Oxygen activation by a mixed-valent, diiron(II/III) cluster in the glycol cleavage reaction catalyzed by myo-inositol oxygenase

myo-Inositol oxygenase (MIOX) catalyzes the ring-cleaving, four-electron oxidation of its cyclohexan-(1,2,3,4,5,6-hexa)-ol substrate (myo-inositol, MI) to d-glucuronate (DG). The preceding paper [Xing, G., Hoffart, L. M., Diao, Y., Prabhu, K. S., Arner, R. J., Reddy, C. C., Krebs, C., and Bollinger, J. M., Jr. (2006) Biochemistry 45, 5393-5401] demonstrates by M?ssbauer and electron paramagnetic resonance (EPR) spectroscopies that MIOX can contain a non-heme dinuclear iron cluster, which, in its mixed-valent (II/III) and fully oxidized (III/III) states, is perturbed by binding of MI in a manner consistent with direct coordination. In the study presented here, the redox form of the enzyme that activates O(2) has been identified. l-Cysteine, which was previously reported to accelerate turnover, reduces the fully oxidized enzyme to the mixed-valent form, and O(2), the cosubstrate, oxidizes the fully reduced form to the mixed-valent form with a stoichiometry of one per O(2). Both observations implicate the mixed-valent, diiron(II/III) form of the enzyme as the active state. Stopped-flow absorption and freeze-quench EPR data from the reaction of the substrate complex of mixed-valent MIOX [MIOX(II/III).MI] with limiting O(2) in the presence of excess, saturating MI reveal the following cycle: (1) MIOX(II/III).MI reacts rapidly with O(2) to generate an intermediate (H) with a rhombic, g < 2 EPR spectrum; (2) a form of the enzyme with the same absorption features as MIOX(II/III) develops as H decays, suggesting that turnover has occurred; and (3) the starting MIOX(II/III).MI complex is then quantitatively regenerated. This cycle is fast enough to account for the catalytic rate. The DG/O(2) stoichiometry in the reaction, 0.8 +/- 0.1, is similar to the theoretical value of 1, whereas significantly less product is formed in the corresponding reaction of the fully reduced enzyme with limiting O(2). The DG/O(2) yield in the latter reaction decreases as the enzyme concentration is increased, consistent with the hypothesis that initial conversion of the reduced enzyme to the MIOX(II/III).MI complex and subsequent turnover by the mixed-valent form is responsible for the product in this case. The use of the mixed-valent, diiron(II/III) cluster by MIOX represents a significant departure from the mechanisms of other known diiron oxygenases, which all involve activation of O(2) from the II/II manifold.     

Extensive misfolding in the refolding reaction of alkaline ferrocytochrome C

This work describes an extensively misfolded kinetic intermediate in the folding of horse ferrocytochrome c. Under absolute native conditions, the alkali-unfolded protein liganded with carbon-monoxide exhibits misfolding. The misfolded product, apparently an off-pathway intermediate, requires large-scale unfolding in order to have a chance to fold correctly to the native state. The rate of unfolding of the misfolded intermediate limits the overall rate of protein folding. The high level of observed misfolding possibly results from a failure of the polypeptide chain to achieve by stochastic search the transition state relevant for successful folding. Such misfolding may be analogous to the failure of a sizable set of proteins in the intracellular milieu to fold to the functionally active native state.     

The function and structural influence of selective relaxed constraint at functional intracellular loop3 of 5-HT(1A) serotonin-1 receptor family

Superoxide dismutases (SODs) are metalloenzymes that represent one important line of defense against reactive oxygen species (ROS). In this paper, two novel SOD genes, MdSOD1 and MdSOD2, which putatively encode 261 and 214 amino acid residues respectively were identified and characterized from the housefly Musca domestica. The high similarity of MdSOD1 and MdSOD2 with SODs from other organisms indicated that they should be two new members of the SOD family. qPCR exhibited a universal expression of MdSOD1 and MdSOD2 detected in various tissues of housefly larva, including the fat body, gut, hemocyte and epidermis. Expression profiling reveals that MdSOD1 and MdSOD2 can be induced significantly via not only heat shock and cadmium (Cd) stress but also Escherichia coli and Staphylococcus aureus challenge. The two genes were cloned into the prokaryotic expression vector pET-28a to obtain the fusion proteins rMdSOD1 and rMdSOD2. Between them, the activity of rMdSOD2 was found by visual assay methods. ESI-LC-MS/MS analysis showed that three peptide fragments of the protein rMdSOD2 were identical to the corresponding sequence of M. domestica MdSOD2. MdSOD1 and MdSOD2 in housefly larvae were abrogated by feeding bacteria expressing dsRNA. High mortalities were observed in the larvae treated with dsRNA of SODs at heat shock, Cd stress and bacterial invasion. This phenomenon indicated that MdSOD1 and MdSOD2 are related to the survival of M. domestica under stress. This may provide new insights into the role of the two SOD genes in protecting M. domestica against both stress and bacterial invasion.     

