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TitleMechanism and reconstitution of circadian transcription in cyanobacteria.
Journal, issue, pagesNat Struct Mol Biol, Vol. 33, Issue 2, Page 275-281, Year 2026
Publish dateFeb 10, 2026
AuthorsMingxu Fang / Yajie Gu / Miron Leanca / Mariusz Matyszewski / Andy LiWang / Yulia Yuzenkova / Kevin D Corbett / Susan S Golden /
PubMed AbstractCircadian 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 ...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.
External linksNat Struct Mol Biol / PubMed:41667880 / PubMed Central
MethodsEM (single particle)
Resolution2.5 - 3.74 Å
Structure data

47221

9dvs

EMDB-47221, PDB-9dvs:
CryoEM structure of Syn7942 RNAP-SigA holoenzyme
Method: EM (single particle) / Resolution: 2.5 Å

47222

9dvt

EMDB-47222, PDB-9dvt:
Cryo-EM structure of RpaA bound to PkaiBC DNA and the CTD of the alpha subunit of RNAP from the cyanobacterium Synechococcus elongatus
Method: EM (single particle) / Resolution: 3.74 Å

47223

9dvu

EMDB-47223, PDB-9dvu:
CryoEM structure of RpaA bound to PkaiBC DNA and Syn7942 RNAP-SigA holoenzyme
Method: EM (single particle) / Resolution: 3.7 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

Source
  • synechococcus elongatus (bacteria)
  • synthetic construct (others)
  • synechococcus elongatus pcc 7942 = fachb-805 (bacteria)
KeywordsDNA BINDING PROTEIN/DNA / SigA / RNAP / TAC / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex / alpha subunit of RNAP / PkaiBC DNA / RpaA / transcription factor / Response regulator / transcriptional regulator

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