Structural basis of CueR-dependent transcription activation

Abstract Bacteriophage T4 middle promoters are activated through a process called σ appropriation, which requires the concerted effort of two T4-encoded transcription factors: AsiA and MotA. Despite extensive biochemical and genetic analyses, puzzle remains, in part, because of a lack of precise structural information for σ appropriation complex. Here, we report a single-particle cryo-electron microscopy (cryo-EM) structure of an intact σ appropriation complex, comprising AsiA, MotA, Escherichia coli RNA polymerase (RNAP), σ70 and a T4 middle promoter. As expected, AsiA binds to and remodels σ region 4 to prevent its contact with host promoters. Unexpectedly, AsiA undergoes a large conformational change, takes over the job of σ region 4 and provides an anchor point for the upstream double-stranded DNA. Because σ region 4 is conserved among bacteria, other transcription factors may use the same strategy to alter the landscape of transcription immediately. Together, the structure provides a foundation for understanding σ appropriation and transcription activation.

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Structural basis of transcription activation by the global regulator Spx

Nucleic Acids Research ◽

10.1093/nar/gkab790 ◽

2021 ◽

Vol 49 (18) ◽

pp. 10756-10769

Author(s):

Jing Shi ◽

Fangfang Li ◽

Aijia Wen ◽

Libing Yu ◽

Lu Wang ◽

...

Keyword(s):

Transcriptional Regulator ◽

Transcription Activation ◽

Structural Basis ◽

Active Conformation ◽

Multiple Target ◽

Global Regulator ◽

Gram Positive Bacteria ◽

Bacterial Transcription ◽

Promoter Dna ◽

Transcription Activators

Abstract Spx is a global transcriptional regulator in Gram-positive bacteria and has been inferred to efficiently activate transcription upon oxidative stress by engaging RNA polymerase (RNAP) and promoter DNA. However, the precise mechanism by which it interacts with RNAP and promoter DNA to initiate transcription remains obscure. Here, we report the cryo-EM structure of an intact Spx-dependent transcription activation complex (Spx–TAC) from Bacillus subtilis at 4.2 Å resolution. The structure traps Spx in an active conformation and defines key interactions accounting for Spx-dependent transcription activation. Strikingly, an oxidized Spx monomer engages RNAP by simultaneously interacting with the C-terminal domain of RNAP alpha subunit (αCTD) and σA. The interface between Spx and αCTD is distinct from those previously reported activators, indicating αCTD as a multiple target for the interaction between RNAP and various transcription activators. Notably, Spx specifically wraps the conserved –44 element of promoter DNA, thereby stabilizing Spx–TAC. Besides, Spx interacts extensively with σA through three different interfaces and promotes Spx-dependent transcription activation. Together, our structural and biochemical results provide a novel mechanistic framework for the regulation of bacterial transcription activation and shed new light on the physiological roles of the global Spx-family transcription factors.

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Structural basis of bacterial transcription activation

Science ◽

10.1126/science.aao1923 ◽

2017 ◽

Vol 358 (6365) ◽

pp. 947-951 ◽

Cited By ~ 24

Author(s):

Bin Liu ◽

Chuan Hong ◽

Rick K. Huang ◽

Zhiheng Yu ◽

Thomas A. Steitz

Keyword(s):

High Resolution ◽

De Novo ◽

Transcription Activation ◽

Class I ◽

Receptor Protein ◽

Structural Basis ◽

Complete Class ◽

Bacterial Transcription ◽

Cryo Electron Microscopy ◽

Promoter Dna

In bacteria, the activation of gene transcription at many promoters is simple and only involves a single activator. The cyclic adenosine 3′,5′-monophosphate receptor protein (CAP), a classic activator, is able to activate transcription independently through two different mechanisms. Understanding the class I mechanism requires an intact transcription activation complex (TAC) structure at a high resolution. Here we report a high-resolution cryo–electron microscopy structure of an intact Escherichia coli class I TAC containing a CAP dimer, a σ70–RNA polymerase (RNAP) holoenzyme, a complete class I CAP-dependent promoter DNA, and a de novo synthesized RNA oligonucleotide. The structure shows how CAP wraps the upstream DNA and how the interactions recruit RNAP. Our study provides a structural basis for understanding how activators activate transcription through the class I recruitment mechanism.

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