Article

The Escherichia coli thioredoxin homolog YbbN/Trxsc is a chaperone and a weak protein oxidoreductase.

Stress Molecules, Institut Jacques Monod, Université Paris 7, 2 place Jussieu, 75005 Paris, France.
Biochemical and Biophysical Research Communications (impact factor: 2.48). 06/2006; 343(3):780-6. DOI:10.1016/j.bbrc.2006.03.028 pp.780-6
Source: PubMed

ABSTRACT Escherichia coli contains two thioredoxins, Trx1 and Trx2, and a thioredoxin-like protein, YbbN, which presents a strong homology in its N-terminal part with thioredoxin 1 and 2. YbbN, however, does not possess the canonical Cys-x-x-Cys active site of thioredoxins, but instead a Ser-x-x-Cys site. In addition to Cys-38, located in the SxxC site, it contains a second cysteine, Cys-63, close to Cys-38 in the 3D model. Cys-38 and Cys-63 undergo an oxidoreduction process, suggesting that YbbN functions with two redox cysteines. Accordingly, YbbN catalyzes the oxidation of reduced RNase and the isomerization of scrambled RNase. Moreover, upon oxidation, its oligomeric state changes from dimers to tetramers and higher oligomers. YbbN also possesses chaperone properties, promoting protein folding after urea denaturation and forming complexes with unfolded proteins. This is the first biochemical characterization of a member of the YbbN class of bacterial thioredoxin-like proteins, and in vivo experiments will allow to determine the importance of its redox and chaperone properties in the cellular physiology.

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    Article: Interactive visualization of clusters in microarray data: an efficient tool for improved metabolic analysis of E. coli
    Theresa Scharl, Florentina Potschacher, Gerald Striedner, Karl Bayer, Friedrich Leisch
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    ABSTRACT: Background Interpretation of comprehensive DNA microarray data sets is a challenging task for biologists and process engineers where scientific assistance of statistics and bioinformatics is essential. Interdisciplinary cooperation and concerted development of software-tools for simplified and accelerated data analysis and interpretation is the key to overcome the bottleneck in data-analysis workflows. This approach is exemplified by gcExplorer an interactive visualization toolbox based on cluster analysis. Clustering is an important tool in gene expression data analysis to find groups of co-expressed genes which can finally suggest functional pathways and interactions between genes. The visualization of gene clusters gives practitioners an understanding of the cluster structure of their data and makes it easier to interpret the cluster results. Results In this study the interactive visualization toolbox gcExplorer is applied to the interpretation of E. coli microarray data. The data sets derive from two fedbatch experiments conducted in order to investigate the impact of different induction strategies on the host metabolism and product yield. The software enables direct graphical comparison of these two experiments. The identification of potentially interesting gene candidates or functional groups is substantially accelerated and eased. Conclusion It was shown that gcExplorer is a very helpful tool to gain a general overview of microarray experiments. Interesting gene expression patterns can easily be found, compared among different experiments and combined with information about gene function from publicly available databases.
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Keywords

3D model
 
bacterial thioredoxin-like proteins
 
canonical Cys-x-x-Cys active site
 
cellular physiology
 
Escherichia coli
 
first biochemical characterization
 
N-terminal part
 
oligomeric state changes
 
oxidation
 
redox cysteines
 
RNase
 
second cysteine
 
strong homology
 
thioredoxin 1
 
thioredoxin-like protein
 
thioredoxins
 
Trx1
 
urea denaturation
 
YbbN class
 
YbbN functions