Liquid–Liquid Phase Separation by Intrinsically Disordered Protein Regions of Viruses: Roles in Viral Life Cycle and Control of Virus–Host Interactions

Brocca, Stefania; Grandori, Rita; Longhi, Sonia; Uversky, Vladimir N.

doi:10.3390/ijms21239045

Cited by 125 publications

(125 citation statements)

References 249 publications

(352 reference statements)

Supporting

Mentioning

122

Contrasting

Order By: Relevance

“…It is now clear that a wide variety of compartments likely form using the process of liquid-liquid phase separation (LLPS), which leads to a condensation of specific compo-nents out of bulk cytosol or nucleoplasm (1). The protein components of condensates tend to contain intrinsically disordered or low-complexity sequences and RNA-binding domains (2). Many condensates also contain nucleic acids, and indeed, RNA can promote phase separation in many instances (3).…”

Section: Introductionmentioning

confidence: 99%

Role of spatial patterning of N-protein interactions in SARS-CoV-2 genome packaging

Seim

Roden

Gladfelter

2021

Biophysical Journal

View full text Add to dashboard Cite

Viruses must efficiently and specifically package their genomes while excluding cellular nucleic acids and viral sub-genomic fragments. Some viruses use specific packaging signals, which are conserved sequence/structure motifs present only in the full-length genome. Recent work has shown that viral proteins important for packaging can undergo liquid-liquid phase separation (LLPS), where one or two viral nucleic acid binding proteins condense with the genome. The compositional simplicity of viral components lends itself well to theoretical modeling compared to more complex cellular organelles. Viral LLPS can be limited to one or two viral proteins and a single genome that is enriched in LLPS-promoting features. In our previous study, we observed that LLPS-promoting sequences of SARS-CoV-2 are located at the 5′ and 3′ ends of the genome, whereas the middle of the genome is predicted to consist mostly of solubilizing elements. Is this arrangement sufficient to drive single genome packaging, genome compaction, and genome cyclization? We addressed these questions using a coarse-grained polymer model, LASSI, to study the LLPS of nucleocapsid protein with RNA sequences that either promote LLPS or solubilization. With respect to genome cyclization, we find the most optimal arrangement restricts LLPS-promoting elements to the 5′ and 3′ ends of the genome, consistent with the native spatial patterning. Genome compaction is enhanced by clustered LLPS-promoting binding sites, while single genome packaging is most efficient when binding sites are distributed throughout the genome. These results suggest that many and variably positioned LLPS-promoting signals can support packaging in the absence of a singular packaging signal which argues against necessity of such a feature. We hypothesize that this model should be generalizable to multiple viruses as well as cellular organelles like paraspeckles, which enrich specific, long RNA sequences in a defined arrangement.

show abstract

Section: Introductionmentioning

confidence: 99%

Role of spatial patterning of N-protein interactions in SARS-CoV-2 genome packaging

Seim

Roden

Gladfelter

2021

Biophysical Journal

View full text Add to dashboard Cite

show abstract

“…The NCAPs of Ebola and Measles, among others, also undergo LLPS as part of their viral life cycles. The LLPS of Measles’s NCAP was shown to mature from a liquid-like to a gel-like state, possibly as a mechanism to control phase separation( 41 ). We similarly observed a transformation from a liquid-like to a gel-like state of the LCD segment upon extended incubation with Site2hp RNA (Figure 4).…”

Section: Discussionmentioning

confidence: 99%

Inhibition of amyloid formation of the Nucleoprotein of SARS-CoV-2

Tayeb-Fligelman

Cheng

Tai

et al. 2021

Preprint

View full text Add to dashboard Cite

The SARS-CoV-2 Nucleoprotein (NCAP) functions in RNA packaging during viral replication and assembly. Computational analysis of its amino acid sequence reveals a central low-complexity domain (LCD) having sequence features akin to LCDs in other proteins known to function in liquid-liquid phase separation. Here we show that in the presence of viral RNA, NCAP, and also its LCD segment alone, form amyloid-like fibrils when undergoing liquid-liquid phase separation. Within the LCD we identified three 6-residue segments that drive amyloid fibril formation. We determined atomic structures for fibrils formed by each of the three identified segments. These structures informed our design of peptide inhibitors of NCAP fibril formation and liquid-liquid phase separation, suggesting a therapeutic route for Covid-19.

show abstract

“…Viruses present an opportunity to dissect LLPS-promoting interactions between proteins and nucleic acids because of their limited proteome that must engage with specific viral nucleic acids (i.e., viral genome). Indeed, proteins and nucleic acids from many different viruses have now been shown to undergo LLPS (Brocca et al, 2020; Guseva et al, 2020; Heinrich et al, 2018; Nikolic et al, 2017; Rincheval et al, 2017). Importantly, viral model systems involving one LLPS promoting protein and one genomic nucleic acid (such as RNA), can reveal new principals for nucleic acid sequence- and structure-encoded LLPS.…”

Section: Introductionmentioning

confidence: 99%

Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures

Roden

Dai

Seim

et al. 2021

Preprint

View full text Add to dashboard Cite

Betacoronavirus SARS-CoV-2 infections caused the global Covid-19 pandemic. The nucleocapsid protein (N-protein) is required for multiple steps in the betacoronavirus replication cycle. SARS-CoV-2-N-protein is known to undergo liquid-liquid phase separation (LLPS) with specific RNAs at particular temperatures to form condensates. We show that N-protein recognizes at least two separate and distinct RNA motifs, both of which require double-stranded RNA (dsRNA) for LLPS. These motifs are separately recognized by N-protein's two RNA binding domains (RBDs). Addition of dsRNA accelerates and modifies N-protein LLPS in vitro and in cells and controls the temperature condensates form. The abundance of dsRNA tunes N-protein-mediated translational repression and may confer a switch from translation to genome packaging. Thus, N-protein's two RBDs interact with separate dsRNA motifs, and these interactions impart distinct droplet properties that can support multiple viral functions. These experiments demonstrate a paradigm of how RNA structure can control the properties of biomolecular condensates.

show abstract

Liquid–Liquid Phase Separation by Intrinsically Disordered Protein Regions of Viruses: Roles in Viral Life Cycle and Control of Virus–Host Interactions

Cited by 125 publications

References 249 publications

Role of spatial patterning of N-protein interactions in SARS-CoV-2 genome packaging

Role of spatial patterning of N-protein interactions in SARS-CoV-2 genome packaging

Inhibition of amyloid formation of the Nucleoprotein of SARS-CoV-2

Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures

Contact Info

Product

Resources

About