Novel zinc finger motif in the basal transcriptional machinery: Three-dimensional NMR studies of the nucleic acid binding domain of transcriptional elongation factor TFIIS

Qian, Xiuqi; Gozani, Shai N.; Yoon, Ho Sup; Jeon, Choon Ju; Agarwal, Kan; Weiss, Michael A.

doi:10.1021/bi00089a010

Cited by 120 publications

(126 citation statements)

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“…Amino acid sequences of Elf1 homologues are conserved among yeast, humans, A. thaliana, C. reinhardtii, the unicellular red alga Cyanidioschyzon merolae and P. yezoensis, containing a C4 type-zinc finger as the DNA-binding region (Fig. 2); this is also found in other transcriptional elongation factors including Spt4 and TFIIS (Malone et al 1993;Qian et al 1993). …”

Section: Cloning and Structural Characterization Of Transcription Facmentioning

confidence: 99%

Visualization of Nuclear Localization of Transcription Factors with Cyan and Green Fluorescent Proteins in the Red Alga Porphyra yezoensis

et al. 2009

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Running titleFollowing molecular cloning and characterization of transcription factors DP-E2F-like 1 (PyDEL1), transcription elongation factor 1 (PyElf1) and multiprotein bridging factor 1 (PyMBF1), we then demonstrated that ZsGFP and AmCFP can be used to visualize nuclear localization of PyElf1 and PyMBF1. This is the first report to perform visualization of subcellular localization of transcription factors as genome-encoded proteins in red algae.3

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Section: Cloning and Structural Characterization Of Transcription Facmentioning

confidence: 99%

Visualization of Nuclear Localization of Transcription Factors with Cyan and Green Fluorescent Proteins in the Red Alga Porphyra yezoensis

et al. 2009

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“…Solution structures have previously been reported for the three-helix bundle of domain II of yeast TFIIS (3) and the zinc ribbon of domain III of human TFIIS (9,33). Individually, these domains are inactive for stimulation of transcript elongation.…”

Section: Mapping Of the Minimal Transcriptionally Active Regionmentioning

confidence: 99%

Yeast Transcript Elongation Factor (TFIIS), Structure and Function

Olmsted¹,

Awrey²,

Koth³

et al. 1998

Journal of Biological Chemistry

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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 all of domains II and III. We confirm that the structure of domain II in the context of fully active yTFIIS is the same as that determined previously for a shorter construct. We have determined the structure of the C-terminal zinc ribbon domain of active yTFIIS and shown that it is similar to that reported for a shorter construct of human TFIIS. The region linking domain II with the zinc ribbon of domain III appears to be conformationally flexible and does not adopt a single defined tertiary structure. NMR analysis of inactive mutants of yTFIIS support a role for the linker region in interactions with the transcription elongation complex.The rate of transcript elongation by RNA polymerase II is regulated by elongation factors, of which there are two classes with different mechanisms of action. One class, which includes elongin, ELL, pTEFb, and RAP74 stimulates the rate of nucleotide incorporation. The other class, includes TFIIS, its viral and archael sequence homologues, and the bacterial proteins, greA and greB. These proteins do not affect the rate of nucleotide incorporation, but rather stimulate an activity in RNA polymerase II that enables it to transcribe throught blocks to elongation such as DNA-binding proteins, DNA-binding drugs, or particular sequences of DNA that promote transcription arrest (1).Although TFIIS 1 and its bacterial homologues have very similar mechanisms of action, their primary sequences and three-dimensional structures are quite different. GreA and greB each comprise 160 amino acids that form two 80-residue structural domains. In greA, the N-terminal domain is composed of two extended, coiled antiparallel ␣-helices, and can be cross-linked to the nascent RNA when bound to RNA polymerase in a stalled elongation complex (2). The C-terminal domain of greA is globular and is composed of a ␤-sheet that cradles an ␣-helix. GreB is a sequence homologue of greA and likely has an identical tertiary structure. yTFIIS is composed of three domains (domains I, II, and III) as defined by limited proteolysis and structural studies using nuclear magnetic resonance (NMR) spectroscopy (3) (see Fig. 1). Domains II and III, which together extend from residues 131-309 in yeast, are sufficient for transcription activity. Domain II (residues 131-240 in yeast) contains a three-helix bundle (3) and domain III is a zinc ribbon, which contains a three-stranded ␤-sheet, stabilized by a tetrad of cysteine residues that chelate a zinc ion (4). Domain II is conserved in TFIIS homologues and is postulated to int...

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“…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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“…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).…”

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“…Mutagenesis has determined that domain III is critical for TFIIS function (29,(32)(33)(34). This region possesses a zinc ribbon motif that shares similarity to several small subunits of nuclear polymerases: RPB9 of RNA polymerase II, C11 of RNA polymerase III, and A12.2 of RNA polymerase I (3,(35)(36)(37), as well as TFIIB (38). This region is able to interact with nucleic acids in vitro, although very weakly, and the functional significance of this interaction is not known.…”

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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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Novel zinc finger motif in the basal transcriptional machinery: Three-dimensional NMR studies of the nucleic acid binding domain of transcriptional elongation factor TFIIS

Cited by 120 publications

References 54 publications

Visualization of Nuclear Localization of Transcription Factors with Cyan and Green Fluorescent Proteins in the Red Alga Porphyra yezoensis

Visualization of Nuclear Localization of Transcription Factors with Cyan and Green Fluorescent Proteins in the Red Alga Porphyra yezoensis

Yeast Transcript Elongation Factor (TFIIS), Structure and Function

Structural Basis for the Species-specific Activity of TFIIS

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