1. Structural Biology and Molecular Biophysics
  2. Plant Biology
Download icon

Kinetics of the LOV domain of ZEITLUPE determine its circadian function in Arabidopsis

  1. Ashutosh Pudasaini
  2. Jae Sung Shim
  3. Young Hun Song
  4. Hua Shi
  5. Takatoshi Kiba
  6. David E Somers
  7. Takato Imaizumi
  8. Brian D Zoltowski  Is a corresponding author
  1. Southern Methodist University, United States
  2. University of Washington, United States
  3. Ohio State University, United States
  4. RIKEN Center for Sustainable Resource Science, Japan
Research Article
  • Cited 24
  • Views 3,174
  • Annotations
Cite this article as: eLife 2017;6:e21646 doi: 10.7554/eLife.21646

Abstract

A LOV (Light, Oxygen, or Voltage) domain containing blue-light photoreceptor ZEITLUPE (ZTL) directs circadian timing by degrading clock proteins in plants. Functions hinge upon allosteric differences coupled to the ZTL photocycle; however, structural and kinetic information was unavailable. Herein, we tune the ZTL photocycle over two orders of magnitude. These variants reveal that ZTL complexes with targets independent of light, but dictates enhanced protein degradation in the dark. In vivo experiments definitively show photocycle kinetics dictate the rate of clock component degradation, thereby impacting circadian period. Structural studies demonstrate that photocycle dependent activation of ZTL depends on an unusual dark-state conformation of ZTL. Crystal structures of ZTL LOV domain confirm delineation of structural and kinetic mechanisms and identify an evolutionarily selected allosteric hinge differentiating modes of PAS/LOV signal transduction. The combined biochemical, genetic and structural studies provide new mechanisms indicating how PAS/LOV proteins integrate environmental variables in complex networks.

Article and author information

Author details

  1. Ashutosh Pudasaini

    Department of Chemistry, Southern Methodist University, Dallas, United States
    Competing interests
    The authors declare that no competing interests exist.

  2. Jae Sung Shim

    Department of Biology, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.

  3. Young Hun Song

    Department of Biology, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.

  4. Hua Shi

    Department of Molecular Genetics, Ohio State University, Columbus, United States
    Competing interests
    The authors declare that no competing interests exist.

  5. Takatoshi Kiba

    RIKEN Center for Sustainable Resource Science, Yokohama, Japan
    Competing interests
    The authors declare that no competing interests exist.

  6. David E Somers

    Department of Molecular Genetics, Ohio State University, Columbus, United States
    Competing interests
    The authors declare that no competing interests exist.

  7. Takato Imaizumi

    Department of Biology, University of Washington, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.

  8. Brian D Zoltowski

    Department of Chemistry, Southern Methodist University, Dallas, United States
    For correspondence
    bzoltowski@smu.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6749-0743

Funding

National Institutes of Health (R15GM109282)

  • Brian D Zoltowski

Herman Frasch Foundation for Chemical Research (739-HF12)

  • Brian D Zoltowski

Rural Development Administration (PJ011175)

  • Young Hun Song
  • Takato Imaizumi

National Science Foundation (MCB 1613643)

  • Brian D Zoltowski

National Institutes of Health (R01GM079712)

  • Takato Imaizumi

National Institutes of Health (R01GM093285)

  • David E Somers

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Richard Amasino, University of Wisconsin, United States

Publication history

  1. Received: September 19, 2016
  2. Accepted: February 26, 2017
  3. Accepted Manuscript published: February 28, 2017 (version 1)
  4. Version of Record published: March 28, 2017 (version 2)
  5. Version of Record updated: March 29, 2017 (version 3)

Copyright

© 2017, Pudasaini 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

  • 3,174
    Page views
  • 674
    Downloads
  • 24
    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)

Categories and tags

Research organism

    1. Of interest

    The structures of Secretory and dimeric Immunoglobulin A

    Sonya Kumar Bharathkar et al.
  2. Further reading

Further reading

    1. Immunology and Inflammation
    2. Structural Biology and Molecular Biophysics

    The structures of Secretory and dimeric Immunoglobulin A

    Sonya Kumar Bharathkar et al.
    Research Article

    Secretory (S) Immunoglobulin (I) A is the predominant mucosal antibody, which binds pathogens and commensal microbes. SIgA is a polymeric antibody, typically containing two copies of IgA that assemble with one joining-chain (JC) to form dimeric (d) IgA that is bound by the polymeric Ig-receptor ectodomain, called secretory component (SC). Here we report the cryo-electron microscopy structures of murine SIgA and dIgA. Structures reveal two IgAs conjoined through four heavy-chain tailpieces and the JC that together form a b-sandwich-like fold. The two IgAs are bent and tilted with respect to each other, forming distinct concave and convex surfaces. In SIgA, SC is bound to one face, asymmetrically contacting both IgAs and JC. The bent and tilted arrangement of complex components limits the possible positions of both sets of antigen binding fragments (Fabs) and preserves steric accessibility to receptor binding sites, likely influencing antigen binding and effector functions.

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Uncovering the basis of protein-protein interaction specificity with a combinatorially complete library

    Thuy-Lan V Lite et al.
    Research Article

    Protein-protein interaction specificity is often encoded at the primary sequence level. However, the contributions of individual residues to specificity are usually poorly understood and often obscured by mutational robustness, sequence degeneracy, and epistasis. Using bacterial toxin-antitoxin systems as a model, we screened a combinatorially complete library of antitoxin variants at three key positions against two toxins. This library enabled us to measure the effect of individual substitutions on specificity in hundreds of genetic backgrounds. These distributions allow inferences about the general nature of interface residues in promoting specificity. We find that positive and negative contributions to specificity are neither inherently coupled nor mutually exclusive. Further, a wild-type antitoxin appears optimized for specificity as no substitutions improve discrimination between cognate and non-cognate partners. By comparing crystal structures of paralogous complexes, we provide a rationale for our observations. Collectively, this work provides a generalizable approach to understanding the logic of molecular recognition.

    1. Microbiology and Infectious Disease
    2. Structural Biology and Molecular Biophysics

    Ebola and Marburg virus matrix layers are locally ordered assemblies of VP40 dimers

    William Wan et al.
    Research Article Updated

    Filoviruses such as Ebola and Marburg virus bud from the host membrane as enveloped virions. This process is achieved by the matrix protein VP40. When expressed alone, VP40 induces budding of filamentous virus-like particles, suggesting that localization to the plasma membrane, oligomerization into a matrix layer, and generation of membrane curvature are intrinsic properties of VP40. There has been no direct information on the structure of VP40 matrix layers within viruses or virus-like particles. We present structures of Ebola and Marburg VP40 matrix layers in intact virus-like particles, and within intact Marburg viruses. VP40 dimers assemble extended chains via C-terminal domain interactions. These chains stack to form 2D matrix lattices below the membrane surface. These lattices form a patchwork assembly across the membrane and suggesting that assembly may begin at multiple points. Our observations define the structure and arrangement of the matrix protein layer that mediates formation of filovirus particles.