1. Biochemistry and Chemical Biology
  2. Cell Biology
Download icon

Targeting of the Fun30 nucleosome remodeller by the Dpb11 scaffold facilitates cell cycle-regulated DNA end resection

  1. Susanne CS Bantele
  2. Pedro Ferreira
  3. Dalia Gritenaite
  4. Dominik Boos
  5. Boris Pfander  Is a corresponding author
  1. Max Planck Institute of Biochemistry, Germany
  2. University Duisburg-Essen, Germany
Research Article
  • Cited 34
  • Views 2,306
  • Annotations
Cite this article as: eLife 2017;6:e21687 doi: 10.7554/eLife.21687

Abstract

DNA double strand breaks (DSBs) can be repaired by either recombination-based or direct ligation-based mechanisms. Pathway choice is made at the level of DNA end resection, a nucleolytic processing step, which primes DSBs for repair by recombination. Resection is thus under cell cycle control, but additionally regulated by chromatin and nucleosome remodellers. Here we show that both layers of control converge in the regulation of resection by the evolutionarily conserved Fun30/SMARCAD1 remodeller. Yeast Fun30 and human SMARCAD1 are cell cycle-regulated by interaction with the DSB-localized scaffold proteins Dpb11 and TOPBP1, respectively. In yeast this protein assembly additionally comprises the 9-1-1 damage sensor, is involved in localizing Fun30 to damaged chromatin and thus is required for efficient long-range resection of DSBs. Notably, artificial targeting of Fun30 to DSBs is sufficient to bypass the cell cycle regulation of long-range resection, indicating that chromatin remodelling during resection is underlying DSB repair pathway choice.

Article and author information

Author details

  1. Susanne CS Bantele

    DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
    Competing interests
    The authors declare that no competing interests exist.
  2. Pedro Ferreira

    Centre for Medical Biotechnology, University Duisburg-Essen, Essen, Germany
    Competing interests
    The authors declare that no competing interests exist.
  3. Dalia Gritenaite

    DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
    Competing interests
    The authors declare that no competing interests exist.
  4. Dominik Boos

    Centre for Medical Biotechnology, University Duisburg-Essen, Essen, Germany
    Competing interests
    The authors declare that no competing interests exist.
  5. Boris Pfander

    DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
    For correspondence
    bpfander@biochem.mpg.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2180-5054

Funding

Deutsche Forschungsgemeinschaft (Project Grant,PF794/3-1)

  • Boris Pfander

Max-Planck-Gesellschaft (Grant)

  • Boris Pfander

Fonds der chemischen Industrie (Fellowship)

  • Susanne CS Bantele

NRW Rueckkehrerprogramm from the stae of North-Rhine-Westphalia (Grant)

  • Dominik Boos

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

Reviewing Editor

  1. Gregory Ira, Baylor College of Medicine, United States

Publication history

  1. Received: September 21, 2016
  2. Accepted: January 3, 2017
  3. Accepted Manuscript published: January 7, 2017 (version 1)
  4. Accepted Manuscript updated: January 12, 2017 (version 2)
  5. Version of Record published: February 9, 2017 (version 3)

Copyright

© 2017, Bantele 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

  • 2,306
    Page views
  • 719
    Downloads
  • 34
    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
    Nazia Ahmad et al.
    Research Article Updated

    L,D-transpeptidase function predominates in atypical 3 → 3 transpeptide networking of peptidoglycan (PG) layer in Mycobacterium tuberculosis. Prior studies of L,D-transpeptidases have identified only the catalytic site that binds to peptide moiety of the PG substrate or β-lactam antibiotics. This insight was leveraged to develop mechanism of its activity and inhibition by β-lactams. Here, we report identification of an allosteric site at a distance of 21 Å from the catalytic site that binds the sugar moiety of PG substrates (hereafter referred to as the S-pocket). This site also binds a second β-lactam molecule and influences binding at the catalytic site. We provide evidence that two β-lactam molecules bind co-operatively to this enzyme, one non-covalently at the S-pocket and one covalently at the catalytic site. This dual β-lactam-binding phenomenon is previously unknown and is an observation that may offer novel approaches for the structure-based design of new drugs against M. tuberculosis.

    1. Biochemistry and Chemical Biology
    Erika Alden DeBenedictis et al.
    Research Article Updated

    Translation using four-base codons occurs in both natural and synthetic systems. What constraints contributed to the universal adoption of a triplet codon, rather than quadruplet codon, genetic code? Here, we investigate the tolerance of the Escherichia coli genetic code to tRNA mutations that increase codon size. We found that tRNAs from all 20 canonical isoacceptor classes can be converted to functional quadruplet tRNAs (qtRNAs). Many of these selectively incorporate a single amino acid in response to a specified four-base codon, as confirmed with mass spectrometry. However, efficient quadruplet codon translation often requires multiple tRNA mutations. Moreover, while tRNAs were largely amenable to quadruplet conversion, only nine of the twenty aminoacyl tRNA synthetases tolerate quadruplet anticodons. These may constitute a functional and mutually orthogonal set, but one that sharply limits the chemical alphabet available to a nascent all-quadruplet code. Our results suggest that the triplet codon code was selected because it is simpler and sufficient, not because a quadruplet codon code is unachievable. These data provide a blueprint for synthetic biologists to deliberately engineer an all-quadruplet expanded genetic code.