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Contents and Chemical Biology

Integrative Biology issue 1 contents pages

Shedding light on the efficacy of laboratory evolution based on iterative saturation mutagenesis

Assessment of the CFTR and ENaC association

Predicting protein evolution in vitro by phage escape technology

Metallo-complex activation of neuroprotective signalling pathways as a therapeutic treatment for Alzheimer’s disease

MAR elements regulate the probability of epigenetic switching between active and inactive gene expression

The use of cyan fluorescent protein variants with a distinctive lifetime signature

Transcript stability in the protein interaction network of Escherichia coli

Human cyt P450 mediated metabolic toxicity of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) evaluated using electrochemiluminescent arrays

A comparative evolutionary study of transcription networks. The global role of feedback and hierachical structures

Identification of metabolites in human hepatic bile using 800 MHz ¹H NMR spectroscopy, HPLC-NMR/MS and UPLC-MS

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Molecular BioSystems Vol -4

Molecular BioSystems Vol -3

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Transcript stability in the protein interaction network of Escherichia coli

Content Provider	Royal Society of Chemistry (RSC)
Author	Babu, M. Madan Janga, Sarath Chandra
Copyright Year	2009
Abstract	Gene expression is a dynamic process which can be controlled by a number of mechanisms as genetic information flows from nucleic acids to proteins. The study of gene expression in the steady state, while informative, overlooks the underlying dynamics of the processes. Steady-state transcript levels are a result of both RNA synthesis and degradation, and as such, measurements of degradation rates can be used to determine their rates of synthesis as well as reveal regulation that occurs via changes in RNA stability. Messenger RNA degradation plays a central role in diverse cellular processes and is controlled primarily by the activity of the degradosome in prokaryotes. In this study, we use the currently available network of protein–protein interactions (PPIs) and mRNA half-lives in Escherichia coli to demonstrate that centrality of a protein in the PPI network is strongly correlated with its mRNA half-life. We find that interacting proteins tend to show similar half-lives, commonly referred to as assortative behavior in networks, which is frequently found in biological and social networks. While a major fraction of the interacting proteins show significantly lower differences in mRNA stabilities, a smaller but significant number of protein pairs tend to show higher differences than expected by chance. Higher differences in transcript stabilities often involved those that encode for transcription factors and enzymes, suggesting a feedback link at the post-translational level. We also note that although essential genes, which act as a proxy for in vivo centrality in PPI networks, are highly expressed compared to non-essential ones, they do not encode for more stable transcripts than non-essential genes. Our results provide a direct link between mRNA stability and centrality of a protein in PPI network indicating the importance of post-transcriptional mechanisms on nascent RNAs in the cell.
Starting Page	154
Ending Page	162
Page Count	9
File Format	HTM / HTML PDF
ISSN	1742206X
Volume Number	5
Issue Number	2
Journal	Molecular BioSystems
DOI	10.1039/b816845h
Language	English
Publisher	Royal Society of Chemistry
Access Restriction	Open
Subject Keyword	Escherichia Messenger RNA Gene RNA Escherichia coli Half-life Gene expression Protein
Content Type	Text
Resource Type	Article
Subject	Molecular Biology Biotechnology

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Dual role of transcription and transcript stability in the regulation of gene expression in Escherichia coli cells cultured on glucose at different growth rates

Escherichia coli achieves faster growth by increasing catalytic and translation rates of proteins

Bacterial small RNA-based negative regulation: Hfq and its accomplices.

Optimizing Granulocyte Colony-Stimulating Factor Transcript for Enhanced Expression in Escherichia coli

Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation.

Posttranscriptional Regulation of tnaA by Protein-RNA Interaction Mediated by Ribosomal Protein L4 in Escherichia coli.

Towards inferring time dimensionality in protein–protein interaction networks by integrating structures: the p53 example

Coding-sequence determinants of gene expression in Escherichia coli.

Cloning and expression of human erythropoietin cDNA in Escherichia coli.

Transcript stability in the protein interaction network of Escherichia coli

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Dual role of transcription and transcript stability in the regulation of gene expression in Escherichia coli cells cultured on glucose at different growth rates

Escherichia coli achieves faster growth by increasing catalytic and translation rates of proteins

Bacterial small RNA-based negative regulation: Hfq and its accomplices.

Optimizing Granulocyte Colony-Stimulating Factor Transcript for Enhanced Expression in Escherichia coli

Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation.

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Coding-sequence determinants of gene expression in Escherichia coli.

Cloning and expression of human erythropoietin cDNA in Escherichia coli.

Transcript stability in the protein interaction network of Escherichia coli