1. Cell Biology
  2. Chromosomes and Gene Expression

S-adenosylmethionine synthases specify distinct H3K4me3 populations and gene expression patterns during heat stress

  1. Adwait A Godbole
  2. Sneha Gopalan
  3. Thien-Kim Nguyen
  4. Alexander L Munden
  5. Dominique S Lui
  6. Matthew G Fanelli
  7. Paula Vo
  8. Caroline A Lewis
  9. Jessica B Spinelli
  10. Thomas G Fazzio
  11. Amy K Walker  Is a corresponding author
  1. University of Massachusetts Medical School, United States
https://doi.org/10.7554/eLife.79511
Share this article
Cite this article
  1. Adwait A Godbole
  2. Sneha Gopalan
  3. Thien-Kim Nguyen
  4. Alexander L Munden
  5. Dominique S Lui
  6. Matthew G Fanelli
  7. Paula Vo
  8. Caroline A Lewis
  9. Jessica B Spinelli
  10. Thomas G Fazzio
  11. Amy K Walker
(2023)
S-adenosylmethionine synthases specify distinct H3K4me3 populations and gene expression patterns during heat stress
eLife 12:e79511.
https://doi.org/10.7554/eLife.79511
  2. Download BibTeX
  3. Download .RIS

Abstract

Methylation is a widely occurring modification that requires the methyl donor S-adenosylmethionine (SAM) and acts in regulation of gene expression and other processes. SAM is synthesized from methionine, which is imported or generated through the 1-carbon cycle (1CC). Alterations in 1CC function have clear effects on lifespan and stress responses, but the wide distribution of this modification has made identification of specific mechanistic links difficult. Exploiting a dynamic stress-induced transcription model, we find that two SAM synthases in Caenorhabditis elegans, SAMS-1 and SAMS-4, contribute differently to modification of H3K4me3, gene expression and survival. We find that sams-4 enhances H3K4me3 in heat shocked animals lacking sams-1, however, sams-1 cannot compensate for sams-4, which is required to survive heat stress. This suggests that the regulatory functions of SAM depend on its enzymatic source and that provisioning of SAM may be an important regulatory step linking 1CC function to phenotypes in aging and stress.

Data availability

Sequencing data have been deposited in GEO under accession code GSE223597.

The following previously published data sets were used

Article and author information

Author details

  1. Adwait A Godbole

    Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.

  2. Sneha Gopalan

    Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.

  3. Thien-Kim Nguyen

    Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.

  4. Alexander L Munden

    Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.

  5. Dominique S Lui

    Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.

  6. Matthew G Fanelli

    Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.

  7. Paula Vo

    Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.

  8. Caroline A Lewis

    Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.

  9. Jessica B Spinelli

    Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.

  10. Thomas G Fazzio

    3.Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0353-7466

  11. Amy K Walker

    3.Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
    For correspondence
    amy.walker@umassmed.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1899-8916

Funding

National Institutes of Health (1R01AG053355)

  • Amy K Walker

National Institutes of Health (R01HD072122)

  • Thomas G Fazzio

National Institutes of Health (K99CA273420)

  • Sneha Gopalan

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

Reviewing Editor

  1. Jan Gruber, Yale-NUS College, Singapore

Publication history

  1. Preprint posted: March 30, 2022 (view preprint)
  2. Received: April 15, 2022
  3. Accepted: February 7, 2023
  4. Accepted Manuscript published: February 9, 2023 (version 1)
  5. Accepted Manuscript updated: February 10, 2023 (version 2)
  6. Version of Record published: March 3, 2023 (version 3)

Copyright

© 2023, Godbole 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

  • 1,150
    Page views
  • 166
    Downloads
  • 0
    Citations

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

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. Adwait A Godbole
  2. Sneha Gopalan
  3. Thien-Kim Nguyen
  4. Alexander L Munden
  5. Dominique S Lui
  6. Matthew G Fanelli
  7. Paula Vo
  8. Caroline A Lewis
  9. Jessica B Spinelli
  10. Thomas G Fazzio
  11. Amy K Walker
(2023)
S-adenosylmethionine synthases specify distinct H3K4me3 populations and gene expression patterns during heat stress
eLife 12:e79511.
https://doi.org/10.7554/eLife.79511

Categories and tags

Research organism

Further reading

    1. Cell Biology

    The Uso1 globular head interacts with SNAREs to maintain viability even in the absence of the coiled-coil domain

