The transcriptionally active fragment of the yeast RNA polymerase II transcription elongation factor, TFIIS, comprises a three-helix bundle and a zinc ribbon motif joined by a linker region. We have probed the function of this fragment of TFIIS using structureguided mutagenesis. The helix bundle domain binds RNA polymerase II with the same affinity as does the full-length TFIIS, and this interaction is mediated by a basic patch on the outer face of the third helix. TFIIS mutants that were unable to bind RNA polymerase II were inactive for transcription activity, confirming the central role of polymerase binding in the TFIIS mechanism of action. The linker and zinc ribbon regions play roles in promoting cleavage of the nascent transcript and read-through past the block to elongation. Mutation of three aromatic residues in the zinc ribbon domain (Phe 269 , Phe 296 , and Phe 308 ) impaired both transcript cleavage and read-through. Mutations introduced in the linker region between residues 240 and 245 and between 250 and 255 also severely impaired both transcript cleavage and read-through activities. Our analysis suggests that the linker region of TFIIS probably adopts a critical structure in the context of the elongation complex.Elongating RNA polymerase II stalls upon encountering blocks to elongation in vitro (1). In some cases, these transiently stalled polymerases convert to very stable arrested complexes. Arrested complexes are unable to resume transcription even after hours to weeks of incubation (2). The inability of such complexes to resume transcription results from a structural change in the stalled polymerase, which causes the active site to disengage from the 3Ј-end of the transcript (3). The general elongation factor TFIIS 1 reactivates arrested transcription complexes within minutes (4). The reactivation process involves a TFIIS-stimulated endonucleolytic cleavage of the transcript by the RNA polymerase II (5, 6), which relocates the polymerase active site to the new 3Ј-end of the RNA chain and allows for chain extension. The reactivation of stalled elongation complexes involves multiple steps, with the first being the interaction of TFIIS with RNA polymerase II. The TFIIS-binding domain on RNA polymerase II was identified by Friesen and colleagues (7), who discovered mutants in the largest subunit of RNA polymerase II, RPB1, that displayed the same phenotype as a strain deleted for the TFIIS gene (sensitivity to the drug 6-azauracil) and that also could be suppressed by overexpression of TFIIS. These mutants localized to a part of RPB1 between regions G and H, which are conserved from bacteria to man and are in close proximity to the RNA polymerase active site (8, 9). The genetic evidence for a TFIIS interacting domain was confirmed biochemically, when two of the mutant RNA polymerases were purified and shown directly to have 500-fold lower affinity for TFIIS compared with the wild-type polymerase (10).Transcript cleavage is the next essential step in the reactivation process. It is now clear that R...

The micropig model of chronic alcoholism was used to study the relationship of lipid composition and physical properties in three different tissue membranes from the same animals. Ethanol feeding reduced membrane anisotropy, as measured with the diphenylhexatriene probe, in liver plasma and kidney brush-border membranes but not in jejunal brush-border membranes. Preincubation with ethanol reduced anisotropy in each of the three control membranes, whereas all three membranes from the ethanol-fed group were relatively tolerant to the acute effect of ethanol. In liver and kidney membranes, ethanol feeding increased levels of linoleic (18:2 omega 6) acid and decreased levels of arachidonic (20:4 omega 6) and docosahexaenoic (22:6 omega 3) acids and their specific double-bond positions, consistent with reduced activities of delta 6 and delta 5 fatty acid desaturases. In liver and kidney membranes, anisotropy parameters and the acute effect of ethanol correlated inversely with levels of linoleic acid and directly with levels of arachidonic and docosahexaenoic acids and their specific double bonds. Levels of docosahexaenoic acid correlated with the acute effect of ethanol in all three membranes. Phospholipid fatty acid profiles were similar in jejunal brush-border membranes and terminal bile samples, suggesting that the effects of ethanol on jejunal fatty acids and physical properties are modulated by intraluminal biliary phospholipids. The effect of ethanol on anisotropy could not be attributed to changes in membrane cholesterol/phospholipid ratios. These studies affirm the value of this new animal model of chronic alcoholism and provide comprehensive evidence for the central role of fatty acid desaturation in the membrane-associated effects of ethanol exposure.

Many proteins involved in eukaryotic transcription are similar in function and in sequence between organisms. Despite the sequence similarities, there are many factors that do not function across species. For example, transcript elongation factor TFIIS is highly conserved among eukaryotes, and yet the TFIIS protein from Saccharomyces cerevisiae cannot function with mammalian RNA polymerase II and vice versa. To determine the reason for this species specificity, chimeras were constructed linking three structurally independent regions of the TFIIS proteins from yeast and human cells. Two independently folding domains, II and III, have been examined previously using NMR (1-3). Yeast domain II alone is able to bind yeast RNA polymerase II with the same affinity as the full-length TFIIS protein, and this domain was expected to confer the species selectivity. Domain III has previously been shown to be readily exchanged between mammalian and yeast factors. However, the results presented here indicate that domain II is insufficient to confer species selectivity, and a primary determinant lies in a 30-amino acid highly conserved linker region connecting domain II with domain III. These 30 amino acids may physically orient domains II and III to support functional interactions between TFIIS and RNA polymerase II.In vivo, RNA polymerase II transcription units can vary from several hundreds to millions of base pairs, and these transcribed sequences contain information that regulates the elongation reaction for RNA polymerase II. Several types of blocks to elongation have been identified (4), and these include nucleosomes, DNA lesions, DNA binding proteins, and specific DNA sequences themselves. Thus, modulating the ability of RNA polymerase to recognize and overcome these blocks can regulate gene expression in the cell (4 -7). Several proteins have been identified in vitro that affect transcript elongation by RNA polymerase II. One regulatory protein is TFIIS, a factor that enables RNA polymerase II to transcribe through a variety of blocks to elongation in vitro (4, 5, 8 -11). In mammalian cells, there is a family of TFIIS gene sequences, and these are expressed in a tissue-or development-specific pattern (12-17). In Saccharomyces cerevisiae the gene encoding TFIIS, PPR2 (18,19), is single copy but not essential. Disruption strains have several moderate phenotypes but are quite sensitive to the drug 6-azauracil (20).Across species, TFIIS proteins share a high degree of sequence conservation (21). Despite this similarity, S. cerevisiae does not function with metazoan polymerases and vice versa (22, 23). Indeed, even Schizosaccharomyces pombe and S. cerevisiae do not stimulate each other's polymerases (21). This species specificity is somewhat surprising given the striking similarity of amino acid sequences across these species in the functionally sufficient carboxyl-terminal half of the protein (11). This region of TFIIS carries out all known functions in vitro, and these functions include stimulating an arrested RNA polymer...