Archaeal RNA polymerase (RNAP) is widely recognized as the structural and functional ancestor of eukaryotic RNA polymerase II (Pol II). This chapter examines the evolutionary diversification of RNAP subunits and associated transcription factors, with emphasis on their roles in the emergence of complex regulatory systems. Key molecular components—Rpo3, Rpo4/7, TFE, Spt4/5, and TFS—are analyzed in terms of their conserved core structures and lineage-specific adaptations. Comparative structural studies reveal that, while the catalytic architecture of RNAP has been preserved, regulatory domains and additional functionalities have been incrementally acquired. Notably, the incorporation of an iron–sulfur (Fe–S) cluster in Rpo3 and the expansion of KOW domains in the elongation factor Spt5 are interpreted as critical steps toward coupling transcription with RNA processing. These findings support the view that increasing transcriptional complexity evolved through elaboration upon ancient molecular scaffolds. A conceptual framework is thus proposed to trace the evolutionary transition from archaeal transcription to the eukaryotic gene regulatory machinery.

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From Simplicity to Complexity: The Evolution of RNA Polymerase II from Its Archaeal Ancestor

  • Akira Hirata

摘要

Archaeal RNA polymerase (RNAP) is widely recognized as the structural and functional ancestor of eukaryotic RNA polymerase II (Pol II). This chapter examines the evolutionary diversification of RNAP subunits and associated transcription factors, with emphasis on their roles in the emergence of complex regulatory systems. Key molecular components—Rpo3, Rpo4/7, TFE, Spt4/5, and TFS—are analyzed in terms of their conserved core structures and lineage-specific adaptations. Comparative structural studies reveal that, while the catalytic architecture of RNAP has been preserved, regulatory domains and additional functionalities have been incrementally acquired. Notably, the incorporation of an iron–sulfur (Fe–S) cluster in Rpo3 and the expansion of KOW domains in the elongation factor Spt5 are interpreted as critical steps toward coupling transcription with RNA processing. These findings support the view that increasing transcriptional complexity evolved through elaboration upon ancient molecular scaffolds. A conceptual framework is thus proposed to trace the evolutionary transition from archaeal transcription to the eukaryotic gene regulatory machinery.