1. Biochemistry and Chemical Biology
  2. Chromosomes and Gene Expression
Download icon

Chemical perturbation of an intrinsically disordered region of TFIID distinguishes two modes of transcription initiation

  1. Zhengjian Zhang  Is a corresponding author
  2. Zarko Boskovic
  3. Mahmud M Hussain
  4. Wenxin Hu
  5. Carla Inouye
  6. Han-Je Kim
  7. A Katherine Abole
  8. Mary K Doud
  9. Timothy A Lewis
  10. Angela N Koehler
  11. Stuart L Schreiber
  12. Robert Tjian
  1. Janelia Research Campus, Howard Hughes Medical Institute, United States
  2. Howard Hughes Medical Institute, Harvard University, United States
  3. Howard Hughes Medical Institute, University of California, Berkeley, United States
  4. Broad Institute, United States
  5. University of California, Berkeley, United States
Research Article
  • Cited 26
  • Views 2,498
  • Annotations
Cite this article as: eLife 2015;4:e07777 doi: 10.7554/eLife.07777

Abstract

Intrinsically disordered protein regions (IDRs) are peptide segments that fail to form stable 3-dimensional structures in the absence of partner proteins. They are abundant in eukaryotic proteomes and are often associated with human diseases, but their biological functions have been elusive to study. Here we report the identification of a tin(IV) oxochloride-derived cluster that binds an evolutionarily conserved IDR within the metazoan TFIID transcription complex. Binding arrests an isomerization of promoter-bound TFIID that is required for the engagement of Pol II during the first (de novo) round of transcription initiation. However, the specific chemical probe does not affect reinitiation, which requires the re-entry of Pol II, thus, mechanistically distinguishing these two modes of transcription initiation. This work also suggests a new avenue for targeting the elusive IDRs by harnessing certain features of metal-based complexes for mechanistic studies, and for the development of novel pharmaceutical interventions.

Article and author information

Author details

  1. Zhengjian Zhang

    Transcription Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
    For correspondence
    zhangzh@janelia.hhmi.org
    Competing interests
    No competing interests declared.
  2. Zarko Boskovic

    Department of Chemistry and Chemical Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
    Competing interests
    No competing interests declared.
  3. Mahmud M Hussain

    Department of Chemistry and Chemical Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
    Competing interests
    No competing interests declared.
  4. Wenxin Hu

    Transcription Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
    Competing interests
    No competing interests declared.
  5. Carla Inouye

    Li Ka Shing Center for Biomedical and Health Sciences, Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
    Competing interests
    No competing interests declared.
  6. Han-Je Kim

    Center for the Science of Therapeutics, Broad Institute, Cambridge, United States
    Competing interests
    No competing interests declared.
  7. A Katherine Abole

    Department of Chemistry, University of California, Berkeley, Berkeley, United States
    Competing interests
    No competing interests declared.
  8. Mary K Doud

    Center for the Science of Therapeutics, Broad Institute, Cambridge, United States
    Competing interests
    No competing interests declared.
  9. Timothy A Lewis

    Center for the Science of Therapeutics, Broad Institute, Cambridge, United States
    Competing interests
    No competing interests declared.
  10. Angela N Koehler

    Center for the Science of Therapeutics, Broad Institute, Cambridge, United States
    Competing interests
    No competing interests declared.
  11. Stuart L Schreiber

    Department of Chemistry and Chemical Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
    Competing interests
    No competing interests declared.
  12. Robert Tjian

    Transcription Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
    Competing interests
    Robert Tjian, President of the Howard Hughes Medical Institute (2009-present), one of the three founding funders of eLife, and a member of eLife's Board of Directors.

Reviewing Editor

  1. Danny Reinberg, Howard Hughes Medical Institute, New York University School of Medicine, United States

Publication history

  1. Received: March 29, 2015
  2. Accepted: August 27, 2015
  3. Accepted Manuscript published: August 28, 2015 (version 1)
  4. Version of Record published: September 25, 2015 (version 2)

Copyright

© 2015, Zhang et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 2,498
    Page views
  • 576
    Downloads
  • 26
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, Scopus, PubMed Central.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Download citations (links to download the citations from this article in formats compatible with various reference manager tools)

Open citations (links to open the citations from this article in various online reference manager services)

Further reading

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Paul Fischer et al.
    Research Article

    Enzymerhodopsins represent a recently discovered class of rhodopsins which includes histidine kinase rhodopsin, rhodopsin phosphodiesterases and rhodopsin guanylyl cyclases (RGCs). The regulatory influence of the rhodopsin domain on the enzyme activity is only partially understood and holds the key for a deeper understanding of intra-molecular signaling pathways. Here we present a UV-Vis and FTIR study about the light-induced dynamics of a RGC from the fungus Catenaria anguillulae, which provides insights into the catalytic process. After the spectroscopic characterization of the late rhodopsin photoproducts, we analyzed truncated variants and revealed the involvement of the cytosolic N-terminus in the structural rearrangements upon photo-activation of the protein. We tracked the catalytic reaction of RGC and the free GC domain independently by UV-light induced release of GTP from the photolabile NPE-GTP substrate. Our results show substrate binding to the dark-adapted RGC and GC alike and reveal differences between the constructs attributable to the regulatory influence of the rhodopsin on the conformation of the binding pocket. By monitoring the phosphate rearrangement during cGMP and pyrophosphate formation in light-activated RGC, we were able to confirm the M state as the active state of the protein. The described setup and experimental design enable real-time monitoring of substrate turnover in light-activated enzymes on a molecular scale, thus opening the pathway to a deeper understanding of enzyme activity and protein-protein interactions.

    1. Biochemistry and Chemical Biology
    2. Chromosomes and Gene Expression
    Gemma LM Fisher et al.
    Research Article Updated

    Structural Maintenance of Chromosomes (SMC) complexes have ubiquitous roles in compacting DNA linearly, thereby promoting chromosome organization-segregation. Interaction between the Escherichia coli SMC complex, MukBEF, and matS-bound MatP in the chromosome replication termination region, ter, results in depletion of MukBEF from ter, a process essential for efficient daughter chromosome individualization and for preferential association of MukBEF with the replication origin region. Chromosome-associated MukBEF complexes also interact with topoisomerase IV (ParC2E2), so that their chromosome distribution mirrors that of MukBEF. We demonstrate that MatP and ParC have an overlapping binding interface on the MukB hinge, leading to their mutually exclusive binding, which occurs with the same dimer to dimer stoichiometry. Furthermore, we show that matS DNA competes with the MukB hinge for MatP binding. Cells expressing MukBEF complexes that are mutated at the ParC/MatP binding interface are impaired in ParC binding and have a mild defect in MukBEF function. These data highlight competitive binding as a means of globally regulating MukBEF-topoisomerase IV activity in space and time.