Large RNP granules in <i>Caenorhabditis elegans</i> oocytes have distinct phases of RNA-binding proteins

Elaswad, Mohamed T.; Watkins, Brooklynne M; Sharp, Katherine G; Munderloh, Chloe; Schisa, Jennifer A

doi:10.1093/g3journal/jkac173

Cited by 9 publications

(7 citation statements)

References 44 publications

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“…Our data are also consistent with a model where the MEX-3, CGH-1, and MEG-3 phases of large RNP granules are less liquid-like than PGL-1, since PGL-1 is sensitive to imaging-associated stress in both diakinesis and arrested oocytes. Our companion article tests this model of distinct phases using multiple functional assays ( Elaswad et al 2022 ).…”

Section: Resultsmentioning

confidence: 99%

Imaging-associated stress causes divergent phase transitions of RNA-binding proteins in the Caenorhabditis elegans germ line

Elaswad

Munderloh

Watkins

et al. 2022

G3 Genes|Genomes|Genetics

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One emerging paradigm of cellular organization of RNA and RNA binding proteins is the formation of membraneless organelles (MLOs). Examples of MLOs include several types of ribonucleoprotein granules that form via phase separation. A variety of intracellular pH changes and post-translational modifications, as well as extracellular stresses can stimulate the condensation of proteins into granules. For example, the assembly of stress granules induced by oxidative stress, osmotic stress, and heat stress has been well-characterized in a variety of somatic cell types. In the germ line, similar stress-induced condensation of proteins occurs; however, less is known about the role of phase separation during gamete production. Researchers who study phase transitions often make use of fluorescent reporters to study the dynamics of RNA binding proteins during live-cell imaging. In this report, we demonstrate that common conditions of live-imaging C. elegans can cause an inadvertent stress and trigger phase transitions of RNA binding proteins. We show this imaging-associated stress stimulates decondensation of multiple germ granule proteins, and condensation of several P-body proteins. Proteins within larger RNP granules in meiotically-arrested oocytes do not appear to be as sensitive to the stress as proteins in diakinesis oocytes of young hermaphrodites, with the exception of the germ granule protein PGL-1. Our results have important methodological implications for all researchers using live-cell imaging techniques. The data also suggest that the RNA binding proteins within large RNP granules of arrested oocytes may have distinct phases which we characterize in our companion paper.

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Section: Resultsmentioning

confidence: 99%

Imaging-associated stress causes divergent phase transitions of RNA-binding proteins in the Caenorhabditis elegans germ line

Elaswad

Munderloh

Watkins

et al. 2022

G3 Genes|Genomes|Genetics

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“…In the cell, the RNA binding proteins (RBPs) and their RNAs always form the phase separating condensation to proceed with the RNA highly efficiently. Recent research also mentioned that ceMEX-3 can form RNP granules in the oocytes of C. elegans but is isolated from the other phases in the P-granule to handle the RNA individually 38 . The C-terminus of ceMEX-3 is the potential phase separation driver based on the sequence, while there is a similar long intrinsically disordered region in hMEX3B connecting the KH domains and RING domain.…”

Section: Discussionmentioning

confidence: 99%

Molecular mechanism of specific HLA-A mRNA recognition by the RNA-binding-protein hMEX3B to promote tumor immune escape

Yang,

Chen,

et al. 2024

Commun Biol

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Immunotherapy, including immune checkpoint inhibitors and adoptive cell transfer, has obtained great progress, but their efficiencies vary among patients due to the genetic and epigenetic differences. Human MEX3B (hMEX3B) protein is an RNA-binding protein that contains two KH domains at the N-terminus and a RING domain at its C-terminus, which has the activity of E3 ubiquitin ligase and is essential for RNA degradation. Current evidence suggests that hMEX3B is involved in many important biological processes, including tumor immune evasion and HLA-A regulation, but the sequence of substrate RNA recognized by hMEX3B and the functional molecular mechanisms are unclear. Here, we first screened the optimized hMEX3B binding sequence on the HLA-A mRNA and reported that the two tandem KH domains can bind with their substrate one hundred times more than the individual KH domains. We systematically investigated the binding characteristics between the two KH domains and their RNA substrates by nuclear magnetic resonance (NMR). Based on this information and the small-angle X-ray scattering (SAXS) data, we used molecular dynamics simulations to obtain structural models of KH domains in complex with their corresponding RNAs. By analyzing the models, we noticed that on the KH domains’ variable loops, there were two pairs of threonines and arginines that can disrupt the recognition of the RNA completely, and this influence had also been verified both in vitro and in vivo. Finally, we presented a functional model of the hMEX3B protein, which indicated that hMEX3B regulated the degradation of its substrate mRNAs in many biological processes. Taken together, our research illustrated how the hMEX3B protein played a key role in translation inhibition during the immune response to tumor cells and provided an idea and a lead for the study of the molecular mechanism and function of other MEX3 family proteins.

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“…Oocyte-specific proteins could promote the observed TIAR-1 and PrD6-mutant TIAR-1 association to SG’s and resistance to disassembly. Large condensates formed in arrested oocytes of C. elegans gonads depleted of sperm or when animals are exposed to different types of stress ( Elaswad et al, 2022 ). Proteins found associated with these large oocyte condensates can show different liquid phases.…”

Section: Discussionmentioning

confidence: 99%

Two predicted α-helices within the prion-like domain of TIAR-1 play a crucial role in its association with stress granules in Caenorhabditis elegans

Fuentes-Jiménez,

Salinas,

Morales-Oliva

et al. 2023

Front. Cell Dev. Biol.

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Stress granules (SGs) are sites for mRNA storage, protection, and translation repression. TIA1 and TIAR1 are two RNA-binding proteins that are key players in SGs formation in mammals. TIA1/TIAR have a prion-like domain (PrD) in their C-terminal that promotes liquid-phase separation. Lack of any TIA1/TIAR has severe consequences in mice. However, it is not clear whether the failure to form proper SGs is the cause of any of these problems. We disrupted two predicted α-helices within the prion-like domain of the Caenohabditis elegans TIA1/TIAR homolog, TIAR-1, to test whether its association with SGs is important for the nematode. We found that tiar-1 PrD mutant animals continued to form TIAR-1 condensates under stress in the C. elegans gonad. Nonetheless, TIAR-1 condensates appeared fragile and disassembled quickly after stress. Apparently, the SGs continued to associate regularly as observed with CGH-1, an SG marker. Like tiar-1-knockout nematodes, tiar-1 PrD mutant animals exhibited fertility problems and a shorter lifespan. Notwithstanding this, tiar-1 PrD mutant nematodes were no sensitive to stress. Our data demonstrate that the predicted prion-like domain of TIAR-1 is important for its association with stress granules. Moreover, this domain may also play a significant role in various TIAR-1 functions unrelated to stress, such as fertility, embryogenesis and lifespan.

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Large RNP granules in Caenorhabditis elegans oocytes have distinct phases of RNA-binding proteins

Cited by 9 publications

References 44 publications

Imaging-associated stress causes divergent phase transitions of RNA-binding proteins in the Caenorhabditis elegans germ line

Imaging-associated stress causes divergent phase transitions of RNA-binding proteins in the Caenorhabditis elegans germ line

Molecular mechanism of specific HLA-A mRNA recognition by the RNA-binding-protein hMEX3B to promote tumor immune escape

Two predicted α-helices within the prion-like domain of TIAR-1 play a crucial role in its association with stress granules in Caenorhabditis elegans

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