Genomic SELEX Screening of Regulatory Targets of Escherichia coli Transcription Factors

Author(s):  
Tomohiro Shimada ◽  
Hiroshi Ogasawara ◽  
Akira Ishihama
2015 ◽  
Vol 58 ◽  
pp. 93-103 ◽  
Author(s):  
Ernesto Pérez-Rueda ◽  
Silvia Tenorio-Salgado ◽  
Alejandro Huerta-Saquero ◽  
Yalbi I. Balderas-Martínez ◽  
Gabriel Moreno-Hagelsieb

2019 ◽  
Vol 161 ◽  
pp. 70-77
Author(s):  
Tatiana A. Bessonova ◽  
Natalia V. Lekontseva ◽  
Uliana S. Shvyreva ◽  
Alexey D. Nikulin ◽  
Maria N. Tutukina ◽  
...  

FEBS Journal ◽  
2020 ◽  
Vol 287 (21) ◽  
pp. 4767-4782
Author(s):  
Ashok Kumar Madikonda ◽  
Akbarpasha Shaikh ◽  
Sonali Khanra ◽  
Harshita Yakkala ◽  
Sailu Yellaboina ◽  
...  

2012 ◽  
Vol 194 (18) ◽  
pp. 4867-4875 ◽  
Author(s):  
Lon M. Chubiz ◽  
George D. Glekas ◽  
Christopher V. Rao

ABSTRACTBacteria possess multiple mechanisms to survive exposure to various chemical stresses and antimicrobial compounds. In the enteric bacteriumEscherichia coli, three homologous transcription factors—MarA, SoxS, and Rob—play a central role in coordinating this response. Three separate systems are known to regulate the expression and activities of MarA, SoxS, and Rob. However, a number of studies have shown that the three do not function in isolation but rather are coregulated through transcriptional cross talk. In this work, we systematically investigated the extent of transcriptional cross talk in themar-sox-robregulon. While the three transcription factors were found to have the potential to regulate each other's expression when ectopically expressed, the only significant interactions observed under physiological conditions were betweenmarandrobsystems. MarA, SoxS, and Rob all activate themarRABpromoter, more so when they are induced by their respective inducers: salicylate, paraquat, and decanoate. None of the three proteins affects thesoxSpromoter, though unexpectedly, it was mildly repressed by decanoate by an unknown mechanism. SoxS is the only one of the three proteins to repress therobpromoter. Surprisingly, salicylate somewhat activates transcription ofrob, while decanoate represses it a bit. Rob, in turn, activates not only its downstream promoters in response to salicylate but also themarRABpromoter. These results demonstrate that themarandrobsystems function together in response to salicylate.


2007 ◽  
Vol 189 (18) ◽  
pp. 6655-6664 ◽  
Author(s):  
Sang Kyun Ahn ◽  
Kapil Tahlan ◽  
Zhou Yu ◽  
Justin Nodwell

ABSTRACT The SCO7222 protein and ActR are two of ∼150 TetR-like transcription factors encoded in the Streptomyces coelicolor genome. Using bioluminescence as a readout, we have developed Escherichia coli-based biosensors that accurately report the regulatory activity of these proteins and used it to investigate their interactions with DNA and small-molecule ligands. We found that the SCO7222 protein and ActR repress the expression of their putative target genes, SCO7223 and actII-ORF2 (actA), respectively, by interacting with operator sequence in the promoters. The operators recognized by the two proteins are related such that O 7223 (an operator for SCO7223) could be bound by both the SCO7222 protein and ActR with similar affinities. In contrast, Oact (an operator for actII-ORF2) was bound tightly by ActR and more weakly by the SCO7222 protein. We demonstrated ligand specificity of these proteins by showing that while TetR (but not ActR or the SCO7222 protein) interacts with tetracyclines, ActR (but not TetR or the SCO7222 protein) interacts with actinorhodin and related molecules. Through operator-targeted mutagenesis, we found that at least two nucleotide changes in O 7223 were required to disrupt its interaction with SCO7222 protein, while ActR was more sensitive to changes on Oact . Most importantly, we found that the interaction of each protein with wild-type and mutant operator sequences in vivo and in vitro correlated perfectly. Our data suggest that E. coli-based biosensors of this type should be broadly applicable to TetR-like transcription factors.


