1. Cell Biology
  2. Structural Biology and Molecular Biophysics

The Nse5/6-like SIMC1-SLF2 complex localizes SMC5/6 to viral replication centers

  1. Martina Oravcová
  2. Minghua Nie
  3. Nicola Zilio
  4. Shintaro Maeda
  5. Yasaman Jami-Alahmadi
  6. Eros Lazzerini-Denchi
  7. James A Wohlschlegel
  8. Helle D Ulrich
  9. Takanori Otomo
  10. Michael Boddy  Is a corresponding author
  1. Scripps Research Institute, United States
  2. Institute of Molecular Biology, Germany
  3. University of California, Los Angeles, United States
  4. National Cancer Institute, United States
https://doi.org/10.7554/eLife.79676
Share this article
Cite this article
  1. Martina Oravcová
  2. Minghua Nie
  3. Nicola Zilio
  4. Shintaro Maeda
  5. Yasaman Jami-Alahmadi
  6. Eros Lazzerini-Denchi
  7. James A Wohlschlegel
  8. Helle D Ulrich
  9. Takanori Otomo
  10. Michael Boddy
(2022)
The Nse5/6-like SIMC1-SLF2 complex localizes SMC5/6 to viral replication centers
eLife 11:e79676.
https://doi.org/10.7554/eLife.79676
  2. Download BibTeX
  3. Download .RIS

Abstract

The human SMC5/6 complex is a conserved guardian of genome stability and an emerging component of antiviral responses. These disparate functions likely require distinct mechanisms of SMC5/6 regulation. In yeast, Smc5/6 is regulated by its Nse5/6 subunits, but such regulatory subunits for human SMC5/6 are poorly defined. Here, we identify a novel SMC5/6 subunit called SIMC1 that contains SUMO interacting motifs (SIMs) and an Nse5-like domain. We isolated SIMC1 from the proteomic environment of SMC5/6 within polyomavirus large T antigen (LT)-induced subnuclear compartments. SIMC1 uses its SIMs and Nse5-like domain to localize SMC5/6 to polyomavirus replication centers (PyVRCs) at SUMO-rich PML nuclear bodies. SIMC1's Nse5-like domain binds to the putative Nse6 orthologue SLF2 to form an anti-parallel helical dimer resembling the yeast Nse5/6 structure. SIMC1-SLF2 structure-based mutagenesis defines a conserved surface region containing the N-terminus of SIMC1's helical domain that regulates SMC5/6 localization to PyVRCs. Furthermore, SLF1, which recruits SMC5/6 to DNA lesions via its BRCT and ARD motifs, binds SLF2 analogously to SIMC1 and forms a separate Nse5/6-like complex. Thus, two Nse5/6-like complexes with distinct recruitment domains control human SMC5/6 localization.

Data availability

The SMC5 and SIMC1 BioID datasets have been deposited to the PRIDE database (85) as follows: Protein interaction AP-MS data: PRIDE PXD033923. Cryo-EM density map and atomic coordinates of the SIMC1-SLF2 complex have been deposited to the Electron Microscopy Data Bank and wwPDB, respectively, under accession codes EMD-25706 and PDB 7T5P.

The following data sets were generated

Article and author information

Author details

  1. Martina Oravcová

    Department of Molecular Medicine, Scripps Research Institute, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.

  2. Minghua Nie

    Department of Molecular Medicine, Scripps Research Institute, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.

  3. Nicola Zilio

    Institute of Molecular Biology, Mainz, Germany
    Competing interests
    The authors declare that no competing interests exist.

  4. Shintaro Maeda

    Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.

  5. Yasaman Jami-Alahmadi

    Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States
    Competing interests
    The authors declare that no competing interests exist.

  6. Eros Lazzerini-Denchi

    Laboratory of Genome Integrity, National Cancer Institute, Bethesda, United States
    Competing interests
    The authors declare that no competing interests exist.

  7. James A Wohlschlegel

    Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States
    Competing interests
    The authors declare that no competing interests exist.

  8. Helle D Ulrich

    Institute of Molecular Biology, Mainz, Germany
    Competing interests
    The authors declare that no competing interests exist.

  9. Takanori Otomo

    Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3589-238X

  10. Michael Boddy

    Department of Molecular Medicine, Scripps Research Institute, La Jolla, United States
    For correspondence
    nboddy@scripps.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7618-4449

Funding

National Institute of General Medical Sciences (GM136273)

  • Michael Boddy

National Institute of General Medical Sciences (GM089788)

  • James A Wohlschlegel

National Institute of General Medical Sciences (GM092740)

  • Takanori Otomo

Deutsche Forschungsgemeinschaft (393547839 - SFB 1361,sub-project 07)

  • Helle D Ulrich

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

Copyright

This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

Metrics

  • 2,066
    views
  • 290
    downloads
  • 15
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

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)

