Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity

• Published in: The EMBO journal 2011-04, Vol.30 (7), p.1302-1310
• Main Authors: Martinez-Rucobo, Fuensanta W, Sainsbury, Sarah, Cheung, Alan CM, Cramer, Patrick
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Cells; Chromosomal Proteins, Non-Histone - chemistry; Crystallography, X-Ray; DNA-Directed RNA Polymerases - chemistry; EMBO09; EMBO40; gene regulation; gene transcription; Genes; Models, Molecular; Molecular Sequence Data; multiprotein complex structure; Nucleic acids; Polymerization; Protein Binding; Protein Structure, Quaternary; Pyrococcus furiosus - chemistry; Pyrococcus furiosus - enzymology; Repressor Proteins - chemistry; Ribonucleic acid; RNA; RNA polymerase elongation; Saccharomyces cerevisiae - chemistry; Saccharomyces cerevisiae - enzymology; Sequence Homology, Amino Acid; transcription elongation factor; Transcriptional Elongation Factors - chemistry; Yeasts
• ISSN: 0261-4189; 1460-2075
• DOI: 10.1038/emboj.2011.64

Related RNA polymerases (RNAPs) carry out cellular gene transcription in all three kingdoms of life. The universal conservation of the transcription machinery extends to a single RNAP‐associated factor, Spt5 (or NusG in bacteria), which renders RNAP processive and may have arisen early to permit evolution of long genes. Spt5 associates with Spt4 to form the Spt4/5 heterodimer. Here, we present the crystal structure of archaeal Spt4/5 bound to the RNAP clamp domain, which forms one side of the RNAP active centre cleft. The structure revealed a conserved Spt5–RNAP interface and enabled modelling of complexes of Spt4/5 counterparts with RNAPs from all kingdoms of life, and of the complete yeast RNAP II elongation complex with bound Spt4/5. The N‐terminal NGN domain of Spt5/NusG closes the RNAP active centre cleft to lock nucleic acids and render the elongation complex stable and processive. The C‐terminal KOW1 domain is mobile, but its location is restricted to a region between the RNAP clamp and wall above the RNA exit tunnel, where it may interact with RNA and/or other factors. Spt5 and NusG play a conserved role in stimulating RNA polymerase II transcription elongation and processivity. Here, the crystal structure of Spt4/5 bound to the RNA polymerase clamp domain reveals that the factor binds above DNA and RNA in the active centre cleft preventing premature dissociation of the polymerase.