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Title: Structural dissection of an interaction between transcription initiation and termination factors implicated in promoter-terminator cross-talk

Abstract

Functional cross-talk between the promoter and terminator of a gene has long been noted. Promoters and terminators are juxtaposed to form gene loops in several organisms, and gene looping is thought to be involved in transcriptional regulation. The general transcription factor IIB (TFIIB) and the C-terminal domain phosphatase Ssu72, essential factors of the transcription preinitiation complex and the mRNA processing and polyadenylation complex, respectively, are important for gene loop formation. TFIIB and Ssu72 interact both genetically and physically, but the molecular basis of this interaction is not known. Here we present a crystal structure of the core domain of TFIIB in two new conformations that differ in the relative distance and orientation of the two cyclin-like domains. The observed extraordinary conformational plasticity may underlie the binding of TFIIB to multiple transcription factors and promoter DNAs that occurs in distinct stages of transcription, including initiation, reinitiation, and gene looping. We mapped the binding interface of the TFIIB-Ssu72 complex using a series of systematic, structure-guided in vitro binding and site-specific photocross-linking assays. Our results indicate that Ssu72 competes with acidic activators for TFIIB binding and that Ssu72 disrupts an intramolecular TFIIB complex known to impede transcription initiation. We also show that themore » TFIIB-binding site on Ssu72 overlaps with the binding site of symplekin, a component of the mRNA processing and polyadenylation complex. Here, we propose a hand-off model in which Ssu72 mediates a conformational transition in TFIIB, accounting for the role of Ssu72 in transcription reinitiation, gene looping, and promoter-terminator cross-talk.« less

Authors:
 [1];  [2];  [2];  [1];  [2];  [1]
  1. Univ. of Texas Southwestern Medical Center, Dallas, TX (United States)
  2. Hong Kong Univ. of Science and Technology, Hong Kong (China)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22). Scientific User Facilities Division; Welch Foundation; USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); Rita Allen Foundation; UT Southwestern Medical Center Endowed Scholar; National Inst. of Health; Hong Kong Research Grant Council
OSTI Identifier:
1511721
Grant/Contract Number:  
[AC02-06CH11357; AC02-05CH11231; AC02-76SF00515; P41GM103393; I-1790; R1119; GM114576; GM121662; HKUST C6009–15G]
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Biological Chemistry
Additional Journal Information:
[ Journal Volume: 293; Journal Issue: 5]; Journal ID: ISSN 0021-9258
Publisher:
American Society for Biochemistry and Molecular Biology
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; general transcription factor (GTF); RNA polymerase II; transcription initiation factor; transcription regulation; transcription termination; gene looping; promoter-terminator cross-talk; TFIIB; Ssu72

Citation Formats

Bratkowski, Matthew, Unarta, Ilona Christy, Zhu, Lizhe, Shubbar, Murtada, Huang, Xuhui, and Liu, Xin. Structural dissection of an interaction between transcription initiation and termination factors implicated in promoter-terminator cross-talk. United States: N. p., 2017. Web. doi:10.1074/jbc.M117.811521.
Bratkowski, Matthew, Unarta, Ilona Christy, Zhu, Lizhe, Shubbar, Murtada, Huang, Xuhui, & Liu, Xin. Structural dissection of an interaction between transcription initiation and termination factors implicated in promoter-terminator cross-talk. United States. doi:10.1074/jbc.M117.811521.
Bratkowski, Matthew, Unarta, Ilona Christy, Zhu, Lizhe, Shubbar, Murtada, Huang, Xuhui, and Liu, Xin. Mon . "Structural dissection of an interaction between transcription initiation and termination factors implicated in promoter-terminator cross-talk". United States. doi:10.1074/jbc.M117.811521. https://www.osti.gov/servlets/purl/1511721.
@article{osti_1511721,
title = {Structural dissection of an interaction between transcription initiation and termination factors implicated in promoter-terminator cross-talk},
author = {Bratkowski, Matthew and Unarta, Ilona Christy and Zhu, Lizhe and Shubbar, Murtada and Huang, Xuhui and Liu, Xin},
abstractNote = {Functional cross-talk between the promoter and terminator of a gene has long been noted. Promoters and terminators are juxtaposed to form gene loops in several organisms, and gene looping is thought to be involved in transcriptional regulation. The general transcription factor IIB (TFIIB) and the C-terminal domain phosphatase Ssu72, essential factors of the transcription preinitiation complex and the mRNA processing and polyadenylation complex, respectively, are important for gene loop formation. TFIIB and Ssu72 interact both genetically and physically, but the molecular basis of this interaction is not known. Here we present a crystal structure of the core domain of TFIIB in two new conformations that differ in the relative distance and orientation of the two cyclin-like domains. The observed extraordinary conformational plasticity may underlie the binding of TFIIB to multiple transcription factors and promoter DNAs that occurs in distinct stages of transcription, including initiation, reinitiation, and gene looping. We mapped the binding interface of the TFIIB-Ssu72 complex using a series of systematic, structure-guided in vitro binding and site-specific photocross-linking assays. Our results indicate that Ssu72 competes with acidic activators for TFIIB binding and that Ssu72 disrupts an intramolecular TFIIB complex known to impede transcription initiation. We also show that the TFIIB-binding site on Ssu72 overlaps with the binding site of symplekin, a component of the mRNA processing and polyadenylation complex. Here, we propose a hand-off model in which Ssu72 mediates a conformational transition in TFIIB, accounting for the role of Ssu72 in transcription reinitiation, gene looping, and promoter-terminator cross-talk.},
doi = {10.1074/jbc.M117.811521},
journal = {Journal of Biological Chemistry},
number = [5],
volume = [293],
place = {United States},
year = {2017},
month = {11}
}

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