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

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

  1. Martina Oravcová
  2. Minghua Nie
  3. Nicola Zilio
  4. Shintaro Maeda
  5. Yasaman Jami-Alahmadi
  6. Eros Lazzerini-Denchi
  7. James A Wohlschlegel
  8. Helle D Ulrich
  9. Takanori Otomo
  10. Michael Boddy
(2022)
The Nse5/6-like SIMC1-SLF2 complex localizes SMC5/6 to viral replication centers
eLife 11:e79676.
https://doi.org/10.7554/eLife.79676

Share this article

https://doi.org/10.7554/eLife.79676

Categories and tags

Research organism

Further reading

    1. Cell Biology
    2. Computational and Systems Biology

    Unbiased identification of cell identity in dense mixed neural cultures

    Sarah De Beuckeleer, Tim Van De Looverbosch ... Winnok H De Vos
    Research Article

    Induced pluripotent stem cell (iPSC) technology is revolutionizing cell biology. However, the variability between individual iPSC lines and the lack of efficient technology to comprehensively characterize iPSC-derived cell types hinder its adoption in routine preclinical screening settings. To facilitate the validation of iPSC-derived cell culture composition, we have implemented an imaging assay based on cell painting and convolutional neural networks to recognize cell types in dense and mixed cultures with high fidelity. We have benchmarked our approach using pure and mixed cultures of neuroblastoma and astrocytoma cell lines and attained a classification accuracy above 96%. Through iterative data erosion, we found that inputs containing the nuclear region of interest and its close environment, allow achieving equally high classification accuracy as inputs containing the whole cell for semi-confluent cultures and preserved prediction accuracy even in very dense cultures. We then applied this regionally restricted cell profiling approach to evaluate the differentiation status of iPSC-derived neural cultures, by determining the ratio of postmitotic neurons and neural progenitors. We found that the cell-based prediction significantly outperformed an approach in which the population-level time in culture was used as a classification criterion (96% vs 86%, respectively). In mixed iPSC-derived neuronal cultures, microglia could be unequivocally discriminated from neurons, regardless of their reactivity state, and a tiered strategy allowed for further distinguishing activated from non-activated cell states, albeit with lower accuracy. Thus, morphological single-cell profiling provides a means to quantify cell composition in complex mixed neural cultures and holds promise for use in the quality control of iPSC-derived cell culture models.

    1. Cell Biology

    Endocytic recycling is central to circadian collagen fibrillogenesis and disrupted in fibrosis

    Joan Chang, Adam Pickard ... Karl E Kadler
    Research Article

    Collagen-I fibrillogenesis is crucial to health and development, where dysregulation is a hallmark of fibroproliferative diseases. Here, we show that collagen-I fibril assembly required a functional endocytic system that recycles collagen-I to assemble new fibrils. Endogenous collagen production was not required for fibrillogenesis if exogenous collagen was available, but the circadian-regulated vacuolar protein sorting (VPS) 33b and collagen-binding integrin α11 subunit were crucial to fibrillogenesis. Cells lacking VPS33B secrete soluble collagen-I protomers but were deficient in fibril formation, thus secretion and assembly are separately controlled. Overexpression of VPS33B led to loss of fibril rhythmicity and overabundance of fibrils, which was mediated through integrin α11β1. Endocytic recycling of collagen-I was enhanced in human fibroblasts isolated from idiopathic pulmonary fibrosis, where VPS33B and integrin α11 subunit were overexpressed at the fibrogenic front; this correlation between VPS33B, integrin α11 subunit, and abnormal collagen deposition was also observed in samples from patients with chronic skin wounds. In conclusion, our study showed that circadian-regulated endocytic recycling is central to homeostatic assembly of collagen fibrils and is disrupted in diseases.

    1. Cell Biology

    Hypersensitive intercellular responses of endometrial stromal cells drive invasion in endometriosis

    Chun-Wei Chen, Jeffery B Chavez ... Bruce J Nicholson
    Research Article Updated

    Endometriosis is a debilitating disease affecting 190 million women worldwide and the greatest single contributor to infertility. The most broadly accepted etiology is that uterine endometrial cells retrogradely enter the peritoneum during menses, and implant and form invasive lesions in a process analogous to cancer metastasis. However, over 90% of women suffer retrograde menstruation, but only 10% develop endometriosis, and debate continues as to whether the underlying defect is endometrial or peritoneal. Processes implicated in invasion include: enhanced motility; adhesion to, and formation of gap junctions with, the target tissue. Endometrial stromal (ESCs) from 22 endometriosis patients at different disease stages show much greater invasiveness across mesothelial (or endothelial) monolayers than ESCs from 22 control subjects, which is further enhanced by the presence of EECs. This is due to the enhanced responsiveness of endometriosis ESCs to the mesothelium, which induces migration and gap junction coupling. ESC-PMC gap junction coupling is shown to be required for invasion, while coupling between PMCs enhances mesothelial barrier breakdown.