus strain Tubercularia sp. TF5, originally separated from the inner bark of Taxus mairei obtained in Fujian Province, Southeast China. The structures of compounds 1–3 were elucidated by spectroscopic methods. The antimicrobial and cytotoxic activities of 1 were analyzed but it showed no significant activities.     

Expression of a <Emphasis Type="Italic">hemA</Emphasis> Gene from <Emphasis Type="Italic">Agrobacterium radiobacter</Emphasis> in a Rare Codon Optimizing <Emphasis Type="Italic">Escherichia coli</Emphasis> for Improving 5-aminolevulinate Production

The 5-aminolevulinate (ALA) synthase gene (hemA) from Agrobacterium radiobacter zju-0121, which was cloned previously in our laboratory, contains several rare codons. To enhance the expression of this gene, Escherichia coli Rosetta(DE3), which is a rare codon optimizer strain, was picked out as the host to construct an efficient recombinant strain. Cell extracts of the recombinant E. coli were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis under the appropriate conditions. The results indicated that the activity of ALA synthase expressed in Rosetta(DE3)/pET-28a(+)-hemA was about 20% higher than that in E. coli BL21(DE3). Then the effects of precursors (glycine and succinate) and glucose, which is an inhibitor for ALA dehydratase as well as the carbon sources for cell growth, on the production of 5-aminolevulinate were investigated. Based on an optimal fed-batch culture system described in our previous work, up to 6.5 g/l (50 mM) ALA was produced in a 15-l fermenter.     

Heat capacities and thermodynamic properties of (<Emphasis Type="Italic">S</Emphasis>)-<Emphasis Type="Italic">tert</Emphasis>-butyl 1-phenylethylcarbamate

An N-tert-butyloxycarbonylated organic synthesis intermediate, (S)-tert-butyl 1-phenylethylcarbamate, was prepared and investigated by means of differential scanning calorimetry (DSC) and thermogravimetry (TG). The molar heat capacities of (S)-tert-butyl 1-phenylethylcarbamate were precisely determined by means of adiabatic calorimetry over the temperature range of 80-380 K. There was a solid–liquid phase transition exhibited during the heating process with the melting point of 359.53 K. The molar enthalpy and entropy of this transition were determined to be 29.73 kJ mol⁻¹ and 82.68 J K⁻¹ mol⁻¹ based on the experimental C _p–T curve, respectively. The thermodynamic functions, [H_T⁰ - H_298.15⁰ H_{T}^{0} - H_{298.15}^{0} ] and [S_T⁰ - S_298.15⁰ S_{T}^{0} - S_{298.15}^{0} ], were calculated from the heat capacity data in the temperature range of 80–380 K with an interval of 5 K. TG experiment showed that the pyrolysis of the compound was started at the temperature of 385 K and terminated at 510 K within one step.     

<Emphasis Type="Italic">N</Emphasis>-allyl and <Emphasis Type="Italic">N</Emphasis>-propargyl trifluoromethanesulfonimides. Theoretical analysis

Tautomers of N-allyl- and N-propargyl-substituted trifluoromethanesulfonimides (CF₃SO₂)₂NR (R = CH₂CH=CH₂, Z/E-CH=CHMe, CH₂C≡CH, CH=CH=CH₂, C≡CCH₂) were calculated by the DFT (B3LYP, wB97XD, PBE1PBE), MP2, and CBS-QB3 methods. The results were compared with the theoretical data for the corresponding amines and amides NHRR¹ (R¹ = H, CF₃SO₂). It was shown that there is no conjugation between the nitrogen atom and C=C bond and that conjugation exists with the C≡C bond with electron density displacement toward the nitrogen atom. The calculations of anions derived from N-allyl- and N-propargyl-trifluoromethanesulfonimides revealed the possibility of their rearrangement with elimination of trifluoromethanesulfinate anion and formation of its H-complex with N-(prop-2-en-1-ylidene)trifluoromethanesulfonamide or N-(prop-2-yn-1-ylidene)trifluoromethanesulfonamide.     

