Transcript stability in the protein interaction network of Escherichia coli.
Transcript stability in the protein interaction network of Escherichia coli.
复制标题
大肠杆菌蛋白质相互作用网络中的转录稳定性。
DOI：
10.1039/b816845h
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发表时间：
2009
影响因子：
--
通讯作者：
M. M. Babu
中科院分区：
文献类型：
--
作者：
S. Janga;M. M. Babu
基因表达是一个动态的过程，当遗传信息从核酸流向蛋白质时，可以由许多机制控制。对稳定状态下的基因表达的研究，虽然提供了信息，但忽略了过程的潜在动态。稳定状态的转录水平是RNA合成和降解的结果，因此，降解速率的测量可以用来确定它们的合成速率，并揭示通过RNA稳定性的变化而发生的调节。信使RNA的降解在多种细胞过程中起着核心作用，主要受原核生物中降解体的活性控制。在这项研究中，我们使用目前可用的蛋白质-蛋白质相互作用网络(PPI)和大肠杆菌中的mRNA半衰期来证明蛋白质在PPI网络中的中心性与其mRNA半衰期密切相关。我们发现相互作用的蛋白质往往呈现类似的半衰期，通常被称为网络中的分类行为，这在生物和社会网络中经常存在。虽然大部分相互作用的蛋白质在mRNA稳定性上表现出显著的差异，但少数但数量可观的蛋白质对往往比预期的表现出更高的差异。转录稳定性的较高差异通常与转录因子和酶的编码有关，这表明在翻译后水平上存在反馈联系。我们还注意到，尽管在PPI网络中作为体内中心性代理的必需基因比非必需基因高表达，但它们并不比非必需基因编码更稳定的转录本。我们的结果提供了PPI网络中蛋白质的信使核糖核酸稳定性和中心性之间的直接联系，表明了细胞中新生RNA的转录后机制的重要性。
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.
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影响因子：
7
作者：
Jordan, IK;Rogozin, IB;Koonin, EV
通讯作者：
Koonin, EV
影响因子：
5.6
作者：
McDowall, KJ;Cohen, SN
通讯作者：
Cohen, SN
影响因子：
14.9
作者：
Zuo, YH;Deutscher, MP
通讯作者：
Deutscher, MP
DOI：
10.1073/pnas.0308747101
发表时间：
2004-03-02
影响因子：
11.1
作者：
Bernstein, JA;Lin, PH;Lin-Chao, S
通讯作者：
Lin-Chao, S