Transcription factors in Escherichia coli prefer the holo conformation.
Transcription factors in Escherichia coli prefer the holo conformation.
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DOI：
10.1371/journal.pone.0065723
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Collado-Vides J
中科院分区：
文献类型：
--
作者：
Balderas-Martínez YI;Savageau M;Salgado H;Pérez-Rueda E;Morett E;Collado-Vides J
The transcriptional regulatory network of Escherichia coli K-12 is among the best studied gene networks of any living cell. Transcription factors bind to DNA either with their effector bound (holo conformation), or as a free protein (apo conformation) regulating transcription initiation. By using RegulonDB, the functional conformations (holo or apo) of transcription factors, and their mode of regulation (activator, repressor, or dual) were exhaustively analyzed. We report a striking discovery in the architecture of the regulatory network, finding a strong under-representation of the apo conformation (without allosteric metabolite) of transcription factors when binding to their DNA sites to activate transcription. This observation is supported at the level of individual regulatory interactions on promoters, even if we exclude the promoters regulated by global transcription factors, where three-quarters of the known promoters are regulated by a transcription factor in holo conformation. This genome-scale analysis enables us to ask what are the implications of these observations for the physiology and for our understanding of the ecology of E. coli. We discuss these ideas within the framework of the demand theory of gene regulation.
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影响因子：
14.9
作者：
Salgado H;Peralta-Gil M;Gama-Castro S;Santos-Zavaleta A;Muñiz-Rascado L;García-Sotelo JS;Weiss V;Solano-Lira H;Martínez-Flores I;Medina-Rivera A;Salgado-Osorio G;Alquicira-Hernández S;Alquicira-Hernández K;López-Fuentes A;Porrón-Sotelo L;Huerta AM;Bonavides-Martínez C;Balderas-Martínez YI;Pannier L;Olvera M;Labastida A;Jiménez-Jacinto V;Vega-Alvarado L;Del Moral-Chávez V;Hernández-Alvarez A;Morett E;Collado-Vides J
通讯作者：
Collado-Vides J
DOI：
10.1073/pnas.0808500106
发表时间：
2009-06-02
影响因子：
11.1
作者：
Gerland, Ulrich;Hwa, Terence
通讯作者：
Hwa, Terence
影响因子：
11.4
作者：
Merino, E;Yanofsky, C
通讯作者：
Yanofsky, C
影响因子：
12.3
作者：
Freyre-González JA;Alonso-Pavón JA;Treviño-Quintanilla LG;Collado-Vides J
通讯作者：
Collado-Vides J
DOI：
10.1089/omi.1.2000.5.205
发表时间：
2000-01-01
期刊：
Microbial and Comparative Genomics
影响因子：
--
作者：
Serres, Margrethe Hauge;Riley, Monica
通讯作者：
Riley, Monica