A study of the biosynthesis of phenazine-1-carboxylic acid

Washed cell preparations of Pseudomonas aureofaciens synthesize phenazine-1-carboxylic acid in a medium consisting of 0.2 M glycerol and 0.02 M-lysine. Experiments with C14-labeled substrates indicate that all of the carbon atoms in the phenazine-1-carboxylic acid are derived from glycerol. Anthranilic acid inhibits synthesis of this phenazine compound. Incorporation of label from H3-shikimic acid has been demonstrated. In addition, a decrease in the incorporation of label from glycerol-1,3-C14 into phenazine-1-carboxylic acid has been demonstrated in the presence of unlabeled shikimic acid.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/32163/1/0000218.pd

The Dynamics of Zeroth-Order Ultrasensitivity: A Critical Phenomenon in Cell Biology

It is well known since the pioneering work of Goldbeter and Koshland [Proc. Natl. Acad. Sci. USA, vol. 78, pp. 6840-6844 (1981)] that cellular phosphorylation- dephosphorylation cycle (PdPC), catalyzed by kinase and phosphatase under saturated condition with zeroth order enzyme kinetics, exhibits ultrasensitivity, sharp transition. We analyse the dynamics aspects of the zeroth order PdPC kinetics and show a critical slowdown akin to the phase transition in condensed matter physics. We demonstrate that an extremely simple, though somewhat mathematically "singular" model is a faithful representation of the ultrasentivity phenomenon. The simplified mathematical model will be valuable, as a component, in developing complex cellular signaling network theory as well as having a pedagogic value.Comment: 8 pages, 3 figure

Law of Genome Evolution Direction : Coding Information Quantity Grows

The problem of the directionality of genome evolution is studied. Based on the analysis of C-value paradox and the evolution of genome size we propose that the function-coding information quantity of a genome always grows in the course of evolution through sequence duplication, expansion of code, and gene transfer from outside. The function-coding information quantity of a genome consists of two parts, p-coding information quantity which encodes functional protein and n-coding information quantity which encodes other functional elements except amino acid sequence. The evidences on the evolutionary law about the function-coding information quantity are listed. The needs of function is the motive force for the expansion of coding information quantity and the information quantity expansion is the way to make functional innovation and extension for a species. So, the increase of coding information quantity of a genome is a measure of the acquired new function and it determines the directionality of genome evolution.Comment: 16 page

Oxygen radical-mediated oxidation reactions of an alanine peptide motif - density functional theory and transition state theory study

<p>Abstract</p> <p>Background</p> <p>Oxygen-base (O-base) oxidation in protein backbone is important in the protein backbone fragmentation due to the attack from reactive oxygen species (ROS). In this study, an alanine peptide was used model system to investigate this O-base oxidation by employing density functional theory (DFT) calculations combining with continuum solvent model. Detailed reaction steps were analyzed along with their reaction rate constants.</p> <p>Results</p> <p>Most of the O-base oxidation reactions for this alanine peptide are exothermic except for the bond-breakage of the C_α-N bond to form hydroperoxy alanine radical. Among the reactions investigated in this study, the activated energy of OH α-H abstraction is the lowest one, while the generation of alkylperoxy peptide radical must overcome the highest energy barrier. The aqueous situation facilitates the oxidation reactions to generate hydroxyl alanine peptide derivatives except for the fragmentations of alkoxyl alanine peptide radical. The C_α-C_βbond of the alkoxyl alanine peptide radical is more labile than the peptide bond.</p> <p>Conclusion</p> <p>the rate-determining step of oxidation in protein backbone is the generation of hydroperoxy peptide radical via the reaction of alkylperoxy peptide radical with HO₂. The stabilities of alkylperoxy peptide radical and complex of alkylperoxy peptide radical with HO₂are crucial in this O-base oxidation reaction.</p

Diversity of Protein and mRNA Forms of Mammalian Methionine Sulfoxide Reductase B1 Due to Intronization and Protein Processing

Background: Methionine sulfoxide reductases (Msrs) are repair enzymes that protect proteins from oxidative stress by catalyzing stereospecific reduction of oxidized methionine residues. MsrB1 is a selenocysteine-containing cytosolic/nuclear Msr with high expression in liver and kidney. Principal Findings: Here, we identified differences in MsrB1 gene structure among mammals. Human MsrB1 gene consists of four, whereas the corresponding mouse gene of five exons, due to occurrence of an additional intron that flanks the stop signal and covers a large part of the 3′-UTR. This intron evolved in a subset of rodents through intronization of exonic sequences, whereas the human gene structure represents the ancestral form. In mice, both splice forms were detected in liver, kidney, brain and heart with the five-exon form being the major form. We found that both mRNA forms were translated and supported efficient selenocysteine insertion into MsrB1. In addition, MsrB1 occurs in two protein forms that migrate as 14 and 5 kDa proteins. We found that each mRNA splice form generated both protein forms. The abundance of the 5 kDa form was not influenced by protease inhibitors, replacement of selenocysteine in the active site or mutation of amino acids in the cleavage site. However, mutation of cysteines that coordinate a structural zinc decreased the levels of 5 and 14 kDa forms, suggesting importance of protein structure for biosynthesis and/stability of these forms. Conclusions: This study characterized unexpected diversity of protein and mRNA forms of mammalian selenoprotein MsrB1

