1,231 research outputs found
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<sub>α</sub>-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<sub>α</sub>-C<sub>β </sub>bond 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 HO<sub>2</sub>. The stabilities of alkylperoxy peptide radical and complex of alkylperoxy peptide radical with HO<sub>2 </sub>are 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
Size matters: a view of selenocysteine incorporation from the ribosome
This review focuses on the known factors required for selenocysteine (Sec) incorporation in eukaryotes and highlights recent findings that have compelled us to propose a new model for the mechanism of Sec incorporation. In light of this data we also review the controversial aspects of the previous modelspecifically regarding the proposed interaction between SBP2 and eEFSec. In addition, the relevance of two recently discovered factors in the recoding of Sec are reviewed. The role of the ribosome in this process is emphasized along with a detailed analysis of kinkturn structures present in the ribosome and the L7Ae RNA-binding motif present in SBP2 and other proteins
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
Identification of oxidation products and free radicals of tryptophan by mass spectrometry
Oxr1 Is Essential for Protection against Oxidative Stress-Induced Neurodegeneration
Oxidative stress is a common etiological feature of neurological disorders, although the pathways that govern defence against reactive oxygen species (ROS) in neurodegeneration remain unclear. We have identified the role of oxidation resistance 1 (Oxr1) as a vital protein that controls the sensitivity of neuronal cells to oxidative stress; mice lacking Oxr1 display cerebellar neurodegeneration, and neurons are less susceptible to exogenous stress when the gene is over-expressed. A conserved short isoform of Oxr1 is also sufficient to confer this neuroprotective property both in vitro and in vivo. In addition, biochemical assays indicate that Oxr1 itself is susceptible to cysteine-mediated oxidation. Finally we show up-regulation of Oxr1 in both human and pre-symptomatic mouse models of amyotrophic lateral sclerosis, indicating that Oxr1 is potentially a novel neuroprotective factor in neurodegenerative disease
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