Insight into pattern of codon biasness and nucleotide base usage in serotonin receptor gene family from different mammalian species

5-HT (5-Hydroxy-tryptamine) or serotonin receptors are found both in central and peripheral nervous system as well as in non-neuronal tissues. In the animal and human nervous system, serotonin produces various functional effects through a variety of membrane bound receptors. In this study, we focus on 5-HT receptor family from different mammals and examined the factors that account for codon and nucleotide usage variation. A total of 110 homologous coding sequences from 11 different mammalian species were analyzed using relative synonymous codon usage (RSCU), correspondence analysis (COA) and hierarchical cluster analysis together with nucleotide base usage frequency of chemically similar amino acid codons. The mean effective number of codon (ENc) value of 37.06 for 5-HT(6) shows very high codon bias within the family and may be due to high selective translational efficiency. The COA and Spearman's rank correlation reveals that the nucleotide compositional mutation bias as the major factors influencing the codon usage in serotonin receptor genes. The hierarchical cluster analysis suggests that gene function is another dominant factor that affects the codon usage bias, while species is a minor factor. Nucleotide base usage was reported using Goldman, Engelman, Stietz (GES) scale reveals the presence of high uracil (>45%) content at functionally important hydrophobic regions. Our in silico approach will certainly help for further investigations on critical inference on evolution, structure, function and gene expression aspects of 5-HT receptors family which are potential antipsychotic drug targets.     

A 12-deoxywithastramonolide-rich somaclonal variant in Withania somnifera (L.) Dunal—molecular cytogenetic analysis and significance as a chemotypic resource

Withania somnifera, commonly known as ashwagandha or Indian ginseng, is a valuable medicinal plant, synthesizing a wide array of pharmacologically active secondary metabolites known as withanolides. In this study, we investigated variation among 54 regenerated plants attained through indirect organogenesis from leaf explants. Organogenic calli were induced on Murashige and Skoog medium containing 2?mg?l^?1 kinetin and 1?mg?l^?1 indole-3-butyric acid. High-performance liquid chromatography was used for quantitative determination of the major withanolides in the somaclones. One somaclone (WS-R-1) showed significantly higher accumulation of 12-deoxywithastramonolide (WS-12D; 0.516%) compared to the explant donor mother plant (0.002%). The incidence of somaclonal variation at the cytological level was investigated by studying mitosis and meiosis in relation to chromosome number and structural organization. There were no alterations in chromosome phenotypes, somatic chromosome count, or meiotic behavior. Fidelity at genomic level was evaluated by random amplification of polymorphic DNA (RAPD) analyses, which revealed multiple genetic polymorphisms between the WS-12D over-producing somaclone and the explant donor mother plant. This study demonstrates the capability of inducing chemotypic variability for the development of high-yielding clones due to molecular instability in W. somnifera using an in vitro approach.     

Identification, purification and characterization of laterosporulin, a novel bacteriocin produced by Brevibacillus sp. strain GI-9

Background

Bacteriocins are antimicrobial peptides that are produced by bacteria as a defense mechanism in complex environments. Identification and characterization of novel bacteriocins in novel strains of bacteria is one of the important fields in bacteriology.

Methodology/Findings

The strain GI-9 was identified as Brevibacillus sp. by 16 S rRNA gene sequence analysis. The bacteriocin produced by strain GI-9, namely, laterosporulin was purified from supernatant of the culture grown under optimal conditions using hydrophobic interaction chromatography and reverse-phase HPLC. The bacteriocin was active against a wide range of Gram-positive and Gram-negative bacteria. MALDI-TOF experiments determined the precise molecular mass of the peptide to be of 5.6 kDa and N-terminal sequencing of the thermo-stable peptide revealed low similarity with existing antimicrobial peptides. The putative open reading frame (ORF) encoding laterosporulin and its surrounding genomic region was fished out from the draft genome sequence of GI-9. Sequence analysis of the putative bacteriocin gene did not show significant similarity to any reported bacteriocin producing genes in database.

Conclusions

We have identified a bacteriocin producing strain GI-9, belonging to the genus Brevibacillus sp. Biochemical and genomic characterization of laterosporulin suggests it as a novel bacteriocin with broad spectrum antibacterial activity.     

NeMedPlant: a database of therapeutic applications and chemical constituents of medicinal plants from north-east region of India

The North-East region of India is one of the twelve mega biodiversity region, containing many rare and endangered species. A curated database of medicinal and aromatic plants from the regions called NeMedPlant is developed. The database contains traditional, scientific and medicinal information about plants and their active constituents, obtained from scholarly literature and local sources. The database is cross-linked with major biochemical databases and analytical tools. The integrated database provides resource for investigations into hitherto unexplored medicinal plants and serves to speed up the discovery of natural productsbased drugs. AVAILABILITY: The database is available for free at http://bif.uohyd.ac.in/nemedplant/orhttp://202.41.85.11/nemedplant/     

System modeling and identification in indicator dilution method for assessment of Ejection Fraction and Pulmonary Blood Volume

Clinically relevant cardiovascular parameters, such as pulmonary blood volume (PBV) and ejection fraction (EF), can be assessed through indicator dilution techniques. Among these techniques, which are typically invasive due to the need for central catheterization, contrast ultrasonography provides a new emerging minimally invasive option. PBV and EF are then measured by a dilution system identification algorithm after detection of multiple dilution curves by an ultrasound scanner. In this paper, dilution systems are represented by parametric models. Since the measured indicator dilution curves (IDCs) are corrupted by measurement artifacts and outliers, the use of conventional least square error (LSE) estimator for estimating system parameters is not optimal. Different estimators are therefore proposed for estimating the system parameters. Comparison of these estimators with the LSE estimator in assessing EF and PBV is performed on simulated, in vitro and patient data. The results show that the proposed total least absolute deviation estimator (TLAD) outperforms other estimators. The measured IDCs are highly corrupted by noise, which affect the estimation of EF and PBV. Therefore, a two stage denoising method capable of removing outliers is also proposed for removing noise in IDCs.