2007 ◽  
Vol 189 (6) ◽  
pp. 2359-2368 ◽  
Author(s):  
Yusuke Terui ◽  
Kyohei Higashi ◽  
Shiho Taniguchi ◽  
Ai Shigemasa ◽  
Kazuhiro Nishimura ◽  
...  

ABSTRACT Proteins whose synthesis is enhanced by polyamines at the level of translation were identified in a polyamine-requiring mutant cultured in the presence of 0.1% glucose and 0.02% glutamate instead of 0.4% glucose as an energy source. Under these conditions, enhancement of cell growth by polyamines was almost the same as that in the presence of 0.4% glucose. It was found that synthesis of RpoN, Cra, and H-NS was enhanced by polyamines at the level of translation at the early logarithmic phase of growth (A 540 of 0.15). The effects of polyamines on synthesis of RpoN, H-NS, and Cra were due to the existence of unusual Shine-Dalgarno sequences (RpoN and H-NS) and an inefficient GUG initiation codon (Cra) in their mRNAs. Thus, rpoN, cra, and hns genes were identified as new members of the polyamine modulon. Because most of the polyamine modulon genes thus far identified encode transcription factors (RpoS [σ38], Cya, FecI [σ18], Fis, RpoN [σ54], Cra, and H-NS), DNA microarray analysis of mRNA expressed in cells was performed. At the early logarithmic phase of growth, a total of 97 species of mRNAs that were up-regulated by polyamines more than twofold were under the control of seven polyamine modulon genes mentioned above.


2014 ◽  
Vol 12 (02) ◽  
pp. 1441006 ◽  
Author(s):  
Yuri A. Purtov ◽  
Olga A. Glazunova ◽  
Sergey S. Antipov ◽  
Viktoria O. Pokusaeva ◽  
Eugeny E. Fesenko ◽  
...  

Seventy-eight promoter islands with an extraordinarily high density of potential promoters have been recently found in the genome of Escherichia coli. It has been shown that RNA polymerase binds internal promoters of these islands and produces short oligonucleotides, while the synthesis of normal mRNAs is suppressed. This quenching may be biologically relevant, as most islands are associated with foreign genes, which expression may deplete cellular resources. However, a molecular mechanism of silencing with the participation of these promoter-rich regions remains obscure. It has been demonstrated that all islands interact with histone-like protein H-NS — a specific sentinel of foreign genes. In this study, we demonstrated the inhibitory effect of H-NS using Δhns mutant of Escherichia coli and showed that deletion of dps, encoding another protein of bacterial nucleoid, tended to decrease rather than increase the amount of island-specific transcripts. This observation precluded consideration of promoter islands as sites for targeted heterochromatization only and a computer search for the binding sites of 53 transcription factors (TFs) revealed six proteins, which may specifically regulate their transcriptional output.


2005 ◽  
Vol 187 (9) ◽  
pp. 3282-3286 ◽  
Author(s):  
Alice Boulanger ◽  
Anne Francez-Charlot ◽  
Annie Conter ◽  
Marie-Pierre Castanié-Cornet ◽  
Kaymeuang Cam ◽  
...  

ABSTRACT Transcription of the Escherichia coli osmB gene is induced by several stress conditions. osmB is expressed from two promoters, osmBp1 and osmBp2. The downstream promoter, osmBp2, is induced after osmotic shock or upon entry into stationary phase in a σS-dependent manner. The upstream promoter, osmBp1, is independent of σS and is activated by RcsB, the response regulator of the His-Asp phosphorelay signal transduction system RcsCDB. RcsB is responsible for the induction of osmBp1 following treatment with chlorpromazine. Activation of osmBp1 by RcsB requires a sequence upstream of its −35 element similar to the RcsB binding site consensus, suggesting a direct regulatory role. osmB appears as another example of a multistress-responsive gene whose transcription involves both a σS-dependent promoter and a second one independent of σS but controlled by stress-specific transcription factors.


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