Transcription elongation factor SII

Abstract

RNA chain elongation by RNA polymerase II (pol II) is a complex and regulated process which is coordinated with capping, splicing, and polyadenylation of the primary transcript. Numerous elongation factors that enable pol II to transcribe faster and/or more efficiently have been purified. SII is one such factor. It helps pol II bypass specific blocks to elongation that are encountered during transcript elongation. SII was first identified biochemically on the basis of its ability to enable pol II to synthesize long transcripts. ((1)) Both the high resolution structure of SII and the details of its novel mechanism of action have been refined through mutagenesis and sophisticated in vitro assays. SII engages transcribing pol II and assists it in bypassing blocks to elongation by stimulating a cryptic, nascent RNA cleavage activity intrinsic to RNA polymerase. The nuclease activity can also result in removal of misincorporated bases from RNA. Molecular genetic experiments in yeast suggest that SII is generally involved in mRNA synthesis in vivo and that it is one type of a growing collection of elongation factors that regulate pol II. In vertebrates, a family of related SII genes has been identified; some of its members are expressed in a tissue-specific manner. The principal challenge now is to understand the isoform-specific functional differences and the biology of regulation exerted by the SII family of proteins on target genes, particularly in multicellular organisms.

Figure 1

Structure of transcript cleavage and elongation factors SII and GreA. A) Schematic montage of the tripartite SII domain structure based upon the NMR derived models of domain II of yeast SII (modified from ref. 46) and the domain III zinc ribbon of human SII (modified from ref. 48). Domain I (yellow line) NMR structure will be presented elsewhere (V. Olmsted and C. Arrowsmith, personal communication). The flexible linker between domains II and III is represented as a dashed yellow line. Amino acid side chains that constitute a hydrophobic core of domain II are shown in green, yellow, red, and fuchsia. The approximate positions of critical aspartic (D) and glutamic acid (E) residues in the loop of the zinc ribbon are indicated. The position of four cysteine residues (C) shown chelating (dotted lines) a zinc ion (sphere) were sketched onto the zinc ribbon structure. The relative sizes of the domains are not to scale. B) Structure of E. coli GreA protein as determined by X-ray crystallography (modified from ref. 45). RNA in an elongation complex crosslinks to the tip of the extended α-helical “finger” domain.⁽⁴⁵⁾ The aminoterminal (N) helical finger is responsible for activating transcript cleavage and elongation. The carboxy-terminal (C) globular domain is largely responsible for GreA binding to E. coli RNA polymerase.⁽⁴⁵⁾

Figure 2

Summary of a network of genetic interactions (arrows) between the SII gene DST1 (triangle), and genes encoding RNA polymerase II subunits (rectangles), chromatin related proteins (circles and ellipse), and subunits of the Elongator complex (squares).