    Ignacio Bravo-Plaza, Victor G Tagua ... Miguel A Peñalva
    Research Article

    Uso1/p115 and RAB1 tether ER-derived vesicles to the Golgi. Uso1/p115 contains a globular-head-domain (GHD), a coiled-coil (CC) mediating dimerization/tethering and a C-terminal region (CTR) interacting with golgins. Uso1/p115 is recruited to vesicles by RAB1. Genetic studies placed Uso1 paradoxically acting upstream of, or in conjunction with RAB1 (Sapperstein et al., 1996). We selected two missense mutations in uso1 resulting in E6K and G540S in the GHD that rescued lethality of rab1-deficient Aspergillus nidulans. The mutations are phenotypically additive, their combination suppressing the complete absence of RAB1, which emphasizes the key physiological role of the GHD. In living hyphae Uso1 recurs on puncta (60 sec half-life) colocalizing partially with the Golgi markers RAB1, Sed5 and GeaA/Gea1/Gea2, and totally with the retrograde cargo receptor Rer1, consistent with Uso1 dwelling in a very early Golgi compartment from which ER residents reaching the Golgi recycled back to the ER. Localization of Uso1, but not of Uso1E6K/G540S, to puncta is abolished by compromising RAB1 function, indicating that E6K/G540S creates interactions bypassing RAB1. That Uso1 delocalization correlates with a decrease in the number of Gea1 cisternae supports that Uso1-and-Rer1-containing puncta are where the protein exerts its physiological role. In S-tag-coprecipitation experiments Uso1 is an associate of the Sed5/Bos1/Bet1/Sec22 SNARE complex zippering vesicles with the Golgi, with Uso1E6K/G540S showing stronger association. Using purified proteins, we show that Bos1 and Bet1 bind the Uso1 GHD directly. However, Bet1 is a strong E6K/G540S-independent binder, whereas Bos1 is weaker but becomes as strong as Bet1 when the GHD carries E6K/G540S. G540S alone markedly increases GHD binding to Bos1, whereas E6K causes a weaker effect, correlating with their phenotypic contributions. AlphaFold2 predicts that G540S increases binding of the GHD to the Bos1 Habc domain. In contrast, E6K lies in an N-terminal, potentially alpha-helical, region that sensitive genetic tests indicate as required for full Uso1 function. Remarkably, this region is at the end of the GHD basket opposite to the end predicted to interact with Bos1. We show that unlike dimeric full-length and CTR∆ Uso1 proteins, the GHD lacking the CC/CTR dimerization domain, whether originating from bacteria or Aspergillus extracts and irrespective of whether it carries or not E6K/G540S, would appear to be monomeric. With the finding that overexpression of E6K/G540S and wild-type GHD complement uso1∆, our data indicate that the GHD monomer is capable of providing, at least partially, the essential Uso1 functions, and that long-range tethering activity is dispensable. Rather, these findings strongly suggest that the essential role of Uso1 involves the regulation of SNAREs.

    1. Cell Biology

    Global analysis of contact-dependent human-to-mouse intercellular mRNA and lncRNA transfer in cell culture

    Sandipan Dasgupta, Daniella Y Dayagi ... Jeffrey E Gerst
    Research Article

    Full-length mRNAs transfer between adjacent mammalian cells via direct cell-to-cell connections called tunneling nanotubes (TNTs). However, the extent of mRNA transfer at the transcriptome-wide level (the 'transferome') is unknown. Here, we analyzed the transferome in an in vitro human-mouse cell co-culture model using RNA-sequencing. We found that mRNA transfer is non-selective, prevalent across the human transcriptome, and that the amount of transfer to mouse embryonic fibroblasts (MEFs) strongly correlates with the endogenous level of gene expression in donor human breast cancer cells. Typically, <1% of endogenous mRNAs undergo transfer. Non-selective, expression-dependent RNA transfer was further validated using synthetic reporters. RNA transfer appears contact-dependent via TNTs, as exemplified for several mRNAs. Notably, significant differential changes in the native MEF transcriptome were observed in response to co-culture, including the upregulation of multiple cancer and cancer-associated fibroblast-related genes and pathways. Together, these results lead us to suggest that TNT-mediated RNA transfer could be a phenomenon of physiological importance under both normal and pathogenic conditions.

    1. Cell Biology

    Insights into cargo sorting by SNX32 and its role in neurite outgrowth

    Jini Sugatha, Amulya Priya ... Sunando Datta
    Research Article Updated

    Sorting nexins (SNX) are a family of proteins containing the Phox homology domain, which shows a preferential endo-membrane association and regulates cargo sorting processes. Here, we established that SNX32, an SNX-BAR (Bin/Amphiphysin/Rvs) sub-family member associates with SNX4 via its BAR domain and the residues A226, Q259, E256, R366 of SNX32, and Y258, S448 of SNX4 that lie at the interface of these two SNX proteins mediate this association. SNX32, via its PX domain, interacts with the transferrin receptor (TfR) and Cation-Independent Mannose-6-Phosphate Receptor (CIMPR), and the conserved F131 in its PX domain is important in stabilizing these interactions. Silencing of SNX32 leads to a defect in intracellular trafficking of TfR and CIMPR. Further, using SILAC-based differential proteomics of the wild-type and the mutant SNX32, impaired in cargo binding, we identified Basigin (BSG), an immunoglobulin superfamily member, as a potential interactor of SNX32 in SHSY5Y cells. We then demonstrated that SNX32 binds to BSG through its PX domain and facilitates its trafficking to the cell surface. In neuroglial cell lines, silencing of SNX32 leads to defects in neuronal differentiation. Moreover, abrogation in lactate transport in the SNX32-depleted cells led us to propose that SNX32 may contribute to maintaining the neuroglial coordination via its role in BSG trafficking and the associated monocarboxylate transporter activity. Taken together, our study showed that SNX32 mediates the trafficking of specific cargo molecules along distinct pathways.