A working model for condensate RNA-binding proteins as matchmakers for protein complex assembly

Abstract

Most cellular processes are carried out by protein complexes, but it is still largely unknown how the subunits of lowly expressed complexes find each other in the crowded cellular environment. Here, we will describe a working model where RNA-binding proteins in cytoplasmic condensates act as matchmakers between their bound proteins (called protein targets) and newly translated proteins of their RNA targets to promote their assembly into complexes. Different RNA-binding proteins act as scaffolds for various cytoplasmic condensates with several of them supporting translation. mRNAs and proteins are recruited into the cytoplasmic condensates through binding to specific domains in the RNA-binding proteins. Scaffold RNA-binding proteins have a high valency. In our model, they use homotypic interactions to assemble condensates and they use heterotypic interactions to recruit protein targets into the condensates. We propose that unoccupied binding sites in the scaffold RNA-binding proteins transiently retain recruited and newly translated proteins in the condensates, thus promoting their assembly into complexes. Taken together, we propose that lowly expressed subunits of protein complexes combine information in their mRNAs and proteins to colocalize in the cytoplasm. The efficiency of protein complex assembly is increased by transient entrapment accomplished by multivalent RNA-binding proteins within cytoplasmic condensates.

Keywords: cooperativity between mRNA and protein motifs; cytoplasmic compartmentalization: subcellular organization; function of biomolecular condensates; localized processes; protein–protein interaction.

FIGURE 1.

Model for condensate RNA-binding proteins to serve as protein matchmakers for complex assembly. (A) An RNA-binding protein (red) assembles into a cytoplasmic condensate that supports translation. (B) The RNA-binding protein (red) binds to specific mRNAs (mRNA target of the RNA-binding protein, light blue) which results in mRNA enrichment in the cytoplasmic condensate. (C) The RNA-binding protein (red) uses specific protein domains (yellow dots) to bind to specific proteins (protein target of the RNA-binding protein, blue dots) which results in their recruitment into the condensate. The protein interaction domains are used for homotypic interaction to assemble the condensate and for heterotypic interaction to recruit and retain protein targets in the condensate. The multivalent protein interaction domains provide specificity for the enriched proteins in the condensate which serve as potential subunits of complexes. (D) Translation of the mRNA target allows the newly translated protein to form protein–protein interactions with a protein target in cis. A fully formed protein complex is indicated by the black outline of the proteins and signifies that all potential retention sites are masked. This allows the fully formed complex to leave the condensate. (E) As in D, but the proximity of other mRNA and protein targets also allows interactions in trans between protein targets recruited by neighboring mRNAs and among newly translated mRNA targets. (F) Unoccupied multivalent interaction domains of the RNA-binding protein allow recruited proteins and newly translated proteins to be transiently retained within the condensate network. Repeated binding allows them to scan the condensate to increase the chance of encounter of specific interactors. After complex assembly, they leave the condensate through masking of the retention sites. (G) Without visualizing the protein matchmakers that consist of the condensate RNA-binding protein and the bound mRNAs, protein complex assembly appears to occur through diffusion and random encounter.

FIGURE 2.

Functional submodules of RNA regulons. (A) We propose that cobinding of two or more RNA-binding proteins to groups of mRNAs define functionally related subgroups of mRNAs. A single RNA-binding protein, such as HuR, often has thousands of mRNA targets. The universe of mRNAs with HuR binding sites is shown on the left. Subgroups of these mRNAs are cobound by other RNA-binding proteins (for example TIS11B or Staufen; shown on the right), thus potentially representing groups of mRNA with shared functions, called functional submodules. (B) We propose that cooperative action between motifs in mRNAs and their encoded proteins defines functionally related groups of proteins. The universe of mRNAs with HuR binding sites is shown on the left. Groups of mRNAs with HuR binding sites may encode proteins containing shared domains, thus potentially reflecting functional submodules. Shown are HuR mRNA targets that encode proteins with Armadillo/HEAT repeats. These proteins may share functions such as the regulation of splicing and nuclear export. Another group of HuR mRNA targets that encode proteins with so far unknown shared motifs may regulate other functions known to be regulated by HuR.