Yeast Transcript Elongation Factor (TFIIS), Structure and Function

Olmsted, Valerie K.; Awrey, Donald E.; Koth, Christopher M.; Shan, Xi; Morin, Paul E.; Kazanis, Sophia; Edwards, A.M.; Arrowsmith, C.H.

doi:10.1074/jbc.273.35.22589

Journal of Biological Chemistry

1998

DOI: 10.1074/jbc.273.35.22589

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Yeast Transcript Elongation Factor (TFIIS), Structure and Function

Valerie K. Olmsted¹,

Donald E. Awrey²,

Christopher M. Koth³

et al.

Abstract: TFIIS is a general transcription elongation factor that helps arrested RNA polymerase II elongation complexes resume transcription. We have previously shown that yeast TFIIS (yTFIIS) comprises three structural domains (I-III). The three-dimensional structures of domain II and part of domain III have been previously reported, but neither domain can autonomously stimulate transcription elongation. Here we report the NMR structural analysis of residues 131-309 of yTFIIS which retains full activity and contains al… Show more

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Cited by 43 publications

(41 citation statements)

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(32 reference statements)

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“…TFIIS is composed of three domains that fold independently, as demonstrated by NMR analysis of its structure (6,7). Cleavage-stimulating activity minimally requires the Cterminal two-thirds of the protein, that is, its domain II and III separated by a 15-aa linker (7,8).…”

mentioning

confidence: 99%

TFIIS elongation factor and Mediator act in conjunction during transcription initiation in vivo

Guglielmi

Soutourina

Esnault

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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The transcription initiation and elongation steps of protein-coding genes usually rely on unrelated protein complexes. However, the TFIIS elongation factor is implicated in both processes. We found that, in the absence of the Med31 Mediator subunit, yeast cells required the TFIIS polymerase II (Pol II)-binding domain but not its RNA cleavage stimulatory activity that is associated with its elongation function. We also found that the TFIIS Pol II-interacting domain was needed for the full recruitment of Pol II to several promoters in the absence of Med31. This work demonstrated that, in addition to its thoroughly characterized role in transcription elongation, TFIIS is implicated through its Pol II-binding domain in the formation or stabilization of the transcription initiation complex in vivo.RNA polymerase II ͉ Saccharomyces cerevisiae ͉ transcription regulation ͉ Med31 ͉ Mediator subunit T he transcription of protein-coding eukaryotic genes by RNA polymerase II (Pol II) requires three successive steps: initiation, elongation, and termination. Transcription initiation of class II genes involves the binding of activators to regulatory sequences; the recruitment of RNA Pol II to the core promoter via interactions with activators, coactivators, and general transcription factors; and the initiation reaction per se with DNA strand opening and abortive initiation (1). A major coactivator target of transcriptional activators is the Mediator (2, 3). One of its activities is the recruitment and/or stabilization of Pol II at core promoters (4). After transcription initiation, Pol II enters elongation, during which it can be arrested because of the presence of specific DNA sequences that promote pausing, or because of obstacles such as DNA damage or bound proteins. To avoid or escape arrest, Pol II requires different elongation factors, including TFIIS (5). Evidence suggests that TFIIS could be implicated in both initiation and elongation.In vitro, TFIIS can reactivate arrested elongation complexes by stimulating endonucleolytic cleavage by Pol II of the nascent RNA (5). TFIIS is composed of three domains that fold independently, as demonstrated by NMR analysis of its structure (6, 7). Cleavage-stimulating activity minimally requires the Cterminal two-thirds of the protein, that is, its domain II and III separated by a 15-aa linker (7,8). Domain II forms a three-helix bundle followed by three short helices, with a basic patch on the third helix (␣-3) that is essential for TFIIS binding to Pol II (7). Crystallographic analysis of a TFIIS-Pol II complex confirmed that this basic patch lies at the TFIIS-Pol II interface (7,8). TFIIS binding to Pol II is required for domain III to reach the Pol II active site. Domain III forms a zinc ribbon that contains a conserved RSADE motif, responsible for the stimulation of RNA cleavage (7,8).TFIIS is also implicated in transcription initiation. First, the deletion of the DST1 gene, encoding TFIIS in yeast, is colethal with the deletion of the gene encoding the Med31 subunit of the Medi...

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mentioning

confidence: 99%

TFIIS elongation factor and Mediator act in conjunction during transcription initiation in vivo

Guglielmi

Soutourina

Esnault

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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“…The second domain of TFIIS, residues 131-240 in yeast, is ␣-helical (1,2). Deletion analysis as well as site-directed mutagenesis have shown that this region of the protein binds to the polymerase (27,28,30).…”

mentioning

confidence: 99%

“…This region is able to interact with nucleic acids in vitro, although very weakly, and the functional significance of this interaction is not known. Domains II and III are connected with a linker region of about 30 amino acids (2). In yeast TFIIS, this linker region had no defined conformation based on NMR analysis, but also it was not fully flexible (2).…”

mentioning

confidence: 99%

“…The most highly conserved region of TFIIS lies within domain III (residues 279 -309) (2,3). Mutagenesis has determined that domain III is critical for TFIIS function (29,(32)(33)(34).…”

mentioning

confidence: 99%

“…The carboxyl-terminal half of TFIIS also is sufficient to complement the drug sensitivity of ppr2⌬ strains in vivo (11,22). Based on protease digestion studies and NMR structure analysis, yeast TFIIS consists of three major structural domains (1)(2)(3). Domain I, the amino-terminal portion of TFIIS (amino acids 1-130 in yeast), shows the least relatedness across species.…”

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confidence: 99%

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Structural Basis for the Species-specific Activity of TFIIS

Shimasaki

Kane

2000

Journal of Biological Chemistry

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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...

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Transcription elongation factor SII

2000

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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. BioEssays 22:327–336, 2000. © 2000 John Wiley & Sons, Inc.

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Yeast Transcript Elongation Factor (TFIIS), Structure and Function

Cited by 43 publications

References 33 publications

TFIIS elongation factor and Mediator act in conjunction during transcription initiation in vivo

TFIIS elongation factor and Mediator act in conjunction during transcription initiation in vivo

Structural Basis for the Species-specific Activity of TFIIS

Transcription elongation factor SII

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