Self-assembly of tris(2-ureidobenzyl)amines with <Emphasis Type="Italic">C</Emphasis><Subscript>1</Subscript> symmetry

Abstract  

Tris(2-ureidobenzyl)amines bearing three differentially substituted arms have been synthesized. They possess an asymmetric nitrogen atom, the pivotal one, and thus they feature C ₁ symmetry. The self-assembly of these C ₁-symmetric tris(2-ureidobenzyl)amines may potentially lead to multiple regio- and diastereoisomeric capsules coming from the pairing of the four stereoisomeric monomers with configurations (R, P), (S, P), (R, M) and (S, M). The ¹H- and ¹⁹F{¹H}-NMR spectra confirm the presence of dimeric aggregates, as a mixture of several regio- and diastereoisomeric species.     

Delineation of the <Emphasis Type="Italic">Pasteurellaceae</Emphasis>-specific GbpA-family of glutathione-binding proteins

Background

The Gram-negative bacterium Haemophilus influenzae is a glutathione auxotroph and acquires the redox-active tripeptide by import. The dedicated glutathione transporter belongs to the ATP-binding cassette (ABC)-transporter superfamily and displays more than 60% overall sequence identity with the well-studied dipeptide (Dpp) permease of Escherichia coli. The solute binding protein (SBP) that mediates glutathione transport in H. influenzae is a lipoprotein termed GbpA and is 54% identical to E. coli DppA, a well-studied member of family 5 SBP's. The discovery linking GbpA to glutathione import came rather unexpectedly as this import-priming SBP was previously annotated as a heme-binding protein (HbpA), and was thought to mediate heme acquisition. Nonetheless, although many SBP's have been implicated in more than one function, a prominent physiological role for GbpA and its partner permease in heme acquisition appears to be very unlikely. Here, we sought to characterize five representative GbpA homologs in an effort to delineate the novel GbpA-family of glutathione-specific family 5 SBPs and to further clarify their functional role in terms of ligand preferences.

Results

Lipoprotein and non-lipoprotein GbpA homologs were expressed in soluble form and substrate specificity was evaluated via a number of ligand binding assays. A physiologically insignificant affinity for hemin was observed for all five GbpA homologous test proteins. Three out of five test proteins were found to bind glutathione and some of its physiologically relevant derivatives with low- or submicromolar affinity. None of the tested SBP family 5 allocrites interacted with the remaining two GbpA test proteins. Structure-based sequence alignments and phylogenetic analysis show that the two binding-inert GbpA homologs clearly form a separate phylogenetic cluster. To elucidate a structure-function rationale for this phylogenetic differentiation, we determined the crystal structure of one of the GbpA family outliers from H. parasuis. Comparisons thereof with the previously determined structure of GbpA in complex with oxidized glutathione reveals the structural basis for the lack of allocrite binding capacity, thereby explaining the outlier behavior.

Conclusions

Taken together, our studies provide for the first time a collective functional look on a novel, Pasteurellaceae-specific, SBP subfamily of glutathione binding proteins, which we now term GbpA proteins. Our studies strongly implicate GbpA family SBPs in the priming step of ABC-transporter-mediated translocation of useful forms of glutathione across the inner membrane, and rule out a general role for GbpA proteins in heme acquisition.

     

Immunoaffinity purification and characterization of mitochondrial membrane-bound D-3-hydroxybutyrate dehydrogenase from <Emphasis Type="Italic">Jaculus orientalis</Emphasis>

Background  

The interconversion of two important energy metabolites, 3-hydroxybutyrate and acetoacetate (the major ketone bodies), is catalyzed by D-3-hydroxybutyrate dehydrogenase (BDH¹: EC 1.1.1.30), a NAD⁺-dependent enzyme. The eukaryotic enzyme is bound to the mitochondrial inner membrane and harbors a unique lecithin-dependent activity. Here, we report an advanced purification method of the mammalian BDH applied to the liver enzyme from jerboa (Jaculus orientalis), a hibernating rodent adapted to extreme diet and environmental conditions.