operator binding
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Microbiology ◽  
2021 ◽  
Vol 167 (12) ◽  
Takeshi Shimizu ◽  
Manami Onuki ◽  
Shin Suzuki ◽  
Shinichiro Hirai ◽  
Eiji Yokoyama ◽  

Enterohaemorrhagic Escherichia coli (EHEC) produces Shiga toxin 1 (Stx1) and Shiga toxin 2 (Stx2). Although stx1 and stx2 were found within the late operons of the Stx-encoding phages (Stx-phages), stx1 could mainly be transcribed from the stx1 promoter (P Stx1), which represents the functional operator-binding site (Fur box) for the transcriptional regulator Fur (ferric uptake regulator), upstream of stx1. In this study, we found that the production of Stx1 by EHEC was affected by oxygen concentration. Increased Stx1 production in the presence of oxygen is dependent on Fur, which is an Fe2+-responsive transcription factor. The intracellular Fe2+ pool was lower under microaerobic conditions than under anaerobic conditions, suggesting that lower Fe2+ availability drove the formation of less Fe2+-Fur, less DNA binding to the P Stx1 region, and an increase in Stx1 production.

2020 ◽  
Vol 114 (2) ◽  
pp. 262-278 ◽  
Mareike Lembke ◽  
Thomas Höfler ◽  
Ada‐Natsuko Walter ◽  
Sarah Tutz ◽  
Vera Fengler ◽  

2020 ◽  
Anja Pavlin ◽  
Gregor Bajc ◽  
Nadine Fornelos ◽  
Douglas F. Browning ◽  
Matej Butala

AbstractAcinetobacter baumannii poses a great threat in healthcare settings worldwide with clinical isolates revealing an ever evolving multidrug-resistance. Here, we report the molecular mechanisms governing the tight repression of the error-prone DNA polymerase umuDC genes in this important bacterial human pathogen. We demonstrate that the small DdrR protein directly interacts with the UmuDAb transcription repressor, which possesses some similarities to LexA proteins from other bacteria, to increase the repressor’s affinity for target sequences in the umuDC operon. These data reveal that DdrR forms a stable complex with free UmuDAb but is released upon association of this repressor complex with target DNA. We show that DdrR also interacts with UmuD, a component of DNA polymerase V and that DdrR enhances the operator binding of LexA repressors from Clostridium difficile, Bacillus thuringiensis and Staphylococcus aureus. Our results suggest that proteins that assist the action of LexA-like transcription factors may be common to many, if not all, bacteria that mount the SOS response.

2016 ◽  
Vol 113 (18) ◽  
pp. E2480-E2488 ◽  
Minsik Kim ◽  
Hee Jung Kim ◽  
Sang Hyeon Son ◽  
Hye Jin Yoon ◽  
Youngbin Lim ◽  

DNA-binding repressors are involved in transcriptional repression in many organisms. Disabling a repressor is a crucial step in activating expression of desired genes. Thus, several mechanisms have been identified for the removal of a stably bound repressor (Rep) from the operator. Here, we describe an uncharacterized mechanism of noncanonical DNA binding and induction by a Rep from the temperate Salmonella phage SPC32H; this mechanism was revealed using the crystal structures of homotetrameric Rep (92–198) and a hetero-octameric complex between the Rep and its antirepressor (Ant). The canonical method of inactivating a repressor is through the competitive binding of the antirepressor to the operator-binding site of the repressor; however, these studies revealed several noncanonical features. First, Ant does not compete for the DNA-binding region of Rep. Instead, the tetrameric Ant binds to the C-terminal domains of two asymmetric Rep dimers. Simultaneously, Ant facilitates the binding of the Rep N-terminal domains to Ant, resulting in the release of two Rep dimers from the bound DNA. Second, the dimer pairs of the N-terminal DNA-binding domains originate from different dimers of a Rep tetramer (trans model). This situation is different from that of other canonical Reps, in which two N-terminal DNA-binding domains from the same dimeric unit form a dimer upon DNA binding (cis model). On the basis of these observations, we propose a noncanonical model for the reversible inactivation of a Rep by an Ant.

Chung-Hye Han

AbstractThere are two main approaches to the syntax of Korean relative clauses: the operator-movement analysis and the operator-binding analysis. Although the predictions made by the two analyses are clear, no consensus is found in the literature regarding the two approaches, as there is disagreement on what the facts are. This situation thus calls for adopting a controlled experimental methodology to obtain the relevant data. In this article, I present findings from two magnitude estimation task experiments that support the operator-movement analysis. Experiment 1 tested whether a subject gap can occur in islands in relative clauses and whether it can be replaced with an overt pronoun, and Experiment 2 tested whether an object gap can occur in islands in relative clauses and whether it can be replaced with an overt pronoun. In both experiments, a gap could not occur in an island and could not be replaced with an overt pronoun. According to these findings, relativization into islands is ruled out in Korean, and thus the operator-movement analysis is supported.

Biopolymers ◽  
2013 ◽  
pp. n/a-n/a
Andrew V. Colasanti ◽  
Michael A. Grosner ◽  
Pamela J. Perez ◽  
Nicolas Clauvelin ◽  
Xiang-Jun Lu ◽  

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