RNA polymerase comes into focus

Abstract

Understanding the mechanism and regulation of RNA synthesis is a key objective in molecular biology. In recent years a plethora of factors that regulate transcription has been identified. Most of these factors either facilitate or impair access of RNA polymerases to template DNA. Crosslinking and mutational studies have provided key information regarding the mechanism of RNA synthesis. Nonetheless, the structural basis of RNA synthesis has remained elusive. Until now, structural information for multisubunit RNA polymerases was limited to low-resolution electron crystallography of yeast and bacterial enzymes.We now enter a new era with high-resolution X-ray crystal structures for eukaryotic and bacterial RNA polymerases. Poglitsch et al.1xElectron crystal structure of an RNA polymerase II transcription elongation complex. Poglitsch, C.L. et al. Cell. 1999; 98: 791–798Abstract | Full Text | Full Text PDF | PubMed | Scopus (55)See all References1 have extended the low-resolution structure of yeast RNA polymerase II to an active transcription complex that includes template DNA and product RNA. In addition to identifying the catalytic region of the enzyme, this structure defines a novel path for the DNA template across one face of the enzyme. Furthermore, Fu et al.2xYeast RNA polymerase II at 5 A resolution. Fu, J. et al. Cell. 1999; 98: 799–810Abstract | Full Text | Full Text PDF | PubMed | Scopus (104)See all References2 have solved the X-ray structure of yeast RNA polymerase II in the absence of nucleic acid at 5 A resolution. Comparison of this structure with the transcriptionally active complex identified two flexible domains as potential DNA and RNA clamps. Zhang et al.3xCrystal structure of Thermus aquaticus core RNA polymerase at 3.3 A resolution. Zhang, G. et al. Cell. 1999; 98: 811–824Abstract | Full Text | Full Text PDF | PubMed | Scopus (548)See all References3 treat us to an even clearer view of the enzyme with the crystal structure of bacterial core RNA polymerase at 3.3 A resolution. This is truly a landmark achievement that defines the overall architecture of RNA polymerase, subunit structures and interactions, and the active center of the enzyme. The results from DNA and RNA crosslinking studies could also be mapped onto this structure to define components involved in DNA and RNA binding. These X-ray structures are consistent with the earlier electron crystallographic structures and most features are conserved between the bacterial and yeast enzymes. We can now anticipate seeing more refined structures of RNA polymerases and their complexes trapped at different stages of the transcription cycle. A detailed mechanistic understanding of this most fundamental process in gene expression is rapidly coming into focus.