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The prevalence and distribution in genomes of low-complexity, amyloid-like, reversible, kinked segment (LARKS), a common structural motif in amyloid-like fibrils

View ORCID ProfileMichael P. Hughes, Luki Goldschmidt, View ORCID ProfileDavid S. Eisenberg
doi: https://doi.org/10.1101/2020.12.08.415679
Michael P. Hughes
Department of Biological Chemistry, UCLA-DOE Institute, HHMI, and Molecular Biology Institute, UCLA, Los Angeles 90095-1570
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Luki Goldschmidt
Department of Biological Chemistry, UCLA-DOE Institute, HHMI, and Molecular Biology Institute, UCLA, Los Angeles 90095-1570
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David S. Eisenberg
Department of Biological Chemistry, UCLA-DOE Institute, HHMI, and Molecular Biology Institute, UCLA, Los Angeles 90095-1570
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  • ORCID record for David S. Eisenberg
  • For correspondence: david@mbi.ucla.edu
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Abstract

Membraneless Organelles (MLOs) are vital and dynamic reaction centers in cells that organize metabolism in the absence of a membrane. Multivalent interactions between protein Low-Complexity Domains (LCDs) contribute to MLO organization. Our previous work used computational methods to identify structural motifs termed Low-complexity Amyloid-like Reversible Kinked Segments (LARKS) that can phase-transition to form hydrogels and are common in human proteins that participate in MLOs. Here we searched for LARKS in proteomes of six model organisms: Homo sapiens, Drosophila melanogaster, Plasmodium falciparum, Saccharomyces cerevisiae, Mycobacterium tuberculosis, and Escherichia coli. We find LARKS are abundant in M. tuberculosis, D. melanogaster, and H. sapiens, but not in S. cerevisiae or P. falciparum. Abundant LARKS require high glycine content, which enables kinks to form in LARKS as is illustrated in the known LARKS-rich amyloid structures of TDP43, FUS, and hnRNPA2, three proteins that participate in MLOs. These results support the idea of LARKS as an evolved structural motif and we offer the LARKSdb webserver which permits users to search for LARKS in their protein sequences of interest.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ↵* Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA

  • ↵# Department of Biochemistry University of Washington Seattle, WA

  • ↵** Email: david{at}mbi.ucla.edu

  • https://servicesn.mbi.ucla.edu/LARKSdb/index.py

  • Abbreviations

    LARKS
    Low Complexity, Amyloid-like Reversible Kinked Segments
    LCDs
    Low-Complexity Domains
    PrLDs
    Prion-like Domains
    IDRs
    Intrinsically Disordered Regions
    LLPS
    Liquid-Liquid Phase Separation
    MLOs
    Membraneless Organelles
    LARKS∩LCD protein
    protein that has at least one LCD and for which the fraction of LARKS is greater than average for its proteome
    LARKS∩LCD residue
    an amino acid residue that is a predicted LARKS within a LCD
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    The prevalence and distribution in genomes of low-complexity, amyloid-like, reversible, kinked segment (LARKS), a common structural motif in amyloid-like fibrils
    Michael P. Hughes, Luki Goldschmidt, David S. Eisenberg
    bioRxiv 2020.12.08.415679; doi: https://doi.org/10.1101/2020.12.08.415679
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    The prevalence and distribution in genomes of low-complexity, amyloid-like, reversible, kinked segment (LARKS), a common structural motif in amyloid-like fibrils
    Michael P. Hughes, Luki Goldschmidt, David S. Eisenberg
    bioRxiv 2020.12.08.415679; doi: https://doi.org/10.1101/2020.12.08.415679

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