Unexpected expression of carbonic anhydrase I and selenium‐binding protein as the only major non‐heme proteins in erythrocytes of the subterranean mole rat (Spalax ehrenbergi)

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/117190/1/feb2s0014579398006905.pd

Antioxidant defence of colostrum and milk in consecutive lactations in sows

<p>Abstract</p> <p>Background</p> <p>Parturition is supposed to be related to oxidative stress, not only for the mother, but also for the newborn. Moreover, it is not clear whether consecutive pregnancies, parturitions, and lactations are similar to each other in regards to intensity of metabolic processes or differ from each other. The aim of the study was to compare dynamic changes of antioxidative parameters in colostrum and milk of sows taken during 72 h postpartum from animals in consecutive lactations. Activities of glutathione peroxidase (GSH-Px), glutathione transferase (GSH-Tr), and superoxide dismutase (SOD), and amount of vitamin A and C were measured. Healthy pregnant animals were divided into 4 groups according to the assessed lactation: A -1^stlactation (n = 10), B - 2^ndand 3^rdlactation (n = 7), C - 4^thand 5^thlactation (n = 11), D - 6^th- 8^thlactation (n = 8). The colostrum was sampled immediately after parturition and after 6, 12, 18 and 36 h while the milk was assessed at 72 h after parturition. Spectrophotometric methods were used for measurements.</p> <p>Results</p> <p>The activity of antioxidative enzymes and the concentration of vitamin A increased with time postpartum. The concentration of vitamin C was the highest between the 18th and 36th h postpartum.</p> <p>Conclusions</p> <p>Dynamic changes in the values of antioxidant parameters measured during the study showed that sows milk provides the highest concentration of antioxidants in the 2^ndand 3^rdand 4^thand 5^thlactation giving the best defence against reactive oxygen species to newborns and mammary glands.</p

Molecular and Structural Discrimination of Proline Racemase and Hydroxyproline-2-Epimerase from Nosocomial and Bacterial Pathogens

The first eukaryotic proline racemase (PRAC), isolated from the human Trypanosoma cruzi pathogen, is a validated therapeutic target against Chagas' disease. This essential enzyme is implicated in parasite life cycle and infectivity and its ability to trigger host B-cell nonspecific hypergammaglobulinemia contributes to parasite evasion and persistence. Using previously identified PRAC signatures and data mining we present the identification and characterization of a novel PRAC and five hydroxyproline epimerases (HyPRE) from pathogenic bacteria. Single-mutation of key HyPRE catalytic cysteine abrogates enzymatic activity supporting the presence of two reaction centers per homodimer. Furthermore, evidences are provided that Brucella abortus PrpA [for ‘proline racemase’ virulence factor A] and homologous proteins from two Brucella spp are bona fide HyPREs and not ‘one way’ directional PRACs as described elsewhere. Although the mechanisms of aminoacid racemization and epimerization are conserved between PRAC and HyPRE, our studies demonstrate that substrate accessibility and specificity partly rely on contraints imposed by aromatic or aliphatic residues distinctively belonging to the catalytic pockets. Analysis of PRAC and HyPRE sequences along with reaction center structural data disclose additional valuable elements for in silico discrimination of the enzymes. Furthermore, similarly to PRAC, the lymphocyte mitogenicity displayed by HyPREs is discussed in the context of bacterial metabolism and pathogenesis. Considering tissue specificity and tropism of infectious pathogens, it would not be surprising if upon infection PRAC and HyPRE play important roles in the regulation of the intracellular and extracellular amino acid pool profiting the microrganism with precursors and enzymatic pathways of the host

Microbial transformations of selenite by methane-oxidizing bacteria

Abstract Methane oxidizing bacteria are well known for their role in the global methane cycle and their potential for microbial transformation of wide range of hydrocarbon and chlorinated hydrocarbon pollution. Recently, it has also emerged that methane-oxidizing bacteria interact with inorganic pollutants in the environment. Here we report what we believe to be the first study of the interaction of pure strains of methane-oxidizing bacteria with selenite. Results indicate that the commonly used laboratory model strains of methane oxidizing bacteria, Methylococcus capsulatus (Bath) and Methylosinus trichosporium OB3b are both able to reduce the toxic selenite (SeO32-) but not selenate (SeO42-) to red spherical nanoparticulate elemental selenium (Se0), which was characterised via EDX and EXAFS. The cultures also produced volatile selenium-containing species, which suggests that both strains may have an additional activity that can either transform Se0 or selenite into volatile methylated forms of selenium. Transmission electron microscopy (TEM) measurements and experiments with the cell fractions: cytoplasm, cell wall and cell membrane show that the nanoparticles are formed mainly on the cell wall. Collectively these results are promising for the use of methane-oxidizing bacteria for bioremediation or suggest possible uses in the production of selenium nanoparticles for biotechnology