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.

Extended disordered regions of ribosome-associated NAC proteins paralogs belong only to the germline in Drosophila melanogaster

“…Comparing the amino acid sequence patterns of the ubiquitous and germinal NAC subunits revealed the significantly extended IDRs at the C- and N-termini of the β- and α-subunits of gNAC, respectively. The burst of interest to IDRs stems from a large amount of the recently accumulated data demonstrating the wide functional role of IDRs in protein–protein interactions and the formation of biocondensates 40 , 41 . IDRs are protein unfolded parts providing protein–protein interactions 42 , which are considered to be necessary for the functionality of the ubiquitous NAC and its chaperone activity in C. elegans 31 .…”

An RNA binding protein, RNP1A, works with Contractility Kit proteins to facilitate macropinocytosis

“…However, it was extremely difficult to co-express fluorophore labeled RNP1A with IQGAP2, and therefore we could not acquire enough data to obtain conclusive results. RBPs have been proposed to act as protein-protein interaction hubs due to their multi-valency and presence of intrinsically disordered regions (Chen & Mayr, 2022). Therefore, we tested if knocking down rnp1A changes the overall size of Cortexillin I-containing CKs by comparing the in vivo diffusion time of Cortexillin I in wild type control and rnp1A knockdown cell lines as a proxy.…”

Large protein complex interfaces have evolved to promote cotranslational assembly

“…The strong trend in E. coli supports this idea, because polycistronic gene structure is more compatible with sequential assembly. In eukaryotes, large complexes and subunits of lowly abundant complexes may require an additional biological process to ensure their transcripts are colocalised for simultaneous assembly and to facilitate further assembly steps (Keene, 2007; Chen and Mayr, 2022). Sequential assembly, on the other hand, may have evolved to exploit large interface areas for the recruitment of partner subunits.…”

“…Although homomers may benefit from polysome-driven assembly, it requires allocation of cellular resources to ensure at least two ribosomes are actively translating the same mRNA at any one time (Liu, Beyer and Aebersold, 2016). On the other hand, heteromers, products of different genes that physically interact, can only employ the trans mode of assembly in eukaryotes, providing mechanisms that colocalise their transcripts exist (Liu et al ., 2016; Pizzinga et al ., 2019; Wang et al ., 2020; Chen and Mayr, 2022). In contrast to homomers, cotranslational assembly of heteromers may only require a single ribosome on each mRNA, which could allow lowly abundant regulatory proteins to cotranslationally assemble (Heyer and Moore, 2016; Biever et al ., 2020).…”