Phase separation of the LINE-1 ORF1 protein is mediated by the N-terminus and coiled-coil domain

Newton, Jocelyn C.; Naik, Mandar T.; Li, Grace Y.; Murphy, E.; Fawzi, Nicolas L.; Sedivy, John M.; Jogl, G.

doi:10.1016/j.bpj.2021.03.028

Cited by 36 publications

(24 citation statements)

References 59 publications

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“…Considering that ORF1p interacts with ribosomes, as shown by orthogonal approaches, we propose that ORF1p might interact with ribosome-associated RNAs. Notably, our observations in vivo agree with recent reports of ORF1p capacity to phase separate and form condensates with RNAs that are required for L1 retrotransposition, further supporting the leading role of ORF1p in LBs formation 89, 90 .…”

Section: Discussionsupporting

confidence: 91%

Ribonucleoprotein condensation driven by retrotransposon LINE-1 sustains RNA integrity and translation in mouse spermatocytes

Luca

Gupta

Bortvin

2023

Preprint

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Transposable elements (TE) are mobile DNA sequences whose excessive proliferation endangers the host. Although animals have evolved robust TE-targeting defenses, including Piwi- interacting (pi)RNAs, retrotransposon LINE-1 (L1) still thrives in humans and mice. To gain insights into L1 endurance, we characterized L1 Bodies (LBs) and ORF1p complexes in germ cells of piRNA-deficient Maelstrom null mice. We report that ORF1p interacts with TE RNAs, genic mRNAs, and stress granule proteins, consistent with earlier studies. We also show that ORF1p associates with the CCR4-NOT deadenylation complex and PRKRA, a Protein Kinase R factor. Despite ORF1p interactions with these negative regulators of RNA expression, the stability and translation of LB-localized mRNAs remain unchanged. To scrutinize these findings, we studied the effects of PRKRA on L1 in cultured cells and showed that it elevates ORF1p levels and L1 retrotransposition. These results suggest that ORF1p-driven condensates promote L1 propagation, without affecting the metabolism of endogenous RNAs.

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Section: Discussionsupporting

confidence: 91%

Ribonucleoprotein condensation driven by retrotransposon LINE-1 sustains RNA integrity and translation in mouse spermatocytes

Luca

Gupta

Bortvin

2023

Preprint

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“…Constituent subunits of condensates, including SC proteins, can enter and exit condensates and move within them. Coiled-coils can facilitate phase-separation (47,48), potentially by promoting multivalent interactions (49,50). This is consistent with the poor per-site conservation of SC proteins, since multivalent interactions can rely on molecular features exhibited by groups of amino acids (e.g., charge or hydrophobicity) rather than tight, 'lock-and-key' interfaces formed by specific tertiary structures.…”

Section: Discussionsupporting

confidence: 56%

Unconventional conservation reveals structure-function relationships in the synaptonemal complex

Kursel

Cope

Rog

2021

Preprint

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Functional requirements constrain protein evolution, commonly manifesting in conserved primary amino acid sequence. Here, we extend this idea to secondary structural features by tracking their conservation in essential meiotic proteins with highly diverged sequences. The synaptonemal complex (SC) aligns parental chromosome pairs and regulates exchanges between them. In electron micrographs of meiocytes from all eukaryotic clades, the SC appears as a ~100 nm-wide ladder-like structure with regular striations. Despite the conserved ultrastructure and functions, the proteins that make up the SC are highly divergent in sequence. Here we found that, within the Caenorhabditis genus, SC proteins are significantly more diverged than other proteins. However, SC proteins have highly conserved protein length and coiled-coil domain structure. The same unconventional conservation signature holds true for SC proteins in Drosophila and mammals, suggesting it could be a universal feature of SC proteins. We used this evolutionary signature to identify a novel SC protein in the nematode Pristionchus pacificus, Ppa-SYP-1, which has no significant homology to any protein outside of Pristionchus. Our work suggests that the length and relative arrangement of coiled-coils play a key role in the structure and function of the SC. Furthermore, our analysis implies that expanding sequence analysis beyond measures of per-site identity or similarity can enhance our understanding of protein evolution and function.

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“…Both full-length and truncated ORF1p that contain the intrinsically disordered N-terminal domain (ORF 1–53 ) and coiled-coil domain (ORF1 1–152 ) are capable of robust phase separation that form dynamic cytoplasmic membraneless condensates [ 747 , 748 ]. Even though the disordered N-terminal domain promotes LLPS, phase separation of ORF1p is dependent upon the interactions between the N-terminal and coiled-coil domains; furthermore, LLPS of ORF1p can be inhibited by high salt concentration [ 747 ], where no condensate formation was observed above 300 mM potassium chloride (KCl) [ 748 ]. Decreasing the ratio of ORF1p to RNA changes the viscosity and surface tension of condensates, slowing droplet fusion kinetics, and even alters the physical properties of L1 condensates [ 748 ].…”

Section: Melatonin Regulates Sars-cov-2-mediated Crosstalk Between Th...mentioning

confidence: 99%

Melatonin: Regulation of Viral Phase Separation and Epitranscriptomics in Post-Acute Sequelae of COVID-19

Loh¹,

Reíter

2022

IJMS

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The relentless, protracted evolution of the SARS-CoV-2 virus imposes tremendous pressure on herd immunity and demands versatile adaptations by the human host genome to counter transcriptomic and epitranscriptomic alterations associated with a wide range of short- and long-term manifestations during acute infection and post-acute recovery, respectively. To promote viral replication during active infection and viral persistence, the SARS-CoV-2 envelope protein regulates host cell microenvironment including pH and ion concentrations to maintain a high oxidative environment that supports template switching, causing extensive mitochondrial damage and activation of pro-inflammatory cytokine signaling cascades. Oxidative stress and mitochondrial distress induce dynamic changes to both the host and viral RNA m6A methylome, and can trigger the derepression of long interspersed nuclear element 1 (LINE1), resulting in global hypomethylation, epigenetic changes, and genomic instability. The timely application of melatonin during early infection enhances host innate antiviral immune responses by preventing the formation of “viral factories” by nucleocapsid liquid-liquid phase separation that effectively blockades viral genome transcription and packaging, the disassembly of stress granules, and the sequestration of DEAD-box RNA helicases, including DDX3X, vital to immune signaling. Melatonin prevents membrane depolarization and protects cristae morphology to suppress glycolysis via antioxidant-dependent and -independent mechanisms. By restraining the derepression of LINE1 via multifaceted strategies, and maintaining the balance in m6A RNA modifications, melatonin could be the quintessential ancient molecule that significantly influences the outcome of the constant struggle between virus and host to gain transcriptomic and epitranscriptomic dominance over the host genome during acute infection and PASC.

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Phase separation of the LINE-1 ORF1 protein is mediated by the N-terminus and coiled-coil domain

Cited by 36 publications

References 59 publications

Ribonucleoprotein condensation driven by retrotransposon LINE-1 sustains RNA integrity and translation in mouse spermatocytes

Ribonucleoprotein condensation driven by retrotransposon LINE-1 sustains RNA integrity and translation in mouse spermatocytes

Unconventional conservation reveals structure-function relationships in the synaptonemal complex

Melatonin: Regulation of Viral Phase Separation and Epitranscriptomics in Post-Acute Sequelae of COVID-19

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