9DVT

Cryo-EM structure of RpaA bound to PkaiBC DNA and the CTD of the alpha subunit of RNAP from the cyanobacterium Synechococcus elongatus

Summary for 9DVT

• Entry DOI: 10.2210/pdb9dvt/pdb
• EMDB information: 47222
• Descriptor: Non-template DNA, Template DNA, DNA-directed RNA polymerase subunit alpha, ... (5 entities in total)
• Functional Keywords: alpha subunit of rnap, pkaibc dna, rpaa, transcription factor, dna binding protein, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Synechococcus elongatus; More
• Total number of polymer chains: 6
• Total formula weight: 201538.06

Authors

Fang, M.,Gu, Y.,Matyszewski, M.,Leanca, M.,LiWang, A.,Yuzenkova, Y.,Corbett, K.D.,Golden, S.E. (deposition date: 2024-10-08, release date: 2025-10-15, Last modification date: 2026-03-04)

Primary citation

Fang, M.,Gu, Y.,Leanca, M.,Matyszewski, M.,LiWang, A.,Yuzenkova, Y.,Corbett, K.D.,Golden, S.S.
Mechanism and reconstitution of circadian transcription in cyanobacteria.
Nat.Struct.Mol.Biol., 33:275-281, 2026

PubMed Abstract: Circadian biological clocks evolved across kingdoms of life as an adaptation to predictable cycles of sunrise and sunset. In the cyanobacterium Synechococcus elongatus, a protein-based clock precisely controls when different genes are turned on and off during the 24-h day but the phasing mechanism remains unclear. Here we show the molecular basis of this regulation and reconstitute clock-controlled transcription in vitro using purified components. Biochemical and structural analyses revealed that the clock-regulated transcription factor RpaA can function as either an activator or a repressor of cyanobacterial RNA polymerase, depending on its binding position relative to core promoter elements. Leveraging the repressor mechanism, we developed a heterologous in vitro system driven by bacteriophage T7 RNA polymerase that sustains circadian transcription for multiple days. These findings explain how a single clock output generates opposite phases of gene expression and define the minimal components for circadian clock function, enabling synthetic or biotechnological applications.

PubMed: 41667880
DOI: 10.1038/s41594-025-01740-0

Experimental method

ELECTRON MICROSCOPY (3.74 Å)